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Sample records for acid site density

  1. Support Effects on Bronsted acid site densities and alcohol dehydration turnover rates on tungsten oxide domains

    SciTech Connect

    Macht, Josef; Baertsch, Chelsey D.; May-Lozano, Marcos; Soled, Stuart L.; Wang, Yong; Iglesia, Enrique

    2005-03-01

    Initial activity and acid site density of several WAl, WSi (MCM41) and one WSn sample were determined. Trans/cis 2-butene selectivity is dependent on the support. Presumably, these differences are due to subtle differences in base strengths. 2-Butanol dehydration rates (per W-atom) reached maximum values at intermediate WOx surface densities on WAl, as reported for 2-butanol dehydration reactions on WZr. Titration results indicate that Bronsted acid sites are required for 2-butanol dehydration on WAl, WSi and WSn. UV-visible studies suggest that WAl is much more difficult to reduce than WZr. The detection of reduced centers on WAl, the number of which correlates to Bronsted acid site density and catalyst activity, as well as the temperature dependence of Bronsted acid site density indicate the in-situ formation of these active sites. We infer that this mechanism is common among all supported WOx samples described in this study. Turnover rates are a function of Bronsted acid site density only. High acid site densities lead to high turnover rates. Higher active site densities may cause stronger conjugate bases, as a higher electron density has to be stabilized, and thus weaker acidity, enabling a faster rate of product desorption. The maximum achievable active site density is dependent on the support. WZr reaches a higher active site density than WAl.

  2. Surface site density, silicic acid retention and transport properties of compacted magnetite powder

    NASA Astrophysics Data System (ADS)

    Mayant, C.; Grambow, B.; Abdelouas, A.; Ribet, S.; Leclercq, S.

    In France, within the framework of investigations of the feasibility of deep geological disposal of high-level radioactive waste, studies on corrosion products of steel over packs are ongoing. Such studies concern silica and radionuclide retention. The objective of the present work is to study sorption of silicic acid on compacted magnetite in percolation cells to attempt to simulate confined site conditions. Potentiometric titration of commercial magnetite was carried out with both dispersed and compacted magnetite. The titration of the magnetite suspension has been made with two different methods: a batch method (several suspensions) and a direct fast method (one suspension). The Gran’s function gave 1.7 (±0.4) and 2.4 (±0.5) sorption sites nm -2 with these respective methods but site densities as high as 20/nm 2 could be obtained by modelling. The titration of magnetite compacted at 120 bars showed that the evolution of charge density on magnetite surfaces is similar for compacted and dispersed magnetite. Silicic acid sorption onto dispersed and compacted magnetite was similar with sorption site densities ranging between 2.2 and 4.4/nm 2.

  3. The significance of erythrocyte antigen site density

    PubMed Central

    Hoyer, Leon W.; Trabold, Norma C.

    1971-01-01

    The importance of antigen site density has been studied by means of a model passive hemolysis system using red cells coupled with sulfanilic acid groups. Relative site numbers were estimated from the covalent linkage of sulfanilic acid-35S to red cell membrane protein, and the effective antigen site number was determined with 125I-labeled rabbit IgG anti-sulfanilic acid (anti-S). Immune hemolysis was demonstrated for red cells which had greater than a threshold number of antigen sites, the value of which was different for normal human cells (80,000 sites/cell), cells from a patient with paroxysmal nocturnal hemoglobinuria (PNH) (40,000 sites/cell), and sheep red blood cells (RBC) (15,000 sites/cell). Cells with antigen site densities below these values did not hemolyze when tested with 1 mg/ml purified rabbit IgM anti-S. 2-8 times greater antigen site densities were required to obtain hemolysis with IgG anti-S. Above the threshold value, hemolysis titers were proportional to the antigen site number until maximal values were obtained. The greater hemolytic efficiency of IgM antibody was demonstrated in this system, and it was established that the magnitude of the difference was related to the test cell antigen site density. These data, taken with previously reported hemagglutination studies, have been used to develop a general classification of immune hemolysis and hemagglutination based on antigen site density and antibody class. It is suggested that the heterogeneity of blood group systems is caused by differences in the site separation of erythrocyte membrane antigens. PMID:5105661

  4. The significance of erythrocyte antigen site density

    PubMed Central

    Hoyer, Leon W.; Trabold, Norma C.

    1970-01-01

    The importance of antigen site density has been studied by means of a model passive hemagglutination system using human red cells coupled with sulfanilic acid groups. Relative site numbers were estimated from the covalent linkage of sulfanilic acid-35S to red cell membrane protein and the effective antigen site number was determined with 125I-labeled rabbit IgG antisulfanilic acid. Cells which had fewer than 20,000 antigen sites per cell were not agglutinated. As greater numbers of sulfanilic groups were coupled to the red cells, the agglutination titers increased to maximum values with red fanilic groups were coupled to the red cells, the agglutination titers of purified IgM antibody were 10-20 times greater than IgG antibody when preparations with the same protein concentration were compared, but this difference was not noted when IgG antibody was measured by antiglobulin reactions. These findings emphasize the need to consider differences in antigen site density when comparing blood group systems. They are consistent with the hypothesis that those blood group antigens which have a very low site number will not be detected by IgG antibodies in saline hemagglutination determinations. PMID:5409811

  5. Incorporation and electron transfer of anthracene in pores of ZSM-5 zeolites. Effect of Brønsted acid site density.

    PubMed

    Hureau, Matthieu; Moissette, Alain; Marquis, Séverine; Brémard, Claude; Vezin, Hervé

    2009-08-01

    The sorption course of anthracene (ACENE-3) into Brønsted-acidic medium pore MFI zeolites was monitored by in situ EPR and diffuse reflectance UV-visible absorption over one year. Weighed amounts of solid ACENE-3 were merely exposed to H(n)ZSM-5 (H(n)(AlO(2))(n)(SiO(2))(96-n)), with the following Brønsted acid site (BAS) densities, n = 0.0, 0.17, 0.57, 0.95, 2.0, 3.4, 6.6, dehydrated at 623 K under argon. The weighed amounts correspond to 1 ACENE-3 per zeolite unit cell. ACENE-3 is found to be incorporated as intact molecules in purely siliceous MFI (silicalite-1). Monte Carlo simulations indicate that ACENE-3 lies in the intersection of straight and zigzag channels. In contrast, the presence of BASs on the inner surface of channels induces spontaneous ionization of ACENE-3 (ionization potential = 7.44 eV). The charge separation as ACENE-3*(+)@H(n)ZSM-5*(-) is caused by the strong Coulombic field gradient of Si-O(-)(H(+))-Al BAS in the absence of any Lewis acid site. The rate and yield of ionization are found to increase dramatically with BAS density increase. The stabilization of ACENE-3*(+)@H(n)ZSM-5*(-) is explained by the tight fit between the rod-shape ACENE-3 and the channel dimensions and especially by the compartmentalization of ejected electrons as AlO(4)H*(-) centers away from the initial site of ionization. The final charge recombination occurs after more than one year and leads to ACENE-3 occluded in the straight channel in close proximity to BAS without any protonation of ACENE-3 (pK(a) = -13.5).

  6. Nanoelectrode Arrays Based on Low Site Density Aligned Carbon Nanotubes

    SciTech Connect

    Yi, Tu; Lin, Yuehe ); Ren, Zhifeng N.

    2003-01-29

    Nanoelectrode arrays (NEAs) were fabricated from the low site density aligned carbon nanotubes (CNTs). The CNTs were grown by plasma enhanced chemical vapor deposition (PECVD) on Ni nanoparticles made by the electrochemical deposition.

  7. Ligand electronic properties modulate tau filament binding site density

    PubMed Central

    Cisek, Katryna; Jensen, Jordan R.; Honson, Nicolette S.; Schafer, Kelsey N.; Cooper, Grace L.; Kuret, Jeff

    2012-01-01

    Small molecules that bind tau-bearing neurofibrillary lesions are being sought for premortem diagnosis, staging, and treatment of Alzheimer’s disease and other tauopathic neurodegenerative diseases. The utility of these agents will depend on both their binding affinity and binding site density (Bmax). Previously we identified polarizability as a descriptor of protein aggregate binding affinity. To examine its contribution to binding site density, we investigated the ability of two closely related benzothiazole derivatives ((E)-2-[[4-(dimethylamino)phenyl]azo]-6-methoxybenzothiazole) and ((E)-2-[2-[4-(dimethylamino)phenyl]ethenyl]-6-methoxybenzothiazole)) that differed in polarizability to displace probes of high (Thioflavin S) and low (radiolabeled (E,E)-1-iodo-2,5-bis(3-hydroxycarbonyl-4-methoxy)styrylbenzene; IMSB) density sites. Consistent with their site densities, Thioflavin S completely displaced radiolabeled IMSB, but IMSB was incapable of displacing Thioflavin S. Although both benzothiazoles displaced the low Bmax IMSB probe, only the highly polarizable analog displaced near saturating concentrations of the Thioflavin S probe. Quantum calculations showed that high polarizability reflected extensive pi-electron delocalization fostered by the presence of electron donating and accepting groups. These data suggest that electron delocalization promotes ligand binding at a subset of sites on tau aggregates that are present at high density, and that optimizing this aspect of ligand structure can yield tau-directed agents with superior diagnostic and therapeutic performance. PMID:23072817

  8. Density functional theory study of the oligomerization of carboxylic acids.

    PubMed

    Di Tommaso, Devis; Watson, Ken L

    2014-11-20

    We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid, and benzoic acid) in water, chloroform, and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6). The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution, and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, located new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid, and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution. (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents. (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (CA)4,(D+D) are the most stable type of tetramers, but their formation from the self-association of classic carboxylic dimers is highly unfavorable. (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (CA)4,(D+D) and (CA)3 + CA → (CA)4,(D+D) are exoergonic, but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species. (v) For tetrolic acid the prenucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α and β solid forms of tetrolic acid. (vi) Stable tetramers of

  9. Topological analysis of the electronic charge density in the ethene protonation reaction catalyzed by acidic zeolite.

    PubMed

    Zalazar, M Fernanda; Peruchena, Nélida M

    2007-08-16

    In the present work, the distribution of the electronic charge density in the ethene protonation reaction by a zeolite acid site is studied within the framework of the density functional theory and the atoms in molecules (AIM) theory. The key electronic effects such as topological distribution of the charge density involved in the reaction are presented and discussed. The results are obtained at B3LYP/6-31G(**) level theory. Attention is focused on topological parameters such as electron density, its Laplacian, kinetic energy density, potential energy density, and electronic energy density at the bond critical points (BCP) in all bonds involved in the interaction zone, in the reactants, pi-complex, transition state, and alkoxy product. In addition, the topological atomic properties are determined on the selected atoms in the course of the reaction (average electron population, N(Omega), atomic net charge, q(Omega), atomic energy, E(Omega), atomic volume, v(Omega), and first moment of the atomic charge distribution, M(Omega)) and their changes are analyzed exhaustively. The topological study clearly shows that the ethene interaction with the acid site of the zeolite cluster, T5-OH, in the ethene adsorbed, is dominated by a strong O-H...pi interaction with some degree of covalence. AIM analysis based on DFT calculation for the transition state (TS) shows that the hydrogen atom from the acid site in the zeolitic fragment is connected to the carbon atom by a covalent bond with some contribution of electrostatic interaction and to the oxygen atom by closed shell interaction with some contribution of covalent character. The C-O bond formed in the alkoxy product can be defined as a weaker shared interaction. Our results show that in the transition state, the dominant interactions are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the concentration and accumulation of the charge density along the bond path between

  10. Competitive sorption of copper and lead at the oxide-water interface: Implications for surface site density

    NASA Astrophysics Data System (ADS)

    Christl, Iso; Kretzschmar, Ruben

    1999-10-01

    The competitive sorption of Cu(II) and Pb(II) to colloidal hematite was investigated as a function of pH and total metal concentration. Acid-base titrations of the hematite and single-metal sorption experiments for Cu and Pb at low to medium surface coverages were used to calibrate two surface complexation models, the triple layer model, and a 2-pK basic Stern model with ion-pair formation. The surface site density was systematically varied from 2 to 20 sites/nm2. Three different metal surface complexes were considered: (1) an inner-sphere metal complex; (2) an outer-sphere metal complex; and (3) an outer-sphere complex of singly hydrolyzed metal cations. Both models provided excellent fits to acid-base titration and single-metal sorption data, regardless of the surface site density used. With increasing site density, ΔpK of the stability constants for protonation reactions increased and metal surface complexes decreased steadily. The calibrated models based on different site densities were used to predict competitive sorption effects between Cu and Pb and single-metal sorption at higher total metal concentrations. Precipitation of oversaturated solid phases was included in the calculations. Best predictions of competitive sorption effects were obtained with surface site densities between 5 and 10 sites/nm2. The results demonstrate that surface site density is a key parameter if surface complexation models are exposed to more complex, multicomponent environments. We conclude that competitive metal sorption experiments can be used to obtain additional information about the relevant surface site density of oxide mineral surfaces.

  11. Biomimetic high density lipoprotein nanoparticles for nucleic acid delivery.

    PubMed

    McMahon, Kaylin M; Mutharasan, R Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K; Luthi, Andrea J; Helfand, Brian T; Ardehali, Hossein; Mirkin, Chad A; Volpert, Olga; Thaxton, C Shad

    2011-03-01

    We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy that combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy, and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery.

  12. Predicting Pb bioavailability to freshwater microalgae in the presence of fulvic acid: algal cell density as a variable.

    PubMed

    Slaveykova, Vera I

    2007-11-01

    In order to better understand the relationship between lead speciation and its bioavailability in natural waters, the interactions between Pb(II), fulvic acid and the freshwater alga, Chlorella kesslerii were studied at various algal cell densities. An increase in cellular lead or fulvic acid adsorbed to algae was observed with decrease of the cell density from ca. 10(7) to 10(5)cells ml(-1). In the presence of fulvic acid, cellular Pb was greater than that expected for the same free lead ion concentrations in the absence of fulvic acid in agreement to our previous study. This effect was found to be more pronounced at lower cell density, in accordance with increased fulvic acid adsorption to algae. Good fit between experimental observations and model predictions of cellular Pb at various cell densities, was observed by assuming that fulvic acid adsorbed to algae give rise to additional binding sites for Pb(II). The findings of this study indicate that a further extension of the biotic ligand model which includes the formation of a ternary complex and cell density (or concentration) as an input parameter is needed to improve its site-specific predictive capacity, especially in the case of dissolved organic matter-rich surface waters. This extension of predictive capacity would allow to reduce the deviations from the BLM model predictions for microalgae in the presence of dissolved organic matter and hence will serve as a mechanistic tool for establishing ambient site-specific water quality criteria. PMID:17555791

  13. Adverse experiences with nitric acid at the Savannah River Site

    SciTech Connect

    Durant, W.S.; Craig, D.K.; Vitacco, M.J.; McCormick, J.A.

    1991-06-01

    Nitric acid is used routinely at the Savannah River Site (SRS) in many processes. However, the site has experienced a number of adverse situations in handling nitric acid. These have ranged from minor injuries to personnel to significant explosions. This document compiles many of these events and includes discussions of process upsets, fires, injuries, and toxic effects of nitric acid and its decomposition products. The purpose of the publication is to apprise those using the acid that it is a potentially dangerous material and can react in many ways as demonstrated by SRS experience. 10 refs.

  14. Economies of density for on-site waste water treatment.

    PubMed

    Eggimann, Sven; Truffer, Bernhard; Maurer, Max

    2016-09-15

    Decentralised wastewater treatment is increasingly gaining interest as a means of responding to sustainability challenges. Cost comparisons are a crucial element of any sustainability assessment. While the cost characteristics of centralised waste water management systems (WMS) have been studied extensively, the economics of decentralised WMS are less understood. A key motivation for studying the costs of decentralised WMS is to compare the cost of centralised and decentralised WMS in order to decide on cost-efficient sanitation solutions. This paper outlines a model designed to assess those costs which depend on the spatial density of decentralised wastewater treatment plants in a region. Density-related costs are mostly linked to operation and maintenance activities which depend on transportation, like sludge removal or the visits of professionals to the plants for control, servicing or repairs. We first specify a modelled cost-density relationship for a region in a geometric two-dimensional space by means of heuristic routing algorithms that consider time and load-capacity restrictions. The generic model is then applied to a Swiss case study for which we specify a broad range of modelling parameters. As a result, we identify a 'hockey-stick'-shaped cost curve that is characterised by strong cost reductions at high density values which level out at around 1 to 1.5 plants per km(2). Variations in the cost curves are mostly due to differences in management approaches (scheduled or unscheduled emptying). In addition to the well-known diseconomies of scale in the case of centralised sanitation, we find a similar generic cost behaviour for decentralised sanitation due to economies of density. Low densities in sparsely populated regions thus result in higher costs for both centralised and decentralised system. Policy implications are that efforts to introduce decentralised options in a region should consider the low-density/high-cost problem when comparing centralised

  15. Economies of density for on-site waste water treatment.

    PubMed

    Eggimann, Sven; Truffer, Bernhard; Maurer, Max

    2016-09-15

    Decentralised wastewater treatment is increasingly gaining interest as a means of responding to sustainability challenges. Cost comparisons are a crucial element of any sustainability assessment. While the cost characteristics of centralised waste water management systems (WMS) have been studied extensively, the economics of decentralised WMS are less understood. A key motivation for studying the costs of decentralised WMS is to compare the cost of centralised and decentralised WMS in order to decide on cost-efficient sanitation solutions. This paper outlines a model designed to assess those costs which depend on the spatial density of decentralised wastewater treatment plants in a region. Density-related costs are mostly linked to operation and maintenance activities which depend on transportation, like sludge removal or the visits of professionals to the plants for control, servicing or repairs. We first specify a modelled cost-density relationship for a region in a geometric two-dimensional space by means of heuristic routing algorithms that consider time and load-capacity restrictions. The generic model is then applied to a Swiss case study for which we specify a broad range of modelling parameters. As a result, we identify a 'hockey-stick'-shaped cost curve that is characterised by strong cost reductions at high density values which level out at around 1 to 1.5 plants per km(2). Variations in the cost curves are mostly due to differences in management approaches (scheduled or unscheduled emptying). In addition to the well-known diseconomies of scale in the case of centralised sanitation, we find a similar generic cost behaviour for decentralised sanitation due to economies of density. Low densities in sparsely populated regions thus result in higher costs for both centralised and decentralised system. Policy implications are that efforts to introduce decentralised options in a region should consider the low-density/high-cost problem when comparing centralised

  16. Effect of ethyl esterification of phenolic acids on low-density lipoprotein oxidation.

    PubMed

    Chalas, J; Claise, C; Edeas, M; Messaoudi, C; Vergnes, L; Abella, A; Lindenbaum, A

    2001-02-01

    Inhibition of copper-induced low-density lipoprotein (LDL) oxidation by phenolic acids and their ethyl esters was investigated. LDL oxidation was evaluated by the hydroperoxide concentration and the chromatographic pattern of apoprotein fractions after fast protein liquid chromatography (FPLC). Antiradical properties against 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical and 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH) were also investigated, and lipophilicity determined by thin-layer chromatography. Caffeic acid at 5 microM and sinapic acid at 10 microM protected LDL against oxidation, inhibiting both hydroperoxide formation and the increase of apoprotein negative charge. Ferulic, gallic and p-hydroxy cinnamic acids were ineffective. Ethyl esterification increased the lipophilicity of the five acids, and enhanced the antioxidant properties of caffeic, sinapic and ferulic acids. Ethyl caffeate was protective at 1 microM. In contrast, gallic and p-hydroxy cinnamic ethyl esters were ineffective. Our results indicate that ethyl esterification of phenolic acids increases lipophilicity of their ethyl esters and may enable a better incorporation into the lipid layer of the LDL particle and the exertion of their antioxidant effect in the true site of lipoperoxidation. However, increasing lipophilicity is not the only mechanism able to potentiate preexisting antioxidant properties of molecules, and probably other mechanisms are implicated.

  17. High cell density propionic acid fermentation with an acid tolerant strain of Propionibacterium acidipropionici.

    PubMed

    Wang, Zhongqiang; Jin, Ying; Yang, Shang-Tian

    2015-03-01

    Propionic acid is an important chemical with wide applications and its production via fermentation is of great interest. However, economic production of bio-based propionic acid requires high product titer, yield, and productivity in the fermentation. A highly efficient and stable high cell density (HCD) fermentation process with cell recycle by centrifugation was developed for propionic acid production from glucose using an acid-tolerant strain of Propionibacterium acidipropionici, which had a higher specific growth rate, productivity, and acid tolerance compared to the wild type ATCC 4875. The sequential batch HCD fermentation at pH 6.5 produced propionic acid at a high titer of ∼40 g/L and productivity of 2.98 g/L h, with a yield of ∼0.44 g/g. The product yield increased to 0.53-0.62 g/g at a lower pH of 5.0-5.5, which, however, decreased the productivity to 1.28 g/L h. A higher final propionic acid titer of >55 g/L with a productivity of 2.23 g/L h was obtained in fed-batch HCD fermentation at pH 6.5. A 3-stage simulated fed-batch process in serum bottles produced 49.2 g/L propionic acid with a yield of 0.53 g/g and productivity of 0.66 g/L h. These productivities, yields and propionic acid titers were among the highest ever obtained in free-cell propionic acid fermentation.

  18. Limitations of the potentiometric titration technique in determining the proton active site density of goethite surfaces

    NASA Astrophysics Data System (ADS)

    Lützenkirchen, Johannes; Boily, Jean-François; Lövgren, Lars; Sjöberg, Staffan

    2002-10-01

    Density of proton active surface sites at mineral surfaces is a property of fundamental importance in equilibrium modeling of surface complexation reactions. In this article, methods for an experimental determination of these sites at the surface of α-FeOOH (goethite) are explored. It is shown that previously obtained saturation data of goethite with respect to protons do not yield a site density that can be considered as an intrinsic sorbent property: the results are below crystallographically expected values and values for different ionic media in terms of composition and concentration yield different numbers - for example, chloride would yield higher values than nitrate at the same concentration, and higher electrolyte concentration would favor higher apparent maxima. Although site saturation might be explained by electrostatic repulsion, which is more efficient at high electrolyte concentration or for certain ions, further independent experimental results show that no saturation occurs on goethite down to ph ≡ -log[H +] = 2.2 and possibly to ph = 1.0 in 0.6 M NaCl. For those very low pH values, the experimental charging curve was obtained by coulometric back titration (using the Gran plot) or titrations with tris (hydroxymethyl)-aminomethane of the supernatant of acidified goethite suspension. These experimental data are to our knowledge the first high quality data at such low pHs. However, small errors in the determination of proton concentrations (1%) are shown to strongly affect the shape of the charging curve for ph < 2. Furthermore, goethite dissolution (proton consumption and iron reduction in coulometric titrations) and liquid junction effects interfere at low ph, hampering the straightforward application of coulometric Gran titrations over the whole pH range. From these experiments, it can nonetheless be ascertained that a minimum of 2.5 protons/nm 2 can be adsorbed at the goethite surface from the point of zero charge (ph 9.4) to pH 0.9. Although

  19. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  20. Synthesis of kojic acid derivatives as secondary binding site probes of D-amino acid oxidase

    PubMed Central

    Raje, Mithun; Hin, Niyada; Duvall, Bridget; Ferraris, Dana V.; Berry, James F.; Thomas, Ajit G.; Alt, Jesse; Rojas, Camilo; Slusher, Barbara S.; Tsukamoto, Takashi

    2013-01-01

    A series of kojic acid (5-hydroxy-2-hydroxymethyl-4H-pyran-4-one) derivatives were synthesized and tested for their ability to inhibit D-amino acid oxidase (DAAO). Various substituents were incorporated into kojic acid at its 2-hydroxymethyl group. These analogs serve as useful molecular probes to explore the secondary binding site, which can be exploited in designing more potent DAAO inhibitors. PMID:23683589

  1. Dehydration of lactic acid to acrylic acid over lanthanum phosphate catalysts: the role of Lewis acid sites.

    PubMed

    Guo, Zhen; Theng, De Sheng; Tang, Karen Yuanting; Zhang, Lili; Huang, Lin; Borgna, Armando; Wang, Chuan

    2016-09-14

    Lanthanum phosphate (LaP) nano-rods were synthesized using n-butylamine as a shape-directing agent (SDA). The resulting catalysts were applied in the dehydration of lactic acid to acrylic acid. Aiming to understand the nature of the active sites, the chemical and physical properties of LaP materials were studied using a variety of characterization techniques. This study showed that the SDA not only affected the porosity of the LaP materials but also modified the acid-base properties. Clearly, the modification of the acid-base properties played a more critical role in determining the catalytic performance than porosity. An optimized catalytic performance was obtained on the LaP catalyst with a higher concentration of Lewis acid sites. Basic sites showed negative effects on the stability of the catalysts. Good stability was achieved when the catalyst was prepared using the appropriate SDA/La ratio. PMID:27514871

  2. Dehydration of lactic acid to acrylic acid over lanthanum phosphate catalysts: the role of Lewis acid sites.

    PubMed

    Guo, Zhen; Theng, De Sheng; Tang, Karen Yuanting; Zhang, Lili; Huang, Lin; Borgna, Armando; Wang, Chuan

    2016-09-14

    Lanthanum phosphate (LaP) nano-rods were synthesized using n-butylamine as a shape-directing agent (SDA). The resulting catalysts were applied in the dehydration of lactic acid to acrylic acid. Aiming to understand the nature of the active sites, the chemical and physical properties of LaP materials were studied using a variety of characterization techniques. This study showed that the SDA not only affected the porosity of the LaP materials but also modified the acid-base properties. Clearly, the modification of the acid-base properties played a more critical role in determining the catalytic performance than porosity. An optimized catalytic performance was obtained on the LaP catalyst with a higher concentration of Lewis acid sites. Basic sites showed negative effects on the stability of the catalysts. Good stability was achieved when the catalyst was prepared using the appropriate SDA/La ratio.

  3. Acid aerosol measurements at a suburban Connecticut site

    NASA Astrophysics Data System (ADS)

    Keeler, Gerald J.; Spengler, John D.; Castillo, Raymond A.

    Atmospheric acidity data were gathered during a year-long field project investigating the possible health effects of acid aerosol in a rural community in southwestern Connecticut. This site was chosen because the air quality is frequently influenced by pollutants transported from the New York-New Jersey corridor as well as from the Midwest U.S. An annular denuder filter-pack system utilized to obtain daily measurements of gaseous HNO 3, HONO, SO 2, and NH 3; plus fine particle SO 42-, NO 3-, and H +. Fine particle mass ( d ⩽ 2.1 μm) and PM10 (particles d ⩽ 10 μm) were also measured. Ozone concentrations and basic meteorological data were also obtained continuously. The atmosphere was acidic with average concentrations of HONO (16 nmol m -3), HNO 3 (42 nmol m -3), and H + (42 nmol m -3), observed from May to September 1988. Atmospheric ammonia concentrations were fairly low averaging 34 nmol m -3 during the same period, and suggesting the neutralizing capacity of the air was significant to neutralize all the acidic species present. Neutralization of acidic particles by reactions on the filter media after collection resulted in a loss of approximately 10% of the measured particle strong acidity for the summertime period investigated. Concentrations of ozone and acidic gases tended to peak with mixed layer flow from the south-southwest while particulate acidity was highest with flow predominantly from the west-soutwest. Hourly ozone concentrations greater than 100 ppb were observed on 31 different days during the monitoring, and concentrations greater than 150 ppb measured on 14 days. HNO 3 and aerosol strong acidity (H +) concentrations reached 174 and 199 nmol m -3, respectively during the summer months.

  4. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  5. Computational studies of Bronsted acid sites in zeolites

    SciTech Connect

    Curtiss, L.A.; Iton, L.E.; Zygmunt, S.A.

    1995-01-01

    The authors have performed high-level ab initio calculations using both Hartree-Fock (HF) and Moller-Plesset perturbation theory (MP2) to study the geometry and energetics of the adsorption complex involving H{sub 2}O and the Bronsted acid site in the zeolite H-ZSM-5. In these calculations, which use aluminosilicate cluster models for the zeolite framework with as many a 28 T atoms (T = Si, Al), we included geometry optimization in the local vicinity of the acid site at the HF/6-31G(d) level of theory, and have calculated corrections for zero-point energies, extensions for zero-point energies, extensions to higher basis sets, and the influence of electron correlation. Results for the adsorption energy and geometry of this complex are reported and compared with previous theoretical and experimental values.

  6. Vole preference of bilberry along gradients of simulated moose density and site productivity.

    PubMed

    Pedersen, Simen; Andreassen, Harry P; Persson, Inga-Lill; Julkunen-Tiitto, Riitta; Danell, Kjell; Skarpe, Christina

    2011-12-01

    Browsing by large herbivores might either increase or decrease preference for the plant by other herbivores, depending on the plant response. Using a cafeteria test, we studied the preference by root voles (Microtus oeconomus [Pallas, 1776]) for bilberry (Vaccinium myrtillus L.) previously subjected to 4 levels of simulated moose (Alces alces [Linnaeus, 1758]) density. The different levels of moose density were simulated at population densities relevant for Fennoscandian conditions, in exclosures situated along a site productivity gradient. We expected: (i) voles to prefer bilberry from high productivity sites over low productivity sites; (ii) voles to prefer browsed bilberry, if plants allocate resources to compensatory growth or to avoid browsed bilberry if plants allocate resources to defense; (iii) these effects to increase with increasing simulated moose density; and (iv) the concentration of plant chemicals and the plant morphology to explain vole preference. Specifically, we predicted that voles would prefer: (i) plants with high nitrogen content; (ii) plants with low content of defensive substances; and (iii) tall plants with long shoots. Voles preferred bilberry from the high productivity sites compared to the low productivity sites. We also found an interaction between site productivity and simulated moose density, where voles preferred unbrowsed plants at low productivity sites and intermediate levels of browsing at high productivity sites. There was no effect of plant chemistry or morphology on vole preference. We conclude that moose browsing impacts the food preference of voles. With the current high densities of moose in Fennoscandia, this could potentially influence vole food selection and population dynamics over large geographical areas.

  7. Efficient solid acid catalyst containing Lewis and Brønsted Acid sites for the production of furfurals.

    PubMed

    Mazzotta, Michael G; Gupta, Dinesh; Saha, Basudeb; Patra, Astam K; Bhaumik, Asim; Abu-Omar, Mahdi M

    2014-08-01

    Self-assembled nanoparticulates of porous sulfonated carbonaceous TiO2 material that contain Brønsted and Lewis acidic sites were prepared by a one-pot synthesis method. The material was characterized by XRD, FTIR spectroscopy, NH3 temperature-programmed desorption, pyridine FTIR spectroscopy, field-emission scanning electron microscopy, high-resolution transmission electron microscopy, N2 -sorption, atomic absorbance spectroscopy, and inductively coupled plasma optical emission spectroscopy. The carbonaceous heterogeneous catalyst (Glu-TsOH-Ti) with a Brønsted-to-Lewis acid density ratio of 1.2 and more accessible acid sites was effective to produce 5-hydroxymethylfurfural and furfural from biomass-derived mono- and disaccharides and xylose in a biphasic solvent that comprised water and biorenewable methyltetrahydrofuran. The catalyst was recycled in four consecutive cycles with a total loss of only 3 % activity. Thus, Glu-TsOH-Ti, which contains isomerization and dehydration catalytic sites and is based on a cheap and biorenewable carbon support, is a sustainable catalyst for the production of furfurals, platform chemicals for biofuels and chemicals. PMID:24807741

  8. Absolute acidity of clay edge sites from ab-initio simulations

    NASA Astrophysics Data System (ADS)

    Tazi, Sami; Rotenberg, Benjamin; Salanne, Mathieu; Sprik, Michiel; Sulpizi, Marialore

    2012-10-01

    We provide a microscopic understanding of the solvation structure and reactivity of the edges of neutral clays. In particular we address the tendency to deprotonation of the different reactive groups on the (0 1 0) face of pyrophyllite. Such information cannot be inferred directly from titration experiments, which do not discriminate between different sites and whose interpretation resorts to macroscopic models. The determination of the corresponding pKa then usually relies on bond valence models, sometimes improved by incorporating some structural information from ab-initio simulations. Here we use density functional theory based molecular dynamics simulations, combined with thermodynamic integration, to compute the free energy of the reactions of water with the different surface groups, leading to a deprotonated site and an aqueous hydronium ion. Our approach consistently describes the clay and water sides of the interface and includes naturally electronic polarization effects. It also allows to investigate the structure and solvation of all sites separately. We find that the most acidic group is SiOH, due to its ability to establish strong hydrogen bonds with adsorbed water, as it also happens on the quartz and amorphous silica surfaces. The acidity constant of AlOH2 is only 1 pKa unit larger. Finally, the pKa of AlOH is outside the possible range in water and this site should not deprotonate in aqueous solution. We show that the solvation of surface sites and hence their acidity is strongly affected by the proximity of other sites, in particular for AlOH and AlOH2 which share the same Al. We discuss the implications of our findings on the applicability of bond valence models to predict the acidity of edge sites of clays.

  9. Density functional theory calculations on dipeptide gallic acid interaction

    NASA Astrophysics Data System (ADS)

    Madhan, B.; Parthasarathi, R.; Subramanian, V.; Raghava Rao, J.; Nair, Balachandran Unni; Ramasami, T.

    2003-02-01

    In the present investigation, an attempt has been made to study the interaction of dipeptides with gallic acid, using Becke3 parameter Lee Yang Parr (B3LYP) method employing 3-21G*, 6-31G* and 6-31+G* basis sets. The interaction energies of the dipeptide-gallic acid complexes are in the range of -5 to -18 kcal/mol depending on the mode of intermolecular complexation. Calculated molecular electrostatic potential (MESP) for the various intermolecular complexes revealed the electrostatic nature of the interaction. Qualitative estimations based on chemical hardness and chemical potential demonstrated fractional electron transfer from dipeptide to gallic acid.

  10. Acidity of edge surface sites of montmorillonite and kaolinite

    NASA Astrophysics Data System (ADS)

    Liu, Xiandong; Lu, Xiancai; Sprik, Michiel; Cheng, Jun; Meijer, Evert Jan; Wang, Rucheng

    2013-09-01

    Acid-base chemistry of clay minerals is central to their interfacial properties, but up to now a quantitative understanding on the surface acidity is still lacking. In this study, with first principles molecular dynamics (FPMD) based vertical energy gap technique, we calculate the acidity constants of surface groups on (0 1 0)-type edges of montmorillonite and kaolinite, which are representatives of 2:1 and 1:1-type clay minerals, respectively. It shows that tbnd Si-OH and tbnd Al-OH2OH groups of kaolinite have pKas of 6.9 and 5.7 and those of montmorillonite have pKas of 7.0 and 8.3, respectively. For each mineral, the calculated pKas are consistent with the experimental ranges derived from fittings of titration curves, indicating that tbnd Si-OH and tbnd Al-OH2OH groups are the major acidic sites responsible to pH-dependent experimental observations. The effect of Mg substitution in montmorillonite is investigated and it is found that Mg substitution increases the pKas of the neighboring tbnd Si-OH and tbnd Si-OH2 groups by 2-3 pKa units. Furthermore, our calculation shows that the pKa of edge tbnd Mg-(OH2)2 is as high as 13.2, indicating the protonated state dominates under common pH. Together with previous adsorption experiments, our derived acidity constants suggest that tbnd Si-O- and tbnd Al-(OH)2 groups are the most probable edge sites for complexing heavy metal cations.

  11. Site-Specific Velocity and Density Model for the Waste Treatment Plant, Hanford, Washington.

    SciTech Connect

    Rohay, Alan C.; Brouns, Thomas M.

    2007-06-27

    This report documents the work conducted under the SBP to develop a shear wave and compressional wave velocity and density model specific to the WTP site. Section 2 provides detailed background information on the WTP site and its underlying geology as well as on the Seismic Boreholes Project activities leading up to the Vs and Vp measurements. In Section 3, methods employed and results obtained are documented for measurements of Vs and Vp velocities in basalts and interbeds. Section 4 provides details on velocity measurements in the sediments underlying the WTP. Borehole gravity measurements of density of the subsurface basalt and sediments are described in Section 5. Section 6 describes the analysis of data presented in section 3-5, and presents the overall velocity and density model for the WTP site.

  12. Evaluation of population density and distribution criteria in nuclear power plant siting

    SciTech Connect

    Young, M.

    1994-06-01

    The NRC has proposed revisions to 10 CFR 100 which include the codification of nuclear reactor site population density limits to 500 people per square mile, at the siting stage, averaged over any radial distance out to 30 miles, and 1,000 people per square mile within the 40-year lifetime of a nuclear plant. This study examined whether there are less restrictive alternative population density and/or distribution criteria which would provide equivalent or better protection to human health in the unlikely event of a nuclear accident. This study did not attempt to directly address the issue of actual population density limits because there are no US risk standards established for the evaluation of population density limits. Calculations were performed using source terms for both a current generation light water reactor (LWR) and an advanced light water reactor (ALWR) design. The results of this study suggest that measures which address the distribution of the population density, including emergency response conditions, could result in lower average individual risks to the public than the proposed guidelines that require controlling average population density. Studies also indicate that an exclusion zone size, determined by emergency response conditions and reactor design (power level and safety features), would better serve to protect public health than a rigid standard applied to all sites.

  13. Physiological responses to acid stress by Saccharomyces cerevisiae when applying high initial cell density

    PubMed Central

    Guo, Zhong-peng; Olsson, Lisbeth

    2016-01-01

    High initial cell density is used to increase volumetric productivity and shorten production time in lignocellulosic hydrolysate fermentation. Comparison of physiological parameters in high initial cell density cultivation of Saccharomyces cerevisiae in the presence of acetic, formic, levulinic and cinnamic acids demonstrated general and acid-specific responses of cells. All the acids studied impaired growth and inhibited glycolytic flux, and caused oxidative stress and accumulation of trehalose. However, trehalose may play a role other than protecting yeast cells from acid-induced oxidative stress. Unlike the other acids, cinnamic acid did not cause depletion of cellular ATP, but abolished the growth of yeast on ethanol. Compared with low initial cell density, increasing initial cell density reduced the lag phase and improved the bioconversion yield of cinnamic acid during acid adaptation. In addition, yeast cells were able to grow at elevated concentrations of acid, probable due to the increase in phenotypic cell-to-cell heterogeneity in large inoculum size. Furthermore, the specific growth rate and the specific rates of glucose consumption and metabolite production were significantly lower than at low initial cell density, which was a result of the accumulation of a large fraction of cells that persisted in a viable but non-proliferating state. PMID:27620460

  14. Inter-site variation in allometry and wood density of Goupia glabra Aubl. in Amazonia.

    PubMed

    Siliprandi, N C; Nogueira, E M; Toledo, J J; Fearnside, P M; Nascimento, H E M

    2016-02-01

    The present study aims to compare the allometry and wood density of Goupia glabra Aubl. (Goupiaceae) in two different terra-firme sites in Amazonian forest. A total of 65 trees ≥ 10 cm DBH was sampled in both sites, with 39 trees in Nova Olinda do Norte (NOlinda, near the Amazon River) and 29 trees in Apuí (near the southern edge of the Amazon forest). Except for the relationship between DBH (diameter at breast height) and Ht (total height), allometric relationships for G.glabra differed significantly between sites. Apuí had lower intercept and greater slope for log10 (DBH) versus log10 (Hs - stem height), and, conversely, greater intercept and lower slope for log10 (DBH) versus log10 (Ch - crown height). The slope differed significantly between the sites for DBH versus Cd (crown diameter), with greater slope found for NOlinda. Mean basic wood density in Apuí was 8.8% lower than in NOlinda. Our findings highlight the variation in adaptive strategy of G. glabra due to environmental differences between sites. This is probably because of different canopy-understory light gradients, which result in differentiation of resource allocation between vertical and horizontal growth, which, in turn, affects mechanical support related to wood density. We also hypothesize that differences in soil fertility and disturbance regimes between sites may act concomitantly with light. PMID:26909641

  15. The impact of on-site wastewater from high density cluster developments on groundwater quality

    NASA Astrophysics Data System (ADS)

    Morrissey, P. J.; Johnston, P. M.; Gill, L. W.

    2015-11-01

    The net impact on groundwater quality from high density clusters of unsewered housing across a range of hydro(geo)logical settings has been assessed. Four separate cluster development sites were selected, each representative of different aquifer vulnerability categories. Groundwater samples were collected on a monthly basis over a two year period for chemical and microbiological analysis from nested multi-horizon sampling boreholes upstream and downstream of the study sites. The field results showed no statistically significant difference between upstream and downstream water quality at any of the study areas, although there were higher breakthroughs in contaminants in the High and Extreme vulnerability sites linked to high intensity rainfall events; these however, could not be directly attributed to on-site effluent. Linked numerical models were then built for each site using HYDRUS 2D to simulate the attenuation of contaminants through the unsaturated zone from which the resulting hydraulic and contaminant fluxes at the water table were used as inputs into MODFLOW MT3D models to simulate the groundwater flows. The results of the simulations confirmed the field observations at each site, indicating that the existing clustered on-site wastewater discharges would only cause limited and very localised impacts on groundwater quality, with contaminant loads being quickly dispersed and diluted downstream due to the relatively high groundwater flow rates. Further simulations were then carried out using the calibrated models to assess the impact of increasing cluster densities revealing little impact at any of the study locations up to a density of 6 units/ha with the exception of the Extreme vulnerability site.

  16. The impact of on-site wastewater from high density cluster developments on groundwater quality.

    PubMed

    Morrissey, P J; Johnston, P M; Gill, L W

    2015-11-01

    The net impact on groundwater quality from high density clusters of unsewered housing across a range of hydro(geo)logical settings has been assessed. Four separate cluster development sites were selected, each representative of different aquifer vulnerability categories. Groundwater samples were collected on a monthly basis over a two year period for chemical and microbiological analysis from nested multi-horizon sampling boreholes upstream and downstream of the study sites. The field results showed no statistically significant difference between upstream and downstream water quality at any of the study areas, although there were higher breakthroughs in contaminants in the High and Extreme vulnerability sites linked to high intensity rainfall events; these however, could not be directly attributed to on-site effluent. Linked numerical models were then built for each site using HYDRUS 2D to simulate the attenuation of contaminants through the unsaturated zone from which the resulting hydraulic and contaminant fluxes at the water table were used as inputs into MODFLOW MT3D models to simulate the groundwater flows. The results of the simulations confirmed the field observations at each site, indicating that the existing clustered on-site wastewater discharges would only cause limited and very localised impacts on groundwater quality, with contaminant loads being quickly dispersed and diluted downstream due to the relatively high groundwater flow rates. Further simulations were then carried out using the calibrated models to assess the impact of increasing cluster densities revealing little impact at any of the study locations up to a density of 6 units/ha with the exception of the Extreme vulnerability site.

  17. Cell density-dependent linoleic acid toxicity to Saccharomyces cerevisiae.

    PubMed

    Ferreira, Túlio César; de Moraes, Lídia Maria Pepe; Campos, Elida Geralda

    2011-08-01

    Since the discovery of the apoptotic pathway in Saccharomyces cerevisiae, several compounds have been shown to cause apoptosis in this organism. While the toxicity of polyunsaturated fatty acids (PUFA) peroxides towards S. cerevisiae has been known for a long time, studies on the effect of nonoxidized PUFA are scarce. The present study deals specifically with linoleic acid (LA) in its nonoxidized form and investigates its toxicity to yeast. Saccharomyces cerevisiae is unable to synthesize PUFA, but can take up and incorporate them into its membranes. Reports from the literature indicate that LA is not toxic to yeast cells. However, we demonstrated that yeast cell growth decreased in cultures treated with 0.1 mM LA for 4 h, and 3-(4,5 dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide reduction (a measure of respiratory activity) decreased by 47%. This toxicity was dependent on the number of cells used in the experiment. We show apoptosis induction by LA concomitant with increases in malondialdehyde, glutathione content, activities of catalase and cytochrome c peroxidase, and decreases in two metabolic enzyme activities. While the main purpose of this study was to show that LA causes cell death in yeast, our results indicate some of the molecular mechanisms of the cell toxicity of PUFA. PMID:21457450

  18. New Osseodensification Implant Site Preparation Method to Increase Bone Density in Low-Density Bone: In Vivo Evaluation in Sheep

    PubMed Central

    Trisi, Paolo; Falco, Antonello; Podaliri Vulpiani, Michele

    2016-01-01

    Purpose: The aim of this study was to evaluate a new surgical technique for implant site preparation that could allow to enhance bone density, ridge width, and implant secondary stability. Materials and Methods: The edges of the iliac crests of 2 sheep were exposed and ten 3.8 × 10-mm Dynamix implants (Cortex) were inserted in the left sides using the conventional drilling method (control group). Ten 5 × 10-mm Dynamix implants (Cortex) were inserted in the right sides (test group) using the osseodensification procedure (Versah). After 2 months of healing, the sheep were killed, and biomechanical and histological examinations were performed. Results: No implant failures were observed after 2 months of healing. A significant increase of ridge width and bone volume percentage (%BV) (approximately 30% higher) was detected in the test group. Significantly better removal torque values and micromotion under lateral forces (value of actual micromotion) were recorded for the test group in respect with the control group. Conclusion: Osseodensification technique used in the present in vivo study was demonstrated to be able to increase the %BV around dental implants inserted in low-density bone in respect to conventional implant drilling techniques, which may play a role in enhancing implant stability and reduce micromotion. PMID:26584202

  19. Site specific passive acoustic detection and densities of humpback whale calls off the coast of California

    NASA Astrophysics Data System (ADS)

    Helble, Tyler Adam

    Passive acoustic monitoring of marine mammal calls is an increasingly important method for assessing population numbers, distribution, and behavior. Automated methods are needed to aid in the analyses of the recorded data. When a mammal vocalizes in the marine environment, the received signal is a filtered version of the original waveform emitted by the marine mammal. The waveform is reduced in amplitude and distorted due to propagation effects that are influenced by the bathymetry and environment. It is important to account for these effects to determine a site-specific probability of detection for marine mammal calls in a given study area. A knowledge of that probability function over a range of environmental and ocean noise conditions allows vocalization statistics from recordings of single, fixed, omnidirectional sensors to be compared across sensors and at the same sensor over time with less bias and uncertainty in the results than direct comparison of the raw statistics. This dissertation focuses on both the development of new tools needed to automatically detect humpback whale vocalizations from single-fixed omnidirectional sensors as well as the determination of the site-specific probability of detection for monitoring sites off the coast of California. Using these tools, detected humpback calls are "calibrated" for environmental properties using the site-specific probability of detection values, and presented as call densities (calls per square kilometer per time). A two-year monitoring effort using these calibrated call densities reveals important biological and ecological information on migrating humpback whales off the coast of California. Call density trends are compared between the monitoring sites and at the same monitoring site over time. Call densities also are compared to several natural and human-influenced variables including season, time of day, lunar illumination, and ocean noise. The results reveal substantial differences in call densities

  20. Specific Initiation Site for Simian Virus 40 Deoxyribonucleic Acid Replication

    PubMed Central

    Thoren, Marilyn M.; Sebring, Edwin D.; Salzman, Norman P.

    1972-01-01

    Replicating simian virus 40 (SV40) deoxyribonucleic acid (DNA) molecules have been isolated under conditions in which the newly synthesized DNA is uniformly labeled with 3H-thymidine. These newly synthesized strands are released from the replicative intermediate molecules by alkaline treatment, and it has been possible to isolate single-stranded SV40 DNA which varies in size from 157,000 daltons (from molecules that are 10% replicated) to 1,360,000 daltons (85% replicated). The rates of duplex formation of newly synthesized DNA have been used to relate their genetic complexity to the extent of DNA replication. As DNA replication proceeds, the time required to effect 50% renaturation of the newly synthesized DNA increases at a proportional rate. The data establish that DNA replication is not initiated at random, but rather that there is a single specific initiation site for DNA replication. PMID:4342054

  1. Efficient production of propionic acid through high density culture with recycling cells of Propionibacterium acidipropionici.

    PubMed

    Liu, Zhen; Ge, Yongsheng; Xu, Jing; Gao, Chao; Ma, Cuiqing; Xu, Ping

    2016-09-01

    The aim of this study was to explore propionic acid production via high density culture of Propionibacterium acidipropionici and recycling of cells. Results showed that final cells of P. acidipropionici from high density culture still had high metabolic activity for reuse. Using our process, 75.9gl(-1) propionic acid was produced, which was 1.84-fold of that in fed-batch fermentation with low cell density (41.2gl(-1)); the corresponding productivity was 100.0% higher than that in fed-batch fermentation with low cell density (0.16gl(-1)h(-1)). This bioprocess may have potential for the industrial production of propionic acid. PMID:27318164

  2. Comparison of charge and dopant densities for DX sites in AlGaAs:Sn

    NASA Astrophysics Data System (ADS)

    Lurio, L. B.; Hayes, T. M.; Pant, J.; Williamson, D. L.; Gibart, P.; Theis, T. N.

    1996-03-01

    X-ray absorption spectroscopy measurements using fluorescence detection have been performed on Sn dopant centers in Al_.33Ga_.77As:Sn. Absolute calibration of the fluorescence yield permits a comparison of dopant and charge carrier densities in the persistent photo-conducting (PPC) state. It is found that the ratio of dopants to carriers is significantly greater than 1:1. In order to understand this discrepancy, we have determined the average local environment of the dopants through analysis of the X-ray absorption fine structure. The reduced carrier density is explained by a combination of inactive donor sites and charge traps. Implications for the nature of the Sn donor sites will be discussed. This research is supported by NSF grant nos. DMR-9006956 and DMR-8902512. The measurements were made at SSRL which is funded by the DOE Office of Basic Energy Sciences and the NIH Biotechnology Research Resource Program.

  3. Iodine 125-lysergic acid diethylamide binds to a novel serotonergic site on rat choroid plexus epithelial cells

    SciTech Connect

    Yagaloff, K.A.; Hartig, P.R.

    1985-12-01

    /sup 125/I-Lysergic acid diethylamide (/sup 125/I-LSD) binds with high affinity to serotonergic sites on rat choroid plexus. These sites were localized to choroid plexus epithelial cells by use of a novel high resolution stripping film technique for light microscopic autoradiography. In membrane preparations from rat choroid plexus, the serotonergic site density was 3100 fmol/mg of protein, which is 10-fold higher than the density of any other serotonergic site in brain homogenates. The choroid plexus site exhibits a novel pharmacology that does not match the properties of 5-hydroxytryptamine-1a (5-HT1a), 5-HT1b, or 5-HT2 serotonergic sites. /sup 125/I-LSD binding to the choroid plexus site is potently inhibited by mianserin, serotonin, and (+)-LSD. Other serotonergic, dopaminergic, and adrenergic agonists and antagonists exhibit moderate to weak affinities for this site. The rat choroid plexus /sup 125/I-LSD binding site appears to represent a new type of serotonergic site which is located on non-neuronal cells in this tissue.

  4. Measuring Oral Fatty Acid Thresholds, Fat Perception, Fatty Food Liking, and Papillae Density in Humans

    PubMed Central

    Haryono, Rivkeh Y.; Sprajcer, Madeline A.; Keast, Russell S. J.

    2014-01-01

    Emerging evidence from a number of laboratories indicates that humans have the ability to identify fatty acids in the oral cavity, presumably via fatty acid receptors housed on taste cells. Previous research has shown that an individual's oral sensitivity to fatty acid, specifically oleic acid (C18:1) is associated with body mass index (BMI), dietary fat consumption, and the ability to identify fat in foods. We have developed a reliable and reproducible method to assess oral chemoreception of fatty acids, using a milk and C18:1 emulsion, together with an ascending forced choice triangle procedure. In parallel, a food matrix has been developed to assess an individual's ability to perceive fat, in addition to a simple method to assess fatty food liking. As an added measure tongue photography is used to assess papillae density, with higher density often being associated with increased taste sensitivity. PMID:24961177

  5. Density fluctuations in the interstellar medium: Evidence for anisotropic magnetogasdynamic turbulence. I - Model and astrophysical sites

    NASA Astrophysics Data System (ADS)

    Higdon, J. C.

    1984-10-01

    A model of anisotropic magnetogasdynamic turbulence is developed in order to investigate quantitatively a turbulent fluid origin for the small spatial scale density fluctuations observed in 1981 by Armstrong, Cordes, and Rickett in the interstellar medium. The anisotropy at these small spatial scales results from the presence of a large-scale approximately uniform magnetic field that is a sum of the steady-state galactic magnetic field and the large-scale turbulent magnetic field fluctuations. The observed density fluctuations are interpreted to be two-dimensional isobaric entropy variations with oppositely directed gradients in temperature and density projected transverse to the local approximately uniform magnetic field. Three possible sites - cloud shell H II regions, diffuse H II regions produced by O stars, and the tenuous intercloud medium - are investigated as possible locations for turbulent flows.

  6. Controlling activation site density by low-energy far-field stimulation in cardiac tissue.

    PubMed

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites ("virtual electrodes") in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  7. Controlling activation site density by low-energy far-field stimulation in cardiac tissue

    NASA Astrophysics Data System (ADS)

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites (“virtual electrodes”) in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  8. Electron Densities in Solar Flare Loops, Chromospheric Evaporation Upflows, and Acceleration Sites

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Benz, Arnold O.

    1996-01-01

    We compare electron densities measured at three different locations in solar flares: (1) in Soft X-Ray (SXR) loops, determined from SXR emission measures and loop diameters from Yohkoh Soft X-Ray Telescope maps (n(sub e, sup SXR) = (0.2-2.5) x 10(exp 11)/ cu cm); (2) in chromospheric evaporation upflows, inferred from plasma frequency cutoffs of decimetric radio bursts detected with the 0.1-3 GHz spectrometer Phoenix of ETH Zuerich (n(sub e, sup upflow) = (0.3-11) x 10(exp 10)/cu cm; and (3) in acceleration sites, inferred from the plasma frequency at the separatrix between upward-accelerated (type III bursts) and downward-accelerated (reverse-drift bursts) electron beams [n(sub e, sup acc) = (0.6-10) x 10(exp 9)/cu cm]. The comparison of these density measurements, obtained from 44 flare episodes (during 14 different flares), demonstrates the compatibility of flare plasma density diagnostics with SXR and radio methods. The density in the upflowing plasma is found to be somewhat lower than in the filled loops, having ratios in a range n(sub e, sup upflow)/n(sub e, sup SXR) = 0.02-1.3, and a factor of 3.6 higher behind the upflow front. The acceleration sites are found to have a much lower density than the SXR-bright flare loops, i.e., n(sub e, sup acc)/n(sub e, sup SXR) = 0.005- 0.13, and thus must be physically displaced from the SXR-bright flare loops. The scaling law between electron time-of-flight distances l' and loop half-lengths s, l'/s = 1.4 +/- 0.3, recently established by Aschwanden et al. suggests that the centroid of the acceleration region is located above the SXR-bright flare loop, as envisioned in cusp geometries (e.g., in magnetic reconnection models).

  9. A Sialic Acid Binding Site in a Human Picornavirus

    PubMed Central

    Frank, Martin; Hähnlein-Schick, Irmgard; Ekström, Jens-Ola; Arnberg, Niklas; Stehle, Thilo

    2014-01-01

    The picornaviruses coxsackievirus A24 variant (CVA24v) and enterovirus 70 (EV70) cause continued outbreaks and pandemics of acute hemorrhagic conjunctivitis (AHC), a highly contagious eye disease against which neither vaccines nor antiviral drugs are currently available. Moreover, these viruses can cause symptoms in the cornea, upper respiratory tract, and neurological impairments such as acute flaccid paralysis. EV70 and CVA24v are both known to use 5-N-acetylneuraminic acid (Neu5Ac) for cell attachment, thus providing a putative link between the glycan receptor specificity and cell tropism and disease. We report the structures of an intact human picornavirus in complex with a range of glycans terminating in Neu5Ac. We determined the structure of the CVA24v to 1.40 Å resolution, screened different glycans bearing Neu5Ac for CVA24v binding, and structurally characterized interactions with candidate glycan receptors. Biochemical studies verified the relevance of the binding site and demonstrated a preference of CVA24v for α2,6-linked glycans. This preference can be rationalized by molecular dynamics simulations that show that α2,6-linked glycans can establish more contacts with the viral capsid. Our results form an excellent platform for the design of antiviral compounds to prevent AHC. PMID:25329320

  10. Gas-phase acidities of o-, m- and p-dehydrobenzoic acid radicals. Determination of the substituent constants for a phenyl radical site

    NASA Astrophysics Data System (ADS)

    Wenthold, Paul G.; Squires, Robert R.

    1998-05-01

    Reaction of CO2 with o-, m-, and p-benzyne radical anions in the gas phase produces o-, m-, and p-dehydrobenzoate radical anions, respectively. The (oxygen) gas-phase basicities of these ions, which are equivalent to the gas-phase acidities of the corresponding dehydrobenzoic acid radicals, [Delta]Gacid(o-, m-, or p-C6H4CO2-H), have been determined with a flowing afterglowtriple quadrupole apparatus by means of the kinetic method. The measured values are (in kcal mol-1): [Delta]Gacid(o-C6H4CO2H) = 330.4 +/- 0.4, [Delta]Gacid(m-C6H4CO2H) = 330.2 +/- 0.4, and [Delta]Gacid(p-C6H4CO2H) = 331.6 +/- 0.4 kcal mol-1. All three radicals are more acidic than benzoic acid ([Delta]Gacid = 333.1 +/- 2.0 kcal mol-1). The measured gas-phase acidities for the meta and para isomers suggest values for the resonance-effect substituent constant, [sigma]R, and the field/inductive effect substituent constant, [sigma]F, for a phenyl radical site of - 0.47 and 0.57, respectively. This classifies a phenyl radical site as a strong inductive withdrawing, and strong resonance donating substituent. Density functional calculations of the gas-phase acidities of dehydrobenzoic acids are in good agreement with the experimental results. The increased acidities of the dehydrobenzoic acids are shown to arise from a balance between the electron withdrawing effect of the electronegative radical site, and a compensating polarization of the [pi] system which mimics the effect of a resonance donor group located at the radical carbon.

  11. Report on Analysis of Forest Floor Bulk Density and Depth at the Savannah River Site.

    SciTech Connect

    Bernard R. Parresol

    2005-10-01

    The forest floor data from the Savannah River Site consists of two layers, the litter layer and the duff layer. The purpose for the study was to determine bulk density conversion factors to convert litter and duff depth values in inches to forest floor fuel values in tons per acre. The primary objective was to collect litter and duff samples to adequately characterize forest floor depth and bulk density for combinations of 4 common forest types (loblolly/slash pine, longleaf pine, pine and hardwood mix, upland hardwood), 3 age classes (5-20, 20-40, 40+ years old) and 3 categories of burning history (0-3, 3-10, 10+ years since last burn).

  12. Communication: Active space decomposition with multiple sites: Density matrix renormalization group algorithm

    SciTech Connect

    Parker, Shane M.; Shiozaki, Toru

    2014-12-07

    We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μE{sub h} or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation.

  13. Goethite surface reactivity: III. Unifying arsenate adsorption behavior through a variable crystal face - Site density model

    NASA Astrophysics Data System (ADS)

    Salazar-Camacho, Carlos; Villalobos, Mario

    2010-04-01

    We developed a model that describes quantitatively the arsenate adsorption behavior for any goethite preparation as a function of pH and ionic strength, by using one basic surface arsenate stoichiometry, with two affinity constants. The model combines a face distribution-crystallographic site density model for goethite with tenets of the Triple Layer and CD-MUSIC surface complexation models, and is self-consistent with its adsorption behavior towards protons, electrolytes, and other ions investigated previously. Five different systems of published arsenate adsorption data were used to calibrate the model spanning a wide range of chemical conditions, which included adsorption isotherms at different pH values, and adsorption pH-edges at different As(V) loadings, both at different ionic strengths and background electrolytes. Four additional goethite-arsenate systems reported with limited characterization and adsorption data were accurately described by the model developed. The adsorption reaction proposed is: lbond2 FeOH +lbond2 SOH +AsO43-+H→lbond2 FeOAsO3[2-]…SOH+HO where lbond2 SOH is an adjacent surface site to lbond2 FeOH; with log K = 21.6 ± 0.7 when lbond2 SOH is another lbond2 FeOH, and log K = 18.75 ± 0.9, when lbond2 SOH is lbond2 Fe 2OH. An additional small contribution of a protonated complex was required to describe data at low pH and very high arsenate loadings. The model considered goethites above 80 m 2/g as ideally composed of 70% face (1 0 1) and 30% face (0 0 1), resulting in a site density for lbond2 FeOH and for lbond2 Fe 3OH of 3.125/nm 2 each. Below 80 m 2/g surface capacity increases progressively with decreasing area, which was modeled by considering a progressively increasing proportion of faces (0 1 0)/(1 0 1), because face (0 1 0) shows a much higher site density of lbond2 FeOH groups. Computation of the specific proportion of faces, and thus of the site densities for the three types of crystallographic surface groups present in

  14. Highly selective Lewis acid sites in desilicated MFI zeolites for dihydroxyacetone isomerization to lactic acid.

    PubMed

    Dapsens, Pierre Y; Mondelli, Cecilia; Pérez-Ramírez, Javier

    2013-05-01

    Desilication of commercial MFI-type (ZSM-5) zeolites in solutions of alkali metal hydroxides is demonstrated to generate highly selective heterogeneous catalysts for the aqueous-phase isomerization of biobased dihydroxyacetone (DHA) to lactic acid (LA). The best hierarchical ZSM-5 sample attains a LA selectivity exceeding 90 %, which is comparable to that of the state-of-the-art catalyst (i.e., the Sn-beta zeolite); this optimized hierarchical catalyst is recyclable over three runs. The Lewis acid sites, which are created through desilication along with the introduction of mesoporosity, are shown to play a crucial role in the formation of the desired product; these cannot be achieved by using other post-synthetic methods, such as steaming or impregnation of aluminum species. Desilication of other metallosilicates, such as Ga-MFI, also leads to high LA selectivity. In the presence of a soluble aluminum source, such as aluminum nitrate, alkaline-assisted alumination can introduce these unique Lewis acid centers in all-silica MFI zeolites. These findings highlight the potential of zeolites in the field of biomass-to-chemical conversion, and expand the applicability of desilication for the generation of selective catalytic centers. PMID:23554234

  15. Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

    PubMed

    Bright, Nicholas A; Davis, Luther J; Luzio, J Paul

    2016-09-12

    The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle. PMID:27498570

  16. Design of a Brønsted acid with two different acidic sites: synthesis and application of aryl phosphinic acid-phosphoric acid as a Brønsted acid catalyst.

    PubMed

    Momiyama, N; Narumi, T; Terada, M

    2015-12-11

    A Brønsted acid with two different acidic sites, aryl phosphinic acid-phosphoric acid, has been synthesized. Its catalytic performance was assessed in the hetero-Diels-Alder reaction of aldehyde hydrates with Danishefsky's diene, achieving high reaction efficiency. PMID:26445921

  17. Amino acid sequence and domain structure of entactin. Homology with epidermal growth factor precursor and low density lipoprotein receptor

    PubMed Central

    1988-01-01

    Entactin (nidogen), a 150-kD sulfated glycoprotein, is a major component of basement membranes and forms a highly stable noncovalent complex with laminin. The complete amino acid sequence of mouse entactin has been derived from sequencing of cDNA clones. The 5.9-kb cDNA contains a 3,735-bp open reading frame followed by a 3'- untranslated region of 2.2 kb. The open reading frame encodes a 1,245- residue polypeptide with an unglycosylated Mr of 136,500, a 28-residue signal peptide, two Asn-linked glycosylation sites, and two potential Ca2+-binding sites. Analysis of the deduced amino acid sequence predicts that the molecule consists of two globular domains of 70 and 36 kD separated by a cysteine-rich domain of 28 kD. The COOH-terminal globular domain shows homology to the EGF precursor and the low density lipoprotein receptor. Entactin contains six EGF-type cysteine-rich repeat units and one copy of a cysteine-repeat motif found in thyroglobulin. The Arg-Gly-Asp cell recognition sequence is present in one of the EGF-type repeats, and a synthetic peptide from the putative cell-binding site of entactin was found to promote the attachment of mouse mammary tumor cells. PMID:3264556

  18. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    PubMed Central

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  19. High-resolution electron density profiles reveal influence of fatty acids on bilayer structure.

    PubMed Central

    Katsaras, J; Stinson, R H

    1990-01-01

    Small-angle x-ray diffraction studies were performed on gel phase-oriented bilayers of dipalmitoylphosphatidylcholine (DPPC) and DPPC containing 40 mol% of either palmitic acid (PA) or palmitic acid brominated at the 2-position (BPA). Oriented samples were prepared using a method developed by us, which is as simple as powder sample preparations while offering all the advantages of oriented samples made by traditional methods. Phases were determined using swelling experiments with structure factors plotted in reciprocal space, creating a relatively smooth curve as the amount of water between the bilayers was changed. Continuous Fourier transforms were also calculated to further test the consistency of the phase assignments. The diffraction data were used to calculate absolute electron density profiles for different bilayers to a resolution of 5-6 A. Analysis indicates the following: (a) The electron density profiles for the three preparations are virtually identical in the hydrocarbon chain region. (b) There is a decrease in the electron density of the glycerol backbone-headgroup region and d-space in DPPC-PA compared to DPPC. (c) The bromine of fatty-acid brominated at the 2-position is in the vicinity of the glycerol backbone. (d) The bilayer thickness of DPPC containing either brominated or unbrominated fatty acid remains relatively constant with increased levels of hydration, unlike DPPC bilayers. PMID:2306509

  20. Ascorbic acid protects lipids in human plasma and low-density lipoprotein against oxidative damage

    SciTech Connect

    Frei, B. )

    1991-12-01

    The authors exposed human blood plasma and low-density lipoprotein (LDL) to many different oxidative challenges and followed the temporal consumption of endogenous antioxidants in relation to the initiation of oxidative damage. Under all types of oxidizing conditions, ascorbic acid completely protects lipids in plasma and LDL against detectable peroxidative damage as assessed by a specific and highly sensitive assay for lipid peroxidation. Ascorbic acid proved to be superior to the other water-soluble plasma antioxidants bilirubin, uric acid, and protein thiols as well as to the lipoprotein-associated antioxidants alpha-tocopherol, ubiquinol-10, lycopene, and beta-carotene. Although these antioxidants can lower the rate of detectable lipid peroxidation, they are not able to prevent its initiation. Only ascorbic acid is reactive enough to effectively intercept oxidants in the aqueous phase before they can attack and cause detectable oxidative damage to lipids.

  1. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2009-04-28

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  2. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2008-10-07

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  3. Site specific incorporation of keto amino acids into proteins

    SciTech Connect

    Schultz, Peter G.; Wang, Lei

    2012-02-14

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  4. Site specific incorporation of keto amino acids into proteins

    SciTech Connect

    Schultz, Peter G.; Wang, Lei

    2011-12-06

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  5. Site specific incorporation of keto amino acids into proteins

    SciTech Connect

    Schultz, Peter G.; Wang, Lei

    2011-03-22

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  6. Solvent extraction study of the thorium nitrate, nitric acid, and tributyl phosphate-dodecane system: density and acidity relationships

    SciTech Connect

    Weinberger, A.J.; Marley, J.L.; Costanzo, D.A.

    1980-05-01

    A solvent extraction study to determine equilibrium conditions of thorium nitrate-nitric acid with 30% tributyl phosphate in normal dodecane has been completed. Experimental conditions studied were 30 to 60{sup 0}C, 0.05 to 1.5 M Th(NO{sub 3}){sub 4}, and 0.0 to 3.0 M HNO{sub 3}. The extractant concentration was constant at 30% tributyl phosphate. The equilibrium experiments have produced data which demonstrate that thorium nitrate concentration, free acid, and density are related in equilibrium behavior between the aqueous and organic phases from 30 to 60{sup 0}C in the 30% tributyl phosphate-dodecane solvent extraction system. The concentration interactions apply to both the two- and three-phase regions. A linear correlation was observed for the density (D) of the aqueous or organic phase and the concentration of thorium and free acid. The general form of the equation is D = a(C/sub Th/ + bC/sub H/) + c, where a is the slope, b is the constant, c is the intercept, and C/sub Th/ and C/sub H/ are the molar concentrations of thorium and free acid respectively. The relationship of temperature, thorium nitrate, and free acid makes possible the definitions of the boundaries between the two- and three-phase regions. This dependence, in turn, permits operational control or simulation studies of the system within the two-phase region. The data demonstrate the interactions of the components of the Thorex system and can be used to improve the mathematical description of equilibrium in the SEPHIS-Thorex computer program.

  7. Interaction of metal ions with acid sites of biosorbents peat moss and Vaucheria and model substances alginic and humic acids

    SciTech Connect

    Crist, R.H.; Martin, J.R.; Crist, D.R.

    1999-07-01

    The interaction between added metal ions and acid sites of two biosorbents, peat moss and the alga Vaucheria, was studied. Results were interpreted in terms of two model substances, alginic acid, a copolymer of guluronic and mannuronic acids present in marine algae, and humic acid in peat moss. For peat moss and Vaucheria at pH 4--6, two protons were displaced per Cd sorbed, after correction for sorbed metals also displaced by the heavy metal. The frequent neglect of exchange of heavy metals for metals either sorbed on the native material or added for pH adjustment leads to erroneous conclusions about proton displacement stoichiometry. Proton displacement constants K{sub ex}{sup H} decreased logarithmically with pH and had similar slopes for alginic acid and biosorbents. This pH effect was interpreted as an electrostatic effect of increasing anionic charge making proton removal less favorable. The maximum number of exchangeable acid sites (capacity C{sub H}) decreased with pH for alginic acid but increased with pH for biosorbents. Consistent with titration behavior, this difference was explained in terms of more weak acid sites in the biosorbents.

  8. An organic-heterojunction diode current equation including random site trap density

    NASA Astrophysics Data System (ADS)

    Kim, SeongMin; Ha, Jaewook; Kim, Jin-Baek

    2016-08-01

    The current-voltage characteristics of an organic heterojunction (HJ), where random site trap density at the donor-acceptor (D-A) interface is included, is numerically investigated based on the polaron-pair (PP) model (Phys. Rev. B. 82, 155305 (2010)). To derive the analytic equation, the electric field FI at the D-A interface, which is included in the field parameter b, is first approximated to estimate the polaron-pair dissociation rate, k_{ppd}. It is then assumed that the quasi-Fermi level E_{Fp/n} at the donor/acceptor lies in the trap energy level ( E_{trap}) at random sites without a direct dependence on applied bias ( Va), but on a HOMO/LUMO with Va dependence. As a result, the low diode current (DC) at forward bias is attributed to the E_{trap}, which is lower than the LUMO at acceptors, and is higher than the HOMO at donors. This implies that the pattern of DC is at forward biases depending upon the position of E_{trap}.

  9. Optimization of Spin-Unrestricted Density Functional Theory for Redox Properties of Rubredoxin Redox Site Analogues

    SciTech Connect

    Niu, Shuqiang; Nichols, Jeffery A.; Ichiye, Toshiko

    2009-05-01

    Systematic studies of the accuracy of density functional theory (DFT) methods, especially the recently developed hybrid generalized gradient approximation (GGA) functionals, for structural and energetic properties of iron-sulfur redox sites are essential before these methods can be used to answer important biological questions about these systems. Here, the geometries, electronic structures, and reduction potentials of redox site analogs of the iron-sulfur protein rubredoxin are investigated using DFT (B3LYP, B97gga1 and BHandH), the Moller-Plesset perturbation theory series (MP2, MP3, MP4SDQ), and coupled cluster (CCSD, CCSD(T)) methods. For the geometries of [Fe(SCH3)4]2-/1- and [Fe(SCH3)3]1-/0, the DFT optimizations give reasonable values and the inclusion of a core electron basis substantially reduces the errors in the calculated geometries. However, for the vertical detachment energy (VDE) and adiabatic detachment energy (ADE) of [Fe(SCH3)4]1- and [Fe(SCH3)3]1-, the B3LYP functional gives the most accurately computed ADE and VDE using DFT, which are comparable with those at the CCSD level of theory. When diffuse functions are added to the sulfur basis set, they have little effect on the geometry optimization but significantly improve the calculated VDE and ADE, which is important for the anionic reduced sites. When multiple polarization functions are added to the sulfur basis set, they lead to a slightly better description of the geometry by giving more angular flexibility but underestimate ADE and VDE, most likely due to overestimating the stabilizing energy of the oxidized sites. Overall, the B3LYP calculations with the more flexible full-core basis sets give a reasonable description both of the geometry and of the ADE and VDE. Thus, improving the basis sets seems to be an efficient and convenient way to obtain reliable reduction potentials of the high-spin iron-sulfur redox sites.

  10. Rapid atomic layer deposition of silica nanolaminates: synergistic catalysis of Lewis/Brønsted acid sites and interfacial interactions

    NASA Astrophysics Data System (ADS)

    Fang, Guoyong; Ma, Jing

    2013-11-01

    Rapid atomic layer deposition (RALD) has been applied to prepare various nanolaminates with repeated multilayer structures. The possible reaction pathways for RALD of the Al2O3/SiO2 nanolaminate using trimethylaluminum (TMA) and tris(tert-butoxy)silanol (TBS) are investigated by using density functional theory (DFT) calculations. The introduction of a Lewis-acid catalyst, TMA, can result in the formation of the catalytic site, which accelerates the propagation of the siloxane polymer. The rate-determining step of whole RALD is the elimination of isobutene of the tert-butoxy groups. The Brønsted acid site of [AlO4] can catalyze the elimination of isobutene. At the same time, the interfacial interactions, such as hydrogen bonding interactions between tert-butoxy groups and the surface, further catalyze the elimination of isobutene and accelerate SiO2 RALD reactions. The synergistic catalysis of Lewis/Brønsted acid sites and interfacial interactions may be applied in the RALD fabrication of other silica nanolaminates, such as HfO2/SiO2, ZrO2/SiO2, and TiO2/SiO2, in microelectronics, catalysis, energy storage, and conversion.Rapid atomic layer deposition (RALD) has been applied to prepare various nanolaminates with repeated multilayer structures. The possible reaction pathways for RALD of the Al2O3/SiO2 nanolaminate using trimethylaluminum (TMA) and tris(tert-butoxy)silanol (TBS) are investigated by using density functional theory (DFT) calculations. The introduction of a Lewis-acid catalyst, TMA, can result in the formation of the catalytic site, which accelerates the propagation of the siloxane polymer. The rate-determining step of whole RALD is the elimination of isobutene of the tert-butoxy groups. The Brønsted acid site of [AlO4] can catalyze the elimination of isobutene. At the same time, the interfacial interactions, such as hydrogen bonding interactions between tert-butoxy groups and the surface, further catalyze the elimination of isobutene and accelerate

  11. Distribution and integrated assessment of lead in an abandoned lead-acid battery site in Southwest China before redevelopment.

    PubMed

    Wang, Mei; Zhang, Chao; Zhang, Zhuo; Li, Fasheng; Guo, Guanlin

    2016-06-01

    Lead-acid battery sites have contributed enormous amounts of lead to the environment, significantly affecting its global biogeochemical cycle and leaving the potential risks to human health. An abandoned lead-acid battery site prepared for redevelopment was selected in order to study the distribution of lead in soils, plants, rhizosphere soils and soil solutions. In total, 197 samples from 77 boreholes were collected and analyzed. Single extractions by acetic acid (HOAc) were conducted to assess the bioavailability and speciation of lead in soils for comparison with the parts of the plants that are aboveground. Health risks for future residential development were evaluated by the integrated exposure uptake biokinetic (IEUBK) model. The results indicated that lead concentrations in 83% of the soil samples exceeded the Chinese Environmental Quality Standard for soil (350 mg/kg for Pb) and mainly occurred at depths between 0 and 1.5 m while accumulating at the surface of demolished construction waste and miscellaneous fill. Lead concentrations in soil solutions and HOAc extraction leachates were linked closely to the contents of aboveground Broussonetia papyrifera and Artemisia annua, two main types of local plants that were found at the site. The probability density of lead in blood (PbB) in excess of 10 µg/dL could overtake the 99% mark in the residential scenario. The findings provided a relatively integrated method to illustrate the onsite investigations and assessment for similar sites before remediation and future development from more comprehensive aspects.

  12. Measurements of mass attenuation coefficient, effective atomic number and electron density of some amino acids

    NASA Astrophysics Data System (ADS)

    Kore, Prashant S.; Pawar, Pravina P.

    2014-05-01

    The mass attenuation coefficients of some amino acids, such as DL-aspartic acid-LR(C4H7NO4), L-glutamine (C4H10N2O3), creatine monohydrate LR(C4H9N3O2H2O), creatinine hydrochloride (C4H7N3O·HCl) L-asparagine monohydrate(C4H9N3O2H2O), L-methionine LR(C5H11NO2S), were measured at 122, 356, 511, 662, 1170, 1275 and 1330 keV photon energies using a well-collimated narrow beam good geometry set-up. The gamma-rays were detected using NaI (Tl) scintillation detection system with a resolution of 0.101785 at 662 keV. The attenuation coefficient data were then used to obtain the effective atomic numbers (Zeff), and effective electron densities (Neff) of amino acids. It was observed that the effective atomic number (Zeff) and effective electron densities (Neff) initially decrease and tend to be almost constant as a function of gamma-ray energy. Zeff and Neff experimental values showed good agreement with the theoretical values with less than 1% error for amino acids.

  13. Distribution and integrated assessment of lead in an abandoned lead-acid battery site in Southwest China before redevelopment.

    PubMed

    Wang, Mei; Zhang, Chao; Zhang, Zhuo; Li, Fasheng; Guo, Guanlin

    2016-06-01

    Lead-acid battery sites have contributed enormous amounts of lead to the environment, significantly affecting its global biogeochemical cycle and leaving the potential risks to human health. An abandoned lead-acid battery site prepared for redevelopment was selected in order to study the distribution of lead in soils, plants, rhizosphere soils and soil solutions. In total, 197 samples from 77 boreholes were collected and analyzed. Single extractions by acetic acid (HOAc) were conducted to assess the bioavailability and speciation of lead in soils for comparison with the parts of the plants that are aboveground. Health risks for future residential development were evaluated by the integrated exposure uptake biokinetic (IEUBK) model. The results indicated that lead concentrations in 83% of the soil samples exceeded the Chinese Environmental Quality Standard for soil (350 mg/kg for Pb) and mainly occurred at depths between 0 and 1.5 m while accumulating at the surface of demolished construction waste and miscellaneous fill. Lead concentrations in soil solutions and HOAc extraction leachates were linked closely to the contents of aboveground Broussonetia papyrifera and Artemisia annua, two main types of local plants that were found at the site. The probability density of lead in blood (PbB) in excess of 10 µg/dL could overtake the 99% mark in the residential scenario. The findings provided a relatively integrated method to illustrate the onsite investigations and assessment for similar sites before remediation and future development from more comprehensive aspects. PMID:26921546

  14. Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids.

    PubMed

    Proudfoot, Andrew; Frank, Andreas O; Ruggiu, Fiorella; Mamo, Mulugeta; Lingel, Andreas

    2016-05-01

    The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density. PMID:27130242

  15. Counting Active Sites on Titanium Oxide-Silica Catalysts for Hydrogen Peroxide Activation through In Situ Poisoning with Phenylphosphonic Acid

    SciTech Connect

    Eaton, Todd R.; Boston, Andrew M.; Thompson, Anthony B.; Gray, Kimberly A.; Notestein, Justin M.

    2015-06-04

    Quantifying specific active sites in supported catalysts improves our understanding and assists in rational design. Supported oxides can undergo significant structural changes as surface densities increase from site-isolated cations to monolayers and crystallites, which changes the number of kinetically relevant sites. Herein, TiOx domains are titrated on TiOx–SiO2 selectively with phenylphosphonic acid (PPA). An ex situ method quantifies all fluid-accessible TiOx, whereas an in situ titration during cis-cyclooctene epoxidation provides previously unavailable values for the number of tetrahedral Ti sites on which H2O2 activation occurs. We use this method to determine the active site densities of 22 different catalysts with different synthesis methods, loadings, and characteristic spectra and find a single intrinsic turnover frequency for cis-cyclooctene epoxidation of (40±7) h-1. This simple method gives molecular-level insight into catalyst structure that is otherwise hidden when bulk techniques are used.

  16. Resolution in QCM Sensors for the Viscosity and Density of Liquids: Application to Lead Acid Batteries

    PubMed Central

    Cao-Paz, Ana María; Rodríguez-Pardo, Loreto; Fariña, José; Marcos-Acevedo, Jorge

    2012-01-01

    In battery applications, particularly in automobiles, submarines and remote communications, the state of charge (SoC) is needed in order to manage batteries efficiently. The most widely used physical parameter for this is electrolyte density. However, there is greater dependency between electrolyte viscosity and SoC than that seen for density and SoC. This paper presents a Quartz Crystal Microbalance (QCM) sensor for electrolyte density-viscosity product measurements in lead acid batteries. The sensor is calibrated in H2SO4 solutions in the battery electrolyte range to obtain sensitivity, noise and resolution. Also, real-time tests of charge and discharge are conducted placing the quartz crystal inside the battery. At the same time, the present theoretical “resolution limit” to measure the square root of the density-viscosity product (ρη) of a liquid medium or best resolution achievable with a QCM oscillator is determined. Findings show that the resolution limit only depends on the characteristics of the liquid to be studied and not on frequency. The QCM resolution limit for ρη measurements worsens when the density-viscosity product of the liquid is increased, but it cannot be improved by elevating the work frequency. PMID:23112618

  17. Resolution in QCM sensors for the viscosity and density of liquids: application to lead acid batteries.

    PubMed

    Cao-Paz, Ana María; Rodríguez-Pardo, Loreto; Fariña, José; Marcos-Acevedo, Jorge

    2012-01-01

    In battery applications, particularly in automobiles, submarines and remote communications, the state of charge (SoC) is needed in order to manage batteries efficiently. The most widely used physical parameter for this is electrolyte density. However, there is greater dependency between electrolyte viscosity and SoC than that seen for density and SoC. This paper presents a Quartz Crystal Microbalance (QCM) sensor for electrolyte density-viscosity product measurements in lead acid batteries. The sensor is calibrated in H(2)SO(4) solutions in the battery electrolyte range to obtain sensitivity, noise and resolution. Also, real-time tests of charge and discharge are conducted placing the quartz crystal inside the battery. At the same time, the present theoretical "resolution limit" to measure the square root of the density-viscosity product [Formula: see text] of a liquid medium or best resolution achievable with a QCM oscillator is determined. Findings show that the resolution limit only depends on the characteristics of the liquid to be studied and not on frequency. The QCM resolution limit for [Formula: see text] measurements worsens when the density-viscosity product of the liquid is increased, but it cannot be improved by elevating the work frequency.

  18. Bile acids reduce endocytosis of high-density lipoprotein (HDL) in HepG2 cells.

    PubMed

    Röhrl, Clemens; Eigner, Karin; Fruhwürth, Stefanie; Stangl, Herbert

    2014-01-01

    High-density lipoprotein (HDL) transports lipids to hepatic cells and the majority of HDL-associated cholesterol is destined for biliary excretion. Cholesterol is excreted into the bile directly or after conversion to bile acids, which are also present in the plasma as they are effectively reabsorbed through the enterohepatic cycle. Here, we provide evidence that bile acids affect HDL endocytosis. Using fluorescent and radiolabeled HDL, we show that HDL endocytosis was reduced in the presence of high concentrations of taurocholate, a natural non-cell-permeable bile acid, in human hepatic HepG2 and HuH7 cells. In contrast, selective cholesteryl-ester (CE) uptake was increased. Taurocholate exerted these effects extracellularly and independently of HDL modification, cell membrane perturbation or blocking of endocytic trafficking. Instead, this reduction of endocytosis and increase in selective uptake was dependent on SR-BI. In addition, cell-permeable bile acids reduced HDL endocytosis by farnesoid X receptor (FXR) activation: chenodeoxycholate and the non-steroidal FXR agonist GW4064 reduced HDL endocytosis, whereas selective CE uptake was unaltered. Reduced HDL endocytosis by FXR activation was independent of SR-BI and was likely mediated by impaired expression of the scavenger receptor cluster of differentiation 36 (CD36). Taken together we have shown that bile acids reduce HDL endocytosis by transcriptional and non-transcriptional mechanisms. Further, we suggest that HDL endocytosis and selective lipid uptake are not necessarily tightly linked to each other.

  19. Bile acids reduce endocytosis of high-density lipoprotein (HDL) in HepG2 cells.

    PubMed

    Röhrl, Clemens; Eigner, Karin; Fruhwürth, Stefanie; Stangl, Herbert

    2014-01-01

    High-density lipoprotein (HDL) transports lipids to hepatic cells and the majority of HDL-associated cholesterol is destined for biliary excretion. Cholesterol is excreted into the bile directly or after conversion to bile acids, which are also present in the plasma as they are effectively reabsorbed through the enterohepatic cycle. Here, we provide evidence that bile acids affect HDL endocytosis. Using fluorescent and radiolabeled HDL, we show that HDL endocytosis was reduced in the presence of high concentrations of taurocholate, a natural non-cell-permeable bile acid, in human hepatic HepG2 and HuH7 cells. In contrast, selective cholesteryl-ester (CE) uptake was increased. Taurocholate exerted these effects extracellularly and independently of HDL modification, cell membrane perturbation or blocking of endocytic trafficking. Instead, this reduction of endocytosis and increase in selective uptake was dependent on SR-BI. In addition, cell-permeable bile acids reduced HDL endocytosis by farnesoid X receptor (FXR) activation: chenodeoxycholate and the non-steroidal FXR agonist GW4064 reduced HDL endocytosis, whereas selective CE uptake was unaltered. Reduced HDL endocytosis by FXR activation was independent of SR-BI and was likely mediated by impaired expression of the scavenger receptor cluster of differentiation 36 (CD36). Taken together we have shown that bile acids reduce HDL endocytosis by transcriptional and non-transcriptional mechanisms. Further, we suggest that HDL endocytosis and selective lipid uptake are not necessarily tightly linked to each other. PMID:25010412

  20. Effects of eicosapentaenoic acid and docosahexaenoic acid on low-density lipoprotein cholesterol and other lipids: a review.

    PubMed

    Jacobson, Terry A; Glickstein, Sara B; Rowe, Jonathan D; Soni, Paresh N

    2012-01-01

    In this exploratory, hypothesis-generating literature review, we evaluated potentially differential effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), and non-HDL-C in published studies of ω-3 fatty acid supplementation or prescription ω-3 fatty acid ethyl esters. Placebo-adjusted changes in mean lipid parameters were compared in randomized, controlled trials in subjects treated for ≥ 4 weeks with DHA or EPA. Of 22 studies identified, 6 compared DHA with EPA directly, 12 studied DHA alone (including 14 DHA-treated groups), and 4 examined EPA alone. In studies directly comparing EPA with DHA, a net increase in LDL-C of 3.3% was observed with DHA (DHA: +2.6%; EPA: -0.7%). In such head-to-head comparative studies, DHA treatment was associated with a net decrease in TG by 6.8% (DHA: -22.4%; EPA: -15.6%); a net increase in non-HDL-C by 1.7% (DHA: -1.2%; EPA -2.9%); and a net increase in HDL-C by 5.9% (DHA: +7.3%; EPA: +1.4%). Increases in LDL-C were also observed in 71% of DHA-alone groups [with demonstrated statistical significance (P < .05) in 67% (8 of 12) DHA-alone studies] but not in any EPA-alone studies. Changes in LDL-C significantly correlated with baseline TG for DHA-treated groups. The range of HDL-C increases documented in DHA-alone vs EPA-alone studies further supports the fact that HDL-C is increased more substantially by DHA than EPA. In total, these findings suggest that DHA-containing supplements or therapies were associated with more significant increases in LDL-C and HDL-C than were EPA-containing supplements or therapies. Future prospective, randomized trials are warranted to confirm these preliminary findings, determine the potential effects of these fatty acids on other clinical outcomes, and evaluate the generalizability of the data to larger and more heterogeneous patient populations. PMID:22264569

  1. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality.

    PubMed

    Bruggeman, Jason E; Swem, Ted; Andersen, David E; Kennedy, Patricia L; Nigro, Debora

    2015-10-01

    Intrinsic and extrinsic factors affect vital rates and population-level processes, and understanding these factors is paramount to devising successful management plans for wildlife species. For example, birds time migration in response, in part, to local and broadscale climate fluctuations to initiate breeding upon arrival to nesting territories, and prolonged inclement weather early in the breeding season can inhibit egg-laying and reduce productivity. Also, density-dependent regulation occurs in raptor populations, as territory size is related to resource availability. Arctic Peregrine Falcons (Falco peregrinus tundrius; hereafter Arctic peregrine) have a limited and northern breeding distribution, including the Colville River Special Area (CRSA) in the National Petroleum Reserve-Alaska, USA. We quantified influences of climate, topography, nest productivity, prey habitat, density dependence, and interspecific competition affecting Arctic peregrines in the CRSA by applying the Dail-Madsen model to estimate abundance and vital rates of adults on nesting cliffs from 1981 through 2002. Arctic peregrine abundance increased throughout the 1980s, which spanned the population's recovery from DDT-induced reproductive failure, until exhibiting a stationary trend in the 1990s. Apparent survival rate (i.e., emigration; death) was negatively correlated with the number of adult Arctic peregrines on the cliff the previous year, suggesting effects of density-dependent population regulation. Apparent survival and arrival rates (i.e., immigration; recruitment) were higher during years with earlier snowmelt and milder winters, and apparent survival was positively correlated with nesting season maximum daily temperature. Arrival rate was positively correlated with average Arctic peregrine productivity along a cliff segment from the previous year and initial abundance was positively correlated with cliff height. Higher cliffs with documented higher productivity (presumably

  2. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality.

    PubMed

    Bruggeman, Jason E; Swem, Ted; Andersen, David E; Kennedy, Patricia L; Nigro, Debora

    2015-10-01

    Intrinsic and extrinsic factors affect vital rates and population-level processes, and understanding these factors is paramount to devising successful management plans for wildlife species. For example, birds time migration in response, in part, to local and broadscale climate fluctuations to initiate breeding upon arrival to nesting territories, and prolonged inclement weather early in the breeding season can inhibit egg-laying and reduce productivity. Also, density-dependent regulation occurs in raptor populations, as territory size is related to resource availability. Arctic Peregrine Falcons (Falco peregrinus tundrius; hereafter Arctic peregrine) have a limited and northern breeding distribution, including the Colville River Special Area (CRSA) in the National Petroleum Reserve-Alaska, USA. We quantified influences of climate, topography, nest productivity, prey habitat, density dependence, and interspecific competition affecting Arctic peregrines in the CRSA by applying the Dail-Madsen model to estimate abundance and vital rates of adults on nesting cliffs from 1981 through 2002. Arctic peregrine abundance increased throughout the 1980s, which spanned the population's recovery from DDT-induced reproductive failure, until exhibiting a stationary trend in the 1990s. Apparent survival rate (i.e., emigration; death) was negatively correlated with the number of adult Arctic peregrines on the cliff the previous year, suggesting effects of density-dependent population regulation. Apparent survival and arrival rates (i.e., immigration; recruitment) were higher during years with earlier snowmelt and milder winters, and apparent survival was positively correlated with nesting season maximum daily temperature. Arrival rate was positively correlated with average Arctic peregrine productivity along a cliff segment from the previous year and initial abundance was positively correlated with cliff height. Higher cliffs with documented higher productivity (presumably

  3. Receptor-mediated uptake of low density lipoprotein stimulates bile acid synthesis by cultured rat hepatocytes

    SciTech Connect

    Junker, L.H.; Davis, R.A. )

    1989-12-01

    The cellular mechanisms responsible for the lipoprotein-mediated stimulation of bile acid synthesis in cultured rat hepatocytes were investigated. Adding 280 micrograms/ml of cholesterol in the form of human or rat low density lipoprotein (LDL) to the culture medium increased bile acid synthesis by 1.8- and 1.6-fold, respectively. As a result of the uptake of LDL, the synthesis of (14C)cholesterol from (2-14C)acetate was decreased and cellular cholesteryl ester mass was increased. Further studies demonstrated that rat apoE-free LDL and apoE-rich high density lipoprotein (HDL) both stimulated bile acid synthesis 1.5-fold, as well as inhibited the formation of (14C)cholesterol from (2-14C)acetate. Reductive methylation of LDL blocked the inhibition of cholesterol synthesis, as well as the stimulation of bile acid synthesis, suggesting that these processes require receptor-mediated uptake. To identify the receptors responsible, competitive binding studies using 125I-labeled apoE-free LDL and 125I-labeled apoE-rich HDL were performed. Both apoE-free LDL and apoE-rich HDL displayed an equal ability to compete for binding of the other, suggesting that a receptor or a group of receptors that recognizes both apolipoproteins is involved. Additional studies show that hepatocytes from cholestyramine-treated rats displayed 2.2- and 3.4-fold increases in the binding of apoE-free LDL and apoE-rich HDL, respectively. These data show for the first time that receptor-mediated uptake of LDL by the liver is intimately linked to processes activating bile acid synthesis.

  4. Stratospheric aerosol acidity, density, and refractive index deduced from SAGE 2 and NMC temperature data

    NASA Technical Reports Server (NTRS)

    Yue, G. K.; Poole, L. R.; Wang, P.-H.; Chiou, E. W.

    1994-01-01

    Water vapor concentrations obtained by the Stratospheric Aerosol and Gas Experiment 2 (SAGE 2) and collocated temperatures provided by the National Meteorological Center (NMC) from 1986 to 1990 are used to deduce seasonally and zonally averaged acidity, density, and refractive index of stratospheric aerosols. It is found that the weight percentage of sulfuric acid in the aerosols increases from about 60 just above the tropopause to about 86 at 35 km. The density increases from about 1.55 to 1.85 g/cu cm between the same altitude limits. Some seasonal variations of composition and density are evident at high latitudes. The refractive indices at 1.02, 0.694, and 0.532 micrometers increase, respectively, from about 1.425, 1.430, and 1.435 just above the tropopause to about 1.445, 1.455, and 1.458 at altitudes above 27 km, depending on the season and latitude. The aerosol properties presented can be used in models to study the effectiveness of heterogeneous chemistry, the mass loading of stratospheric aerosols, and the extinction and backscatter of aerosols at different wavelengths. Computed aerosol surface areas, rate coefficients for the heterogeneous reaction ClONO2 + H2O yields HOCl + HNO3 and aerosol mass concentrations before and after the Pinatubo eruption in June 1991 are shown as sample applications.

  5. Lewis molecular acidity of ionic liquids from empirical energy-density models.

    PubMed

    Contreras, Renato; Aizman, Arie; Tapia, Ricardo A; Cerda-Monje, Andrea

    2013-02-14

    Two complementary models of Lewis molecular acidity are introduced and tested in a wide series of 45 room temperature ionic liquids (RTIL). They are defined in the context of the conceptual density functional theory. The first one, which we tentatively call the excess electronic chemical potential, assesses the electron accepting power of the RTIL by relating the H-bond donor acidity with the charge transfer associated to the acidic H-atom migration at the cation of the RTIL considered as a HB-donor species. This global index accounts for the molecular acidity of the cation moiety of the ionic liquid that takes into account the perturbation of the anionic partner. The second index is defined in terms of the local charge capacity modeled through the maximum electronic charge that the cation, in its valence state, may accept from an unspecified environment. Each model is compared with the experimental HB-donor acidity parameter of the Kamlet Taft model. The best comparison is obtained for a combination of both the excess electronic chemical potential and the local charge capacity. As expected, the correlations with the Kamlet Taft α parameter do not lead to a universal model of HB-donor acidity. Reduced correlations for limited series of structurally related RTIL are obtained instead. Finally, we illustrate the reliability and usefulness of the proposed model of RTIL molecular acidity to explain the cation-dependent solvent effects on the reactivity trends for cycloaddition, Kemp elimination, and Menschutkin reactions, for which experimental rate coefficients are available from literature. PMID:23323706

  6. Influence of different forms of acidities on soil microbiological properties and enzyme activities at an acid mine drainage contaminated site.

    PubMed

    Sahoo, Prafulla Kumar; Bhattacharyya, Pradip; Tripathy, Subhasish; Equeenuddin, Sk Md; Panigrahi, M K

    2010-07-15

    Assessment of microbial parameters, viz. microbial biomass, fluorescence diacetate, microbial respiration, acid phosphatase, beta-glucosidase and urease with respect to acidity helps in evaluating the quality of soils. This study was conducted to investigate the effects of different forms of acidities on soil microbial parameters in an acid mine drainage contaminated site around coal deposits in Jainta Hills of India. Total potential and exchangeable acidity, extractable and exchangeable aluminium were significantly higher in contaminated soil compared to the baseline (p<0.01). Different forms of acidity were significantly and positively correlated with each other (p<0.05). Further, all microbial properties were positively and significantly correlated with organic carbon and clay (p<0.05). The ratios of microbial parameters with organic carbon were negatively correlated with different forms of acidity. Principal component analysis and cluster analyses showed that the microbial activities are not directly influenced by the total potential acidity and extractable aluminium. Though acid mine drainage affected soils had higher microbial biomass and activities due to higher organic matter content than those of the baseline soils, the ratios of microbial parameters/organic carbon indicated suppression of microbial growth and activities due to acidity stress. PMID:20417031

  7. A density functional study of crystalline acetic acid and its proton transfer polymorphic forms

    NASA Astrophysics Data System (ADS)

    Rovira, Carme; Novoa, Juan J.

    2000-11-01

    We present a density functional study of the structure and dynamics of solid acetic acid. Our calculations are based on density functional theory combined with molecular dynamics, within the Car-Parrinello scheme. The computed structure of the acetic acid crystal, optimized without symmetry constraints, is in very good agreement with the experiment and reproduces the changes in the intramolecular structure when going from the gas phase to the solid. The cell parameters of the experimental structure are also well reproduced. Cooperative effects along the molecular chains building the crystal are found to be small (1.2 kcal/mol), although larger than it had been previously estimated. The anti conformation of the COOH fragment leads to a stable structure up to 250 K, with an energy of only 3 kcal/mol above that of the known syn form. The energy barrier associated with the most likely pathway for the syn to anti conformations, involving proton transfer along the OH⋯O units (<5.8 kcal/mol) is much smaller than the experimental barrier for the syn/anti isomerism in gas phase and in solution. Intramolecular and intermolecular reorganizations upon change to the anti structure are analyzed. Overall, our results pinpoint the anti form as a good candidate for a possible acetic acid polymorph.

  8. Evidence that Chemical Chaperone 4-Phenylbutyric Acid Binds to Human Serum Albumin at Fatty Acid Binding Sites

    PubMed Central

    James, Joel; Shihabudeen, Mohamed Sham; Kulshrestha, Shweta; Goel, Varun; Thirumurugan, Kavitha

    2015-01-01

    Endoplasmic reticulum stress elicits unfolded protein response to counteract the accumulating unfolded protein load inside a cell. The chemical chaperone, 4-Phenylbutyric acid (4-PBA) is a FDA approved drug that alleviates endoplasmic reticulum stress by assisting protein folding. It is found efficacious to augment pathological conditions like type 2 diabetes, obesity and neurodegeneration. This study explores the binding nature of 4-PBA with human serum albumin (HSA) through spectroscopic and molecular dynamics approaches, and the results show that 4-PBA has high binding specificity to Sudlow Site II (Fatty acid binding site 3, subdomain IIIA). Ligand displacement studies, RMSD stabilization profiles and MM-PBSA binding free energy calculation confirm the same. The binding constant as calculated from fluorescence spectroscopic studies was found to be kPBA = 2.69 x 105 M-1. Like long chain fatty acids, 4-PBA induces conformational changes on HSA as shown by circular dichroism, and it elicits stable binding at Sudlow Site II (fatty acid binding site 3) by forming strong hydrogen bonding and a salt bridge between domain II and III of HSA. This minimizes the fluctuation of HSA backbone as shown by limited conformational space occupancy in the principal component analysis. The overall hydrophobicity of W214 pocket (located at subdomain IIA), increases upon occupancy of 4-PBA at any FA site. Descriptors of this pocket formed by residues from other subdomains largely play a role in compensating the dynamic movement of W214. PMID:26181488

  9. Determination of a standard site for the measurement of bone mineral density of the human calcaneus

    PubMed Central

    BURSTON, B.; McNALLY, D. S.; NICHOLSON, H. D.

    1998-01-01

    Ultrasound of the calcaneus may be used as a cheap, ionising radiation-free and easy to use indicator of skeletal status, and hence of osteoporotic fracture risk. At present ultrasound is not widely used as it suffers from high precision errors. As ultrasound parameters are determined in part by bone mineral density (BMD), an increase in the accuracy and precision of BMD measurements should reduce the precision error associated with ultrasound measurements. The aim of this study was to define an anatomical site on the calcaneus at which accurate and precise measurements of BMD can be made. Ten dry calcanei and 10 cadaveric feet were scanned using a DXA scanner; 9 anatomically defined regions (1 cm2) were selected in the posterior part of the calcaneus for analysis. The centre of region 1 was positioned halfway along the line joining the anterior border of the calcaneal tubercle and the peak of the posterior superior tubercle, and the remaining 8 regions were placed around this central area. The BMD in these 9 regions was compared with the whole bone BMD and the variability of BMD within each of the 9 regions was measured. The reproducibility of the technique was assessed by taking 10 repeated measurements of 2 bone and 2 cadaveric specimens, each specimen being removed and repositioned between measurements. Region 1 was found to be the most representative of total BMD in cadaveric feet. This region also showed the least variability of BMD and consistently gave the lowest coefficients of variation in the reproducibility study both in the bone and the cadaveric specimens. This region is hence the most suitable site on the calcaneus for measuring absolute values of and changes in BMD. The surface position of region 1 was found to be consistently 5/9 along the line at 45° to the vertical, from the lateral malleolus to the heel. The identification of the surface location of region 1 relative to anatomical landmarks of the foot has enabled the same anatomical site to be

  10. Acid-base site detection and mapping on solid surfaces by Kelvin force microscopy (KFM).

    PubMed

    Gouveia, Rubia F; Bernardes, Juliana S; Ducati, Telma R D; Galembeck, Fernando

    2012-12-01

    Electrostatic potential at the surface of acidic or basic solids changes under higher relative humidity (RH), as determined by using Kelvin force microscopy (KFM). The potential on acid surfaces becomes more negative as the water vapor pressure increases, while it becomes more positive on basic solids. These results verify the following hypothesis: OH(-) or H(+) ions associated with atmospheric water ion clusters are selectively adsorbed on solid surfaces, depending on the respective Brønsted acid or base character. Therefore, Kelvin microscopy, under variable humidity, is a rigorous but convenient alternative to determine the acid-base character of solid surfaces, with a great advantage: it uses only one amphoteric and simple reagent to determine both the acid and base sites. Moreover, this technique provides information on the spatial distribution of acid-base sites, which is currently inaccessible to any other method.

  11. Genetic and environmental correlations between age at menarche and bone mineral density at different skeletal sites.

    PubMed

    Guo, Y; Zhao, L-J; Shen, H; Guo, Y; Deng, H-W

    2005-12-01

    Low bone mineral density (BMD) is an important risk factor for osteoporotic fractures. Though previous studies have demonstrated that age at menarche (AAM) is phenotypically associated with BMD, the contributions of genetic and environmental factors to this association remain unknown. In this study, using variance decomposition analyses, we provided an accurate estimation of the genetic and environmental correlations between AAM and BMD in 2,667 Caucasian women from 512 pedigrees. After adjustment for significant covariates, we detected significant genetic correlations between AAM and BMD at the lumbar spine, femoral neck, and ultradistal radius (rho(G) = -0.1316, -0.1417, and -0.1137, respectively; all P < 0.01). However, all environmental correlations between AAM and BMD were nonsignificant (P > 0.05). We also generated a principal component factor for BMD (PC_BMD) and evaluated the relationship between this factor and AAM. The genetic and environmental correlations between PC_BMD and AAM (rho(P) = -0.0847, P < 0.001; rho(G) = -0.1737, P < 0.01; rho(E) = -0.0348, P > 0.05) were consistent with the results of BMD at the three skeletal sites and AAM. Our results confirmed the significant phenotypic association between BMD and AAM and for the first time suggested that this association is mainly attributable to shared genetic, rather than environmental, factors.

  12. Understanding Rubredoxin Redox Sites by Density Functional Theory Studies of Analogues

    SciTech Connect

    Luo, Yan; Niu, Shuqiang; Ichiye, Toshiko

    2012-09-06

    Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH3)4]0/1-/2-, [Fe(S2-o-xyl)2]0/1-/2-, and Na+[Fe(S2-oxyl) 2]1-/2- in different conformations. In particular, the study of Na+[Fe(S2-o-xyl)2]1-/2- is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ~0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.

  13. PORTSMOUTH ON-SITE DISPOSAL CELL HIGH DENSITY POLYETHYLENE GEOMEMBRANE LONGEVITY

    SciTech Connect

    Phifer, M.

    2012-01-31

    It is anticipated that high density polyethylene (HDPE) geomembranes will be utilized within the liner and closure cap of the proposed On-Site Disposal Cell (OSDC) at the Portsmouth Gaseous Diffusion Plant. The likely longevity (i.e. service life) of HDPE geomembranes in OSDC service is evaluated within the following sections of this report: (1) Section 2.0 provides an overview of HDPE geomembranes, (2) Section 3.0 outlines potential HDPE geomembranes degradation mechanisms, (3) Section 4.0 evaluates the applicability of HDPE geomembrane degradation mechanisms to the Portsmouth OSDC, (4) Section 5.0 provides a discussion of the current state of knowledge relative to the longevity (service life) of HDPE geomembranes, including the relation of this knowledge to the Portsmouth OSDC, and (5) Section 6.0 provides summary and conclusions relative to the anticipated service life of HDPE geomembranes in OSDC service. Based upon this evaluation it is anticipated that the service life of HDPE geomembranes in OSDC service would be significantly greater than the 200 year service life assumed for the OSDC closure cap and liner HDPE geomembranes. That is, a 200 year OSDC HDPE geomembrane service life is considered a conservative assumption.

  14. Measurement of Mars Atmosphere Argon Density with the APXS on the Opportunity site

    NASA Astrophysics Data System (ADS)

    Economou, T. E.; Citron, R. I.; Pierrehumbert, R. T.

    2008-12-01

    Using the APXS on board the Opportunity rover on MER mission, we were able to measure the argon density variation in the martian atmosphere as a function of seasons. The freezing and melting of the CO2 in the martian atmosphere at the poles creates local atmospheric lows/highs that moves the air mass. The argon, however, never freezes and stays in the air. An enhancement of Ar/CO2 mixing ratio by a factor of six at the martian South pole during the winter has been observed by the GRS onboard the Odyssey orbiter. In order to study this effect from the ground at the Opportunity site on MER mission, we have been making dedicated APXS measurements of the Ar in the atmosphere. In this case, the only real peak in the X-ray spectrum is the Ar line. To a good approximation, the APXS count rate is proportional to the number of argon atoms in the sensing volume, and hence measures the atmospheric density of argon, ρAr. If the atmosphere were perfectly mixed, the argon partial pressure would be constant. If we define the Local Mix- ing Ratio (MRlocal) as equal to the ratio of the local Ar partial pressure to the global average, then the measurement PAr/T is proportional to the local mixing ratio. The APXS Ar experiment thus gives a direct measurement of the local mixing ratio at the MER landing sites and it is a direct probe of the global circulation between the polar CO2 resource/sink and the equatorial regions. We have found that the Ar amount in the martian atmosphere at the Opportunity landing site is not constant and it is changing with the changing seasons. The change of the Ar in the atmos-phere follows the overall change in the atmospheric pressure but it is not in phase with it. There is a delay of many months between the maximum in Ar/CO2 mixing ratio and the pressure maximum. In addition, we have even seen the asymmetry between the south and north martian poles due to a different degree of CO2 contribution from both poles during the martian year. The actual Ar

  15. Probing the Binding Site of Bile Acids in TGR5.

    PubMed

    Macchiarulo, Antonio; Gioiello, Antimo; Thomas, Charles; Pols, Thijs W H; Nuti, Roberto; Ferrari, Cristina; Giacchè, Nicola; De Franco, Francesca; Pruzanski, Mark; Auwerx, Johan; Schoonjans, Kristina; Pellicciari, Roberto

    2013-12-12

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure-activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  16. Probing the Binding Site of Bile Acids in TGR5

    PubMed Central

    2013-01-01

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure–activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  17. A multi-point sensor based on optical fiber for the measurement of electrolyte density in lead-acid batteries.

    PubMed

    Cao-Paz, Ana M; Marcos-Acevedo, Jorge; del Río-Vázquez, Alfredo; Martínez-Peñalver, Carlos; Lago-Ferreiro, Alfonso; Nogueiras-Meléndez, Andrés A; Doval-Gandoy, Jesús

    2010-01-01

    This article describes a multi-point optical fiber-based sensor for the measurement of electrolyte density in lead-acid batteries. It is known that the battery charging process creates stratification, due to the different densities of sulphuric acid and water. In order to study this process, density measurements should be obtained at different depths. The sensor we describe in this paper, unlike traditional sensors, consists of several measurement points, allowing density measurements at different depths inside the battery. The obtained set of measurements helps in determining the charge (SoC) and state of health (SoH) of the battery. PMID:22319262

  18. A Multi-Point Sensor Based on Optical Fiber for the Measurement of Electrolyte Density in Lead-Acid Batteries

    PubMed Central

    Cao-Paz, Ana M.; Marcos-Acevedo, Jorge; del Río-Vázquez, Alfredo; Martínez-Peñalver, Carlos; Lago-Ferreiro, Alfonso; Nogueiras-Meléndez, Andrés A.; Doval-Gandoy, Jesús

    2010-01-01

    This article describes a multi-point optical fiber-based sensor for the measurement of electrolyte density in lead-acid batteries. It is known that the battery charging process creates stratification, due to the different densities of sulphuric acid and water. In order to study this process, density measurements should be obtained at different depths. The sensor we describe in this paper, unlike traditional sensors, consists of several measurement points, allowing density measurements at different depths inside the battery. The obtained set of measurements helps in determining the charge (SoC) and state of health (SoH) of the battery. PMID:22319262

  19. Surface charging behavior of nanoparticles by considering site distribution and density, dielectric constant and pH changes--a Monte Carlo approach.

    PubMed

    Clavier, Arnaud; Seijo, Marianne; Carnal, Fabrice; Stoll, Serge

    2015-02-14

    Monte Carlo simulations are used to describe the charging behavior of metal oxide nanoparticles thus enabling a novel and original approach to predict nanoparticle reactivity and the possible interactions with biological and environmental molecules. The charging behavior of spherical nanoparticles is investigated by adjusting the pH of the media and the influence of surface site distribution, density and dielectric constant as well as the acid/base properties of the surface sites and ΔpKa(0) values (difference between two successive deprotonation constants) is systematically studied using a grand canonical Monte Carlo method. A primitive Coulomb model is applied to describe the interaction energies between the explicit discrete sites. Homogeneous/heterogeneous surfaces and patches with homogeneous and heterogeneous distributions are considered in order to reproduce possible site distributions of metal oxide nanoparticles. Two models are used. In the 1-pKa(0) model (one deprotonation step) the results indicate that the deprotonation process is controlled by inter-site distances which are defined by site distributions and densities. It is shown that the homogeneous surface is the most efficient site distribution to obtain high ionization degrees. In the 2-pKa(0) model (two deprotonation steps), the ΔpKa(0) value is found to control the surface charge properties with regard to pH changes. By considering the variation of the total nanoparticle surface charge as a function of pH our results help in the distinction between the zero charge and the isoelectric point and interpretation of experimental NP titration curves. PMID:25579770

  20. Organic acids in cloud water and rainwater at a mountain site in acid rain areas of South China.

    PubMed

    Sun, Xiao; Wang, Yan; Li, Haiyan; Yang, Xueqiao; Sun, Lei; Wang, Xinfeng; Wang, Tao; Wang, Wenxing

    2016-05-01

    To investigate the chemical characteristics of organic acids and to identify their source, cloud water and rainwater samples were collected at Mount Lu, a mountain site located in the acid rain-affected area of south China, from August to September of 2011 and March to May of 2012. The volume-weighted mean (VWM) concentration of organic acids in cloud water was 38.42 μeq/L, ranging from 7.45 to 111.46 μeq/L, contributing to 2.50 % of acidity. In rainwater samples, organic acid concentrations varied from 12.39 to 68.97 μeq/L (VWM of 33.39 μeq/L). Organic acids contributed significant acidity to rainwater, with a value of 17.66 %. Formic acid, acetic acid, and oxalic acid were the most common organic acids in both cloud water and rainwater. Organic acids had an obviously higher concentration in summer than in spring in cloud water, whereas there was much less discrimination in rainwater between the two seasons. The contribution of organic acids to acidity was lower during summer than during spring in both cloud water (2.20 % in summer vs 2.83 % in spring) and rainwater (12.24 % in summer vs 19.89 % in spring). The formic-to-acetic acid ratio (F/A) showed that organic acids were dominated by primary emissions in 71.31 % of the cloud water samples and whole rainwater samples. Positive matrix factorization (PMF) analysis determined four factors as the sources of organic acids in cloud water, including biogenic emissions (61.8 %), anthropogenic emissions (15.28 %), marine emissions (15.07 %) and soil emissions (7.85 %). The findings from this study imply an indispensable role of organic acids in wet deposition, but organic acids may have a limited capacity to increase ecological risks in local environments. PMID:26841776

  1. Organic acids in cloud water and rainwater at a mountain site in acid rain areas of South China.

    PubMed

    Sun, Xiao; Wang, Yan; Li, Haiyan; Yang, Xueqiao; Sun, Lei; Wang, Xinfeng; Wang, Tao; Wang, Wenxing

    2016-05-01

    To investigate the chemical characteristics of organic acids and to identify their source, cloud water and rainwater samples were collected at Mount Lu, a mountain site located in the acid rain-affected area of south China, from August to September of 2011 and March to May of 2012. The volume-weighted mean (VWM) concentration of organic acids in cloud water was 38.42 μeq/L, ranging from 7.45 to 111.46 μeq/L, contributing to 2.50 % of acidity. In rainwater samples, organic acid concentrations varied from 12.39 to 68.97 μeq/L (VWM of 33.39 μeq/L). Organic acids contributed significant acidity to rainwater, with a value of 17.66 %. Formic acid, acetic acid, and oxalic acid were the most common organic acids in both cloud water and rainwater. Organic acids had an obviously higher concentration in summer than in spring in cloud water, whereas there was much less discrimination in rainwater between the two seasons. The contribution of organic acids to acidity was lower during summer than during spring in both cloud water (2.20 % in summer vs 2.83 % in spring) and rainwater (12.24 % in summer vs 19.89 % in spring). The formic-to-acetic acid ratio (F/A) showed that organic acids were dominated by primary emissions in 71.31 % of the cloud water samples and whole rainwater samples. Positive matrix factorization (PMF) analysis determined four factors as the sources of organic acids in cloud water, including biogenic emissions (61.8 %), anthropogenic emissions (15.28 %), marine emissions (15.07 %) and soil emissions (7.85 %). The findings from this study imply an indispensable role of organic acids in wet deposition, but organic acids may have a limited capacity to increase ecological risks in local environments.

  2. Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid.

    PubMed

    Mishra, Soni; Tandon, Poonam; Eravuchira, Pinkie J; El-Abassy, Rasha M; Materny, Arnulf

    2013-03-01

    Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4,5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule.

  3. A density functional study on the acidity properties of pristine and modified SiC nano-sheets

    NASA Astrophysics Data System (ADS)

    Ahmadi Peyghan, Ali; Amir Aslanzadeh, Saeed; Noei, Maziar

    2014-06-01

    Surface acidity is an important property that is frequently used to characterize the reactivity of surfaces. NH3 is well known as a probe molecule in determining the acidity of surfaces experimentally. Here, the adsorption of an NH3 molecule at different sites of a SiC nanosheet was investigated based on density functional theory framework. It was found that NH3 can be weakly adsorbed on the surface of the pristine with the adsorption energy (Ead) of about 3.5 kcal/mol with no sensible effect on the electronic properties of the sheet. Replacing a Si or C atom with both Al and B atoms increases the Ead, indicating that the acidity of SiC sheet can be controlled by doping of B and Al atoms. Relative magnetic order of the acidity for different surfaces was found to be: AlC, a C atom was replaced with a Al, (Ead=86.4 kcal/mol)≫AlSi (Ead=39.2 kcal/mol)>BC (Ead=30.9 kcal/mol)>BSi (Ead=12.3 kcal/mol)≫pristine h-SiC (Ead=3.5 kcal/mol). Moreover, it was found that when a C atom of the sheet was doped by an Al atom, HOMO-LUMO gap of the sheet becomes highly sensitive to NH3 adsorption so that it is decreased by about 31.3% after the adsorption process. It shows that the AlC-doped sheet may be used in the detection of NH3 gas molecules.

  4. Na+ Inhibits the Epithelial Na+ Channel by Binding to a Site in an Extracellular Acidic Cleft*

    PubMed Central

    Kashlan, Ossama B.; Blobner, Brandon M.; Zuzek, Zachary; Tolino, Michael; Kleyman, Thomas R.

    2015-01-01

    The epithelial Na+ channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na+, Cl−, protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na+ concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na+ binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na+. Mutations at selected sites altered the cation inhibitory preference to favor Li+ or K+ rather than Na+. Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na+. Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family. PMID:25389295

  5. Na+ inhibits the epithelial Na+ channel by binding to a site in an extracellular acidic cleft.

    PubMed

    Kashlan, Ossama B; Blobner, Brandon M; Zuzek, Zachary; Tolino, Michael; Kleyman, Thomas R

    2015-01-01

    The epithelial Na(+) channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na(+), Cl(-), protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na(+) concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na(+) binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na(+). Mutations at selected sites altered the cation inhibitory preference to favor Li(+) or K(+) rather than Na(+). Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na(+). Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family. PMID:25389295

  6. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOEpatents

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  7. A stencil printed, high energy density silver oxide battery using a novel photopolymerizable poly(acrylic acid) separator.

    PubMed

    Braam, Kyle; Subramanian, Vivek

    2015-01-27

    A novel photopolymerized poly(acrylic acid) separator is demonstrated in a printed, high-energy-density silver oxide battery. The printed battery demonstrates a high capacity of 5.4 mA h cm(-2) at a discharge current density of 2.75 mA cm(-2) (C/2 rate) while delivering good mechanical flexibility and robustness. PMID:25475759

  8. A stencil printed, high energy density silver oxide battery using a novel photopolymerizable poly(acrylic acid) separator.

    PubMed

    Braam, Kyle; Subramanian, Vivek

    2015-01-27

    A novel photopolymerized poly(acrylic acid) separator is demonstrated in a printed, high-energy-density silver oxide battery. The printed battery demonstrates a high capacity of 5.4 mA h cm(-2) at a discharge current density of 2.75 mA cm(-2) (C/2 rate) while delivering good mechanical flexibility and robustness.

  9. Influence of Regional Difference in Bone Mineral Density on Hip Fracture Site in Elderly Females by Finite Element Analysis.

    PubMed

    Lin, Z L; Li, P F; Pang, Z H; Zheng, X H; Huang, F; Xu, H H; Li, Q L

    2015-11-01

    Hip fracture is a kind of osteoporotic fractures in elderly patients. Its important monitoring indicator is to measure bone mineral density (BMD) using DXA. The stress characteristics and material distribution in different parts of the bones can be well simulated by three-dimensional finite element analysis. Our previous studies have demonstrated a linear positive correlation between clinical BMD and the density of three-dimensional finite element model of the femur. However, the correlation between the density variation between intertrochanteric region and collum femoris region of the model and the fracture site has not been studied yet. The present study intends to investigate whether the regional difference in the density of three-dimensional finite element model of the femur can be used to predict hip fracture site in elderly females. The CT data of both hip joints were collected from 16 cases of elderly female patients with hip fractures. Mimics 15.01 software was used to reconstruct the model of proximal femur on the healthy side. Ten kinds of material properties were assigned. In Abaqus 6.12 software, the collum femoris region and intertrochanteric region were, respectively, drawn for calculating the corresponding regional density of the model, followed by prediction of hip fracture site and final comparison with factual fracture site. The intertrochanteric region/collum femoris region density was [(1.20 ± 0.02) × 10(6)] on the fracture site and [(1.22 ± 0.03) × 10(6)] on the non-fracture site, and the difference was statistically significant (P = 0.03). Among 16 established models of proximal femur on the healthy side, 14 models were consistent with the actual fracture sites, one model was inconsistent, and one model was unpredictable, with the coincidence rate of 87.5 %. The intertrochanteric region or collum femoris region with lower BMD is more prone to hip fracture of the type on the corresponding site. PMID:27352330

  10. Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from DFT Studies

    SciTech Connect

    Das, Ujjal; Zhang, Guanghui; Hu, Bo; Hock, Adam S.; Redfern, Paul C.; Miller, Jeffrey T.; Curtiss, Larry A.

    2015-12-01

    Amorphous silica (SiO2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure and activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. The molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.

  11. Trends in Formic Acid Decomposition on Model Transition Metal Surfaces: A Density Functional Theory Study

    SciTech Connect

    Herron, Jeffrey A.; Scaranto, Jessica; Ferrin, Peter A.; Li, Sha; Mavrikakis, Manos

    2014-12-05

    We present a first-principles, self-consistent periodic density functional theory (PW91-GGA) study of formic acid (HCOOH) decomposition on model (111) and (100) facets of eight fcc metals (Au, Ag, Cu, Pt, Pd, Ni, Ir, and Rh) and (0001) facets of four hcp (Co, Os, Ru, and Re) metals. The calculated binding energies of key formic acid decomposition intermediates including formate (HCOO), carboxyl (COOH), carbon monoxide (CO), water (H2O), carbon dioxide (CO2), hydroxyl (OH), carbon (C), oxygen (O), and hydrogen (H; H2) are presented. Using these energetics, we develop thermochemical potential energy diagrams for both the carboxyl-mediated and the formate-mediated dehydrogenation mechanisms on each surface. We evaluate the relative stability of COOH, HCOO, and other isomeric intermediates (i.e., CO + OH, CO2 + H, CO + O + H) on these surfaces. These results provide insights into formic acid decomposition selectivity (dehydrogenation versus dehydration), and in conjunction with calculated vibrational frequency modes, the results can assist with the experimental search for the elusive carboxyl (COOH) surface intermediate. Results are compared against experimental reports in the literature.

  12. Zinc cysteine active sites of metalloproteins: a density functional theory and x-ray absorption fine structure study.

    PubMed

    Dimakis, Nicholas; Farooqi, Mohammed Junaid; Garza, Emily Sofia; Bunker, Grant

    2008-03-21

    Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)(4-n)(Cys)(n) sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.

  13. Quantitative measurement of the Brönsted acid sites in solid acids: toward a single-site design of Mo-modified ZSM-5 zeolite.

    PubMed

    Tessonnier, Jean-Philippe; Louis, Benoît; Walspurger, Stephane; Sommer, Jean; Ledoux, Marc-Jacques; Pham-Huu, Cuong

    2006-06-01

    On the basis of our previous H/D exchange studies devoted to the quantification of the number of Brönsted acid sites in solid acids, we report here an innovative approach to determine both the amount and the localization of Mo atoms inside the Mo/ZSM-5 catalyst, commonly used for the methane dehydroaromatization reaction. The influence of Mo introduction in the MFI framework was studied by means of BET, X-ray diffraction, 27Al magic angle spinning NMR, NH3 temperature-programmed desorption, and H/D isotopic exchange techniques. A dependence was found between the decrease of acidic OH groups and the Mo content. Depending on the Si/Al ratio of the zeolite, i.e., the proximity of two Brönsted acid sites, the Mo atoms substitute a different number of OH groups. Consequently, a chemical structure was proposed to describe the geometry of the Mo complex in the channels of the ZSM-5 zeolite.

  14. Atmospheric geochemistry of formic and acetic acids at a mid-latitude temperate site

    NASA Technical Reports Server (NTRS)

    Talbot, R. W.; Beecher, K. M.; Harriss, R. C.; Cofer, R. W., III

    1988-01-01

    Tropospheric concentrations of formic and acetic acids in the gas, the aerosol, and the rainwater phases were determined in samples collected 1-2 m above ground level at an open field site in eastern Virginia. These acids were found to occur principally (98 percent or above) in the gas phase, with a marked annual seasonality, averaging 1890 ppt for formate and 1310 ppt for acetate during the growing season, as compared to 695 ppt and 700 ppt, respectively, over the nongrowing season. The data support the hypothesis that biogenic emissions from vegatation are important sources of atmospheric formic and acetic acid during the local growing season. The same time trends were observed for precipitation, although with less defined seasonality. The relative increase of the acetic acid/formic acid ratio during the nongrowing season points to the dominance of anthropogenic inputs of acetic acid from motor vehicles and biomass combustion in the wintertime.

  15. Influences of weather on Ixodes scapularis nymphal densities at long-term study sites in Connecticut.

    PubMed

    Hayes, Laura E; Scott, Jennifer A; Stafford, Kirby C

    2015-04-01

    Tick species worldwide are implicated in transmission of pathogens that cause mild to severe diseases in humans and livestock. Although tick population densities are often highly correlated with tick-borne disease rates, we currently know little about which factors underlie annual changes in those tick population densities. We used a 25-year dataset of Ixodes scapularis drag-sampling surveys at two locations in CT, USA, to investigate the relationship between average nymphal density from mid-May to mid-August and monthly, lagged regional weather variables. The dataset was randomly split into two data subsets, one for hypothesis development and one for hypothesis testing. Nymphal density showed the strongest association with the Standardized Precipitation Index for January of the same year that density data were collected in the analysis based on the hypothesis development data subset. This association was positive; nymphal tick density increased with regional winter precipitation. Nymphal density was positively associated with this same weather variable in the hypothesis testing data subset. Weather conditions during the coldest months of the year may serve as a bottleneck to tick populations, thereby functioning as an important correlate of not only annual blacklegged tick nymphal densities the following summer, but also entomological risk associated with tick-borne pathogens transmitted by this species.

  16. A bidentate Lewis acid with a telluronium ion as an anion-binding site

    NASA Astrophysics Data System (ADS)

    Zhao, Haiyan; Gabbaï, François P.

    2010-11-01

    The search for receptors that can selectively capture small and potentially toxic anions in protic media has sparked a renewed interest in the synthesis and anion-binding properties of polydentate Lewis acids. Seeking new paradigms to enhance the anion affinities of such systems, we synthesized a bidentate Lewis acid that contains a boryl and a telluronium moiety as Lewis acidic sites. Anion-complexation studies indicate that this telluronium borane displays a high affinity for fluoride in methanol. Structural and computational studies show that the unusual fluoride affinity of this bidentate telluronium borane can be correlated with the formation of a B-F --> Te chelate motif supported by a strong lone-pair(F) --> σ*(Te-C) donor-acceptor interaction. These results, which illustrate the viability of heavier chalcogenium centres as anion-binding sites, allow us to introduce a novel strategy for the design of polydentate Lewis acids with enhanced anion affinities.

  17. Site-specific fatty acid-conjugation to prolong protein half-life in vivo.

    PubMed

    Lim, Sung In; Mizuta, Yukina; Takasu, Akinori; Hahn, Young S; Kim, Yong Hwan; Kwon, Inchan

    2013-09-10

    Therapeutic proteins are indispensable in treating numerous human diseases. However, therapeutic proteins often suffer short serum half-life. In order to extend the serum half-life, a natural albumin ligand (a fatty acid) has been conjugated to small therapeutic peptides resulting in a prolonged serum half-life via binding to patients' serum albumin in vivo. However, fatty acid-conjugation has limited applicability due to lack of site-specificity resulting in the heterogeneity of conjugated proteins and a significant loss in pharmaceutical activity. In order to address these issues, we exploited the site-specific fatty acid-conjugation to a permissive site of a protein, using copper-catalyzed alkyne-azide cycloaddition, by linking a fatty acid derivative to p-ethynylphenylalanine incorporated into a protein using an engineered pair of yeast tRNA/aminoacyl tRNA synthetase. As a proof-of-concept, we show that single palmitic acid conjugated to superfolder green fluorescent protein (sfGFP) in a site-specific manner enhanced a protein's albumin-binding in vitro about 20 times and the serum half-life in vivo 5 times when compared to those of the unmodified sfGFP. Furthermore, the fatty acid conjugation did not cause a significant reduction in the fluorescence of sfGFP. Therefore, these results clearly indicate that the site-specific fatty acid-conjugation is a very promising strategy to prolong protein serum half-life in vivo without compromising its folded structure and activity.

  18. Late-Holocene climate evolution at the WAIS Divide site, West Antarctica: Bubble number-density estimates

    USGS Publications Warehouse

    Fegyveresi, John M.; Alley, R.B.; Spencer, M.K.; Fitzpatrick, J.J.; Steig, E.J.; White, J.W.C.; McConnell, J.R.; Taylor, K.C.

    2011-01-01

    A surface cooling of ???1.7??C occurred over the ???two millennia prior to ???1700 CE at the West Antarctic ice sheet (WAIS) Divide site, based on trends in observed bubble number-density of samples from the WDC06A ice core, and on an independently constructed accumulation-rate history using annual-layer dating corrected for density variations and thinning from ice flow. Density increase and grain growth in polar firn are both controlled by temperature and accumulation rate, and the integrated effects are recorded in the number-density of bubbles as the firn changes to ice. Numberdensity is conserved in bubbly ice following pore close-off, allowing reconstruction of either paleotemperature or paleo-accumulation rate if the other is known. A quantitative late-Holocene paleoclimate reconstruction is presented for West Antarctica using data obtained from the WAIS Divide WDC06A ice core and a steady-state bubble number-density model. The resultant temperature history agrees closely with independent reconstructions based on stable-isotopic ratios of ice. The ???1.7??C cooling trend observed is consistent with a decrease in Antarctic summer duration from changing orbital obliquity, although it remains possible that elevation change at the site contributed part of the signal. Accumulation rate and temperature dropped together, broadly consistent with control by saturation vapor pressure.

  19. Vibrational spectroscopy and density functional theory study of 4-mercaptobenzoic acid

    NASA Astrophysics Data System (ADS)

    Li, Ran; Lv, Haiming; Zhang, Xiaolei; Liu, Peipei; Chen, Lei; Cheng, Jianbo; Zhao, Bing

    2015-09-01

    In this paper, 4-mercaptobenzoic acid (4-MBA/pMBA) was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. Based on the modeling results obtained at the B3LYP/6-311++G∗∗ level, all FTIR and Raman bands of the compound obtained experimentally were assigned. Our calculated vibrational frequencies are in good agreement with the experimental vales. The molecular electrostatic potential surface calculation was performed and the result suggested that the 4-MBA had two hydrogen bond donors and three hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311++G∗∗ level.

  20. Extruded films of blended chitosan, low density polyethylene and ethylene acrylic acid.

    PubMed

    Martínez-Camacho, A P; Cortez-Rocha, M O; Graciano-Verdugo, A Z; Rodríguez-Félix, F; Castillo-Ortega, M M; Burgos-Hernández, A; Ezquerra-Brauer, J M; Plascencia-Jatomea, M

    2013-01-16

    The obtaining of chitosan extruded films was possible by using low density polyethylene (LDPE) as a matrix polymer and ethylene-acrylic acid copolymer as an adhesive, in order to ensure adhesion in the interphase of the immiscible polymers. The obtained blend films were resistant; however, a reduction in the mechanical resistance was observed as chitosan concentration increased. The thermal stability of the films showed a certain grade of interaction between polymers as seen in FTIR spectra. The antifungal activity of the extruded films was assessed against Aspergillus niger and high inhibition percentages were observed, which may be mainly attributed to barrier properties of the extruded films and the limited oxygen availability, resulting in the inability of the fungi to grow. A low adherence of fungal spores to the material surface was observed, mainly in areas with chitosan clumps, which can serve as starting points for material degradation.

  1. Infrared and density functional theory studies of formic acid hydrate clusters in noble gas matrices

    NASA Astrophysics Data System (ADS)

    Ito, Fumiyuki

    2016-08-01

    Infrared absorption spectra of formic acid hydrate clusters (HCOOH)m(H2O)n have been measured in noble gas matrices (Ar and Kr). The concentration dependence of the spectra and the comparison with a previous experimental study on HCOOH(H2O) and HCOOH(H2O)2 [Geoge et al., Spectrochim. Acta, Part A 60 (2004) 3225] led to the identification of large clusters. Density functional theory calculations at the B3LYP-DCP/6-31+G(2d,2p) level were carried out to determine the anharmonic vibrational properties of the clusters, enabling a consistent assignment of the observed vibrational peaks to specific clusters.

  2. In vitro enantioselective displacement of propranolol from protein binding sites by acetyl salicylic acid and salicylic acid.

    PubMed

    Rezaei, Z; Khabnadideh, S; Hemmateenejad, B; Dehghani, Z

    2007-09-01

    The influences of acetyl salicylic acid (ASA) and salicylic acid (SA) on the enantioselective binding of propranolol (PL) and its enantiomers to plasma proteins and human serum albumin (HSA) were investigated. The equilibrium dialysis was employed for protein binding studies. We observed statistically significant displacement of racemic-PL, (+)-(R)-PL, and (-)-(S)-PL (0.1-10 microM) from their protein binding sites by ASA (200 microg/ml) and SA (100 microg/ml). ASA and SA displaced PL stereoselectivly from its binding sites. We concluded that ASA and its metabolite SA could change R/S ratio of PL unbound fractions and they might affect pharmacokinetic properties of PL.

  3. Are carboxyl groups the most acidic sites in amino acids? Gas-phase acidities, photoelectron spectra, and computations on tyrosine, p-hydroxybenzoic acid, and their conjugate bases.

    PubMed

    Tian, Zhixin; Wang, Xue-Bin; Wang, Lai-Sheng; Kass, Steven R

    2009-01-28

    Deprotonation of tyrosine in the gas phase was found to occur preferentially at the phenolic site, and the conjugate base consists of a 70:30 mixture of phenoxide and carboxylate anions at equilibrium. This result was established by developing a chemical probe for differentiating these two isomers, and the presence of both ions was confirmed by photoelectron spectroscopy. Equilibrium acidity measurements on tyrosine indicated that deltaG(acid)(o) = 332.5 +/- 1.5 kcal mol(-1) and deltaH(acid)(o) = 340.7 +/- 1.5 kcal mol(-1). Photoelectron spectra yielded adiabatic electron detachment energies of 2.70 +/- 0.05 and 3.55 +/- 0.10 eV for the phenoxide and carboxylate anions, respectively. The H/D exchange behavior of deprotonated tyrosine was examined using three different alcohols (CF3CH2OD, C6H5CH2OD, and CH3CH2OD), and incorporation of up to three deuterium atoms was observed. Two pathways are proposed to account for these results, and all of the experimental findings are supplemented with B3LYP/aug-cc-pVDZ and G3B3 calculations. In addition, it was found that electrospray ionization of tyrosine from a 3:1 (v/v) CH3OH/H2O solution using a commercial source produces a deprotonated [M-H]- anion with the gas-phase equilibrium composition rather than the structure of the ion that exists in aqueous media. Electrospray ionization from acetonitrile, however, leads largely to the liquid-phase (carboxylate) structure. A control molecule, p-hydroxybenzoic acid, was found to behave in a similar manner. Thus, the electrospray conditions that are employed for the analysis of a compound can alter the isomeric composition of the resulting anion.

  4. Dissolution of Simulated and Radioactive Savannah River Site High-Level Waste Sludges with Oxalic Acid & Citric Acid Solutions

    SciTech Connect

    STALLINGS, MARY

    2004-07-08

    This report presents findings from tests investigating the dissolution of simulated and radioactive Savannah River Site sludges with 4 per cent oxalic acid and mixtures of oxalic and citric acid previously recommended by a Russian team from the Khlopin Radium Institute and the Mining and Chemical Combine (MCC). Testing also included characterization of the simulated and radioactive waste sludges. Testing results showed the following: Dissolution of simulated HM and PUREX sludges with oxalic and citric acid mixtures at SRTC confirmed general trends reported previously by Russian testing. Unlike the previous Russian testing six sequential contacts of a mixture of oxalic acid citric acids at a 2:1 ratio (v/w) of acid to sludge did not produce complete dissolution of simulated HM and PUREX sludges. We observed that increased sludge dissolution occurred at a higher acid to sludge ratio, 50:1 (v/w), compared to the recommended ratio of 2:1 (v/w). We observed much lower dissolution of aluminum in a simulated HM sludge by sodium hydroxide leaching. We attribute the low aluminum dissolution in caustic to the high fraction of boehmite present in the simulated sludge. Dissolution of HLW sludges with 4 per cent oxalic acid and oxalic/citric acid followed general trends observed with simulated sludges. The limited testing suggests that a mixture of oxalic and citric acids is more efficient for dissolving HM and PUREX sludges and provides a more homogeneous dissolution of HM sludge than oxalic acid alone. Dissolution of HLW sludges in oxalic and oxalic/citric acid mixtures produced residual sludge solids that measured at higher neutron poison to equivalent 235U weight ratios than that in the untreated sludge solids. This finding suggests that residual solids do not present an increased nuclear criticality safety risk. Generally the neutron poison to equivalent 235U weight ratios of the acid solutions containing dissolved sludge components are lower than those in the untreated

  5. Fibroblast response is enhanced by poly(L-lactic acid) nanotopography edge density and proximity

    PubMed Central

    Milner, Keith R; Siedlecki, Christopher A

    2007-01-01

    The development of scaffolds for use in tissue engineering applications requires careful choice of macroscale properties, such as mechanical characteristics, porosity and biodegradation. The micro- and nano-scale properties of the scaffold surface are also an important design criterion as these influence cell adhesion, proliferation, and differentiation. The cellular response is known to be affected by surface topography but the mechanisms governing this remain unclear. Homogenous poly(L-lactic acid) was textured with surface nanotopographies by two-stage replication molding of heterogeneous demixed polymer films. Initial cell adhesion was improved on nanotextured surfaces compared with smooth controls, but subsequent cell density was significantly reduced on the roughest surfaces. Improvements in cell response were found to correlate with focal contact and actin microfilament development. Cell response was found to trend both with the surface density of topography edges and with inter-topography spacing, indicating possible roles for edges stimulating cell adhesion/proliferation or for spacing to modulate the ability of integrin-ligand bonds to cluster and form focal adhesions. This study furthers understanding of the geometric properties of surface nanotopographies that affect cellular response. It is hoped that identification of the mechanisms governing cell-topography interactions will allow rule-based design of biomaterial surface to engineer specific cellular responses. PMID:17722548

  6. Site-specific incorporation of a fluorescent terphenyl unnatural amino acid.

    PubMed

    Lampkowski, Jessica S; Uthappa, Diya M; Young, Douglas D

    2015-11-15

    The site-specific incorporation of unnatural amino acids into proteins has a wide range of biological implications. Of particular interest is the incorporation of fluorescent probes as a mechanism to track protein function, transport, and folding. Thus, the development of a novel system for the incorporation of new fluorescent unnatural amino acids has significant utility. Specifically, we have elucidated an aminoacyl-tRNA synthetase capable of recognizing a terphenyl UAA derivative, and charging a cognate tRNA with this amino acid for protein incorporation. Moreover, we have successfully incorporated this fluorescent UAA into GFP at several key residues, demonstrating a novel means to modulate fluorescence within the protein.

  7. Protective effect of oleanolic acid on oxidized-low density lipoprotein induced endothelial cell apoptosis.

    PubMed

    Cao, Jianhua; Li, Guanghui; Wang, Meizhi; Li, Hui; Han, Zhiwu

    2015-10-01

    Oleanolic acid (3β-hydroxyolean-12-en-28-oic acid, OA) is a naturally-occurring triterpenoid with various promising pharmacological properties. The present study was conducted to determine the protective effects of OA against oxidized low-density lipoprotein (ox-LDL) induced endothelial cell apoptosis and the possible underlying mechanisms. Our results showed that ox-LDL significantly decreased cell viability and induced apoptosis in human umbilical vein endothelial cells (HUVECs). OA in the co-treatment showed a protective effect against ox-LDL induced loss in cell viability and an increase in apoptosis, which was associated with the modulating effect of OA on ox-LDL induced hypoxia-inducible factor 1α(HIF-1α) expression. Moreover, our results showed that the modulating effect of OA against ox-LDL induced HIF-1α expression was obtained via inhibition of lipoprotein receptor 1 (LOX-1)/reactive oxygen species (ROS) signaling. Collectively, we suggested that the protective effect of OA against ox-LDL induced HUVEC apoptosis might, at least in part, be obtained via inhibition of the LOX-1/ROS/HIF-1α signaling pathway. PMID:26559024

  8. Experimental and theoretical spectroscopic studies of anticancer drug rosmarinic acid using HF and density functional theory

    NASA Astrophysics Data System (ADS)

    Mariappan, G.; Sundaraganesan, N.; Manoharan, S.

    2012-11-01

    In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of anticancer drug of rosmarinic acid. The optimized molecular structure, atomic charges, vibrational frequencies, natural bond orbital analysis and ultraviolet-visible spectral interpretation of rosmarinic acid have been studied by performing HF and DFT/B3LYP/6-31G(d,p) level of theory. The FT-IR (solid and solution phase), FT-Raman (solid phase) spectra were recorded in the region 4000-400 and 3500-50 cm-1, respectively. The UV-Visible absorption spectra of the compound that dissolved in ethanol were recorded in the range of 200-800 nm. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The formation of hydrogen bond was investigated in terms of the charge density by the NBO calculations. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

  9. Protective effect of oleanolic acid on oxidized-low density lipoprotein induced endothelial cell apoptosis.

    PubMed

    Cao, Jianhua; Li, Guanghui; Wang, Meizhi; Li, Hui; Han, Zhiwu

    2015-10-01

    Oleanolic acid (3β-hydroxyolean-12-en-28-oic acid, OA) is a naturally-occurring triterpenoid with various promising pharmacological properties. The present study was conducted to determine the protective effects of OA against oxidized low-density lipoprotein (ox-LDL) induced endothelial cell apoptosis and the possible underlying mechanisms. Our results showed that ox-LDL significantly decreased cell viability and induced apoptosis in human umbilical vein endothelial cells (HUVECs). OA in the co-treatment showed a protective effect against ox-LDL induced loss in cell viability and an increase in apoptosis, which was associated with the modulating effect of OA on ox-LDL induced hypoxia-inducible factor 1α(HIF-1α) expression. Moreover, our results showed that the modulating effect of OA against ox-LDL induced HIF-1α expression was obtained via inhibition of lipoprotein receptor 1 (LOX-1)/reactive oxygen species (ROS) signaling. Collectively, we suggested that the protective effect of OA against ox-LDL induced HUVEC apoptosis might, at least in part, be obtained via inhibition of the LOX-1/ROS/HIF-1α signaling pathway.

  10. The myeloperoxidase product hypochlorous acid generates irreversible high-density lipoprotein receptor inhibitors

    PubMed Central

    Binder, Veronika; Ljubojevic, Senka; Haybaeck, Johannes; Holzer, Michael; El-Gamal, Dalia; Schicho, Rudolf; Pieske, Burkert; Heinemann, Akos; Marsche, Gunther

    2014-01-01

    Objective Elevated levels of advanced oxidation protein products (AOPPs) have been described in several chronic inflammatory diseases, like chronic renal insufficiency, rheumatoid arthritis and atherosclerosis. Recent findings revealed that AOPPs are inhibitors of the major high-density lipoprotein (HDL) receptor, scavenger receptor class B, type 1 (SR-BI). Here we investigated what oxidation induced structural alterations convert plasma albumin into an HDL-receptor inhibitor. Approach and Results Exposure of albumin to the physiological oxidant, hypochlorous acid, generated high affinity SR-BI ligands. Protection of albumin lysine-residues prior exposure to hypochlorous acid as well as regeneration of N-chloramines after oxidation of albumin completely prevented binding of oxidized albumin to SR-BI, indicating that modification of albumin lysine-residues is required to generate SR-BI ligands. Of particular interest, N-chloramines within oxidized albumin promoted irreversible binding to SR-BI, resulting in permanent receptor blockade. We observed that the SR-BI inhibitory activity of albumin isolated from chronic kidney disease patients correlated with the content of the myeloperoxidase-specific oxidation product 3-chlorotyrosine and was associated with alterations in the composition of HDL. Conclusion Given that several potential atheroprotective activities of HDL are mediated by SR-BI, the present results raise the possibility that oxidized plasma albumin, through permanent SR-BI blockade, contributes to the pathophysiology of cardiovascular disease. PMID:23493288

  11. Density functional theory studies on molecular structure, vibrational spectra and electronic properties of cyanuric acid.

    PubMed

    Prabhaharan, M; Prabakaran, A R; Srinivasan, S; Gunasekaran, S

    2015-03-01

    The present work has been carried out a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of cyanuric acid. The FT-IR (100-4000cm(-1)) and FT-Raman spectra (400-4000cm(-1)) of cyanuric acid were recorded. In DFT methods, Becke's three parameter exchange-functional (B3) combined with gradient-corrected correlation functional of Lee, Yang and Parr (LYP) by implementing the split-valence polarized 6-31G(d,p) and 6-31++G(d,p) basis sets have been considered for the computation of the molecular structure optimization, vibrational frequencies, thermodynamic properties and energies of the optimized structures. The density functional theory (DFT) result complements the experimental findings. The electronic properties, such as HOMO-LUMO energies and molecular electrostatic potential (MESP) are also performed. Mulliken population analysis on atomic charges is also calculated. The first order hyperpolarizability (βtotal) of this molecular system and related properties (β, μ and Δα) are calculated using DFT/B3LYP/6-31G (d,p) and B3LYP/6-311++G(d,p) methods. The thermodynamic functions (heat capacity, entropy and enthalpy) from spectroscopic data by statistical methods were also obtained for the range of temperature 50-1000K.

  12. Density functional theory studies on molecular structure, vibrational spectra and electronic properties of cyanuric acid

    NASA Astrophysics Data System (ADS)

    Prabhaharan, M.; Prabakaran, A. R.; Srinivasan, S.; Gunasekaran, S.

    2015-03-01

    The present work has been carried out a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of cyanuric acid. The FT-IR (100-4000 cm-1) and FT-Raman spectra (400-4000 cm-1) of cyanuric acid were recorded. In DFT methods, Becke's three parameter exchange-functional (B3) combined with gradient-corrected correlation functional of Lee, Yang and Parr (LYP) by implementing the split-valence polarized 6-31G(d,p) and 6-31++G(d,p) basis sets have been considered for the computation of the molecular structure optimization, vibrational frequencies, thermodynamic properties and energies of the optimized structures. The density functional theory (DFT) result complements the experimental findings. The electronic properties, such as HOMO-LUMO energies and molecular electrostatic potential (MESP) are also performed. Mulliken population analysis on atomic charges is also calculated. The first order hyperpolarizability (βtotal) of this molecular system and related properties (β, μ and Δα) are calculated using DFT/B3LYP/6-31G (d,p) and B3LYP/6-311++G(d,p) methods. The thermodynamic functions (heat capacity, entropy and enthalpy) from spectroscopic data by statistical methods were also obtained for the range of temperature 50-1000 K.

  13. Parkinson's disease: decreased density of /sup 3/H-imipramine and /sup 3/H-paroxetine binding sites in putamen

    SciTech Connect

    Raisman, R.; Cash, R.; Agid, Y.

    1986-04-01

    The density of high-affinity /sup 3/H-imipramine and /sup 3/H-paroxetine binding sites (two serotonin-uptake blockers) was decreased in the putamen of parkinsonian patients. The correlation between serotonin levels and the number of /sup 3/H-imipramine and /sup 3/H-paroxetine binding sites suggests that they are located on serotoninergic nerve terminals and could be used to study serotoninergic innervation in the human brain. Since imipramine and paroxetine are powerful antidepressants, these results furthermore suggest that decreased serotoninergic transmission may be implicated in the pathophysiology of depression in Parkinson's disease.

  14. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment

    NASA Astrophysics Data System (ADS)

    Astani, Elahe; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L.; Shekarsaraei, Setareh

    2016-04-01

    A theoretical study was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond (HB), in the active site of enzyme human dehydroepiandrosterone sulphotransferase (SULT2A1/DHEA) using the local (M06-L) and hybrid (M06, M06-2X) meta-GGA functionals of density functional theory (DFT). Results revealed that DHEA is able to form HBs with residues His99, Tyr231, Met137 and Met16 in the active site of the SULT2A1/DHEA. It was found that DHEA interacts with the other residues through electrostatic and Van der Waals interactions.

  15. Effect of acidic amino acids engineered into the active site cleft of Thermopolyspora flexuosa GH11 xylanase.

    PubMed

    Li, He; Turunen, Ossi

    2015-01-01

    Thermopolyspora flexuosa GH11 xylanase (XYN11A) shows optimal activity at pH 6-7 and 75-80 °C. We studied how mutation to aspartic acid (N46D and V48D) in the vicinity of the catalytic acid/base affects the pH activity of highly thermophilic GH11 xylanase. Both mutations shifted the pH activity profile toward acidic pH. In general, the Km values were lower at pH 4-5 than at pH 6, and in line with this, the rate of hydrolysis of xylotetraose was slightly faster at pH 4 than at pH 6. The N46D mutation and also lower pH in XYN11A increased the hydrolysis of xylotriose. The Km value increased remarkably (from 2.5 to 11.6 mg/mL) because of V48D, which indicates the weakening of binding affinity of the substrate to the active site. Xylotetraose functioned well as a substrate for other enzymes, but with lowered reaction rate for V48D. Both N46D and V48D increased the enzyme inactivation by ionic liquid [emim]OAc. In conclusion, the pH activity profile could be shifted to acidic pH due to an effect from two different directions, but the tightly packed GH11 active site can cause steric problems for the mutations.

  16. Effective and site-specific phosphoramidation reaction for universally labeling nucleic acids.

    PubMed

    Su, Yu-Chih; Chen, Hsing-Yin; Ko, Ni Chien; Hwang, Chi-Ching; Wu, Min Hui; Wang, Li-Fang; Wang, Yun-Ming; Chang, Sheng-Nan; Wang, Eng-Chi; Wang, Tzu-Pin

    2014-03-15

    Here we report efficient and selective postsynthesis labeling strategies, based on an advanced phosphoramidation reaction, for nucleic acids of either synthetic or enzyme-catalyzed origin. The reactions provided phosphorimidazolide intermediates of DNA or RNA which, whether reacted in one pot (one-step) or purified (two-step), were directly or indirectly phosphoramidated with label molecules. The acquired fluorophore-labeled nucleic acids, prepared from the phosphoramidation reactions, demonstrated labeling efficacy by their F/N ratio values (number of fluorophores per molecule of nucleic acid) of 0.02-1.2 which are comparable or better than conventional postsynthesis fluorescent labeling methods for DNA and RNA. Yet, PCR and UV melting studies of the one-step phosphoramidation-prepared FITC-labeled DNA indicated that the reaction might facilitate nonspecific hybridization in nucleic acids. Intrinsic hybridization specificity of nucleic acids was, however, conserved in the two-step phosphoramidation reaction. The reaction of site-specific labeling nucleic acids at the 5'-end was supported by fluorescence quenching and UV melting studies of fluorophore-labeled DNA. The two-step phosphoramidation-based, effective, and site-specific labeling method has the potential to expedite critical research including visualization, quantification, structural determination, localization, and distribution of nucleic acids in vivo and in vitro.

  17. In Situ Oxalic Acid Injection to Accelerate Arsenic Remediation at a Superfund Site in New Jersey

    PubMed Central

    Wovkulich, Karen; Stute, Martin; Mailloux, Brian J.; Keimowitz, Alison R.; Ross, James; Bostick, Benjamin; Sun, Jing; Chillrud, Steven N.

    2015-01-01

    Arsenic is a prevalent contaminant at a large number of US Superfund sites; establishing techniques that accelerate As remediation could benefit many sites. Hundreds of tons of As were released into the environment by the Vineland Chemical Co. in southern New Jersey during its manufacturing lifetime (1949–1994), resulting in extensive contamination of surface and subsurface soils and sediments, groundwater, and the downstream watershed. Despite substantial intervention at this Superfund site, sufficient aquifer cleanup could require many decades if based on traditional pump and treat technologies only. Laboratory column experiments have suggested that oxalic acid addition to contaminated aquifer solids could promote significant As release from the solid phase. To evaluate the potential of chemical additions to increase As release in situ and boost treatment efficiency, a forced gradient pilot scale study was conducted on the Vineland site. During spring/summer 2009, oxalic acid and bromide tracer were injected into a small portion (~50 m2) of the site for 3 months. Groundwater samples indicate that introduction of oxalic acid led to increased As release. Between 2.9 and 3.6 kg of As were removed from the sampled wells as a result of the oxalic acid treatment during the 3-month injection. A comparison of As concentrations on sediment cores collected before and after treatment and analyzed using X-ray fluorescence spectroscopy suggested reduction in As concentrations of ~36% (median difference) to 48% (mean difference). While further study is necessary, the addition of oxalic acid shows potential for accelerating treatment of a highly contaminated site and decreasing the As remediation time-scale. PMID:25598701

  18. Creative use of pilot points to address site and regional scale heterogeneity in a variable-density model

    USGS Publications Warehouse

    Dausman, Alyssa M.; Doherty, John; Langevin, Christian D.

    2010-01-01

    Pilot points for parameter estimation were creatively used to address heterogeneity at both the well field and regional scales in a variable-density groundwater flow and solute transport model designed to test multiple hypotheses for upward migration of fresh effluent injected into a highly transmissive saline carbonate aquifer. Two sets of pilot points were used within in multiple model layers, with one set of inner pilot points (totaling 158) having high spatial density to represent hydraulic conductivity at the site, while a second set of outer points (totaling 36) of lower spatial density was used to represent hydraulic conductivity further from the site. Use of a lower spatial density outside the site allowed (1) the total number of pilot points to be reduced while maintaining flexibility to accommodate heterogeneity at different scales, and (2) development of a model with greater areal extent in order to simulate proper boundary conditions that have a limited effect on the area of interest. The parameters associated with the inner pilot points were log transformed hydraulic conductivity multipliers of the conductivity field obtained by interpolation from outer pilot points. The use of this dual inner-outer scale parameterization (with inner parameters constituting multipliers for outer parameters) allowed smooth transition of hydraulic conductivity from the site scale, where greater spatial variability of hydraulic properties exists, to the regional scale where less spatial variability was necessary for model calibration. While the model is highly parameterized to accommodate potential aquifer heterogeneity, the total number of pilot points is kept at a minimum to enable reasonable calibration run times.

  19. PHYSICAL SOLUTIONS FOR ACID ROCK DRAINAGE AT REMOTE SITES DEMONSTRATION PROJECT

    EPA Science Inventory

    This report summarizes the results of Mine Waste Technology Program, Activity III, Project 42, Physical Solutions for Acid Rock Drainage at Remote Sites, funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by EPA and the U.S. Department of Energy. A...

  20. LIME TREATMENT LAGOONS TECHNOLOGY FOR TREATING ACID MINE DRAINAGE FROM TWO MINING SITES

    EPA Science Inventory

    Runoff and drainage from active and inactive mines are someof the most environmentally damaging land uses i the US. Acid Mine drainage (AMD) from mining sites across the country requires treatment because of high metal concentrations that exceed regulatory standards for safe disc...

  1. Modeling Analysis for Characterizing Sulfate Reduction at an Acid Mine Drainage Site

    NASA Astrophysics Data System (ADS)

    Sengupta, A.; Ahlfeld, D. P.

    2004-05-01

    A field site has been established at Davis Mine, an abandoned pyrite mine in rural Rowe, Massachusetts in the United States. At the site, attenuation restricts the extent of AMD in both the groundwater and surface water of the area. Current research is examining the Fe(III) and sulfate reduction along with a complex community of acidophilic and acid-tolerant anaerobic microorganisms. In an effort to interlink the geochemical reduction with the microbial community existing in the site, the role of the Fe(III) and sulfate reducing bacteria is being investigated. Initial experimental data and column studies have shown the presence of sulfate reducing bacteria at the site. A detailed groundwater flow model for the affected site has been developed. A model is currently being developed of the various geochemical and biological processes at Davis Mine for use in distinguishing between sulfate reduction and dilution as they affect observed sulfate attenuation.

  2. Firn density profile at Megadunes, East Antarctica, calls for an improved densification model for low accumulation sites.

    NASA Astrophysics Data System (ADS)

    Suwa, M.; Severinghaus, J. P.

    2004-12-01

    We report a density profile of the firn at Megadunes, East Antarctica (80o78'S; 124o50'E). The Megadunes site is characterized by a low mass accumulation rate (2.9 g/cm2/yr) and cold temperature (mean annual = -49.5oC). Validating existing firn densification models using a density profile of such a site is important because such models, either purely empirical or mechanistic, have been calibrated with few sites that are analogous to a glacial condition (ultralow accumulation and temperature). We make use of CO2 concentrations in the lock-in (or non-diffusive) zone to obtain the accumulation rate, assuming that the gas in the lock-in zone ages at the same rate as the surrounding ice [Battle et al., 1996], and assuming that the gas enclosure rate must equal the long-term mean accumulation rate. This estimate is preliminary and may change when results from beta analysis of cores become available. Our density profile shows that the widely used pure empirical model by Herron and Langway [1980] overestimates the close-off depth by 16 %, and the semi-mechanistic model by Pimienta and Barnola [Barnola et al., 1991] also overestimates the close-off depth by 26 %. Our study at the Megadunes site indicates that the δ 15N of N2 paradox for glacial ice from East Antarctica would have partly resulted from a poorly calibrated densification model for a `glacial-like' condition and a thick convective zone as we observed at the Megadunes site [Severinghaus et al., in prep].

  3. Trans-cinnamic acid and coumarin-3-carboxylic acid: experimental charge-density studies to shed light on [2 + 2] cycloaddition reactions.

    PubMed

    Howard, Judith A K; Mahon, Mary F; Raithby, Paul R; Sparkes, Hazel A

    2009-04-01

    As part of an ongoing series of experimental charge-density investigations into the intra- and intermolecular interactions present in compounds which undergo solid-state [2 + 2] cycloaddition reactions, the charge-density analyses of trans-cinnamic acid and coumarin-3-carboxylic acid are reported. Thus, high-resolution single-crystal X-ray diffraction data were recorded at 100 K for trans-cinnamic acid (sin theta/lambda(max) = 1.03 A(-1)) and coumarin-3-carboxylic acid (sin theta/lambda(max) = 1.19 A(-1)). In addition to the anticipated O-H...O hydrogen bonds weak C-H...O interactions were identified in both structures along with very weak intermolecular interactions between pairs of molecules that undergo solid-state [2 + 2] cycloaddition reactions upon irradiation.

  4. Experimental and Mechanistic Understanding of Aldehyde Hydrogenation Using Au25 Nanoclusters with Lewis Acids: Unique Sites for Catalytic Reactions.

    PubMed

    Li, Gao; Abroshan, Hadi; Chen, Yuxiang; Jin, Rongchao; Kim, Hyung J

    2015-11-18

    The catalytic activity of Au25(SR)18 nanoclusters (R = C2H4Ph) for the aldehyde hydrogenation reaction in the presence of a base, e.g., ammonia or pyridine, and transition-metal ions M(z+), such as Cu(+), Cu(2+), Ni(2+) and Co(2+), as a Lewis acid is studied. The addition of a Lewis acid is found to significantly promote the catalytic activity of Au25(SR)18/CeO2 in the hydrogenation of benzaldehyde and a number of its derivatives. Matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry in conjunction with UV-vis spectroscopy confirm the generation of new species, Au25-n(SR)18-n (n = 1-4), in the presence of a Lewis acid. The pathways for the speciation of Au24(SR)17 from its parent Au25(SR)18 nanocluster as well as its structure are investigated via the density functional theory (DFT) method. The adsorption of M(z+) onto a thiolate ligand "-SR-" of Au25(SR)18, followed by a stepwise detachment of "-SR-" and a gold atom bonded to "-SR-" (thus an "Au-SR" unit) is found to be the most likely mechanism for the Au24(SR)17 generation. This in turn exposes the Au13-core of Au24(SR)17 to reactants, providing an active site for the catalytic hydrogenation. DFT calculations indicate that M(z+) is also capable of adsorbing onto the Au13-core surface, producing a possible active metal site of a different kind to catalyze the aldehyde hydrogenation reaction. This study suggests, for the first time, that species with an open metal site like adducts [nanoparticle-M]((z-1)+) or fragments Au25-n(SR)18-n function as the catalysts rather than the intact Au25(SR)18.

  5. RF1 Knockout Allows Ribosomal Incorporation of Unnatural Amino Acids at Multiple Sites

    PubMed Central

    Johnson, David B.F.; Xu, Jianfeng; Shen, Zhouxin; Takimoto, Jeffrey K.; Schultz, Matthew D.; Schmitz, Robert J.; Ecker, Joseph R.; Briggs, Steven P.; Wang, Lei

    2011-01-01

    Stop codons have been exploited for genetic incorporation of unnatural amino acids (Uaas) in live cells, but the efficiency is low possibly due to competition from release factors, limiting the power and scope of this technology. Here we show that the reportedly essential release factor 1 can be knocked out from Escherichia coli by fixing release factor 2. The resultant strain JX33 is stable and independent, and reassigns UAG from a stop signal to an amino acid when a UAG-decoding tRNA/synthetase pair is introduced. Uaas were efficiently incorporated at multiple UAG sites in the same gene without translational termination in JX33. We also found that amino acid incorporation at endogenous UAG codons is dependent on RF1 and mRNA context, which explains why E. coli tolerates apparent global suppression of UAG. JX33 affords a unique autonomous host for synthesizing and evolving novel protein functions by enabling Uaa incorporation at multiple sites. PMID:21926996

  6. Library Off-Site Shelving: Guide for High-Density Facilities.

    ERIC Educational Resources Information Center

    Nitecki, Danuta A., Ed.; Kendrick, Curtis L., Ed.

    This collection of essays addresses the planning, construction, and operating issues relating to high-density library shelving facilities. The volume covers essential topics that address issues relating to the building, its operations, and serving the collections. It begins with an introduction by the volume's editors, "The Paradox and Politics of…

  7. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    SciTech Connect

    Gangi Setty, Thanuja; Cho, Christine; Govindappa, Sowmya; Apicella, Michael A.; Ramaswamy, S.

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  8. CD36 binds oxidized low density lipoprotein (LDL) in a mechanism dependent upon fatty acid binding.

    PubMed

    Jay, Anthony G; Chen, Alexander N; Paz, Miguel A; Hung, Justin P; Hamilton, James A

    2015-02-20

    The association of unesterified fatty acid (FA) with the scavenger receptor CD36 has been actively researched, with focuses on FA and oxidized low density lipoprotein (oxLDL) uptake. CD36 has been shown to bind FA, but this interaction has been poorly characterized to date. To gain new insights into the physiological relevance of binding of FA to CD36, we characterized FA binding to the ectodomain of CD36 by the biophysical method surface plasmon resonance. Five structurally distinct FAs (saturated, monounsaturated (cis and trans), polyunsaturated, and oxidized) were pulsed across surface plasmon resonance channels, generating association and dissociation binding curves. Except for the oxidized FA HODE, all FAs bound to CD36, with rapid association and dissociation kinetics similar to HSA. Next, to elucidate the role that each FA might play in CD36-mediated oxLDL uptake, we used a fluorescent oxLDL (Dii-oxLDL) live cell assay with confocal microscopy imaging. CD36-mediated uptake in serum-free medium was very low but greatly increased when serum was present. The addition of exogenous FA in serum-free medium increased oxLDL binding and uptake to levels found with serum and affected CD36 plasma membrane distribution. Binding/uptake of oxLDL was dependent upon the FA dose, except for docosahexaenoic acid, which exhibited binding to CD36 but did not activate the uptake of oxLDL. HODE also did not affect oxLDL uptake. High affinity FA binding to CD36 and the effects of each FA on oxLDL uptake have important implications for protein conformation, binding of other ligands, functional properties of CD36, and high plasma FA levels in obesity and type 2 diabetes.

  9. A Density Functional Theory Study of Temperature Dependence of Cluster Formation from Sulfuric Acid and Ammonia

    NASA Astrophysics Data System (ADS)

    lin, H.; Chon, N. L.; Lee, S.

    2013-12-01

    Recent atmospheric nucleation studies have shown that acid-base reactions are essential at the initial step of aerosol nucleation. Ammonia is the most abundant base compound present in the atmosphere. Ammonia can directly interact with sulfuric acid clusters to reduce Gibbs free energy of cluster formation and growth, but the role that ammonia plays in atmospheric nucleation is still not well understood, especially at the molecular cluster level. We have performed density functional theory (BL3YP) and ab initio (MP2) calculations to study energetics of cluster formation for (NH3)m(H2SO4) and (NH3)(H2SO4)n (m, n = 1-6) in the temperature range from 200-300 K. For the model (NH3)m(H2SO4) clusters, bindings were predicted to increase from m = 1 to 6 at 200 K, while the most stable complex at 300 K was found to be at m = 2. For the (NH3)(H2SO4)n complexes, enthalpic contributions dominated and the binding is more stable for larger n. The temperature dependency has stronger effects on the (NH3)m(H2SO4) complexes, among which the lowest free energy shifts from m = 6 at T = 200 K to m = 5 around T = 240 K and further to m = 2 at T ≥ 280 K. The effects on the (NH3)(H2SO4)n complexes are much smaller, while there are similar trends that favor larger n for all temperatures between 200 and 300 K. These results thus indicate that the role of ammonia in atmospheric aerosol nucleation is critical in a wide range of atmospheric temperature conditions.

  10. A GIS analysis of suitability for construction aggregate recycling sites using regional transportation network and population density features

    USGS Publications Warehouse

    Robinson, G.R.; Kapo, K.E.

    2004-01-01

    Aggregate is used in road and building construction to provide bulk, strength, support, and wear resistance. Reclaimed asphalt pavement (RAP) and reclaimed Portland cement concrete (RPCC) are abundant and available sources of recycled aggregate. In this paper, current aggregate production operations in Virginia, Maryland, and the District of Columbia are used to develop spatial association models for the recycled aggregate industry with regional transportation network and population density features. The cost of construction aggregate to the end user is strongly influenced by the cost of transporting processed aggregate from the production site to the construction site. More than 60% of operations recycling aggregate in the mid-Atlantic study area are located within 4.8 km (3 miles) of an interstate highway. Transportation corridors provide both sites of likely road construction where aggregate is used and an efficient means to move both materials and on-site processing equipment back and forth from various work sites to the recycling operations. Urban and developing areas provide a high market demand for aggregate and a ready source of construction debris that may be processed into recycled aggregate. Most aggregate recycling operators in the study area are sited in counties with population densities exceeding 77 people/km2 (200 people/mile 2). No aggregate recycling operations are sited in counties with less than 19 people/km2 (50 people/mile2), reflecting the lack of sufficient long-term sources of construction debris to be used as an aggregate source, as well as the lack of a sufficient market demand for aggregate in most rural areas to locate a recycling operation there or justify the required investment in the equipment to process and produce recycled aggregate. Weights of evidence analyses (WofE), measuring correlation on an area-normalized basis, and weighted logistic regression (WLR), are used to model the distribution of RAP and RPCC operations relative

  11. Lipid Classes and Fatty Acids in Ophryotrocha cyclops, a Dorvilleid from Newfoundland Aquaculture Sites

    PubMed Central

    Salvo, Flora; Dufour, Suzanne C.; Hamoutene, Dounia; Parrish, Christopher C.

    2015-01-01

    A new opportunistic annelid (Ophryotrocha cyclops) discovered on benthic substrates underneath finfish aquaculture sites in Newfoundland (NL) may be involved in the remediation of organic wastes. At those aquaculture sites, bacterial mats and O. cyclops often coexist and are used as indicators of organic enrichment. Little is known on the trophic strategies used by these annelids, including whether they might consume bacteria or other aquaculture-derived wastes. We studied the lipid and fatty acid composition of the annelids and their potential food sources (degraded flocculent organic matter, fresh fish pellets and bacterial mats) to investigate feeding relationships in these habitats and compared the lipid and fatty acid composition of annelids before and after starvation. Fish pellets were rich in lipids, mainly terrestrially derived C18 fatty acids (18:1ω9, 18:2ω6, 18:3ω3), while bacterial samples were mainly composed of ω7 fatty acids, and flocculent matter appeared to be a mixture of fresh and degrading fish pellets, feces and bacteria. Ophryotrocha cyclops did not appear to store excessive amounts of lipids (13%) but showed a high concentration of ω3 and ω6 fatty acids, as well as a high proportion of the main fatty acids contained in fresh fish pellets and bacterial mats. The dorvilleids and all potential food sources differed significantly in their lipid and fatty acid composition. Interestingly, while all food sources contained low proportions of 20:5ω3 and 20:2ω6, the annelids showed high concentrations of these two fatty acids, along with 20:4ω6. A starvation period of 13 days did not result in a major decrease in total lipid content; however, microscopic observations revealed that very few visible lipid droplets remained in the gut epithelium after three months of starvation. Ophryotrocha cyclops appears well adapted to extreme environments and may rely on lipid-rich organic matter for survival and dispersal in cold environments. PMID:26308719

  12. Lipid Classes and Fatty Acids in Ophryotrocha cyclops, a Dorvilleid from Newfoundland Aquaculture Sites.

    PubMed

    Salvo, Flora; Dufour, Suzanne C; Hamoutene, Dounia; Parrish, Christopher C

    2015-01-01

    A new opportunistic annelid (Ophryotrocha cyclops) discovered on benthic substrates underneath finfish aquaculture sites in Newfoundland (NL) may be involved in the remediation of organic wastes. At those aquaculture sites, bacterial mats and O. cyclops often coexist and are used as indicators of organic enrichment. Little is known on the trophic strategies used by these annelids, including whether they might consume bacteria or other aquaculture-derived wastes. We studied the lipid and fatty acid composition of the annelids and their potential food sources (degraded flocculent organic matter, fresh fish pellets and bacterial mats) to investigate feeding relationships in these habitats and compared the lipid and fatty acid composition of annelids before and after starvation. Fish pellets were rich in lipids, mainly terrestrially derived C18 fatty acids (18:1ω9, 18:2ω6, 18:3ω3), while bacterial samples were mainly composed of ω7 fatty acids, and flocculent matter appeared to be a mixture of fresh and degrading fish pellets, feces and bacteria. Ophryotrocha cyclops did not appear to store excessive amounts of lipids (13%) but showed a high concentration of ω3 and ω6 fatty acids, as well as a high proportion of the main fatty acids contained in fresh fish pellets and bacterial mats. The dorvilleids and all potential food sources differed significantly in their lipid and fatty acid composition. Interestingly, while all food sources contained low proportions of 20:5ω3 and 20:2ω6, the annelids showed high concentrations of these two fatty acids, along with 20:4ω6. A starvation period of 13 days did not result in a major decrease in total lipid content; however, microscopic observations revealed that very few visible lipid droplets remained in the gut epithelium after three months of starvation. Ophryotrocha cyclops appears well adapted to extreme environments and may rely on lipid-rich organic matter for survival and dispersal in cold environments.

  13. Influence of liquid density on the parametric shape instability of sonoluminescence bubbles in water and sulfuric acid.

    PubMed

    Godínez, F A; Navarrete, M

    2011-07-01

    Parametric shape instability of sonoluminescing argon bubbles in water and aqueous H(2)SO(4) was numerically analyzed considering gas and liquid density variations. The employed model couples Gilmore, Tait (liquid) and van der Waals (gas) equations to simulate radial dynamics and density changes, respectively. Shape stability-instability zones in the P(a)-R(0) space resulted from a linear stability analysis. For the argon-water and argon-water-acid systems, numerical results indicate a rapid rise in both gas and liquid densities during final stages of bubble implosion which result in a stabilizing effect on the parametric instability.

  14. Characterization of Naphthaleneacetic Acid Binding to Receptor Sites on Cellular Membranes of Maize Coleoptile Tissue 1

    PubMed Central

    Ray, Peter M.; Dohrmann, Ulrike; Hertel, Rainer

    1977-01-01

    Characteristics of and optimum conditions for saturable (“specific”) binding of [14C]naphthaleneacetic acid to sites located on membranous particles from maize (Zea mays L.) coleoptiles are described. Most, if not all, of the specific binding appears to be due to a single kinetic class of binding sites having a KD of 5 to 7 × 10−7m for naphthalene-1-acetic acid (NAA). Binding of NAA is insensitive to high monovalent salt concentrations, indicating that binding is not primarily ionic. However, specific binding is inhibited by Mg2+ or Ca2+ above 5 mm. Specific binding is improved by organic acids, especially citrate. Binding is heat-labile and is sensitive to agents that act either on proteins or on lipids. Specific binding is reversibly inactivated by reducing agents such as dithioerythritol; a reducible group, possibly a disulfide group, may be located at the binding site and required for its function. The affinity of the specific binding sites for auxins is modified by an unidentified dialyzable, heat-stable, apparently amphoteric, organic factor (“supernatant factor”) found in maize tissue. PMID:16659851

  15. Zinc-induced oligomerization of zinc α2 glycoprotein reveals multiple fatty acid-binding sites.

    PubMed

    Zahid, Henna; Miah, Layeque; Lau, Andy M; Brochard, Lea; Hati, Debolina; Bui, Tam T T; Drake, Alex F; Gor, Jayesh; Perkins, Stephen J; McDermott, Lindsay C

    2016-01-01

    Zinc α2 glycoprotein (ZAG) is an adipokine with a class I MHC protein fold and is associated with obesity and diabetes. Although its intrinsic ligand remains unknown, ZAG binds the dansylated C11 fatty acid 11-(dansylamino)undecanoic acid (DAUDA) in the groove between the α1 and α2 domains. The surface of ZAG has approximately 15 weak zinc-binding sites deemed responsible for precipitation from human plasma. In the present study the functional significance of these metal sites was investigated. Analytical ultracentrifugation (AUC) and CD showed that zinc, but not other divalent metals, causes ZAG to oligomerize in solution. Thus ZAG dimers and trimers were observed in the presence of 1 and 2 mM zinc. Molecular modelling of X-ray scattering curves and sedimentation coefficients indicated a progressive stacking of ZAG monomers, suggesting that the ZAG groove may be occluded in these. Using fluorescence-detected sedimentation velocity, these ZAG-zinc oligomers were again observed in the presence of the fluorescent boron dipyrromethene fatty acid C16-BODIPY (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-hexadecanoic acid). Fluorescence spectroscopy confirmed that ZAG binds C16-BODIPY. ZAG binding to C16-BODIPY, but not to DAUDA, was reduced by increased zinc concentrations. We conclude that the lipid-binding groove in ZAG contains at least two distinct fatty acid-binding sites for DAUDA and C16-BODIPY, similar to the multiple lipid binding seen in the structurally related immune protein CD1c. In addition, because high concentrations of zinc occur in the pancreas, the perturbation of these multiple lipid-binding sites by zinc may be significant in Type 2 diabetes where dysregulation of ZAG and zinc homoeostasis occurs.

  16. Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD.

    PubMed

    Aidas, Kęstutis; Lanevskij, Kiril; Kubilius, Rytis; Juška, Liutauras; Petkevičius, Daumantas; Japertas, Pranas

    2015-11-01

    Aqueous pK(a) of selected primary benzenesulfonamides are predicted in a systematic manner using density functional theory methods and the SMD solvent model together with direct and proton exchange thermodynamic cycles. Some test calculations were also performed using high-level composite CBS-QB3 approach. The direct scheme generally does not yield a satisfactory agreement between calculated and measured acidities due to a severe overestimation of the Gibbs free energy changes of the gas-phase deprotonation reaction by the used exchange-correlation functionals. The relative pK(a) values calculated using proton exchange method compare to experimental data very well in both qualitative and quantitative terms, with a mean absolute error of about 0.4 pK(a) units. To achieve this accuracy, we find it mandatory to perform geometry optimization of the neutral and anionic species in the gas and solution phases separately, because different conformations are stabilized in these two cases. We have attempted to evaluate the effect of the conformer-averaged free energies in the pK(a) predictions, and the general conclusion is that this procedure is highly too costly as compared with the very small improvement we have gained.

  17. Associations of Polyunsaturated Fatty Acid Intake with Bone Mineral Density in Postmenopausal Women

    PubMed Central

    Harris, Margaret; Farrell, Vanessa; Houtkooper, Linda; Going, Scott; Lohman, Timothy

    2015-01-01

    A secondary analysis of cross-sectional data was analyzed from 6 cohorts (Fall 1995–Fall 1997) of postmenopausal women (n = 266; 56.6 ± 4.7 years) participating in the Bone Estrogen Strength Training (BEST) study (a 12-month, block-randomized, clinical trial). Bone mineral density (BMD) was measured at femur neck and trochanter, lumbar spine (L2–L4), and total body BMD using dual-energy X-ray absorptiometry (DXA). Mean dietary polyunsaturated fatty acids (PUFAs) intakes were assessed using 8 days of diet records. Multiple linear regression was used to examine associations between dietary PUFAs and BMD. Covariates included in the models were total energy intake, body weight at year 1, years after menopause, exercise, use of hormone therapy (HT), total calcium, and total iron intakes. In the total sample, lumbar spine and total body BMD had significant negative associations with dietary PUFA intake at P < 0.05. In the non-HT group, no significant associations between dietary PUFA intake and BMD were seen. In the HT group, significant inverse associations with dietary PUFA intake were seen in the spine, total body, and Ward's triangle BMD, suggesting that HT may influence PUFA associations with BMD. This study is registered with clinicaltrials.gov, identifier: NCT00000399. PMID:25785226

  18. Evidence of sulphur and nitrogen deposition signals at the United Kingdom Acid Waters Monitoring Network sites.

    PubMed

    Cooper, D M

    2005-09-01

    Some recent studies of trends in sulphate in surface waters have alluded to possible lag effects imposed by catchment soils, resulting in discrepancies between trends in deposition and run-off. To assess the extent of these possible effects in the UK, sulphate concentration data from the United Kingdom Acid Waters Monitoring Network (AWMN) sites are compared with estimates of sulphur deposition at each site. From these data, input-output budgets are computed at an annual time scale. The estimated budgets suggest a close association between catchment sulphur inputs and outputs at an annual scale, with well-balanced annual budgets at most sites, indicative of only minor lag effects. A similar analysis of the AWMN site nitrogen budget shows little evidence of an association between nitrogen inputs and outputs at this time scale.

  19. Modeling protein evolution with several amino acid replacement matrices depending on site rates.

    PubMed

    Le, Si Quang; Dang, Cuong Cao; Gascuel, Olivier

    2012-10-01

    Most protein substitution models use a single amino acid replacement matrix summarizing the biochemical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors that influence the substitution patterns. In this paper, we investigate the use of different substitution matrices for different site evolutionary rates. Indeed, the variability of evolutionary rates corresponds to one of the most apparent heterogeneity factors among sites, and there is no reason to assume that the substitution patterns remain identical regardless of the evolutionary rate. We first introduce LG4M, which is composed of four matrices, each corresponding to one discrete gamma rate category (of four). These matrices differ in their amino acid equilibrium distributions and in their exchangeabilities, contrary to the standard gamma model where only the global rate differs from one category to another. Next, we present LG4X, which also uses four different matrices, but leaves aside the gamma distribution and follows a distribution-free scheme for the site rates. All these matrices are estimated from a very large alignment database, and our two models are tested using a large sample of independent alignments. Detailed analysis of resulting matrices and models shows the complexity of amino acid substitutions and the advantage of flexible models such as LG4M and LG4X. Both significantly outperform single-matrix models, providing gains of dozens to hundreds of log-likelihood units for most data sets. LG4X obtains substantial gains compared with LG4M, thanks to its distribution-free scheme for site rates. Since LG4M and LG4X display such advantages but require the same memory space and have comparable running times to standard models, we believe that LG4M and LG4X are relevant alternatives to single replacement matrices. Our models, data, and software are available from http://www.atgc-montpellier.fr/models/lg4x.

  20. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    PubMed Central

    Gangi Setty, Thanuja; Cho, Christine; Govindappa, Sowmya; Apicella, Michael A.; Ramaswamy, S.

    2014-01-01

    Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states. PMID:25004958

  1. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

    PubMed

    Rodrigue, Nicolas; Philippe, Hervé; Lartillot, Nicolas

    2010-03-01

    Modeling the interplay between mutation and selection at the molecular level is key to evolutionary studies. To this end, codon-based evolutionary models have been proposed as pertinent means of studying long-range evolutionary patterns and are widely used. However, these approaches have not yet consolidated results from amino acid level phylogenetic studies showing that selection acting on proteins displays strong site-specific effects, which translate into heterogeneous amino acid propensities across the columns of alignments; related codon-level studies have instead focused on either modeling a single selective context for all codon columns, or a separate selective context for each codon column, with the former strategy deemed too simplistic and the latter deemed overparameterized. Here, we integrate recent developments in nonparametric statistical approaches to propose a probabilistic model that accounts for the heterogeneity of amino acid fitness profiles across the coding positions of a gene. We apply the model to a dozen real protein-coding gene alignments and find it to produce biologically plausible inferences, for instance, as pertaining to site-specific amino acid constraints, as well as distributions of scaled selection coefficients. In their account of mutational features as well as the heterogeneous regimes of selection at the amino acid level, the modeling approaches studied here can form a backdrop for several extensions, accounting for other selective features, for variable population size, or for subtleties of mutational features, all with parameterizations couched within population-genetic theory. PMID:20176949

  2. Site-specific study on stabilization of acid-generating mine tailings using coal fly ash

    SciTech Connect

    Shang, J.Q.; Wang, H.L.; Kovac, V.; Fyfe, J.

    2006-03-15

    A site-specific study on stabilizing acid-generating mine tailings from Sudbury Mine using a coal fly ash from Nanticoke Generating Station is presented in this paper. The objective of the study is to evaluate the feasibility of codisposal of the fly ash and mine tailings to reduce environmental impacts of Sudbury tailings disposal sites. The study includes three phases, i.e., characterization of the mine tailings, and coal fly ash, oxidation tests on the mine tailings and kinetic column permeation tests. The results of the experiments indicate that when permeated with acid mine drainage, the hydraulic conductivity of Nanticoke coal fly ash decreased more than three orders of magnitude (from 1 x 10{sup -6} to 1 x 10{sup -9} cm/s), mainly due to chemical reactions between the ash solids and acid mine drainage. Furthermore, the hydraulic gradient required for acid mine drainage to break through the coal fly ash is increased up to ten times (from 17 to 150) as compared with that for water. The results also show that the leachate from coal fly ash neutralizes the acidic pore fluid of mine tailings. The concentrations of trace elements in effluents from all kinetic column permeation tests indicated that coplacement of coal fly ash with mine tailings has the benefit of immobilizing trace elements, especially heavy metals. All regulated element concentrations from effluent during testing are well below the leachate quality criteria set by the local regulatory authority.

  3. Low urine pH and acid excretion do not predict bone fractures or the loss of bone mineral density: a prospective cohort study

    PubMed Central

    2010-01-01

    Background The acid-ash hypothesis, the alkaline diet, and related products are marketed to the general public. Websites, lay literature, and direct mail marketing encourage people to measure their urine pH to assess their health status and their risk of osteoporosis. The objectives of this study were to determine whether 1) low urine pH, or 2) acid excretion in urine [sulfate + chloride + 1.8x phosphate + organic acids] minus [sodium + potassium + 2x calcium + 2x magnesium mEq] in fasting morning urine predict: a) fragility fractures; and b) five-year change of bone mineral density (BMD) in adults. Methods Design: Cohort study: the prospective population-based Canadian Multicentre Osteoporosis Study. Multiple logistic regression was used to examine associations between acid excretion (urine pH and urine acid excretion) in fasting morning with the incidence of fractures (6804 person years). Multiple linear regression was used to examine associations between acid excretion with changes in BMD over 5-years at three sites: lumbar spine, femoral neck, and total hip (n = 651). Potential confounders controlled included: age, gender, family history of osteoporosis, physical activity, smoking, calcium intake, vitamin D status, estrogen status, medications, renal function, urine creatinine, body mass index, and change of body mass index. Results There were no associations between either urine pH or acid excretion and either the incidence of fractures or change of BMD after adjustment for confounders. Conclusion Urine pH and urine acid excretion do not predict osteoporosis risk. PMID:20459740

  4. Using high-density magnetic and electromagnetic data for waste site characterization: A case study

    SciTech Connect

    Cochran, J.R.; Dalton, K.E.

    1995-03-01

    Magnetometers are frequently used to characterize hazardous waste sites. Due to cost and time considerations, data are typically collected on a coarse grid with nodes on 3 to 6 meter (m) centers. Hardware and software are now available which allow the rapid and cost effective collection of information on a much finer sampling grid. In this paper we present and compare total field magnetometery data collected on 3 m centers to total field magnetometery data collected on a grid with centers of 0.5 m or less. We also compare the magnetometery data to time-domain electromagnetic (EM) data collected on a 1 m by 0.2 m grid using the recently introduced Geonics Ltd. EM61 metal detector. All three data sets were collected at an abandoned landfill radioactive Burial Site No. 11 (RB-11) is located on Kirtland Air Force Base near Albuquerque, New Mexico.

  5. Conversion of α-linolenic acid to long-chain omega-3 fatty acid derivatives and alterations of HDL density subfractions and plasma lipids with dietary polyunsaturated fatty acids in Monk parrots (Myiopsitta monachus).

    PubMed

    Petzinger, C; Larner, C; Heatley, J J; Bailey, C A; MacFarlane, R D; Bauer, J E

    2014-04-01

    The effect of α-linolenic acid from a flaxseed (FLX)-enriched diet on plasma lipid and fatty acid metabolism and possible atherosclerosis risk factors was studied in Monk parrots (Myiopsitta monachus). Twenty-four Monk parrots were randomly assigned to diets containing either 10% ground SUNs or 10% ground FLXs. Feed intake was calculated daily. Blood samples, body condition scores and body weights were obtained at -5 weeks, day 0, 7, 14, 28, 42 and 70. Plasma samples were analysed for total cholesterol, free cholesterol, triacylglycerols and lipoproteins. Phospholipid subfraction fatty acid profiles were determined. By day 70, the FLX group had significantly higher plasma phospholipid fatty acids including 18:3n-3 (α-linolenic acid), 20:5n-3 (eicosapentaenoic acid) and 22:6n-3 (docosahexaenoic acid). The sunflower group had significantly higher plasma phospholipid levels of 20:4n-6 (arachidonic acid). By day 70, the high-density lipoprotein (HDL) peak shifted resulting in significantly different HDL peak densities between the two experimental groups (1.097 g/ml FLX group and 1.095 g/ml SUN group, p = 0.028). The plasma fatty acid results indicate that Monk parrots can readily convert α-linolenic acid to the long-chain omega-3 derivatives including docosahexaenoic acid and reduce 20:4n-6 accumulation in plasma phospholipids. The reason for a shift in the HDL peak density is unknown at this time. PMID:23600588

  6. Conversion of α-linolenic acid to long-chain omega-3 fatty acid derivatives and alterations of HDL density subfractions and plasma lipids with dietary polyunsaturated fatty acids in Monk parrots (Myiopsitta monachus).

    PubMed

    Petzinger, C; Larner, C; Heatley, J J; Bailey, C A; MacFarlane, R D; Bauer, J E

    2014-04-01

    The effect of α-linolenic acid from a flaxseed (FLX)-enriched diet on plasma lipid and fatty acid metabolism and possible atherosclerosis risk factors was studied in Monk parrots (Myiopsitta monachus). Twenty-four Monk parrots were randomly assigned to diets containing either 10% ground SUNs or 10% ground FLXs. Feed intake was calculated daily. Blood samples, body condition scores and body weights were obtained at -5 weeks, day 0, 7, 14, 28, 42 and 70. Plasma samples were analysed for total cholesterol, free cholesterol, triacylglycerols and lipoproteins. Phospholipid subfraction fatty acid profiles were determined. By day 70, the FLX group had significantly higher plasma phospholipid fatty acids including 18:3n-3 (α-linolenic acid), 20:5n-3 (eicosapentaenoic acid) and 22:6n-3 (docosahexaenoic acid). The sunflower group had significantly higher plasma phospholipid levels of 20:4n-6 (arachidonic acid). By day 70, the high-density lipoprotein (HDL) peak shifted resulting in significantly different HDL peak densities between the two experimental groups (1.097 g/ml FLX group and 1.095 g/ml SUN group, p = 0.028). The plasma fatty acid results indicate that Monk parrots can readily convert α-linolenic acid to the long-chain omega-3 derivatives including docosahexaenoic acid and reduce 20:4n-6 accumulation in plasma phospholipids. The reason for a shift in the HDL peak density is unknown at this time.

  7. The control of acid mine drainage at the Summitville Mine Superfund Site

    SciTech Connect

    Ketellapper, V.L.; Williams, L.O.

    1996-11-01

    The Summitville Mine Superfund Site is located about 25 miles south of Del Norte, Colorado, in Rio Grande County. Occurring at an average elevation of 11,500 feet in the San Juan Mountain Range, the mine site is located two miles east of the Continental Divide. Mining at Summitville has occurred since 1870. The mine was most recently operated by Summitville Consolidated Mining Company, Inc. (SCMCI) as an open pit gold mine with extraction by means of a cyanide leaching process. In December of 1992, SCMCI declared bankruptcy and vacated the mine site. At that time, the US Environmental Protection Agency (EPA) took over operations of the water treatment facilities to prevent a catastrophic release of cyanide and metal-laden water from the mine site. Due to high operational costs of water treatment (approximately $50,000 per day), EPA established a goal to minimize active water treatment by reducing or eliminating acid mine drainage (AMD). All of the sources of AMD generation on the mine site were evaluated and prioritized. Of the twelve areas identified as sources of AMD, the Cropsy Waste Pile, the Summitville Dam Impoundment, the Beaver Mud Dump, the Reynolds and Chandler adits, and the Mine Pits were consider to be the most significant contributors to the generation of metal-laden acidic (low pH) water. A two part plan was developed to control AMD from the most significant sources. The first part was initiated immediately to control AMD being released from the Site. This part focused on improving the efficiency of the water treatment facilities and controlling the AMD discharges from the mine drainage adits. The second part of the plan was aimed at reducing the AMD generated in groundwater and surface water runoff from the mine wastes. A lined and capped repository located in the mine pits for acid generating mining waste and water treatment plant sludge was found to be the most feasible alternative.

  8. Moleculary imprinted polymers with metalloporphyrin-based molecular recognition sites coassembled with methacrylic acid.

    PubMed

    Takeuchi, T; Mukawa, T; Matsui, J; Higashi, M; Shimizu, K D

    2001-08-15

    A diastereoselective molecularly imprinted polymer (MIP) for (-)-cinchonidine, PPM(CD), was prepared by the combined use of methacrylic acid and vinyl-substituted zinc(II) porphyrin as functional monomers. Compared to MIPs using only methacrylic acid or zinc porphyrin as a functional monomer, PM(CD) and PP(CD), respectively, PPM(CD) showed higher binding ability for (-)-cinchonidine in chromatographic tests using the MIP-packed columns. Scatchard analysis gave a higher association constant of PPM(CD) for (-)-cinchonidine (1.14 x 10(7) M(-1)) than those of PP(CD) (1.45 x 10(6) M(-1)) and PM(CD) (6.78 x 10(6) M(-1)). The affinity distribution of binding sites estimated by affinity spectrum analysis showed a higher percentage of high-affinity sites and a lower percentage of low-affinity sites in PPM(CD). The MIPs containing a zinc(II) porphyrin in the binding sites, PPM(CD) and PP(CD), showed fluorescence quenching according to the binding of (-)-cinchonidine, and the quenching was significant in the low-concentration range, suggesting that the high-affinity binding sites contain the porphyrin residue. The correlation of the relative fluorescence intensity against log of (-)-cinchonidine concentrations showed a linear relationship. These results revealed that the MIP having highly specific binding sites was assembled by the two functional monomers, vinyl-substituted zinc(II) porphyrin and methacrylic acid, and they cooperatively worked to yield the specific binding. In addition, the zinc(II) porphyrin-based MIPs appeared to act as fluorescence sensor selectively responded by binding events of the template molecule.

  9. Na-K pump site density and ouabain binding affinity in cultured chick heart cells

    SciTech Connect

    Lobaugh, L.A.; Lieberman, M.

    1987-11-01

    The possible existence of multiple (/sup 3/H)ouabain binding sites and the relationship between ouabain binding and Na-K pump inhibition in cardiac muscle were studied using cultured embryonic chick heart cells. (/sup 3/H)ouabain bound to a single class of sites in 0.5 mM K (0.5 Ko) with an association rate constant (k+1) of 3.4 X 10(4) M-1.s-1 and a dissociation rate constant (k-1) of 0.0095 s. Maximal specific (/sup 3/H)ouabain binding RT to myocyte-enriched cultures is 11.7 pmol/mg protein and Kd is 0.43 microM in 0.5 Ko, whereas Kd,apparent is 6.6 microM in 5.4 Ko. The number of binding sites per myocyte was calculated by correcting for the contribution of fibroblasts in myocyte-enriched cultures using data from homogeneous fibroblast cultures (RT = 3.3 pmol/mg protein; Kd = 0.19 microM in 0.5 Ko). Equivalence of (/sup 3/H)ouabain binding sites and Na-K pumps was implied by agreement between maximal specific binding of (/sup 3/H)ouabain and /sup 125/I-labeled monoclonal antibody directed against Na+-K+-ATPase (approximately 2 X 10(6) sites/cell). However, (/sup 3/H)ouabain binding occurred at lower concentrations than inhibition of ouabain-sensitive /sup 42/K uptake in 0.5 Ko. Further studies in both 0.5 K and 5.4 Ko showed that ouabain caused cell Na content Nai to increase over the same range of concentrations that binding occurred, implying that increased Nai may stimulate unbound Na-K pumps and prevent a proportional decrease in /sup 42/K uptake rate. The results show that Na-K pump inhibition occurs as a functional consequence of specific ouabain binding and indicate that the Na-K pump is the cardiac glycoside receptor in cultured heart cells.

  10. A surface structural model for ferrihydrite I: Sites related to primary charge, molar mass, and mass density

    NASA Astrophysics Data System (ADS)

    Hiemstra, Tjisse; Van Riemsdijk, Willem H.

    2009-08-01

    A multisite surface complexation (MUSIC) model for ferrihydrite (Fh) has been developed. The surface structure and composition of Fh nanoparticles are described in relation to ion binding and surface charge development. The site densities of the various reactive surface groups, the molar mass, the mass density, the specific surface area, and the particle size are quantified. As derived theoretically, molecular mass and mass density of nanoparticles will depend on the types of surface groups and the corresponding site densities and will vary with particle size and surface area because of a relatively large contribution of the surface groups in comparison to the mineral core of nanoparticles. The nano-sized (˜2.6 nm) particles of freshly prepared 2-line Fh as a whole have an increased molar mass of M ˜ 101 ± 2 g/mol Fe, a reduced mass density of ˜3.5 ± 0.1 g/cm 3, both relatively to the mineral core. The specific surface area is ˜650 m 2/g. Six-line Fh (5-6 nm) has a molar mass of M ˜ 94 ± 2 g/mol, a mass density of ˜3.9 ± 0.1 g/cm 3, and a surface area of ˜280 ± 30 m 2/g. Data analysis shows that the mineral core of Fh has an average chemical composition very close to FeOOH with M ˜ 89 g/mol. The mineral core has a mass density around ˜4.15 ± 0.1 g/cm 3, which is between that of feroxyhyte, goethite, and lepidocrocite. These results can be used to constrain structural models for Fh. Singly-coordinated surface groups dominate the surface of ferrihydrite (˜6.0 ± 0.5 nm -2). These groups can be present in two structural configurations. In pairs, the groups either form the edge of a single Fe-octahedron (˜2.5 nm -2) or are present at a single corner (˜3.5 nm -2) of two adjacent Fe octahedra. These configurations can form bidentate surface complexes by edge- and double-corner sharing, respectively, and may therefore respond differently to the binding of ions such as uranyl, carbonate, arsenite, phosphate, and others. The relatively low PZC of

  11. Determining generic velocity and density models for crustal amplification calculations, with an update of the Boore and Joyner (1997) Generic Site Amplification for Graphic Site Amplification

    USGS Publications Warehouse

    Boore, David

    2016-01-01

    This short note contains two contributions related to deriving depth‐dependent velocity and density models for use in computing generic crustal amplifications. The first contribution is a method for interpolating two velocity profiles to obtain a third profile with a time‐averaged velocity  to depth Z that is equal to a specified value (e.g., for shear‐wave velocity VS,  for Z=30  m, in which the subscript S has been added to indicate that the average is for shear‐wave velocities). The second contribution is a procedure for obtaining densities from VS. The first contribution is used to extend and revise the Boore and Joyner (1997) generic rock VS model, for which , to a model with the more common . This new model is then used with the densities from the second contribution to compute crustal amplifications for a generic site with .

  12. Structure, spectra and antioxidant action of ascorbic acid studied by density functional theory, Raman spectroscopic and nuclear magnetic resonance techniques.

    PubMed

    Singh, Gurpreet; Mohanty, B P; Saini, G S S

    2016-02-15

    Structure, vibrational and nuclear magnetic resonance spectra, and antioxidant action of ascorbic acid towards hydroxyl radicals have been studied computationally and in vitro by ultraviolet-visible, nuclear magnetic resonance and vibrational spectroscopic techniques. Time dependant density functional theory calculations have been employed to specify various electronic transitions in ultraviolet-visible spectra. Observed chemical shifts and vibrational bands in nuclear magnetic resonance and vibrational spectra, respectively have been assigned with the help of calculations. Changes in the structure of ascorbic acid in aqueous phase have been examined computationally and experimentally by recording Raman spectra in aqueous medium. Theoretical calculations of the interaction between ascorbic acid molecule and hydroxyl radical predicted the formation of dehydroascorbic acid as first product, which has been confirmed by comparing its simulated spectra with the corresponding spectra of ascorbic acid in presence of hydrogen peroxide.

  13. Structure, spectra and antioxidant action of ascorbic acid studied by density functional theory, Raman spectroscopic and nuclear magnetic resonance techniques

    NASA Astrophysics Data System (ADS)

    Singh, Gurpreet; Mohanty, B. P.; Saini, G. S. S.

    2016-02-01

    Structure, vibrational and nuclear magnetic resonance spectra, and antioxidant action of ascorbic acid towards hydroxyl radicals have been studied computationally and in vitro by ultraviolet-visible, nuclear magnetic resonance and vibrational spectroscopic techniques. Time dependant density functional theory calculations have been employed to specify various electronic transitions in ultraviolet-visible spectra. Observed chemical shifts and vibrational bands in nuclear magnetic resonance and vibrational spectra, respectively have been assigned with the help of calculations. Changes in the structure of ascorbic acid in aqueous phase have been examined computationally and experimentally by recording Raman spectra in aqueous medium. Theoretical calculations of the interaction between ascorbic acid molecule and hydroxyl radical predicted the formation of dehydroascorbic acid as first product, which has been confirmed by comparing its simulated spectra with the corresponding spectra of ascorbic acid in presence of hydrogen peroxide.

  14. Recognition of protein phosphorylation site based on amino acids sequence features

    NASA Astrophysics Data System (ADS)

    Zhang, Ying; Ding, Changjiang; Lu, Jun

    2012-09-01

    Protein phosphorylation is one of the most important reversible post-translational modifications (PTMs), and the theoretical recognition of the phosphorylation site is one of the important content of the computational biology. In the paper, we use the amino acid component, the position-dependent residue statistics and the non-adjacent residue pair frequency as the recognition parameters, and use Jensen-Shannon Divergence with Quadratic Discriminant analysis(JSDQD) as the method for predicting the phosphorylation sites. The 7-fold cross-validation test accuracies for the CK2, PKA and PKC kinase families are 90%, 90% and 86%, respectively.

  15. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing.

    PubMed

    Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-Qi; Tan, Cong; Li, Chengdao

    2015-01-01

    Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149

  16. Estimates of cloud water deposition at Mountain Acid Deposition Program sites in the Appalachian Mountains.

    PubMed

    Baumgardner, Ralph E; Isil, Selma S; Lavery, Thomas F; Rogers, Christopher M; Mohnen, Volker A

    2003-03-01

    Cloud water deposition was estimated at three high-elevation sites in the Appalachian Mountains of the eastern United States (Whiteface Mountain, NY; Whitetop Mountain, VA; and Clingman's Dome, TN) from 1994 through 1999 as part of the Mountain Acid Deposition Program (MADPro). This paper provides a summary of cloud water chemistry, cloud liquid water content, cloud frequency, estimates of cloud water deposition of sulfur and nitrogen species, and estimates of total deposition of sulfur and nitrogen at these sites. Other cloud studies in the Appalachians and their comparison to MADPro are also summarized. Whiteface Mountain exhibited the lowest mean and median concentrations of sulfur and nitrogen ions in cloud water, while Clingman's Dome exhibited the highest mean and median concentrations. This geographic gradient is partly an effect of the different meteorological conditions experienced at northern versus southern sites in addition to the difference in pollution content of air masses reaching the sites. All sites measured seasonal cloud water deposition rates of SO4(2-) greater than 50 kg/ha and NO3(-) rates of greater than 25 kg/ha. These high-elevation sites experienced additional deposition loading of SO4(2-) and NO3(-) on the order of 6-20 times greater compared with lower elevation Clean Air Status and Trends Network (CASTNet) sites. Approximately 80-90% of this extra loading is from cloud deposition.

  17. Dietary supplementation of usnic acid, an antimicrobial compound in lichens, does not affect rumen bacterial diversity or density in reindeer.

    PubMed

    Glad, Trine; Barboza, Perry; Mackie, Roderick I; Wright, André-Denis G; Brusetti, Lorenzo; Mathiesen, Svein D; Sundset, Monica A

    2014-06-01

    Reindeer (Rangifer tarandus tarandus) may include large proportions of lichens in their winter diet. These dietary lichens are rich in phenolic secondary compounds, the most well-known being the antimicrobial usnic acid. Previous studies have shown that reindeer host rumen bacteria resistant to usnic acid and that usnic acid is quickly detoxified in their rumen. In the present study, reindeer (n = 3) were sampled before, during, and after usnic acid supplementation to determine the effect on their rumen microbial ecology. Ad libitum intake of usnic acid averaged up to 278 mg/kg body mass. Population densities of rumen bacteria and methanogenic archaea determined by real-time PCR, ranged from 1.36 × 10(9) to 11.8 × 10(9) and 9.0 × 10(5) to 1.35 × 10(8) cells/g wet weight, respectively, and the two populations did not change significantly during usnic acid supplementation (repeated measures ANOVA) or vary significantly between the rumen liquid and particle fraction (paired t test). Rumen bacterial community structure determined by denaturing gradient gel electrophoresis did not change in response to intake of usnic acid. Firmicutes (38.7 %) and Bacteriodetes (27.4 %) were prevalent among the 16S rRNA gene sequences (n = 62) from the DGGE gels, but representatives of the phyla Verrucomicrobia (14.5 %) and Proteobacteria (1.6 %) were also detected. Rapid detoxification of the usnic acid or resistance to usnic acid may explain why the diversity of the dominant bacterial populations and the bacterial density in the reindeer rumen does not change during usnic acid supplementation.

  18. Effects of trap type, placement and ash distribution on emerald ash borer captures in a low density site.

    PubMed

    McCullough, Deborah G; Siegert, Nathan W; Poland, Therese M; Pierce, Steven J; Ahn, Su Zie

    2011-10-01

    Effective methods for early detection of newly established, low density emerald ash borer (Agrilus planipennis Fairmaire) infestations are critically needed in North America. We assessed adult A. planipennis captures on four types of traps in a 16-ha site in central Michigan. The site was divided into 16 blocks, each comprised of four 50- by 50-m cells. Green ash trees (Fraxinus pennsylvanica Marshall) were inventoried by diameter class and ash phloem area was estimated for each cell. One trap type was randomly assigned to each cell in each block. Because initial sampling showed that A. planipennis density was extremely low, infested ash logs were introduced into the center of the site. In total, 87 beetles were captured during the summer. Purple double-decker traps baited with a blend of ash leaf volatiles, Manuka oil, and ethanol captured 65% of all A. planipennis beetles. Similarly baited, green double-decker traps captured 18% of the beetles, whereas sticky bands on girdled trees captured 11% of the beetles. Purple traps baited with Manuka oil and suspended in the canopies of live ash trees captured only 5% of the beetles. At least one beetle was captured on 81% of the purple double-decker traps, 56% of the green double-decker traps, 42% of sticky bands, and 25% of the canopy traps. Abundance of ash phloem near traps had no effect on captures and trap location and sun exposure had only weak effects on captures. Twelve girdled and 29 nongirdled trees were felled and sampled in winter. Current-year larvae were present in 100% of the girdled trees and 72% of the nongirdled trees, but larval density was five times higher on girdled than nongirdled trees.

  19. Simultaneous determination of nitric acid and uranium concentrations in aqueous solution from measurements of electrical conductivity, density, and temperature

    SciTech Connect

    Spencer, B.B.

    1991-01-01

    Nuclear fuel reprocessing plants handle aqueous solutions of nitric acid and uranium in large quantities. Automatic control of process operations requires reliable measurements of these solutes concentration, but this is difficult to directly measure. Physical properties such as solution density and electrical conductivity vary with solute concentration and temperature. Conductivity, density and temperature can be measured accurately with relatively simple and inexpensive devices. These properties can be used to determine solute concentrations will good correlations. This paper provides the appropriate correlations for solutions containing 2 to 6 Molar (M) nitric acid and 0 to 300 g/L uranium metal at temperatures from 25--90{degrees}C. The equations are most accurate below 5 M nitric acid, due to a broad maximum in the conductivity curve at 6 M. 12 refs., 9 figs., 6 tabs.

  20. Site-specific incorporation of keto amino acids into functional G protein-coupled receptors using unnatural amino acid mutagenesis.

    PubMed

    Ye, Shixin; Köhrer, Caroline; Huber, Thomas; Kazmi, Manija; Sachdev, Pallavi; Yan, Elsa C Y; Bhagat, Aditi; RajBhandary, Uttam L; Sakmar, Thomas P

    2008-01-18

    G protein-coupled receptors (GPCRs) are ubiquitous heptahelical transmembrane proteins involved in a wide variety of signaling pathways. The work described here on application of unnatural amino acid mutagenesis to two GPCRs, the chemokine receptor CCR5 (a major co-receptor for the human immunodeficiency virus) and rhodopsin (the visual photoreceptor), adds a new dimension to studies of GPCRs. We incorporated the unnatural amino acids p-acetyl-L-phenylalanine (Acp) and p-benzoyl-L-phenylalanine (Bzp) into CCR5 at high efficiency in mammalian cells to produce functional receptors harboring reactive keto groups at three specific positions. We obtained functional mutant CCR5, at levels up to approximately 50% of wild type as judged by immunoblotting, cell surface expression, and ligand-dependent calcium flux. Rhodopsin containing Acp at three different sites was also purified in high yield (0.5-2 microg/10(7) cells) and reacted with fluorescein hydrazide in vitro to produce fluorescently labeled rhodopsin. The incorporation of reactive keto groups such as Acp or Bzp into GPCRs allows their reaction with different reagents to introduce a variety of spectroscopic and other probes. Bzp also provides the possibility of photo-cross-linking to identify precise sites of protein-protein interactions, including GPCR binding to G proteins and arrestins, and for understanding the molecular basis of ligand recognition by chemokine receptors. PMID:17993461

  1. Surface-mediated control of blood coagulation: the role of binding site densities and platelet deposition.

    PubMed Central

    Kuharsky, A L; Fogelson, A L

    2001-01-01

    A mathematical model of the extrinsic or tissue factor (TF) pathway of blood coagulation is formulated and results from a computational study of its behavior are presented. The model takes into account plasma-phase and surface-bound enzymes and zymogens, coagulation inhibitors, and activated and unactivated platelets. It includes both plasma-phase and membrane-phase reactions, and accounts for chemical and cellular transport by flow and diffusion, albeit in a simplified manner by assuming the existence of a thin, well-mixed fluid layer, near the surface, whose thickness depends on flow. There are three main conclusions from these studies. (i) The model system responds in a threshold manner to changes in the availability of particular surface binding sites; an increase in TF binding sites, as would occur with vascular injury, changes the system's production of thrombin dramatically. (ii) The model suggests that platelets adhering to and covering the subendothelium, rather than chemical inhibitors, may play the dominant role in blocking the activity of the TF:VIIa enzyme complex. This, in turn, suggests that a role of the IXa-tenase pathway for activating factor X to Xa is to continue factor Xa production after platelets have covered the TF:VIIa complexes on the subendothelium. (iii) The model gives a kinetic explanation of the reduced thrombin production in hemophilias A and B. PMID:11222273

  2. Sites of fine-scale electron density turbulence in the interstellar medium

    NASA Technical Reports Server (NTRS)

    Simonetti, John H.

    1992-01-01

    Observations of radio-wave scattering effects probe interstellar electron-density turbulence. But with limited use of complementary data sets only broad conclusions have been obtained. The locations of this turbulence are unknown (phases, objects, etc.), as is the mechanism for its production, although it could play a role in various galactic processes. The IRAS data set was used to search for correlations between scattering and structures traced by infrared emitting dust. The existent HI (21-cm line emission), and 408-MHz radio-continuum all-sky surveys were used to search for correlations between scattering and structures traced by these emissions. Only lines of sight outside the galactic plane were considered (to better delimit the structures which might be causing scattering). No correlation is apparent between 21-cm line emission, or infrared continuum emission and interstellar scattering. However, a correlation exists between the scattering toward extragalactic radio sources and 408-MHz continuum emission.

  3. Ab initio periodic Hartree-Fock investigation of a zeolite acid site

    SciTech Connect

    Nicholas, J.B.; Hess, A.C. )

    1994-06-15

    We have studied theoretical models of a zeolite Bronsted acid site using ab initio periodic Hartree-Fock (PHF) theory. We present results for both one and two acid sites inside a sodalite structure ([beta]-cage). We optimized the geometry of the bridging hydroxyl groups using the STO-3G basis set. All other reported crystal properties were evaluated using the more complete 6-21G (in which the outermost orbital exponents were reoptimized for the solid) level of theory. The results of the periodic calculations are compared to available experimental data, similar periodic calculations of silica sodalite in which there are no acid sites, and calculations of clusters that mimic parts of the periodic structure. The optimized geometry of the single bridging hydroxyl group has internal coordinates of Si-O = 1.64 [angstrom], Al-O = 1.72 [angstrom], O-H = 0.97 [angstrom], Si-O(H)-Al = 136.3[degree], and Si-O-H = 110.7[degree], and the hydrogen is bent 25.2[degrees] out of the Si-O-Al plane. The optimized geometry of the bridging hydroxyl group in the two-acid site model is very similar, with Si-O = 1.65 [angstrom], Al-O = 1.72 [angstrom], O-H = 0.97 [angstrom], Si-O(H)-Al = 135.5[degree], Si-O-H = 112.7[degree], and an out-of-plane angle of 21.5[degree]. 42 refs., 11 figs., 5 tabs.

  4. Disulfide bridge regulates ligand-binding site selectivity in liver bile acid-binding proteins.

    PubMed

    Cogliati, Clelia; Tomaselli, Simona; Assfalg, Michael; Pedò, Massimo; Ferranti, Pasquale; Zetta, Lucia; Molinari, Henriette; Ragona, Laura

    2009-10-01

    Bile acid-binding proteins (BABPs) are cytosolic lipid chaperones that play central roles in driving bile flow, as well as in the adaptation to various pathological conditions, contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Understanding the mode of binding of bile acids with their cytoplasmic transporters is a key issue in providing a model for the mechanism of their transfer from the cytoplasm to the nucleus, for delivery to nuclear receptors. A number of factors have been shown to modulate bile salt selectivity, stoichiometry, and affinity of binding to BABPs, e.g. chemistry of the ligand, protein plasticity and, possibly, the formation of disulfide bridges. Here, the effects of the presence of a naturally occurring disulfide bridge on liver BABP ligand-binding properties and backbone dynamics have been investigated by NMR. Interestingly, the disulfide bridge does not modify the protein-binding stoichiometry, but has a key role in modulating recognition at both sites, inducing site selectivity for glycocholic and glycochenodeoxycholic acid. Protein conformational changes following the introduction of a disulfide bridge are small and located around the inner binding site, whereas significant changes in backbone motions are observed for several residues distributed over the entire protein, both in the apo form and in the holo form. Site selectivity appears, therefore, to be dependent on protein mobility rather than being governed by steric factors. The detected properties further establish a parallelism with the behaviour of human ileal BABP, substantiating the proposal that BABPs have parallel functions in hepatocytes and enterocytes. PMID:19754879

  5. Disulfide bridge regulates ligand-binding site selectivity in liver bile acid-binding proteins.

    PubMed

    Cogliati, Clelia; Tomaselli, Simona; Assfalg, Michael; Pedò, Massimo; Ferranti, Pasquale; Zetta, Lucia; Molinari, Henriette; Ragona, Laura

    2009-10-01

    Bile acid-binding proteins (BABPs) are cytosolic lipid chaperones that play central roles in driving bile flow, as well as in the adaptation to various pathological conditions, contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Understanding the mode of binding of bile acids with their cytoplasmic transporters is a key issue in providing a model for the mechanism of their transfer from the cytoplasm to the nucleus, for delivery to nuclear receptors. A number of factors have been shown to modulate bile salt selectivity, stoichiometry, and affinity of binding to BABPs, e.g. chemistry of the ligand, protein plasticity and, possibly, the formation of disulfide bridges. Here, the effects of the presence of a naturally occurring disulfide bridge on liver BABP ligand-binding properties and backbone dynamics have been investigated by NMR. Interestingly, the disulfide bridge does not modify the protein-binding stoichiometry, but has a key role in modulating recognition at both sites, inducing site selectivity for glycocholic and glycochenodeoxycholic acid. Protein conformational changes following the introduction of a disulfide bridge are small and located around the inner binding site, whereas significant changes in backbone motions are observed for several residues distributed over the entire protein, both in the apo form and in the holo form. Site selectivity appears, therefore, to be dependent on protein mobility rather than being governed by steric factors. The detected properties further establish a parallelism with the behaviour of human ileal BABP, substantiating the proposal that BABPs have parallel functions in hepatocytes and enterocytes.

  6. Conductance based characterization of structure and hopping site density in 2D molecule-nanoparticle arrays.

    PubMed

    McCold, Cliff E; Fu, Qiang; Howe, Jane Y; Hihath, Joshua

    2015-09-28

    Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems.

  7. Elucidating the mechanism and active site of the cyclohexanol dehydrogenation on copper-based catalysts: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Wang, Ziyun; Liu, Xinyi; Rooney, D. W.; Hu, P.

    2015-10-01

    The dehydrogenation of cyclohexanol to cyclohexanone is very important in the manufacture of nylon. Copper-based catalysts are the most popular catalysts for this reaction, and on these catalysts the reaction mechanism and active site are in debate. In order to elucidate the mechanism and active site of the cyclohexanol dehydrogenation on copper-based catalysts, density functional theory with dispersion corrections were performed on up to six facets of copper in two different oxidation states: monovalent copper and metallic copper. By calculating the surface energies of these facets, Cu(111) and Cu2O(111) were found to be the most stable facets for metallic copper and for monovalent copper, respectively. On these two facets, all the possible elementary steps in the dehydrogenation pathway of cyclohexanol were calculated, including the adsorption, dehydrogenation, hydrogen coupling and desorption. Two different reaction pathways for dehydrogenation were considered on both surfaces. It was revealed that the dehydrogenation mechanisms are different on these two surfaces: on Cu(111) the hydrogen belonging to the hydroxyl is removed first, then the hydrogen belonging to the carbon is subtracted, while on Cu2O(111) the hydrogen belonging to the carbon is removed followed by the subtraction of the hydrogen in the hydroxyl group. Furthermore, by comparing the energy profiles of these two surfaces, Cu2O(111) was found to be more active for cyclohexanol dehydrogenation than Cu(111). In addition, we found that the coordinatively unsaturated copper sites on Cu2O(111) are the reaction sites for all the steps. Therefore, the coordinatively unsaturated copper site on Cu2O(111) is likely to be the active site for cyclohexanol dehydrogenation on the copper-based catalysts.

  8. Systemic Free Fatty Acid Disposal Into Very Low-Density Lipoprotein Triglycerides

    PubMed Central

    Koutsari, Christina; Mundi, Manpreet S.; Ali, Asem H.; Patterson, Bruce W.; Jensen, Michael D.

    2013-01-01

    We measured the incorporation of systemic free fatty acids (FFA) into circulating very low-density lipoprotein triglycerides (VLDL-TGs) under postabsorptive, postprandial, and walking conditions in humans. Fifty-five men and 85 premenopausal women with BMI 18–24 (lean) and 27–36 kg/m2 (overweight/obese) received an intravenous bolus injection of [1,1,2,3,3-2H5]glycerol (to measure VLDL-TG kinetics) and either [1-14C]palmitate or [9,10-3H]palmitate to determine the proportion of systemic FFA that is converted to VLDL-TG. Experiments started at 0630 h after a 12-h overnight fast. In the postabsorptive protocol, participants rested and remained fasted until 1330 h. In the postprandial protocol, volunteers ingested frequent portions of a fat-free smoothie. In the walking protocol, participants walked on a treadmill for 5.5 h at ∼3× resting energy expenditure. Approximately 7% of circulating FFA was converted into VLDL-TG. VLDL-TG secretion rates (SRs) were not statistically different among protocols. Visceral fat mass was the only independent predictor of VLDL-TG secretion, explaining 33–57% of the variance. The small proportion of systemic FFA that is converted to VLDL-TG can confound the expected relationship between plasma FFA concentration and VLDL-TG SRs. Regulation of VLDL-TG secretion is complex in that, despite a broad spectrum of physiological FFA concentrations, VLDL-TG SRs did not vary based on different acute substrate availability. PMID:23434937

  9. An economical biorefinery process for propionic acid production from glycerol and potato juice using high cell density fermentation.

    PubMed

    Dishisha, Tarek; Ståhl, Åke; Lundmark, Stefan; Hatti-Kaul, Rajni

    2013-05-01

    An economically sustainable process was developed for propionic acid production by fermentation of glycerol using Propionibacterium acidipropionici and potato juice, a by-product of starch processing, as a nitrogen/vitamin source. The fermentation was done as high-cell-density sequential batches with cell recycle. Propionic acid production and glycerol consumption rates were dependent on initial biomass concentration, and reached a maximum of 1.42 and 2.30 g L(-1) h(-1), respectively, from 50 g L(-1) glycerol at initial cell density of 23.7 gCDW L(-1). Halving the concentration of nitrogen/vitamin source resulted in reduction of acetic and succinic acids yields by ~39% each. At glycerol concentrations of 85 and 120 g L(-1), respectively, 43.8 and 50.8 g L(-1) propionic acid were obtained at a rate of 0.88 and 0.29 g L(-1) h(-1) and yield of 84 and 78 mol%. Succinic acid was 13 g% of propionic acid and could represent a potential co-product covering the cost of nitrogen/vitamin source.

  10. Remaining Sites Verification Package for the 120-B-1, 105-B Battery Acid Sump, Waste Site Reclassification Form 2006-057

    SciTech Connect

    L. M. Dittmer

    2006-09-25

    The 120-B-1 waste site, located in the 100-BC-1 Operable Unit of the Hanford Site, consisted of a concrete battery acid sump that was used from 1944 to 1969 to neutralize the spent sulfuric acid from lead cell batteries of emergency power packs and the emergency lighting system. The battery acid sump was associated with the 105-B Reactor Building and was located adjacent to the building's northwest corner. The results of verification sampling demonstrated that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also showed that residual contaminant concentrations are protective of groundwater and the Columbia River.

  11. Ionization-site effects on the photofragmentation of chloro- and bromoacetic acid molecules

    NASA Astrophysics Data System (ADS)

    Levola, Helena; Itälä, Eero; Schlesier, Kim; Kooser, Kuno; Laine, Sanna; Laksman, Joakim; Ha, Dang Trinh; Rachlew, Elisabeth; Tarkanovskaja, Marta; Tanzer, Katrin; Kukk, Edwin

    2015-12-01

    Fragmentation of gas-phase chloro- and bromoacetic acid samples, particularly its dependency on the atomic site of the initial core ionization, was studied in photoelectron-photoion-photoion coincidence (PEPIPICO) measurements. The fragmentation was investigated after ionizing carbon 1 s and bromine 3 d or chlorine 2 p core orbitals. It was observed that the samples had many similar fragmentation pathways and that their relative weights depended strongly on the initial ionization site. Additional Auger PEPIPICO measurements revealed a clear dependence of fragment pair intensities on the kinetic energy of the emitted Auger electrons. The modeled and measured Auger electron spectra indicated that the average internal energy of the molecule was larger following the carbon 1 s core-hole decay than after the decay of the halogen core hole. This difference in the internal energies was found to be the source of the site-dependent photofragmentation behavior.

  12. Isoferulic Acid Action against Glycation-Induced Changes in Structural and Functional Attributes of Human High-Density Lipoprotein.

    PubMed

    Jairajpuri, D S; Jairajpuri, Z S

    2016-03-01

    Glycation-induced high-density lipoprotein (HDL) modification by aldehydes can result in loss of its antiinflammatory/antioxidative properties, contributing to diabetes-associated cardiovascular diseases. Isoferulic acid, a major active ingredient of Cimicifuga heracleifolia, shows antiinflammatory, antiviral, antioxidant, and antidiabetic properties. Thus, this study investigated the antiglycation effect of isoferulic acid against compositional modifications of HDL and loss of biological activity of HDL-paraoxonase induced on incubation with different aldehydes. Protective effect of isoferulic acid was assessed by subjecting purified HDL from human plasma to glycation with methylglyoxal, glyoxal, or glycolaldehyde and varying concentrations of isoferulic acid. The effect of isoferulic acid was analyzed by determining amino group number, tryptophan and advanced glycation end-product fluorescence, thermal denaturation studies, carboxymethyl lysine content, and activity of HDL-paraoxonase. Concentration-dependent inhibitory action of isoferulic acid was observed against extensive structural perturbations, decrease in amino group number, increase in carboxymethyl lysine content, and decrease in the activity of HDL-paraoxonase caused by aldehyde-associated glycation in the HDL molecule. Isoferulic acid, when taken in concentration equal to that of aldehydes, was most protective, as 82-88% of paraoxonase activity was retained for all studied aldehydes. Isoferulic acid shows antiglycation action against aldehyde-associated glycation in HDL, which indicates its therapeutic potential for diabetic patients, especially those with micro-/macrovascular complications. PMID:27262199

  13. Prey Density Threshold and Tidal Influence on Reef Manta Ray Foraging at an Aggregation Site on the Great Barrier Reef.

    PubMed

    Armstrong, Asia O; Armstrong, Amelia J; Jaine, Fabrice R A; Couturier, Lydie I E; Fiora, Kym; Uribe-Palomino, Julian; Weeks, Scarla J; Townsend, Kathy A; Bennett, Mike B; Richardson, Anthony J

    2016-01-01

    Large tropical and sub-tropical marine animals must meet their energetic requirements in a largely oligotrophic environment. Many planktivorous elasmobranchs, whose thermal ecologies prevent foraging in nutrient-rich polar waters, aggregate seasonally at predictable locations throughout tropical oceans where they are observed feeding. Here we investigate the foraging and oceanographic environment around Lady Elliot Island, a known aggregation site for reef manta rays Manta alfredi in the southern Great Barrier Reef. The foraging behaviour of reef manta rays was analysed in relation to zooplankton populations and local oceanography, and compared to long-term sighting records of reef manta rays from the dive operator on the island. Reef manta rays fed at Lady Elliot Island when zooplankton biomass and abundance were significantly higher than other times. The critical prey density threshold that triggered feeding was 11.2 mg m-3 while zooplankton size had no significant effect on feeding. The community composition and size structure of the zooplankton was similar when reef manta rays were feeding or not, with only the density of zooplankton changing. Higher zooplankton biomass was observed prior to low tide, and long-term (~5 years) sighting data confirmed that more reef manta rays are also observed feeding during this tidal phase than other times. This is the first study to examine prey availability at an aggregation site for reef manta rays and it indicates that they feed in locations and at times of higher zooplankton biomass.

  14. Prey Density Threshold and Tidal Influence on Reef Manta Ray Foraging at an Aggregation Site on the Great Barrier Reef

    PubMed Central

    Armstrong, Asia O.; Armstrong, Amelia J.; Jaine, Fabrice R. A.; Couturier, Lydie I. E.; Fiora, Kym; Uribe-Palomino, Julian; Weeks, Scarla J.; Townsend, Kathy A.; Bennett, Mike B.; Richardson, Anthony J.

    2016-01-01

    Large tropical and sub-tropical marine animals must meet their energetic requirements in a largely oligotrophic environment. Many planktivorous elasmobranchs, whose thermal ecologies prevent foraging in nutrient-rich polar waters, aggregate seasonally at predictable locations throughout tropical oceans where they are observed feeding. Here we investigate the foraging and oceanographic environment around Lady Elliot Island, a known aggregation site for reef manta rays Manta alfredi in the southern Great Barrier Reef. The foraging behaviour of reef manta rays was analysed in relation to zooplankton populations and local oceanography, and compared to long-term sighting records of reef manta rays from the dive operator on the island. Reef manta rays fed at Lady Elliot Island when zooplankton biomass and abundance were significantly higher than other times. The critical prey density threshold that triggered feeding was 11.2 mg m-3 while zooplankton size had no significant effect on feeding. The community composition and size structure of the zooplankton was similar when reef manta rays were feeding or not, with only the density of zooplankton changing. Higher zooplankton biomass was observed prior to low tide, and long-term (~5 years) sighting data confirmed that more reef manta rays are also observed feeding during this tidal phase than other times. This is the first study to examine prey availability at an aggregation site for reef manta rays and it indicates that they feed in locations and at times of higher zooplankton biomass. PMID:27144343

  15. Prey Density Threshold and Tidal Influence on Reef Manta Ray Foraging at an Aggregation Site on the Great Barrier Reef.

    PubMed

    Armstrong, Asia O; Armstrong, Amelia J; Jaine, Fabrice R A; Couturier, Lydie I E; Fiora, Kym; Uribe-Palomino, Julian; Weeks, Scarla J; Townsend, Kathy A; Bennett, Mike B; Richardson, Anthony J

    2016-01-01

    Large tropical and sub-tropical marine animals must meet their energetic requirements in a largely oligotrophic environment. Many planktivorous elasmobranchs, whose thermal ecologies prevent foraging in nutrient-rich polar waters, aggregate seasonally at predictable locations throughout tropical oceans where they are observed feeding. Here we investigate the foraging and oceanographic environment around Lady Elliot Island, a known aggregation site for reef manta rays Manta alfredi in the southern Great Barrier Reef. The foraging behaviour of reef manta rays was analysed in relation to zooplankton populations and local oceanography, and compared to long-term sighting records of reef manta rays from the dive operator on the island. Reef manta rays fed at Lady Elliot Island when zooplankton biomass and abundance were significantly higher than other times. The critical prey density threshold that triggered feeding was 11.2 mg m-3 while zooplankton size had no significant effect on feeding. The community composition and size structure of the zooplankton was similar when reef manta rays were feeding or not, with only the density of zooplankton changing. Higher zooplankton biomass was observed prior to low tide, and long-term (~5 years) sighting data confirmed that more reef manta rays are also observed feeding during this tidal phase than other times. This is the first study to examine prey availability at an aggregation site for reef manta rays and it indicates that they feed in locations and at times of higher zooplankton biomass. PMID:27144343

  16. Characterization of binding sites for acetylated low density lipoprotein in the rat liver in vivo and in vitro.

    PubMed Central

    Dresel, H A; Friedrich, E; Via, D P; Schettler, G; Sinn, H

    1985-01-01

    Acetylated low density lipoprotein (acetyl-LDL) binding to hepatic membrane proteins of rats was analysed in vitro by ligand blotting. Specific binding could be demonstrated to two hepatic proteins with an apparent mol. wt. of 250 kd and 220 kd. Polyanionic competitors and maleylated bovine serum albumin inhibited the binding of acetyl-LDL effectively. To determine the sites of the catabolism of acetyl-LDL, [131I]-acetyl-LDL was injected intravenously into control rats and rats pre-treated with the known competitors of the acetyl-LDL binding. Distribution of the radiolabelled acetyl-LDL was followed by a scintillation camera. Six minutes after injection, the radioactivity was concentrated in the liver. The competitors and unlabelled acetyl-LDL but not native LDL reduced the hepatic uptake of [131I]acetyl-LDL dramatically. Thus, the sensitivity of the 220- and 250-kd membrane binding sites to the competitors for the acetyl-LDL binding resembled that of the hepatic compartment in vivo. Finally, an application of scintigraphy with radiolabelled low density lipoproteins for diagnostic evaluation of tumor compartments is presented. Images Fig. 2. Fig. 4. Fig. 5. PMID:4006910

  17. Investigation of the adsorption of amino acids on Pd(1 1 1): A density functional theory study

    NASA Astrophysics Data System (ADS)

    James, Joanna N.; Han, Jeong Woo; Sholl, David S.

    2014-05-01

    Density functional theory calculations have been used to study the adsorption of glycine, alanine, norvaline, valine, proline, cysteine, and serine on Pd(1 1 1). Most amino acids except cysteine adsorb onto the surface in a tridentate fashion through a nitrogen atom and both oxygen atoms. For cysteine, an additional bond is formed with the surface due to the strong affinity of the sulfur atom, resulting in a significantly larger adsorption energy. The adsorption patterns of amino acids we examined are supported by the shifts in vibrational frequencies associated with NHH and COO. The adsorption strength of amino acids depends on how much the molecules deform during the adsorption process. Understanding the adsorption of amino acids on Pd(1 1 1) provides fundamental information for future consideration of the interactions between their derivatives or more complicated biomolecules and metal surfaces.

  18. Groundwater flow near the Shoal Site, Sand Springs Range, Nevada: Impact of density-driven flow

    SciTech Connect

    Chapman, J.; Mihevc, T.; McKay, A.

    1994-09-01

    The nature of flow from a highland recharge area in a mountain range in north-central Nevada to discharge areas on either side of the range is evaluated to refine a conceptual model of contaminant transport from an underground nuclear test conducted beneath the range. The test, known as the Shoal event, was conducted in 1963 in granitic rocks of the Sand Springs Range. Sparse hydraulic head measurements from the early 1960s suggest flow from the shot location to the east to Fairview Valley, while hydrochemistry supports flow to salt pans in Fourmile Flat to the west. Chemical and isotopic data collected from water samples and during well-logging arc best explained by a reflux brine system on the west side of the Sand Springs Range, rather than a typical local flow system where all flow occurs from recharge areas in the highlands to a central discharge area in a playa. Instead, dense saline water from the playa is apparently being driven toward the range by density contrasts. The data collected between the range and Fourmile Flat suggest the groundwater is a mixture of younger, fresher recharge water with older brine. Chemical contrasts between groundwater in the east and west valleys reflect the absence of re-flux water in Fairview Valley because the regional discharge area is distant and thus there is no accumulation of salts. The refluxing hydraulic system probably developed after the end of the last pluvial period and differences between the location of the groundwater divide based on hydraulic and chemical indicators could reflect movement of the divide as the groundwater system adjusts to the new reflux condition.

  19. A comparative density functional theory study of electronic structure and optical properties of γ-aminobutyric acid and its cocrystals with oxalic and benzoic acid

    NASA Astrophysics Data System (ADS)

    da Silva Filho, J. G.; Freire, V. N.; Caetano, E. W. S.; Ladeira, L. O.; Fulco, U. L.; Albuquerque, E. L.

    2013-11-01

    In this letter, we study the electronic structure and optical properties of the active medicinal component γ-aminobutyric acid (GABA) and its cocrystals with oxalic (OXA) and benzoic (BZA) acid by means of the density functional theory formalism. It is shown that the cocrystallization strongly weakens the zwitterionic character of the GABA molecule leading to striking differences among the electronic band structures and optical absorption spectra of the GABA crystal and GABA:OXA, GABA:BZA cocrystals, originating from distinct sets of hydrogen bonds. Calculated band widths and Δ-sol band gap estimates indicate that both GABA and GABA:OXA, GABA:BZA cocrystals are indirect gap insulators.

  20. Microbial Communities in Biofilms of an Acid Mine Drainage Site Determined by Phospholipid Analysis

    NASA Astrophysics Data System (ADS)

    Das Gupta, S.; Fang, J.

    2008-12-01

    Phospholipids were extracted to determine the microbial biomass and community structure of biofims from an acid mine drainage (AMD) at the Green Valley coal mine site (GVS) in western Indiana. The distribution of specific biomarkers indicated the presence of a variety of microorganisms. Phototrophic microeukaryotes, which include Euglena mutabilis, algae, and cyanobacteria were the most dominant organisms, as indicated by the presence of polyunsaturated fatty acids. The presence of terminally methyl branched fatty acids suggests the presence of Gram-positive bacteria, and the mid-methyl branched fatty acids indicates the presence of sulfate-reducing bacteria. Fungi appear to also be an important part of the AMD microbial communities as suggested by the presence of 18:2 fatty acid. The acidophilic microeukaryotes Euglena dominated the biofilm microbial communities. These microorganisms appear to play a prominent role in the formation and preservation of stromatolites and in releasing oxygen to the atmosphere by oxygenic photosynthesis. Thus, the AMD environment comprises a host of microorganisms spreading out within the phylogenetic tree of life. Novel insights on the roles of microbial consortia in the formation and preservation of stromatolites and the production of oxygen through photosynthesis in AMD systems may have significance in the understanding of the interaction of Precambrian microbial communities in environments that produced microbially-mediated sedimentary structures and that caused oxygenation of Earth's atmosphere.

  1. Oxygen-enhanced biodegradation of phenoxy acids in ground water at contaminated sites.

    PubMed

    Tuxen, Nina; Reitzel, Lotte A; Albrechtsen, Hans-Jørgen; Bjerg, Poul L

    2006-01-01

    The effects of adding oxygen to anaerobic aquifer materials on biodegradation of phenoxy acid herbicides were studied by laboratory experiments with aquifer material from two contaminated sites (a former agricultural machinery service and an old landfill). At both sites, the primary pollutants were phenoxy acids and related chlorophenols. It was found that addition of oxygen enhanced degradation of the six original phenoxy acids and six original chlorophenols. Inverse modeling on 14C 4-chloro-2-methylphenoxypropanoic acid (MCPP) degradation curves revealed that increasing the oxygen concentrations from <0.3 mg/L up to 7 to 8 mg/L shortened the lag phases (from approximately 150 d to 5 to 25 d) and increased first-order degradation rate constants by 1 order of magnitude (from approximately 5 x 10(-2) d(-1) to up to 30 x 10(-2) d(-1)). Additionally, the degree of MCPP mineralization was increased (30% to 50% mineralized at low oxygen concentrations and 50% to 70% mineralized at high oxygen concentrations, based on 14CO2 recovery). These positive effects on degradation were observed even at relatively low oxygen concentrations (2 mg/L). Furthermore, effects related to the addition of oxygen on the general geochemistry were studied. An oxygen consumption of 2.2 to 2.6 mg O2/g dw was observed due to oxidation of solid organic matter and, to some extent (0.5% to 11% of the total oxygen consumption), water-soluble compounds such as Fe2+, dissolved Mn, nonvolatile organic carbon, and NH4+. Overall, the results suggest that stimulated biodegradation by addition of oxygen might be a feasible remediation technology at herbicide-contaminated sites, although oxygen consumption by the sediment could limit the applicability.

  2. Characterizing Surface Acidic Sites in Mesoporous-Silica-Supported Tungsten Oxide Catalysts Using Solid State NMR and Quantum Chemistry Calculations

    SciTech Connect

    Hu, Jian Z.; Kwak, Ja Hun; Wang, Yong; Hu, Mary Y.; Turcu, Romulus VF; Peden, Charles HF

    2011-10-18

    The acidic sites in dispersed tungsten oxide supported on SBA-15 mesoporous silica were investigated using a combination of pyridine titration, both fast-, and slow-MAS {sup 15}N NMR, static {sup 2}H NMR, and quantum chemistry calculations. It is found that the bridged acidic -OH groups in surface adsorbed tungsten dimers (i.e., W-OH-W) are the Broensted acid sites. The unusually strong acidity of these Broensted acid sites is confirmed by quantum chemistry calculations. In contrast, terminal W-OH sites are very stable and only weakly acidic as are terminal Si-OH sites. Furthermore, molecular interactions between pyridine molecules and the dimer Broensted and terminal W-OH sites for dispersed tungsten oxide species is strong. This results in restricted molecular motion for the interacting pyridine molecules even at room temperature, i.e., a reorientation mainly about the molecular 2-fold axis. This restricted reorientation makes it possible to estimate the relative ratio of the Broensted (tungsten dimer) to the weakly acidic terminal W-OH sites in the catalyst using the slow-MAS {sup 1}H-{sup 15}N CP PASS method.

  3. Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: A comparison between density functional theory and density functional tight binding results

    NASA Astrophysics Data System (ADS)

    große Holthaus, Svea; Köppen, Susan; Frauenheim, Thomas; Ciacchi, Lucio Colombi

    2014-06-01

    We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (10bar{1}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

  4. Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: a comparison between density functional theory and density functional tight binding results.

    PubMed

    grosse Holthaus, Svea; Köppen, Susan; Frauenheim, Thomas; Ciacchi, Lucio Colombi

    2014-06-21

    We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101̄0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields. PMID:24952560

  5. Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: A comparison between density functional theory and density functional tight binding results

    SciTech Connect

    Holthaus, Svea große; Köppen, Susan Frauenheim, Thomas; Ciacchi, Lucio Colombi

    2014-06-21

    We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101{sup ¯}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

  6. Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control.

    PubMed

    Kumar, N V Suresh; Priyakumar, U Deva; Singh, Harjinder; Roy, Saumya; Chakraborty, Tushar Kanti

    2012-07-01

    Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.

  7. Crystal Structure of Species D Adenovirus Fiber Knobs and Their Sialic Acid Binding Sites

    PubMed Central

    Burmeister, Wim P.; Guilligay, Delphine; Cusack, Stephen; Wadell, Göran; Arnberg, Niklas

    2004-01-01

    Adenovirus serotype 37 (Ad37) belongs to species D and can cause epidemic keratoconjunctivitis, whereas the closely related Ad19p does not. Primary cell attachment by adenoviruses is mediated through receptor binding of the knob domain of the fiber protein. The knobs of Ad37 and Ad19p differ at only two positions, Lys240Glu and Asn340Asp. We report the high-resolution crystal structures of the Ad37 and Ad19p knobs, both native and in complex with sialic acid, which has been proposed as a receptor for Ad37. Overall, the Ad37 and Ad19p knobs are very similar to previously reported knob structures, especially to that of Ad5, which binds the coxsackievirus-adenovirus receptor (CAR). Ad37 and Ad19p knobs are structurally identical with the exception of the changed side chains and are structurally most similar to CAR-binding knobs (e.g., that of Ad5) rather than non-CAR-binding knobs (e.g., that of Ad3). The two mutations in Ad19p result in a partial loss of the exceptionally high positive surface charge of the Ad37 knob but do not affect sialic acid binding. This site is located on the top of the trimer and binds both α(2,3) and α(2,6)-linked sialyl-lactose, although only the sialic acid residue makes direct contact. Amino acid alignment suggests that the sialic acid binding site is conserved in several species D serotypes. Our results show that the altered viral tropism and cell binding of Ad19p relative to those of Ad37 are not explained by a different binding ability toward sialyl-lactose. PMID:15220447

  8. Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site.

    PubMed

    Martin, Erik; Samoilova, Rimma I; Narasimhulu, Kupala V; Lin, Tzu-Jen; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A

    2011-04-13

    In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q

  9. Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors

    NASA Astrophysics Data System (ADS)

    Sato, Ryuma; Kitoh-Nishioka, Hirotaka; Ando, Koji; Yamato, Takahisa

    2015-07-01

    To examine the functional roles of the active site methionine (M-site) and glutamic acid (E-site) residues of blue-light photoreceptors, we performed in silico mutation at the M-site in a systematic manner and focused on the hydrogen bonding between the E-site and the substrate: the cyclobutane-pyrimidine dimer (CPD). Fragment molecular orbital calculations with electron correlations demonstrated that substitution of the M-site methionine with either alanine or glutamine always destabilizes the interaction energy between the E-site and the CPD by more than 12.0 kcal/mol, indicating that the methionine and glutamic acid residues cooperatively facilitate the enzymatic reaction in the active site.

  10. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    DOE PAGES

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; Nash, Connor; Steirer, K. Xerxes; Clark, Jared; Robichaud, David J.; Ruddy, Daniel A.

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, anmore » abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

  11. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

    PubMed Central

    Miao, Zhichao; Westhof, Eric

    2015-01-01

    Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i) the definition of nucleic acid binding sites; ii) the training and test datasets; iii) the algorithmic methods for the prediction strategies; iv) the performance measures and v) the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy…) are applied. We found that i) the tools have been greatly improved over the years; ii) some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii) RNA binding and DNA binding appear to follow similar driving forces and iv) dataset bias may exist in some methods. PMID:26681179

  12. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2015-12-01

    Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i) the definition of nucleic acid binding sites; ii) the training and test datasets; iii) the algorithmic methods for the prediction strategies; iv) the performance measures and v) the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy…) are applied. We found that i) the tools have been greatly improved over the years; ii) some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii) RNA binding and DNA binding appear to follow similar driving forces and iv) dataset bias may exist in some methods. PMID:26681179

  13. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites.

    PubMed

    Johnson, David B F; Xu, Jianfeng; Shen, Zhouxin; Takimoto, Jeffrey K; Schultz, Matthew D; Schmitz, Robert J; Xiang, Zheng; Ecker, Joseph R; Briggs, Steven P; Wang, Lei

    2011-11-01

    Stop codons have been exploited for genetic incorporation of unnatural amino acids (Uaas) in live cells, but their low incorporation efficiency, which is possibly due to competition from release factors, limits the power and scope of this technology. Here we show that the reportedly essential release factor 1 (RF1) can be knocked out from Escherichia coli by 'fixing' release factor 2 (RF2). The resultant strain JX33 is stable and independent, and it allows UAG to be reassigned from a stop signal to an amino acid when a UAG-decoding tRNA-synthetase pair is introduced. Uaas were efficiently incorporated at multiple UAG sites in the same gene without translational termination in JX33. We also found that amino acid incorporation at endogenous UAG codons is dependent on RF1 and mRNA context, which explains why E. coli tolerates apparent global suppression of UAG. JX33 affords a unique autonomous host for synthesizing and evolving new protein functions by enabling Uaa incorporation at multiple sites. PMID:21926996

  14. Identification of a lithium interaction site in the gamma-aminobutyric acid (GABA) transporter GAT-1.

    PubMed

    Zhou, Yonggang; Zomot, Elia; Kanner, Baruch I

    2006-08-01

    The sodium- and chloride-dependent electrogenic gamma-aminobutyric acid (GABA) transporter GAT-1, which transports two sodium ions together with GABA, is essential for synaptic transmission by this neurotransmitter. Although lithium by itself does not support GABA transport, it has been proposed that lithium can replace sodium at one of the binding sites but not at the other. To identify putative lithium selectivity determinants, we have mutated the five GAT-1 residues corresponding to those whose side chains participate in the sodium binding sites Na1 and Na2 of the bacterial leucine-transporting homologue LeuT(Aa). In GAT-1 and in most other neurotransmitter transporter family members, four of these residues are conserved, but aspartate 395 replaces the Na2 residue threonine 354. At varying extracellular sodium, lithium stimulated sodium-dependent transport currents as well as [3H]GABA uptake in wild type GAT-1. The extent of this stimulation was dependent on the GABA concentration. In mutants in which aspartate 395 was replaced by threonine or serine, the stimulation of transport by lithium was abolished. Moreover, these mutants were unable to mediate the lithium leak currents. This phenotype was not observed in mutants at the four other positions, although their transport properties were severely impacted. Thus at saturating GABA, the site corresponding to Na2 behaves as a low affinity sodium binding site where lithium can replace sodium. We propose that GABA participates in the other sodium binding site, just like leucine does in the Na1 site, and that at limiting GABA, this site determines the apparent sodium affinity of GABA transport.

  15. Modelling metal centres, acid sites and reaction mechanisms in microporous catalysts.

    PubMed

    O'Malley, Alexander J; Logsdail, A J; Sokol, A A; Catlow, C R A

    2016-07-01

    We discuss the role of QM/MM (embedded cluster) computational techniques in catalytic science, in particular their application to microporous catalysis. We describe the methodologies employed and illustrate their utility by briefly summarising work on metal centres in zeolites. We then report a detailed investigation into the behaviour of methanol at acidic sites in zeolites H-ZSM-5 and H-Y in the context of the methanol-to-hydrocarbons/olefins process. Studying key initial steps of the reaction (the adsorption and subsequent methoxylation), we probe the effect of framework topology and Brønsted acid site location on the energetics of these initial processes. We find that although methoxylation is endothermic with respect to the adsorbed system (by 17-56 kJ mol(-1) depending on the location), there are intriguing correlations between the adsorption/reaction energies and the geometries of the adsorbed species, of particular significance being the coordination of methyl hydrogens. These observations emphasise the importance of adsorbate coordination with the framework in zeolite catalysed conversions, and how this may vary with framework topology and site location, particularly suited to investigation by QM/MM techniques. PMID:27136967

  16. Determination of Vocs in groundwater at an industrial contamination site using a homemade low-density polyethylene passive diffusion sampler.

    PubMed

    Ma, Xu; Tan, Zhiqiang; Pang, Long; Liu, Jingfu

    2013-11-01

    A home-made inexpensive passive diffusion bag (PDB) sampler, prepared by filling deionized water in low-density polyethylene (LDPE) tubes, was evaluated for volatile organic compounds (VOC) sampling in groundwater at industrial contamination sites. Impacts of environmentally relevant conditions on the sampling equilibration time and partitioning of VOCs between the sampler and the water sample were investigated. Sample salinity, agitation and temperature can influence the equilibration time, but generally sampling equilibration was obtained in 14 days under real field sampling of VOCs in groundwater. Both laboratory study and field testing in a contaminated site showed that the VOC concentrations in the developed sampler were equal to those in the water samples at equilibrium. Coupled with a purge and trap concentrator-gas chromatograph-mass spectrometer (P&T-GC-MS), the developed PDB sampler provided a low-cost sampling device for routine monitoring of VOCs in groundwater in wells, with LODs in the range of 2.9-10 microg/L. The proposed PDB was applied to determine VOCs in groundwater at an industrial contamination site, and the present results agreed well with those determined using conventional pump-and-sample monitoring. All the studied 13 VOCs were tested in the four wells in the industrial contamination sites, with their concentrations in the range of 12-73660 microg/L. In addition, while benzene and toluene were heavily contaminated up to a maximum concentration of 74000 tg/L and 6000 microg/L, respectively, 1,2,3-trichlorobenzene and bromobenzene had relatively low contamination levels (below 25 microg/L).

  17. Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

    PubMed Central

    Risso, Valeria A.; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A.; Gaucher, Eric A.; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

    2015-01-01

    Local protein interactions (“molecular context” effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  18. The synergic effect between Mo species and acid sites in Mo/HMCM-22 catalysts for methane aromatization.

    PubMed

    Ma, Ding; Zhu, Qingjun; Wu, Zili; Zhou, Danhong; Shu, Yuying; Xin, Qin; Xu, Yide; Bao, Xinhe

    2005-08-21

    The acid properties of Mo/HMCM-22 catalyst, which is the precursor form of the working catalyst for methane aromatization reaction, and the synergic effect between Mo species and acid sites were studied and characterized by various characterization techniques. It is concluded that Brønsted and Lewis acidities of HMCM-22 are modified due to the introduction of molybdenum. We suggest a monomer of Mo species is formed by the exchange of Mo species with the Brønsted acid sites. On the other hand, coordinate unsaturated sites (CUS) are suggested to be responsible for the formation of newly detected Lewis acid sites. Computer modelling is established and coupling with experimental results, it is then speculated that the effective activation of methane is properly accomplished on Mo species accommodated in the 12 MR supercages of MCM-22 zeolite whereas the Brønsted acid sites in the same channel system play a key role for the formation of benzene. A much more pronounced volcano-typed reactivity curve of the Mo/HMCM-22 catalysts, as compared with that of the Mo/HZSM-5, with respect to Mo loading is found and this can be well understood due to the unique channel structure of MCM-22 zeolite and synergic effect between Mo species and acid sites.

  19. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

    PubMed

    Risso, Valeria A; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A; Gaucher, Eric A; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2015-02-01

    Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.

  20. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

    PubMed

    Risso, Valeria A; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A; Gaucher, Eric A; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2015-02-01

    Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  1. Induced resistance in groundnut by jasmonic acid and salicylic acid through alteration of trichome density and oviposition by Helicoverpa armigera (Lepidoptera: Noctuidae)

    PubMed Central

    War, Abdul Rashid; Hussain, Barkat; Sharma, Hari C.

    2013-01-01

    Jasmonic acid (JA) and salicylic acid (SA) are important phytohormones involved in plant resistance against insect herbivory and pathogen infection. Application of JA and SA induces several defensive traits in plants. Here we investigated the effect of JA and SA on trichome density in five groundnut genotypes [ICGV 86699, ICGV 86031, ICG 2271, ICG 1697 (resistant) and JL 24 (susceptible)]. The effect of JA- and SA-induced resistance on the oviposition behaviour of Helicoverpa armigera on different groundnut genotypes was also studied. Pre-treatment with JA increased numbers of trichomes in the insect-resistant genotypes, ICGV 86699, ICGV 86031, ICG 2271, and ICG 1697. The induction was greater at 10 days after treatment. Jasmonic acid- and SA-treated plants showed a substantial effect on the oviposition behaviour of H. armigera. Jasmonic acid application and herbivory reduced the number of eggs laid by H. armigera in all the groundnut genotypes tested. However, a greater reduction was recorded on plants pre-treated with JA. More egg laying was recorded in JL 24 in all the treatments as compared to the insect-resistant genotypes. These results suggested that pre-treatment with JA increased trichome density in groundnut plants, which conferred antixenosis for oviposition by H. armigera.

  2. Impact of food supplementation and methionine on high densities of cotton rats: Support of the amino-acid-quality hypothesis?

    USGS Publications Warehouse

    Webb, R.E.; Leslie, David M.; Lochmiller, R.L.; Masters, R.E.

    2005-01-01

    Considerable research supports the tenet that quantity and quality of food limit vertebrate populations. We evaluated predictions that increased availabilities of food and the essential amino acid methionine were related to population limitation of the hispid cotton rat (Sigmodon hispidus). Effects of supplemental food and methionine on density, survival, and reproductive parameters of wild cotton rats were assessed in north-central Oklahoma in 1998-1999. Twelve enclosed groups of 16 adult cotton rats each (8 male, 8 female) were randomly assigned to either no supplementation (control), supplementation with a mixed ration that had methionine at slightly below maintenance levels (0.20%), or a methionine-enhanced mixed ration (1.20%). In general, densities of cotton rats were twice as high and were sustained longer with dietary supplementation, and methionine-supplemented populations maintained the highest densities. Treatment effects on survival depended on time of year, with higher survival in supplemented enclosures in October and November. Per capita recruitment was highest with methionine-enhanced food. Treatment effects on proportions of overall and female cotton rats in reproductive condition depended on sampling date, but males were most reproductively active with methionine supplementation. Methionine supplementation resulted in an earlier and longer reproductive season. Density-dependent and density-independent factors no doubt interplay to determine population dynamics of cotton rats, but our results suggest that methionine plays a role in the population dynamics of wild cotton rats, apparently by enhancing overall density, recruitment, and reproductive activity of males.

  3. Refractive Index and Density Measurements of Peanut Oil for Determining Oleic and Linoleic Acid Contents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut seed are approximately 50% oil of which > 80% is either oleic or linoleic acid. The oleic/linoleic acid (O/L) ratio largely influences oxidative stability and hence peanut shelf life. Traditional peanut seed have O/L ratios near 1.5-2.0; however, many new cultivars are “high oleic” with O/L...

  4. Density and Refractive Index Measurements of Peanut Oil to Determine Oleic and Linoleic Acid Content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut seed are approximately 50% oil of which > 80% is either oleic or linoleic acid. The oleic/linoleic acid (O/L) ratio largely influences oxidative stability and hence peanut shelf life. Traditional peanut seed have O/L ratios near 2.5; however, many new cultivars are “high oleic” with O/L rat...

  5. Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns

    NASA Astrophysics Data System (ADS)

    Lu, Wen; Liu, Hai-yan

    2007-02-01

    Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to non-native local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.

  6. The mechanism of reduction of single-site redox proteins by ascorbic acid.

    PubMed Central

    Al-Ayash, A I; Wilson, M T

    1979-01-01

    The reduction of single-site haem and copper redox proteins by ascorbic acid was studied as a function of pH. Evidence is presented that indicates that the double-deprotonated ascorbate anion, ascorbate2-, is the reducing agent, and the pH-independent second-order rate constants for reduction by this species are given. Investigation of the temperature dependences of these rate constants have yielded the values of the activation parameters (delta H++ and delta S++) for reduction. These values, together with ligand-replacement studies, suggest that ascorbate2- acts as an outer-sphere reductant for these proteins. Reasons to account for the apparent inability of ascorbic acid to reduce the alkaline conformer of mammalian ferricytochrome c are suggested. PMID:35158

  7. REMOVING SLUDGE HEELS FROM SAVANNAH RIVER SITE WASTE TANKS BY OXALIC ACID DISSOLUTION

    SciTech Connect

    Poirier, M; David Herman, D; Fernando Fondeur, F; John Pareizs, J; Michael Hay, M; Bruce Wiersma, B; Kim Crapse, K; Thomas Peters, T; Samuel Fink, S; Donald Thaxton, D

    2009-03-01

    The Savannah River Site (SRS) will remove sludge as part of waste tank closure operations. Typically the bulk sludge is removed by mixing it with supernate to produce a slurry, and transporting the slurry to a downstream tank for processing. Experience shows that a residual heel may remain in the tank that cannot be removed by this conventional technique. In the past, SRS used oxalic acid solutions to disperse or dissolve the sludge heel to complete the waste removal. To better understand the actual conditions of oxalic acid cleaning of waste from carbon steel tanks, the authors developed and conducted an experimental program to determine its effectiveness in dissolving sludge, the hydrogen generation rate, the generation rate of other gases, the carbon steel corrosion rate, the impact of mixing on chemical cleaning, the impact of temperature, and the types of precipitates formed during the neutralization process. The test samples included actual SRS sludge and simulated SRS sludge. The authors performed the simulated waste tests at 25, 50, and 75 C by adding 8 wt % oxalic acid to the sludge over seven days. They conducted the actual waste tests at 50 and 75 C by adding 8 wt % oxalic acid to the sludge as a single batch. Following the testing, SRS conducted chemical cleaning with oxalic acid in two waste tanks. In Tank 5F, the oxalic acid (8 wt %) addition occurred over seven days, followed by inhibited water to ensure the tank contained enough liquid to operate the mixer pumps. The tank temperature during oxalic acid addition and dissolution was approximately 45 C. The authors analyzed samples from the chemical cleaning process and compared it with test data. The conclusions from the work are: (1) Oxalic acid addition proved effective in dissolving sludge heels in the simulant demonstration, the actual waste demonstration, and in SRS Tank 5F. (2) The oxalic acid dissolved {approx} 100% of the uranium, {approx} 100% of the iron, and {approx} 40% of the manganese

  8. Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

    NASA Astrophysics Data System (ADS)

    Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

    2015-05-01

    The immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles was investigated. For all particle sizes investigated, a leveling off of the frozen droplet fraction was observed reaching a plateau within the heterogeneous freezing temperature regime (T >- 38°C). The frozen fraction in the plateau region was proportional to the particle surface area. Based on these findings, an asymptotic value for ice active surface site density ns, which we named ns⋆, could be determined for the investigated feldspar sample. The comparison of these results with those of other studies not only elucidates the general feasibility of determining such an asymptotic value but also shows that the value of ns⋆ strongly depends on the method of the particle surface area determination. However, such an asymptotic value might be an important input parameter for atmospheric modeling applications. At least it shows that care should be taken when ns is extrapolated to lower or higher temperature.

  9. The species- and site-specific acid-base properties of penicillamine and its homodisulfide

    NASA Astrophysics Data System (ADS)

    Mirzahosseini, Arash; Szilvay, András; Noszál, Béla

    2014-08-01

    Penicillamine, penicillamine disulfide and 4 related compounds were studied by 1H NMR-pH titrations and case-tailored evaluation methods. The resulting acid-base properties are quantified in terms of 14 macroscopic and 28 microscopic protonation constants and the concomitant 7 interactivity parameters. The species- and site-specific basicities are interpreted by means of inductive and shielding effects through various intra- and intermolecular comparisons. The thiolate basicities determined this way are key parameters and exclusive means for the prediction of thiolate oxidizabilities and chelate forming properties in order to understand and influence chelation therapy and oxidative stress at the molecular level.

  10. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    PubMed Central

    2012-01-01

    Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

  11. Ab initio and density functional theory calculations of molecular structure and vibrational spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid

    NASA Astrophysics Data System (ADS)

    Kumar, J. Sharmi; Devi, T. S. Renuga; Ramkumaar, G. R.; Bright, A.

    2016-01-01

    The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. 1H and 13C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.

  12. Ab initio and density functional theory calculations of molecular structure and vibrational spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid.

    PubMed

    Kumar, J Sharmi; Devi, T S Renuga; Ramkumaar, G R; Bright, A

    2016-01-01

    The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. (1)H and (13)C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.

  13. Effect of a diet enriched with monounsaturated or polyunsaturated fatty acids on levels of low-density and high-density lipoprotein cholesterol in healthy women and men.

    PubMed

    Mensink, R P; Katan, M B

    1989-08-17

    Polyunsaturated fatty acids are thought to lower the serum cholesterol level more effectively than monounsaturated fatty acids. It is unclear whether the difference--if any--is due to a lowering of the level of high-density lipoprotein (HDL) or low-density lipoprotein (LDL) cholesterol. We therefore placed 31 women and 27 men on a mixed natural diet rich in saturated fat (19.3 percent of their daily energy intake from saturated fat, 11.5 percent from monounsaturated fat, and 4.6 percent from polyunsaturated fat) for 17 days. For the next 36 days, they received a mixed diet with the same total fat content, but enriched with olive oil and sunflower oil ("monounsaturated-fat diet": 12.9 percent saturated fat, 15.1 percent monounsaturated fat, and 7.9 percent polyunsaturated fat) or with sunflower oil alone ("polyunsaturated-fat diet": 12.6 percent saturated fat, 10.8 percent monounsaturated fat, and 12.7 percent polyunsaturated fat). The serum LDL cholesterol level decreased by 17.9 percent in those on the monounsaturated-fat diet and by 12.9 percent in those on the polyunsaturated-fat diet (95 percent confidence interval for the difference between the effects of the two unsaturated-fat diets, -9.9 percent to 0.0 percent). In men, the HDL cholesterol level fell slightly but not significantly with both diets. In women, the HDL cholesterol level did not change with either. We conclude that a mixed diet rich in monounsaturated fat was as effective as a diet rich in (n-6)polyunsaturated fat in lowering LDL cholesterol. Both diets lowered the level of HDL cholesterol slightly in men but not in women.

  14. Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

    NASA Astrophysics Data System (ADS)

    Rovira, Carme; Novoa, Juan J.; Ballone, Pietro

    2001-10-01

    Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure.

  15. Locations of the three primary binding sites for long-chain fatty acids on bovine serum albumin

    SciTech Connect

    Hamilton, J.A.; Era, S.; Bhamidipati, S.P. ); Reed, R.G. )

    1991-03-15

    Binding of {sup 13}C-enriched oleic acid to bovine serum albumin and to three large proteolytic fragments of albumin - two complementary fragments corresponding to the two halved of albumin and one fragment corresponding to the carboxyl-terminal domain - yielded unique patterns of NMR resonances (chemical shifts and relative intensities) that were used to identify the locations of binding of the first 5 mol of oleic acid to the multidomain albumin molecule. The first 3 mol of oleic acid added to intact albumin generated three distinct NMR resonances as a result of simultaneous binding of oleic acid to three heterogeneous sites (primary sites). This distribution suggests albumin to be a less symmetrical binding molecule than theoretical models predict. This work also demonstrates the power of NMR for the study of microenvironments of individual fatty acid binding sites in specific domain.

  16. The effect of the distance between acidic site and basic site immobilized on mesoporous solid on the activity in catalyzing aldol condensation

    SciTech Connect

    Yu Xiaofang; Yu Xiaobo; Wu Shujie; Liu Bo; Liu Heng; Guan Jingqi; Kan Qiubin

    2011-02-15

    Acid-base bifunctional heterogeneous catalysts containing carboxylic and amine groups, which were immobilized at defined distance from one another on the mesoporous solid were synthesized by immobilizing lysine onto carboxyl-SBA-15. The obtained materials were characterized by X-ray diffraction (XRD), N{sub 2} adsorption, Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), scanning electron micrographs (SEM), transmission electron micrographs (TEM), elemental analysis, and back titration. Proximal-C-A-SBA-15 with a proximal acid-base distance was more active than maximum-C-A-SBA-15 with a maximum acid-base distance in aldol condensation reaction between acetone and various aldehydes. It appears that the distance between acidic site and basic site immobilized on mesoporous solid should be an essential factor for catalysis optimization. -- Graphical abstract: Proximal-C-A-SBA-15 with a proximal acid-base distance and maximum-C-A-SBA-15 with a maximum acid-base distance were synthesized by immobilizing lysine onto carboxyl-SBA-15. Display Omitted Research highlights: {yields} Proximal-C-A-SBA-15 with a proximal acid-base distance. {yields} Maximum-C-A-SBA-15 with a maximum acid-base distance. {yields} Compared to maximum-C-A-SBA-15, proximal-C-A-SBA-15 was more active toward aldol condensation reaction between acetone and various aldehydes.

  17. Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

    PubMed

    Turan, Başak; Selçuki, Cenk

    2014-09-01

    Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

  18. Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

    PubMed

    Turan, Başak; Selçuki, Cenk

    2014-09-01

    Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers. PMID:25135067

  19. Hydrological parameter estimations from a conservative tracer test with variable-density effects at the Boise Hydrogeophysical Research Site

    NASA Astrophysics Data System (ADS)

    Dafflon, B.; Barrash, W.; Cardiff, M.; Johnson, T. C.

    2011-12-01

    Reliable predictions of groundwater flow and solute transport require an estimation of the detailed distribution of the parameters (e.g., hydraulic conductivity, effective porosity) controlling these processes. However, such parameters are difficult to estimate because of the inaccessibility and complexity of the subsurface. In this regard, developments in parameter estimation techniques and investigations of field experiments are still challenging and necessary to improve our understanding and the prediction of hydrological processes. Here we analyze a conservative tracer test conducted at the Boise Hydrogeophysical Research Site in 2001 in a heterogeneous unconfined fluvial aquifer. Some relevant characteristics of this test include: variable-density (sinking) effects because of the injection concentration of the bromide tracer, the relatively small size of the experiment, and the availability of various sources of geophysical and hydrological information. The information contained in this experiment is evaluated through several parameter estimation approaches, including a grid-search-based strategy, stochastic simulation of hydrological property distributions, and deterministic inversion using regularization and pilot-point techniques. Doing this allows us to investigate hydraulic conductivity and effective porosity distributions and to compare the effects of assumptions from several methods and parameterizations. Our results provide new insights into the understanding of variable-density transport processes and the hydrological relevance of incorporating various sources of information in parameter estimation approaches. Among others, the variable-density effect and the effective porosity distribution, as well as their coupling with the hydraulic conductivity structure, are seen to be significant in the transport process. The results also show that assumed prior information can strongly influence the estimated distributions of hydrological properties.

  20. SAVANNAH RIVER SITE TANK CLEANING: CORROSION RATE FOR ONE VERSUS EIGHT PERCENT OXALIC ACID SOLUTION

    SciTech Connect

    Ketusky, E.; Subramanian, K.

    2011-01-20

    Until recently, the use of oxalic acid for chemically cleaning the Savannah River Site (SRS) radioactive waste tanks focused on using concentrated 4 and 8-wt% solutions. Recent testing and research on applicable dissolution mechanisms have concluded that under appropriate conditions, dilute solutions of oxalic acid (i.e., 1-wt%) may be more effective. Based on the need to maximize cleaning effectiveness, coupled with the need to minimize downstream impacts, SRS is now developing plans for using a 1-wt% oxalic acid solution. A technology gap associated with using a 1-wt% oxalic acid solution was a dearth of suitable corrosion data. Assuming oxalic acid's passivation of carbon steel was proportional to the free oxalate concentration, the general corrosion rate (CR) from a 1-wt% solution may not be bound by those from 8-wt%. Therefore, after developing the test strategy and plan, the corrosion testing was performed. Starting with the envisioned process specific baseline solvent, a 1-wt% oxalic acid solution, with sludge (limited to Purex type sludge-simulant for this initial effort) at 75 C and agitated, the corrosion rate (CR) was determined from the measured weight loss of the exposed coupon. Environmental variations tested were: (a) Inclusion of sludge in the test vessel or assuming a pure oxalic acid solution; (b) acid solution temperature maintained at 75 or 45 C; and (c) agitation of the acid solution or stagnant. Application of select electrochemical testing (EC) explored the impact of each variation on the passivation mechanisms and confirmed the CR. The 1-wt% results were then compared to those from the 8-wt%. The immersion coupons showed that the maximum time averaged CR for a 1-wt% solution with sludge was less than 25-mils/yr for all conditions. For an agitated 8-wt% solution with sludge, the maximum time averaged CR was about 30-mils/yr at 50 C, and 86-mils/yr at 75 C. Both the 1-wt% and the 8-wt% testing demonstrated that if the sludge was removed from

  1. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    PubMed

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  2. Catalytic stimulation by restrained active-site floppiness--the case of high density lipoprotein-bound serum paraoxonase-1.

    PubMed

    Ben-David, Moshe; Sussman, Joel L; Maxwell, Christopher I; Szeler, Klaudia; Kamerlin, Shina C L; Tawfik, Dan S

    2015-03-27

    Despite the abundance of membrane-associated enzymes, the mechanism by which membrane binding stabilizes these enzymes and stimulates their catalysis remains largely unknown. Serum paraoxonase-1 (PON1) is a lipophilic lactonase whose stability and enzymatic activity are dramatically stimulated when associated with high-density lipoprotein (HDL) particles. Our mutational and structural analyses, combined with empirical valence bond simulations, reveal a network of hydrogen bonds that connect HDL binding residues with Asn168--a key catalytic residue residing >15Å from the HDL contacting interface. This network ensures precise alignment of N168, which, in turn, ligates PON1's catalytic calcium and aligns the lactone substrate for catalysis. HDL binding restrains the overall motion of the active site and particularly of N168, thus reducing the catalytic activation energy barrier. We demonstrate herein that disturbance of this network, even at its most far-reaching periphery, undermines PON1's activity. Membrane binding thus immobilizes long-range interactions via second- and third-shell residues that reduce the active site's floppiness and pre-organize the catalytic residues. Although this network is critical for efficient catalysis, as demonstrated here, unraveling these long-rage interaction networks is challenging, let alone their implementation in artificial enzyme design.

  3. Promotion of viral internal ribosomal entry site-mediated translation under amino acid starvation.

    PubMed

    Licursi, Maria; Komatsu, Yumiko; Pongnopparat, Theerawat; Hirasawa, Kensuke

    2012-05-01

    Cap-dependent and internal ribosomal entry site (IRES)-mediated translation are regulated differently within cells. Viral IRES-mediated translation often remains active when cellular cap-dependent translation is severely impaired under cellular stresses induced by virus infection. To investigate how cellular stresses influence the efficiency of viral IRES-mediated translation, we used a bicistronic luciferase reporter construct harbouring IRES elements from the following viruses: encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV), hepatitis C virus (HCV) or human rhinovirus (HRV). NIH3T3 cells transfected with these bicistronic reporter constructs were subjected to different cellular stresses. Increased translation initiation was only observed under amino acid starvation when EMCV or FMDV IRES elements were present. To identify cellular mechanisms that promoted viral IRES-mediated translation, we tested the involvement of eukaryotic initiation factor 4E-binding protein (4E-BP), general control non-depressed 2 (GCN2) and eukaryotic initiation factor 2B (eIF2B), as these are known to be modulated under amino acid starvation. Knockdown of 4E-BP1 impaired the promotion of EMCV and FMDV IRES-mediated translation under amino acid starvation, whereas GCN2 and eIF2B were not involved. To further investigate how 4E-BP1 regulates translation initiated by EMCV and FMDV IRES elements, we used a phosphoinositide kinase-3 inhibitor (LY294002), an mTOR inhibitor (Torin1) or leucine starvation to mimic 4E-BP1 dephosphorylation induced by amino acid starvation. 4E-BP1 dephosphorylation induced by the treatments was not sufficient to promote viral IRES-mediated translation. These results suggest that 4E-BP1 regulates EMCV and FMDV IRES-mediated translation under amino acid starvation, but not via its dephosphorylation. PMID:22302880

  4. Hatching success in salamanders and chorus frogs at two sites in Colorado, USA: Effects of acidic deposition and climate

    USGS Publications Warehouse

    Muths, E.; Campbell, D.H.; Corn, P.S.

    2003-01-01

    The snowpack in the vicinity of the Mount Zirkel Wilderness Area is among the most acidic in the western United States. We analyzed water chemistry and examined hatching success in tiger salamanders and chorus frogs at ponds there and at nearby Rabbit Ears Pass (Dumont) to determine whether acid deposition affects amphibians or their breeding habitats at these potentially sensitive locations. We found a wide range of acid neutralizing capacity among ponds within sites; the minimum pH recorded during the experiment was 5.4 at one of 12 ponds with all others at pH ??? 5.7. At Dumont, hatching success for chorus frogs was greater in ponds with low acid neutralizing capacity; however, lowest pHs were >5.8. At current levels of acid deposition, weather and pond characteristics are likely more important than acidity in influencing hatching success in amphibian larvae at these sites.

  5. The Eastern Australian Childhood Nevus Study: site differences in density and size of melanocytic nevi in relation to latitude and phenotype.

    PubMed

    MacLennan, Robert; Kelly, John W; Rivers, Jason K; Harrison, Simone L

    2003-03-01

    It has been postulated that site-specific variation in melanocytic nevus density and size is explained by differential response to sunlight. We observed the density and size of nevi at different body sites in relation to age, phenotype, latitude, and other measures of ultraviolet exposure. A standard protocol was used to assess nevi, phenotype, and sun exposure in 1123 Australian schoolchildren at 3 contrasting latitudes. Associations with phenotype (red hair, skin reflectance, sun sensitivity, and tanning) varied by body site. In Queensland, gender differences in nevus density on the back and lower limbs, unrelated to sun exposure, were similar to gender differences for melanoma. Small nevi (2-4 mm) were most dense on the arms, whereas large nevi (> or =5 mm) were most dense on the posterior trunk where they were related to age, decreasing latitude, male sex, and freckling. Our findings support the hypothesis of site-specific differences in nevus proliferative potential.

  6. Amino acid sequence surrounding the chondroitin sulfate attachment site of thrombomodulin regulates chondroitin polymerization.

    PubMed

    Izumikawa, Tomomi; Kitagawa, Hiroshi

    2015-05-01

    Thrombomodulin (TM) is a cell-surface glycoprotein and a critical mediator of endothelial anticoagulant function. TM exists as both a chondroitin sulfate (CS) proteoglycan (PG) form and a non-PG form lacking a CS chain (α-TM); therefore, TM can be described as a part-time PG. Previously, we reported that α-TM bears an immature, truncated linkage tetrasaccharide structure (GlcAβ1-3Galβ1-3Galβ1-4Xyl). However, the biosynthetic mechanism to generate part-time PGs remains unclear. In this study, we used several mutants to demonstrate that the amino acid sequence surrounding the CS attachment site influences the efficiency of chondroitin polymerization. In particular, the presence of acidic residues surrounding the CS attachment site was indispensable for the elongation of CS. In addition, mutants defective in CS elongation did not exhibit anti-coagulant activity, as in the case with α-TM. Together, these data support a model for CS chain assembly in which specific core protein determinants are recognized by a key biosynthetic enzyme involved in chondroitin polymerization.

  7. Active-site mutations of diphtheria toxin: effects of replacing glutamic acid-148 with aspartic acid, glutamine, or serine.

    PubMed

    Wilson, B A; Reich, K A; Weinstein, B R; Collier, R J

    1990-09-18

    Glutamic acid-148, an active-site residue of diphtheria toxin identified by photoaffinity labeling with NAD, was replaced with aspartic acid, glutamine, or serine by directed mutagenesis of the F2 fragment of the toxin gene. Wild-type and mutant F2 proteins were synthesized in Escherichia coli, and the corresponding enzymic fragment A moieties (DTA) were derived, purified, and characterized. The Glu----Asp (E148D), Glu----Gln (E148Q), and Glu----Ser (E148S) mutations caused reductions in NAD:EF-2 ADP-ribosyltransferase activity of ca. 100-, 250-, and 300-fold, respectively, while causing only minimal changes in substrate affinity. The effects of the mutations on NAD-glycohydrolase activity were considerably different; only a 10-fold reduction in activity was observed for E148S, and the E148D and E148Q mutants actually exhibited a small but reproducible increase in NAD-glycohydrolytic activity. Photolabeling by nicotinamide-radiolabeled NAD was diminished ca. 8-fold in the E148D mutant and was undetectable in the other mutants. The results confirm that Glu-148 plays a crucial role in the ADP-ribosylation of EF-2 and imply an important function for the side-chain carboxyl group in catalysis. The carboxyl group is also important for photochemical labeling by NAD but not for NAD-glycohydrolase activity. The pH dependence of the catalytic parameters for the ADP-ribosyltransferase reaction revealed a group in DTA-wt that titrates with an apparent pKa of 6.2-6.3 and is in the protonated state in the rate-determining step.(ABSTRACT TRUNCATED AT 250 WORDS)

  8. Leaching of glyphosate and amino-methylphosphonic acid from Danish agricultural field sites.

    PubMed

    Kjaer, Jeanne; Olsen, Preben; Ullum, Marlene; Grant, Ruth

    2005-01-01

    Pesticide leaching is an important process with respect to contamination risk to the aquatic environment. The risk of leaching was thus evaluated for glyphosate (N-phosphonomethyl-glycine) and its degradation product AMPA (amino-methylphosphonic acid) under field conditions at one sandy and two loamy sites. Over a 2-yr period, tile-drainage water, ground water, and soil water were sampled and analyzed for pesticides. At a sandy site, the strong soil sorption capacity and lack of macropores seemed to prevent leaching of both glyphosate and AMPA. At one loamy site, which received low precipitation with little intensity, the residence time within the root zone seemed sufficient to prevent leaching of glyphosate, probably due to degradation and sorption. Minor leaching of AMPA was observed at this site, although the concentration was generally low, being on the order of 0.05 microg L(-1) or less. At another loamy site, however, glyphosate and AMPA leached from the root zone into the tile drains (1 m below ground surface [BGS]) in average concentrations exceeding 0.1 microg L(-1), which is the EU threshold value for drinking water. The leaching of glyphosate was mainly governed by pronounced macropore flow occurring within the first months after application. AMPA was frequently detected more than 1.5 yr after application, thus indicating a minor release and limited degradation capacity within the soil. Leaching has so far been confined to the depth of the tile drains, and the pesticides have rarely been detected in monitoring screens located at lower depths. This study suggests that as both glyphosate and AMPA can leach through structured soils, they thereby pose a potential risk to the aquatic environment.

  9. The reaction mechanism for the SCR process on monomer V(5+) sites and the effect of modified Brønsted acidity.

    PubMed

    Arnarson, Logi; Falsig, Hanne; Rasmussen, Søren B; Lauritsen, Jeppe V; Moses, Poul Georg

    2016-06-22

    The energetics, structures and activity of a monomeric VO3H/TiO2(001) catalyst are investigated for the selective catalytic reduction (SCR) reaction by the use of density functional theory (DFT). Furthermore we study the influences of a dopant substitute in the TiO2 support and its effects on the known properties of the SCR system such as Brønsted acidity and reducibility of vanadium. We find for the reduction part of the SCR mechanism that it involves two Ti-O-V oxygen sites. One is a hydroxyl possessing Brønsted acidity which contributes to the formation of NH4(+), while the other accepts a proton which charge stabilizes the reduced active site. In the reduction the proton is donated to the latter due to a reaction between NH3 and NO that forms a H2NNO molecule which decomposes into N2(g) and H2O(g). A dopant substitution of 10 different dopants: Si, Ge, Se, Zr, Sn, Te, Hf, V, Mo and W at each of the sites, which participate in the reaction, modifies the energetics and therefore the SCR activity. We find that Brønsted acidity is a descriptor for the SCR activity at low temperatures. Based on this descriptor we find that Zr, Hf and Sn have a positive effect as they decrease the activation energy for the SCR reaction. PMID:27297567

  10. A quantum chemical study for exploring the inhibitory effect of nitrogen containing species on the adsorption of polynuclear aromatic hydrocarbons over a Bronsted acid site

    NASA Astrophysics Data System (ADS)

    Celis-Cornejo, C. M.; Garnica Mantilla, M. M.; Baldovino-Medrano, V. G.; Ramírez-Caballero, G. E.

    2016-08-01

    The analysis of the inhibitory effect of nitrogenated compounds on the hydroprocessing and hydropurification of oil derived fuels is important to produce cleaner fuels. In this work, density functional theory calculations were performed to investigate the effect of the nitrogen containing molecules on the adsorption of Polynuclear Aromatic Hydrocarbons (PAHs). Mordenite was chosen as a zeolitic structure for simulating a Bronsted acid site. The character of the acid site was confirmed by both a vibrational frequency calculation and a Bader charge analysis. From the adsorption calculations, it was found that the adsorption energy of PAHs increases with the number of aromatic rings in the structure. Also, the nitrogen containing species possibly inhibit more extensively two and three rings PAHs because of their lower adsorption energies. Finally, it was observed that the nitrogen species tend to drag the proton from the mordenite acid site. This explains the inhibitory effect in the adsorption of PAHs and contributes to understanding the dynamics of hydrocarbon hydroprocessing in refineries.

  11. The reaction mechanism for the SCR process on monomer V(5+) sites and the effect of modified Brønsted acidity.

    PubMed

    Arnarson, Logi; Falsig, Hanne; Rasmussen, Søren B; Lauritsen, Jeppe V; Moses, Poul Georg

    2016-06-22

    The energetics, structures and activity of a monomeric VO3H/TiO2(001) catalyst are investigated for the selective catalytic reduction (SCR) reaction by the use of density functional theory (DFT). Furthermore we study the influences of a dopant substitute in the TiO2 support and its effects on the known properties of the SCR system such as Brønsted acidity and reducibility of vanadium. We find for the reduction part of the SCR mechanism that it involves two Ti-O-V oxygen sites. One is a hydroxyl possessing Brønsted acidity which contributes to the formation of NH4(+), while the other accepts a proton which charge stabilizes the reduced active site. In the reduction the proton is donated to the latter due to a reaction between NH3 and NO that forms a H2NNO molecule which decomposes into N2(g) and H2O(g). A dopant substitution of 10 different dopants: Si, Ge, Se, Zr, Sn, Te, Hf, V, Mo and W at each of the sites, which participate in the reaction, modifies the energetics and therefore the SCR activity. We find that Brønsted acidity is a descriptor for the SCR activity at low temperatures. Based on this descriptor we find that Zr, Hf and Sn have a positive effect as they decrease the activation energy for the SCR reaction.

  12. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

    NASA Astrophysics Data System (ADS)

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  13. Adsorption and oxidation of oxalic acid on anatase TiO2 (001) surface: A density functional theory study.

    PubMed

    Sun, Tao; Wang, Yun; Zhang, Haimin; Liu, Porun; Zhao, Huijun

    2015-09-15

    Anatase TiO2 (001) surfaces have attracted great interest for photo-degradation of organic species recently due to their high reactivity. In this work, adsorption properties and oxidation mechanisms of oxalic acid on the anatase TiO2 (001) surface have been theoretically investigated using the first-principles density functional theory. Various possible adsorption configurations are considered by diversifying the connectivity of carboxylic groups with the surface. It is found that the adsorption of oxalic acid on the anatase (001) surface prefer the dissociative states. A novel double-bidentate configuration has been found due to the structural match between oxalic acid and the (001) surface. More charge is transferred from the adsorbed oxalic acid to the surface with the double-bidentate configuration when comparing with other adsorption structures. Thus, there is a positive correlation relationship between the transferred charge amount and the interfacial bond numbers when oxalic acid adsorbs on the anatase TiO2 (001) surface. The adsorption energies with dispersion corrections have demonstrated that the van der Waals interactions play an important role in the adsorption, especially when adsorbates are close to the surface.

  14. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers.

    PubMed

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  15. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid

    SciTech Connect

    Shaya, D.; Hahn, Bum-Soo; Bjerkan, Tonje Marita; Kim, Wan Seok; Park, Nam Young; Sim, Joon-Soo; Kim, Yeong-Shik; Cygler, M.

    2008-03-19

    Enzymes have evolved as catalysts with high degrees of stereospecificity. When both enantiomers are biologically important, enzymes with two different folds usually catalyze reactions with the individual enantiomers. In rare cases a single enzyme can process both enantiomers efficiently, but no molecular basis for such catalysis has been established. The family of bacterial chondroitin lyases ABC comprises such enzymes. They can degrade both chondroitin sulfate (CS) and dermatan sulfate (DS) glycosaminoglycans at the nonreducing end of either glucuronic acid (CS) or its epimer iduronic acid (DS) by a {beta}-elimination mechanism, which commences with the removal of the C-5 proton from the uronic acid. Two other structural folds evolved to perform these reactions in an epimer-specific fashion: ({alpha}/{alpha}){sub 5} for CS (chondroitin lyases AC) and {beta}-helix for DS (chondroitin lyases B); their catalytic mechanisms have been established at the molecular level. The structure of chondroitinase ABC from Proteus vulgaris showed surprising similarity to chondroitinase AC, including the presence of a Tyr-His-Glu-Arg catalytic tetrad, which provided a possible mechanism for CS degradation but not for DS degradation. We determined the structure of a distantly related Bacteroides thetaiotaomicron chondroitinase ABC to identify additional structurally conserved residues potentially involved in catalysis. We found a conserved cluster located {approx}12 {angstrom} from the catalytic tetrad. We demonstrate that a histidine in this cluster is essential for catalysis of DS but not CS. The enzyme utilizes a single substrate-binding site while having two partially overlapping active sites catalyzing the respective reactions. The spatial separation of the two sets of residues suggests a substrate-induced conformational change that brings all catalytically essential residues close together.

  16. Evaluation Of Sludge Heel Dissolution Efficiency With Oxalic Acid Cleaning At Savannah River Site

    SciTech Connect

    Sudduth, Christie; Vitali, Jason; Keefer, Mark

    2014-01-08

    The chemical cleaning process baseline strategy at the Savannah River Site was revised to improve efficiency during future execution of the process based on lessons learned during previous bulk oxalic acid cleaning activities and to account for operational constraints imposed by safety basis requirements. These improvements were also intended to transcend the difficulties that arise from waste removal in higher rheological yield stress sludge tanks. Tank 12 implemented this improved strategy and the bulk oxalic acid cleaning efforts concluded in July 2013. The Tank 12 radiological removal results were similar to previous bulk oxalic acid cleaning campaigns despite the fact that Tank 12 contained higher rheological yield stress sludge that would make removal more difficult than the sludge treated in previous cleaning campaigns. No appreciable oxalate precipitation occurred during the cleaning process in Tank 12 compared to previous campaigns, which aided in the net volume reduction of 75-80%. Overall, the controls established for Tank 12 provide a template for an improved cleaning process.

  17. Higher Dietary Acidity is Associated with Lower Bone Mineral Density in Postmenopausal Iranian Women, Independent of Dietary Calcium Intake.

    PubMed

    Shariati-Bafghi, Seyedeh-Elaheh; Nosrat-Mirshekarlou, Elaheh; Karamati, Mohsen; Rashidkhani, Bahram

    2014-01-01

    Findings of studies on the link between dietary acid-base balance and bone mass are relatively mixed. We examined the association between dietary acid-base balance and bone mineral density (BMD) in a sample of Iranian women, hypothesizing that a higher dietary acidity would be inversely associated with BMD, even when dietary calcium intake is adequate. In this cross-sectional study, lumbar spine and femoral neck BMDs of 151 postmenopausal women aged 50-85 years were measured using dual-energy x-ray absorptiometry. Dietary intakes were assessed using a validated food frequency questionnaire. Renal net acid excretion (RNAE), an estimate of acid-base balance, was then calculated indirectly from the diet using the formulae of Remer (based on dietary intakes of protein, phosphorus, potassium, and magnesium; RNAERemer) and Frassetto (based on dietary intakes of protein and potassium; RNAEFrassetto), and was energy adjusted by the residual method. After adjusting for potential confounders, multivariable adjusted means of the lumbar spine BMD of women in the highest tertiles of RNAERemer and RNAEFrassetto were significantly lower than those in the lowest tertiles (for RNAERemer: mean difference -0.084 g/cm2; P=0.007 and for RNAEFrassetto: mean difference -0.088 g/cm2; P=0.004). Similar results were observed in a subgroup analysis of subjects with dietary calcium intake of >800 mg/day. In conclusion, a higher RNAE (i. e. more dietary acidity), which is associated with greater intake of acid-generating foods and lower intake of alkali-generating foods, may be involved in deteriorating the bone health of postmenopausal Iranian women, even in the context of adequate dietary calcium intake.

  18. Characteristics of fluoride in pore-water at accidental hydrofluoric acid spillage site, Gumi, Korea

    NASA Astrophysics Data System (ADS)

    Kwon, E. H.; Lee, H. A.; Lee, J.; Kim, D.; Lee, S.; Yoon, H. O.

    2015-12-01

    A leakage accident of hydrofluoric acid (HF) occurred in Gumi, South Korea at Sep. 2012. The study site is located in the borderline between a large-scale industrial complex and a rural area. The HF plume was made immediately, and moved toward the rural area through air. After the accident, 212 ha of farm land were influenced and most of crops were withered. To recover the soil, CaO was applied after six months. Although several studies have done to estimate the extension and movement of HF plume in the air and to assess the impact on human health or plant after the incident, the long-term fate of fluoride (F) in the affected soils is not identified clearly. Thus, this study aimed to understand the behavior of F in the soil after HF releasing from accident site through chemical analysis and geochemical modeling. Within the radius of 1 km of accident site, 16 pore-water and soil samples were collected. The semi-quantitative soil composition (i.e., Al, Ca, Fe, K, Mg, Mn, Na, P, Si, Ti), total F, total P, OM contents in soil, and soil pH have already been measured, and pore-water compositions are also identified. From these experimental and modeling data, we could be evaluate if impact of accident exists until now, and also could be select and identify existing form of fluoride in soil and pore-water.

  19. Low density lipoprotein receptor related protein 1 variant interacts with saturated fatty acids in Puerto Ricans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Low density lipoprotein related receptor protein 1 (LRP1) is a multi-functional endocytic receptor that is highly expressed in adipocytes and the hypothalamus. Animal models and in vitro studies support a role for LRP1 in adipocyte metabolism and leptin signaling, but genetic polymorphisms have not ...

  20. Will reduced sulphur emissions under the Second Sulphur Protocol lead to recovery of acid sensitive sites in UK?

    PubMed

    Jenkins, A; Helliwell, R C; Swingewood, P J; Sefton, C; Renshaw, M; Ferrier, R C

    1998-01-01

    A conceptual model of the combined effects of acid deposition and land-use, Model of Acidification of Groundwater In Catchments (MAGIC), was applied to 21 upland sites in the UK Acid Waters Monitoring Network (AWMN) to assess the likely future recovery in response to the latest international agreements controlling anthropogenic sulphur emissions throughout Europe. Future estimates of sulphur deposition were generated by the Hull Acid Rain Model (HARM), based on the agreed reductions outlined in the Second Sulphur Protocol. The results indicate only a limited degree of recovery in surface-water chemistry at all sites over the next 50 years; moreover, a continuing decline in soil base status is predicted to occur at 70% of sites, resulting in longer term reacidification of surface-water at 38% of sites. However, compared with a 'business as usual' scenario the recovery is pronounced, although acidified sites will require further reductions in acidic deposition if recovery to pre-industrial chemical conditions are to be achieved. Furthermore, land-use scenarios at afforested sites suggest that replanting of felled forest will lead to a further increase in acidification. This strengthens the argument that plantation forestry should be avoided in areas considered geologically sensitive to acidic deposition.

  1. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism.

    PubMed

    Dance, Ian

    2015-11-01

    Nitrogenase contains a well defined and conserved chain of water molecules leading to the FeMo cofactor (FeMo-co, an [Fe7MoCS9] cluster with bidentate chelation of Mo by homocitrate) that is the active site where N2 and other substrates are sequentially hydrogenated using multiple protons and electrons. The function of this chain is proposed to be a proton wire, serially translocating protons to triply-bridging S3B of FeMo-co, where, concomitant with electron transfer to FeMo-co, an H atom is generated on S3B. Density functional simulations of this proton translocation mechanism are reported here, using a large 269-atom model that includes all residues hydrogen bonded to and surrounding the water chain, and likely to influence proton transfer: three carboxylate O atoms of obligatory homocitrate are essential. The mechanism involves the standard two components of the Grotthuss mechanism, namely H atom slides that shift H3O(+) from one water site to the next, and HOH molecular rotations that convert backward (posterior) OH bonds in the water chain to forward (anterior) OH bonds. The topography of the potential energy surface for each of these steps has been mapped. H atom slides pass through very short (ca. 2.5 Å) O-H-O hydrogen bonds, while HOH rotations involve the breaking of O-HO hydrogen bonds, and the occurrence of long (up to 3.6 Å) separations between contiguous water molecules. Both steps involve low potential energy barriers, <7 kcal mol(-1). During operation of the Grotthuss mechanism in nitrogenase there are substantial displacements of water molecules along the chain, occurring as ripples. These characteristics of the 'Grotthuss two-step', coupled with a buffering ability of two carboxylate O atoms of homocitrate, and combined with density functional characterisation of the final proton slide from the ultimate water molecule to S3B (including electron addition), have been choreographed into a complete mechanism for serial hydrogenation of FeMo-co. The

  2. Determination of pKa for Dithiophosphinic Acids using Density Functional Theory

    SciTech Connect

    Michael T. Benson; Megan L. Moser; Dean R. Peterman; Adriana Dinescu

    2008-10-01

    Symmetric aromatic dithiophosphinic acids of the form (XC6H4)2P(=S)(SH), where X = H, o-CH3, p-CH3, p-Cl, p-F, o-CF3, m-CF3, and p-CF3, and asymmetric aromatic acids of the form (X’C6H4)(X”C6H4)P(=S)(SH), where X’ = o-CF3, X” = m-CF3; X’ = H, X” = o-CF3, have been investigated using B3LYP/Gaussian03. Solvation was included in the calculations using the CPCM continuum solvation method. Using the data from vibrational frequency calculations, the pKa was calculated for the acids, and compared to Cyanex-301. The unexpectedly high pKa for bis(o-trifluoromethylphenyl)dithiophosphinic acid, when compared to the ortho-meta, meta-meta, and para-para isomers, is rationalized by e- repulsion between nearby fluorines and the sulfurs in the anion. This repulsion destabilizes the anion, versus the other isomers, thus raising the pKa.

  3. Amino acid conditions near the GPI anchor attachment site of prion protein for the conversion and the GPI anchoring.

    PubMed

    Hizume, Masaki; Kobayashi, Atsushi; Mizusawa, Hidehiro; Kitamoto, Tetsuyuki

    2010-01-22

    Prion protein (PrP) is a glycosylphosphatidylinositol (GPI)-anchored protein, and the C-terminal GPI anchor signal sequence (GPI-SS) of PrP is cleaved before GPI anchoring. However, mutations near the GPI anchor attachment site (the omega site) in the GPI-SS have been recognized in human genetic prion diseases. Moreover, the omega site of PrP has not been identified except hamster, though it is known that amino acid restrictions are very severe at the omega and omega+2 sites in other GPI-anchored proteins. To investigate the effect of mutations near the omega site of PrP on the conversion and the GPI anchoring, and to discover the omega site of murine PrP, we systematically created mutant murine PrP with all possible single amino acid substitutions at every amino acid residue from codon 228 to 240. We transfected them into scrapie-infected mouse neuroblastoma cells and examined the conversion efficiencies and the GPI anchoring of each mutant PrP. Mutations near the omega site altered the conversion efficiencies and the GPI anchoring efficiencies. Especially, amino acid restrictions for the conversion and the GPI anchoring were severe at codons 230 and 232 in murine PrP, though they were less severe than in other GPI-anchored proteins. Only the mutant PrPs presented on a cell surface via a GPI anchor were conversion competent. The present study shows that mutations in the GPI-SS can affect the GPI anchoring and the conversion efficiency of PrP. We clarified for the first time the omega site of murine PrP and the amino acid conditions near the omega site for the conversion as well as GPI anchoring.

  4. Singularity of proton transport in salts of orthoperiodic and orthotellurium acids: theoretical modeling using density functional calculations.

    PubMed

    Zyubina, Tatiana S; Shilov, Gennady V; Dobrovolsky, Yury A; Leonova, Ludmila S; Mebel, Alexander M

    2004-07-21

    Density functional B3LYP calculations have been performed to investigate proton transport in orthoperiodic and orthotellurium acids, their salts MIO(6)H(4)(M = Li, Rb, Cs) and CsH(5)TeO(6), dimers of the salt*acid type MIO(6)H(4)*H(5)IO(6)(M = Rb, Cs), CsIO(6)H(4)*H(6)TeO(6), CsHSO(4)*H(6)TeO(6), Cs(2)SO(4)*H(6)TeO(6), and also in double-substituted and binary salts Rb(2)H(3)IO(6) and Rb(4)H(2)I(2)O(10). It has been shown that the energy of salt dimerization is 33-35 kcal mol(-1) and the activation barrier for proton migration between the neighboring octahedrons of the salt*acid --> acid*salt type is calculated to be 3-13 kcal mol(-1). The activation energy of the proton migration along the octahedron, 20-30 kcal mol(-1), is comparable with the barrier for water molecule separation. Quantum-chemical calculations correlate with the results of X-ray and electrochemical studies.

  5. The species- and site-specific acid-base properties of biological thiols and their homodisulfides.

    PubMed

    Mirzahosseini, Arash; Noszál, Béla

    2014-07-01

    Cysteamine, cysteine, homocysteine, their homodisulfides and 9 related compounds were studied by ¹H NMR-pH titrations and case-tailored evaluation methods. The resulting acid-base properties are quantified in terms of 33 macroscopic and 62 microscopic protonation constants and the concomitant 16 interactivity parameters, providing thus the first complete microspeciation of this vitally important family of biomolecules. The species- and site-specific basicities are interpreted by means of inductive and hydrogen-bonding effects through various intra- and intermolecular comparisons. The pH-dependent distribution of the microspecies is depicted. The thiolate basicities determined this way provide exclusive means for the prediction of thiolate oxidizabilities, a key parameter to understand and influence oxidative stress at the molecular level.

  6. 36C1 measurements and the hydrology of an acid injection site

    USGS Publications Warehouse

    Vourvopoulos, G.; Brahana, J.V.; Nolte, E.; Korschinek, G.; Priller, A.; Dockhorn, B.

    1990-01-01

    In an area in western Tennessee (United States), an industrial firm is injecting acidic (pH = 0.1) iron chloride into permeable zones of carbonate rocks at depths ranging from 1000 to 2200 m below land surface. Overlying the injection zone at a depth of approximately 500 m below land surface is a regional fresh-water aquifer, the Knox aquifer. A study is currently underway to investigate whether the injection wells are hydraulically isolated from the fresh-water aquifer. Drilling of a test well that will reach a total depth of 2700 m has been initiated. The 36Cl content of 15 samples from the Knox aquifer, from monitor wells in the vicinity of the injection site, and from the test well have been analyzed. ?? 1990.

  7. Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

    NASA Astrophysics Data System (ADS)

    Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

    2015-04-01

    The formation of ice in atmospheric clouds has a substantial influence on the radiative properties of clouds as well as on the formation of precipitation. Therefore much effort has been made to understand and quantify the major ice formation processes in clouds. Immersion freezing has been suggested to be a dominant primary ice formation process in low and mid-level clouds (mixed-phase cloud conditions). It also has been shown that mineral dust particles are the most abundant ice nucleating particles in the atmosphere and thus may play an important role for atmospheric ice nucleation (Murray et al., 2012). Additionally, biological particles like bacteria and pollen are suggested to be potentially involved in atmospheric ice formation, at least on a regional scale (Murray et al., 2012). In recent studies for biological particles (SNOMAX and birch pollen), it has been demonstrated that freezing is induced by ice nucleating macromolecules and that an asymptotic value for the mass density of these ice nucleating macromolecules can be determined (Hartmann et al., 2013; Augustin et al., 2013, Wex et al., 2014). The question arises whether such an asymptotic value can also be determined for the ice active surface site density ns, a parameter which is commonly used to describe the ice nucleation activity of e.g., mineral dust. Such an asymptotic value for ns could be an important input parameter for atmospheric modeling applications. In the presented study, we therefore investigated the immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles utilizing the Leipzig Aerosol Cloud Interaction Simulator (LACIS). For all particle sizes considered in the experiments, we observed a leveling off of the frozen droplet fraction reaching a plateau within the heterogeneous freezing temperature regime (T > -38°C) which was proportional to the particle surface area. Based on these findings, we could determine an asymptotic value for the ice

  8. Application of a depositional facies model to an acid mine drainage site.

    PubMed

    Brown, Juliana F; Jones, Daniel S; Mills, Daniel B; Macalady, Jennifer L; Burgos, William D

    2011-01-01

    Lower Red Eyes is an acid mine drainage site in Pennsylvania where low-pH Fe(II) oxidation has created a large, terraced iron mound downstream of an anoxic, acidic, metal-rich spring. Aqueous chemistry, mineral precipitates, microbial communities, and laboratory-based Fe(II) oxidation rates for this site were analyzed in the context of a depositional facies model. Depositional facies were defined as pools, terraces, or microterracettes based on cm-scale sediment morphology, irrespective of the distance downstream from the spring. The sediments were composed entirely of Fe precipitates and cemented organic matter. The Fe precipitates were identified as schwertmannite at all locations, regardless of facies. Microbial composition was studied with fluorescence in situ hybridization (FISH) and transitioned from a microaerophilic, Euglena-dominated community at the spring, to a Betaproteobacteria (primarily Ferrovum spp.)-dominated community at the upstream end of the iron mound, to a Gammaproteobacteria (primarily Acidithiobacillus)-dominated community at the downstream end of the iron mound. Microbial community structure was more strongly correlated with pH and geochemical conditions than depositional facies. Intact pieces of terrace and pool sediments from upstream and downstream locations were used in flowthrough laboratory reactors to measure the rate and extent of low-pH Fe(II) oxidation. No change in Fe(II) concentration was observed with (60)Co-irradiated sediments or with no-sediment controls, indicating that abiotic Fe(II) oxidation was negligible. Upstream sediments attained lower effluent Fe(II) concentrations compared to downstream sediments, regardless of depositional facies.

  9. Activation of the Human Epithelial Sodium Channel (ENaC) by Bile Acids Involves the Degenerin Site.

    PubMed

    Ilyaskin, Alexandr V; Diakov, Alexei; Korbmacher, Christoph; Haerteis, Silke

    2016-09-16

    The epithelial sodium channel (ENaC) is a member of the ENaC/degenerin ion channel family, which also includes the bile acid-sensitive ion channel (BASIC). So far little is known about the effects of bile acids on ENaC function. ENaC is probably a heterotrimer consisting of three well characterized subunits (αβγ). In humans, but not in mice and rats, an additional δ-subunit exists. The aim of this study was to investigate the effects of chenodeoxycholic, cholic, and deoxycholic acid in unconjugated (CDCA, CA, and DCA) and tauro-conjugated (t-CDCA, t-CA, t-DCA) form on human ENaC in its αβγ- and δβγ-configuration. We demonstrated that tauro-conjugated bile acids significantly stimulate ENaC in the αβγ- and in the δβγ-configuration. In contrast, non-conjugated bile acids have a robust stimulatory effect only on δβγENaC. Bile acids stimulate ENaC-mediated currents by increasing the open probability of active channels without recruiting additional near-silent channels known to be activated by proteases. Stimulation of ENaC activity by bile acids is accompanied by a significant reduction of the single-channel current amplitude, indicating an interaction of bile acids with a region close to the channel pore. Analysis of the known ASIC1 (acid-sensing ion channel) crystal structure suggested that bile acids may bind to the pore region at the degenerin site of ENaC. Substitution of a single amino acid residue within the degenerin region of βENaC (N521C or N521A) significantly reduced the stimulatory effect of bile acids on ENaC, suggesting that this site is critical for the functional interaction of bile acids with the channel. PMID:27489102

  10. Site-specific acid-base properties of pholcodine and related compounds.

    PubMed

    Kovács, Z; Hosztafi, S; Noszál, B

    2006-11-01

    The acid-base properties of pholcodine, a cough-depressant agent, and related compounds including metabolites were studied by 1H NMR-pH titrations, and are characterised in terms of macroscopic and microscopic protonation constants. New N-methylated derivatives were also synthesized in order to quantitate site- and nucleus-specific protonation shifts and to unravel microscopic acid-base equilibria. The piperidine nitrogen was found to be 38 and 400 times more basic than its morpholine counterpart in pholcodine and norpholcodine, respectively. The protonation data show that the molecule of pholcodine bears an average of positive charge of 1.07 at physiological pH, preventing it from entering the central nervous system, a plausible reason for its lack of analgesic or addictive properties. The protonation constants of pholcodine and its derivatives are interpreted by comparing with related molecules of pharmaceutical interest. The pH-dependent relative concentrations of the variously protonated forms of pholcodine and morphine are depicted in distribution diagrams.

  11. Site-specific acid-base properties of pholcodine and related compounds.

    PubMed

    Kovács, Z; Hosztafi, S; Noszál, B

    2006-11-01

    The acid-base properties of pholcodine, a cough-depressant agent, and related compounds including metabolites were studied by 1H NMR-pH titrations, and are characterised in terms of macroscopic and microscopic protonation constants. New N-methylated derivatives were also synthesized in order to quantitate site- and nucleus-specific protonation shifts and to unravel microscopic acid-base equilibria. The piperidine nitrogen was found to be 38 and 400 times more basic than its morpholine counterpart in pholcodine and norpholcodine, respectively. The protonation data show that the molecule of pholcodine bears an average of positive charge of 1.07 at physiological pH, preventing it from entering the central nervous system, a plausible reason for its lack of analgesic or addictive properties. The protonation constants of pholcodine and its derivatives are interpreted by comparing with related molecules of pharmaceutical interest. The pH-dependent relative concentrations of the variously protonated forms of pholcodine and morphine are depicted in distribution diagrams. PMID:17004059

  12. Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey.

    PubMed

    Aytar, Pınar; Kay, Catherine Melanie; Mutlu, Mehmet Burçin; Çabuk, Ahmet; Johnson, David Barrie

    2015-04-01

    The biodiversity of acidophilic prokaryotes in two acidic (pH 2.8-3.05) mine drainage (AMD) sites (Balya and Çan) in Turkey was examined using a combined cultivation-based and cultivation-independent approach. The latter included analyzing microbial diversity using fluorescent in situ hybridization (FISH), terminal restriction enzyme fragment length polymorphism (`T-RFLP), and quantitative PCR (qPCR). Numbers of cultivatable heterotrophic acidophilic bacteria were over an order of magnitude greater than those of chemolithotrophic acidophiles in both AMD ponds examined. Isolates identified as strains of Acidithiobacillus ferrivorans, Acidiphilium organovorum, and Ferrimicrobium acidiphilum were isolated from the Balya AMD pond, and others identified as strains of Leptospirillum ferriphilum, Acidicapsa ligni, and Acidiphilium rubrum from Çan AMD. Other isolates were too distantly related (from analysis of their 16S rRNA genes) to be identified at the species level. Archaeal diversity in the two ponds appeared to be far more limited. T-RFLP and qPCR confirmed the presence of Ferroplasma-like prokaryotes, but no archaea were isolated from the two sites. qPCR generated semiquantitative data for genera of some of the iron-oxidizing acidophiles isolated and/or detected, suggesting the order of abundance was Leptospirillum > Ferroplasma > Acidithiobacillus (Balya AMD) and Ferroplasma > Leptospirillum > Acidithiobacillus (Çan AMD).

  13. The Protonation Site of para-Dimethylaminobenzoic Acid Using Atmospheric Pressure Ionization Methods

    NASA Astrophysics Data System (ADS)

    Chai, Yunfeng; Weng, Guofeng; Shen, Shanshan; Sun, Cuirong; Pan, Yuanjiang

    2015-04-01

    The protonation site of para-dimethylaminobenzoic acid ( p-DMABA) was investigated using atmospheric pressure ionization methods (ESI and APCI) coupled with collision-induced dissociation (CID), nuclear magnetic resonance (NMR), and computational chemistry. Theoretical calculations and NMR experiments indicate that the dimethyl amino group is the preferred site of protonation both in the gas phase and aqueous solution. Protonation of p-DMABA occurs at the nitrogen atom by ESI independent of the solvents and other operation conditions under typical thermodynamic control. However, APCI produces a mixture of the nitrogen- and carbonyl oxygen-protonated p-DMABA when aprotic organic solvents (acetonitrile, acetone, and tetrahydrofuran) are used, exhibiting evident kinetic characteristics of protonation. But using protic organic solvents (methanol, ethanol, and isopropanol) in APCI still leads to the formation of thermodynamically stable N-protonated p-DMABA. These structural assignments were based on the different CID behavior of the N- and O-protonated p-DMABA. The losses of methyl radical and water are the diagnostic fragmentations of the N- and O-protonated p-DMABA, respectively. In addition, the N-protonated p-DMABA is more stable than the O-protonated p-DMABA in CID revealed by energy resolved experiments and theoretical calculations.

  14. Studies on the site of biosynthesis of acidic glycoproteins of guinea-pig serum

    PubMed Central

    Simkin, J. L.; Jamieson, J. C.

    1967-01-01

    1. Studies were carried out to determine the cellular and subcellular site of biosynthesis of components of fraction I, an α-globulin fraction containing acidic glycoproteins isolated from guinea-pig serum. l-[U-14C]Leucine or -valine and d-[1-14C]glucosamine were used as precursors. 2. A lag of about 10min. occurred before appreciable label appeared in fraction I of serum after injection of leucine or glucosamine. Label in fraction I after 60min. labelling with glucosamine was present almost entirely in hexosamine and sialic acid. 3. Site of synthesis was investigated by studies in vivo up to 17min. after injection of precursor. Particulate subcellular fractions isolated from liver, spleen and kidney or homogenates of the latter two tissues were extracted with Lubrol. Extracts were allowed to react by double diffusion with antisera to fraction I or to subfractions isolated from it, and gels were subsequently subjected to radioautography. With either amino acid or glucosamine as precursor, only extracts of the microsome fraction of liver formed precipitin lines that were appreciably radioactive. 4. The role of the microsome fraction of liver in the synthesis of these glycoproteins was confirmed by immunological studies after incubation of liver slices with leucine or glucosamine. Incorporation of leucine was also investigated in a cell-free microsome system. 5. Material was also precipitated from certain Lubrol extracts of liver microsomes by direct addition of antiserum and its radioactivity measured. Degradation of material thus precipitated and use of heterologous immune systems showed that labelling of precipitin lines represented biosynthesis. 6. A study of extraction procedures suggested that the substances present in the microsome fraction of liver that react with specific antisera are associated with membranous structures. 7. Most or all precipitin lines formed by Lubrol extracts of liver microsomes interacted with precipitin lines given by guinea

  15. Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites.

    PubMed

    Bettencourt, Raul; Rodrigues, Mónica; Barros, Inês; Cerqueira, Teresa; Freitas, Cátia; Costa, Valentina; Pinheiro, Miguel; Egas, Conceição; Santos, Ricardo Serrão

    2014-08-01

    carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both Menez Gwen and Lucky Strike mussel gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated, in Lucky Strike samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between Menez Gwen and Lucky Strike animals. A differential expression analysis of bacterial genes between Menez Gwen and Lucky Strike mussels indicated a clear expression signature in the latter animal gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at an unpredicted conservation of endosymbiont bacterial loads between Menez Gwen and Lucky Strike samples. Taken together, our results support the hypothesis that B. azoricus exhibits different transcriptional statuses while living in distinct hydrothermal vent sites may result in distinct gene expressions because of physico-chemical and/or symbiont densities differences.

  16. Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites.

    PubMed

    Bettencourt, Raul; Rodrigues, Mónica; Barros, Inês; Cerqueira, Teresa; Freitas, Cátia; Costa, Valentina; Pinheiro, Miguel; Egas, Conceição; Santos, Ricardo Serrão

    2014-08-01

    carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both Menez Gwen and Lucky Strike mussel gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated, in Lucky Strike samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between Menez Gwen and Lucky Strike animals. A differential expression analysis of bacterial genes between Menez Gwen and Lucky Strike mussels indicated a clear expression signature in the latter animal gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at an unpredicted conservation of endosymbiont bacterial loads between Menez Gwen and Lucky Strike samples. Taken together, our results support the hypothesis that B. azoricus exhibits different transcriptional statuses while living in distinct hydrothermal vent sites may result in distinct gene expressions because of physico-chemical and/or symbiont densities differences. PMID:24882018

  17. Chemical characteristics and sources of organic acids in precipitation at a semi-urban site in Southwest China

    NASA Astrophysics Data System (ADS)

    Zhang, Y. L.; Lee, X. Q.; Cao, F.

    2011-01-01

    In order to investigate the chemical characteristics and sources of organic acids in precipitation in Southwest China, 105 rainwater samples were collected at a semi-urban site in Anshun from June 2007 to June 2008. Organic acids and major anions were analyzed along with pH and electrical conductivity. The pH values varied from 3.57 to 7.09 for all the rainfall events sampled, with an average of 4.67 which was typical acidic value. Formic, acetic and oxalic acids were found to be the predominant carboxylic acids and their volume weighted average (VWA) concentrations were 8.77, 6.93 and 2.84 μmol l -1, respectively. These organic acids were estimated to account for 8.1% to the total free acidity (TFA) in precipitation. The concentrations of the majority organic acids at studied site had a clear seasonal pattern, reaching higher levels during the non-growing season than those in growing season, which was attributed to dilution effect of heavy rainfall during the growing season. The seasonal variation of wet deposition flux of these organic acids confirmed higher source strength of biogenic emissions from vegetation during the growing season. Formic-to-acetic acids ratio (F/A), an indicator of primary versus secondary sources of these organic acids, suggested that primary sources from vehicular emission, biomass burning, soil and vegetation emissions were dominant sources. In addition, the lowest concentrations of organic acids were found under type S, when air masses originated from the marine (South China Sea) during Southern Asian Monsoon period. And the highest concentrations were observed in precipitation events from Northeast China (type NE), prevailing mostly during winter with the lowest rainfall.

  18. Halogen bonding from a hard and soft acids and bases perspective: investigation by using density functional theory reactivity indices.

    PubMed

    Pinter, Balazs; Nagels, Nick; Herrebout, Wouter A; De Proft, Frank

    2013-01-01

    Halogen bonds between the trifluoromethyl halides CF(3)Cl, CF(3)Br and CF(3)I, and dimethyl ether, dimethyl sulfide, trimethylamine and trimethyl phosphine were investigated using Pearson's hard and soft acids and bases (HSAB) concept with conceptual DFT reactivity indices, the Ziegler-Rauk-type energy-decomposition analysis, the natural orbital for chemical valence (NOCV) framework and the non-covalent interaction (NCI) index. It is found that the relative importance of electrostatic and orbital (charge transfer) interactions varies as a function of both the donor and acceptor molecules. Hard and soft interactions were distinguished and characterised by atomic charges, electrophilicity and local softness indices. Dual-descriptor plots indicate an orbital σ hole on the halogen similar to the electrostatic σ hole manifested in the molecular electrostatic potential. The predicted high halogen-bond-acceptor affinity of N-heterocyclic carbenes was evidenced in the highest complexation energy for the hitherto unknown CF(3) I·NHC complex. The dominant NOCV orbital represents an electron-density deformation according to a n→σ*-type interaction. The characteristic signal found in the reduced density gradient versus electron-density diagram corresponds to the non-covalent interaction between contact atoms in the NCI plots, which is the manifestation of halogen bonding within the NCI theory. The unexpected C-X bond strengthening observed in several cases was rationalised within the molecular orbital framework.

  19. Halogen bonding from a hard and soft acids and bases perspective: investigation by using density functional theory reactivity indices.

    PubMed

    Pinter, Balazs; Nagels, Nick; Herrebout, Wouter A; De Proft, Frank

    2013-01-01

    Halogen bonds between the trifluoromethyl halides CF(3)Cl, CF(3)Br and CF(3)I, and dimethyl ether, dimethyl sulfide, trimethylamine and trimethyl phosphine were investigated using Pearson's hard and soft acids and bases (HSAB) concept with conceptual DFT reactivity indices, the Ziegler-Rauk-type energy-decomposition analysis, the natural orbital for chemical valence (NOCV) framework and the non-covalent interaction (NCI) index. It is found that the relative importance of electrostatic and orbital (charge transfer) interactions varies as a function of both the donor and acceptor molecules. Hard and soft interactions were distinguished and characterised by atomic charges, electrophilicity and local softness indices. Dual-descriptor plots indicate an orbital σ hole on the halogen similar to the electrostatic σ hole manifested in the molecular electrostatic potential. The predicted high halogen-bond-acceptor affinity of N-heterocyclic carbenes was evidenced in the highest complexation energy for the hitherto unknown CF(3) I·NHC complex. The dominant NOCV orbital represents an electron-density deformation according to a n→σ*-type interaction. The characteristic signal found in the reduced density gradient versus electron-density diagram corresponds to the non-covalent interaction between contact atoms in the NCI plots, which is the manifestation of halogen bonding within the NCI theory. The unexpected C-X bond strengthening observed in several cases was rationalised within the molecular orbital framework. PMID:23169478

  20. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  1. Heavy metal accumulation related to population density in road dust samples taken from urban sites under different land uses.

    PubMed

    Trujillo-González, Juan Manuel; Torres-Mora, Marco Aurelio; Keesstra, Saskia; Brevik, Eric C; Jiménez-Ballesta, Raimundo

    2016-05-15

    Soil pollution is a key component of the land degradation process, but little is known about the impact of soil pollution on human health in the urban environment. The heavy metals Pb, Zn, Cu, Cr, Cd and Ni were analyzed by acid digestion (method EPA 3050B) and a total of 15 dust samples were collected from streets of three sectors of the city with different land uses; commercial, residential and a highway. The purpose was to measure the concentrations of heavy metals in road sediment samples taken from urban sites under different land uses, and to assess pollution through pollution indices, namely the ecological risk index and geoaccumulation index. Heavy metals concentrations (mg/kg) followed the following sequences for each sector: commercial sector Pb (1289.4)>Cu (490.2)>Zn (387.6)>Cr (60.2)>Ni (54.3); highway Zn (133.3)>Cu (126.3)>Pb (87.5)>Cr (9.4)>Ni (5.3); residential sector Zn (108.3)>Pb (26.0)>Cu (23.7)>Cr (7.3)>Ni (7.2). The geoaccumulation index indicated that the commercial sector was moderately to strongly polluted while the other sectors fell into the unpolluted category. Similarly, using the ecological risk index the commercial sector fell into the considerable category while the other sectors classified as low risk. Road dust increased along with city growth and its dynamics, additionally, road dust might cause a number of negative environmental impacts, therefore the monitoring this dust is crucial. PMID:26986764

  2. Plane wave density functional theory studies of the structural and the electronic properties of amino acids attached to graphene oxide via peptide bonding

    NASA Astrophysics Data System (ADS)

    Min, Byeong June; Jeong, Hae Kyung; Lee, ChangWoo

    2015-08-01

    We studied via plane wave pseudopotential total-energy calculations within the local spin density approximation (LSDA) the electronic and the structural properties of amino acids (alanine, glycine, and histidine) attached to graphene oxide (GO) by peptide bonding. The HOMO-LUMO gap, the Hirshfeld charges, and the equilibrium geometrical structures exhibit distinctive variations that depend on the species of the attached amino acid. The GO-amino acid system appears to be a good candidate for a biosensor.

  3. Atmospheric oxalic acid and related secondary organic aerosols in Qinghai Lake, a continental background site in Tibet Plateau

    NASA Astrophysics Data System (ADS)

    Meng, Jingjing; Wang, Gehui; Li, Jianjun; Cheng, Chunlei; Cao, Junji

    2013-11-01

    Summertime PM2.5 aerosols collected from Qinghai Lake (3200 m a.s.l.), a remote continental site in the northeastern part of Tibetan Plateau, were analyzed for dicarboxylic acids (C2-C11), ketocarboxylic acids and α-dicarbonyals. Oxalic acid (C2) is the dominant dicarboxylic acid in the samples, followed by malonic, succinic and azelaic acids. Total dicarboxylic acids (231 ± 119 ng m-3), ketocarboxylic acids (8.4 ± 4.3 ng m-3), and α-dicarbonyls (2.7 ± 2.1 ng m-3) at the Tibetan background site are 2-5 times less than those detected in lowland areas such as 14 Chinese megacities. Compared to those in other urban and marine areas enhancements in relative abundances of C2/total diacids and diacids-C/WSOC of the PM2.5 samples suggest that organic aerosols in the region are more oxidized due to strong solar radiation. Molecular compositions and air mass trajectories demonstrate that the above secondary organic aerosols in the Qinghai Lake atmosphere are largely derived from long-range transport. Ratios of oxalic acid, glyoxal and methylglyoxal to levoglucosan in PM2.5 aerosols emitted from household burning of yak dung, a major energy source for Tibetan in the region, are 30-400 times lower than those in the ambient air, which further indicates that primary emission from biomass burning is a negligible source of atmospheric oxalic acid and α-dicarbonyls at this background site.

  4. Time-dependent density functional theory (TD-DFT) coupled with reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD).

    PubMed

    Yokogawa, D

    2016-09-01

    Theoretical approach to design bright bio-imaging molecules is one of the most progressing ones. However, because of the system size and computational accuracy, the number of theoretical studies is limited to our knowledge. To overcome the difficulties, we developed a new method based on reference interaction site model self-consistent field explicitly including spatial electron density distribution and time-dependent density functional theory. We applied it to the calculation of indole and 5-cyanoindole at ground and excited states in gas and solution phases. The changes in the optimized geometries were clearly explained with resonance structures and the Stokes shift was correctly reproduced. PMID:27608983

  5. Time-dependent density functional theory (TD-DFT) coupled with reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD)

    NASA Astrophysics Data System (ADS)

    Yokogawa, D.

    2016-09-01

    Theoretical approach to design bright bio-imaging molecules is one of the most progressing ones. However, because of the system size and computational accuracy, the number of theoretical studies is limited to our knowledge. To overcome the difficulties, we developed a new method based on reference interaction site model self-consistent field explicitly including spatial electron density distribution and time-dependent density functional theory. We applied it to the calculation of indole and 5-cyanoindole at ground and excited states in gas and solution phases. The changes in the optimized geometries were clearly explained with resonance structures and the Stokes shift was correctly reproduced.

  6. Isotope geochemistry of waters affected by acid mine drainage in old labour sites (SE, Spain).

    NASA Astrophysics Data System (ADS)

    Pérez-Sirvent, Carmen; Martinez-Sanchez, Maria Jose; Garcia-Lorenzo, Maria Luz; Agudo, Ines; Hernandez-Cordoba, Manuel; Recio, Clemente

    2015-04-01

    The ore deposits of this zone have iron, lead and zinc as the main metal components. Iron is present in oxides, hydroxides, sulfides, sulfates, carbonates, and silicates; lead and zinc occur in sulfides (galena and sphalerite, respectively), carbonates, sulfates, and lead or zinc-bearing (manganese, iron) oxides. Mining started with the Romans and activity peaked in the second half of the 19th century and throughout the 20th century until the 1980's. From 1940 to 1957, mineral concentration was made by froth flotation and, prior to this, by gravimetric techniques. The mining wastes, or tailings, with a very fine particle size were deposited inland (tailings dams) and, since 1957, huge releases were made in directly the sea coast. The objective of this work was to evaluate processes affecting waters from abandoned mine sites by way of stable isotopic analysis, particularly H and O stable isotopes from water and S and O from dissolved sulfates. Several common chemical and physical processes, such as evaporation, water-rock interaction and mixing could alter water isotopic composition. Evaporation, which causes an enrichment in δD and δ18O in the residual water, is an important process in semiarid areas. The results obtained indicate that, for sites near the coast, waters are meteoric, and marine infiltration only takes place in the deepest layers near the shore or if water remains stagnated in sediments with low permeability. The main source of sulfate was the oxidation of sulfides, resulting in the liberation of acid, sulfate and metals. In order to assess the mechanism responsible for sulfide oxidation, the stoichiometric isotope balance model and the general isotope balance model were tested, suggesting that the oxidation via Fe3+ was predominant in the surface, and controlled by A. ferrooxidans, while at depth, sulfate reduction occurred.

  7. Beneficial effects of omega-3 fatty acids in the proteome of high-density lipoprotein proteome

    PubMed Central

    2012-01-01

    Background Omega-3 poly-unsaturated fatty acids (ω-3 PUFAs) have demonstrated to be beneficial in the prevention of cardiovascular disease, however, the mechanisms by which they perform their cardiovascular protection have not been clarified. Intriguingly, some of these protective effects have also been linked to HDL. The hypothesis of this study was that ω-3 PUFAs could modify the protein cargo of HDL particle in a triglyceride non-dependent mode. The objective of the study was to compare the proteome of HDL before and after ω-3 PUFAs supplemented diet. Methods A comparative proteomic analysis in 6 smoker subjects HDL before and after a 5 weeks ω-3 PUFAs enriched diet has been performed. Results Among the altered proteins, clusterin, paraoxonase, and apoAI were found to increase, while fibronectin, α-1-antitrypsin, complement C1r subcomponent and complement factor H decreased after diet supplementation with ω-3 PUFAs. Immunodetection assays confirmed these results. The up-regulated proteins are related to anti-oxidant, anti-inflammatory and anti-atherosclerotic properties of HDL, while the down-regulated proteins are related to regulation of complement activation and acute phase response. Conclusions Despite the low number of subjects included in the study, our findings demonstrate that ω-3 PUFAs supplementation modifies lipoprotein containing apoAI (LpAI) proteome and suggest that these protein changes improve the functionality of the particle. PMID:22978374

  8. Early smelter sites: A neglected chapter in the history and geography of acid rain in the United States

    NASA Astrophysics Data System (ADS)

    Quinn, M.-L.

    Dominant spatial and temporal theories of acid rain in the U.S. are identified, followed by brief comments on how historical data have generally been used in modern acid rain research. A frequently-cited 1982 article by E.B. Cowling is examined, one that has influenced much thinking on the history of acid rain. The article overlooks early American smelters, however, and the role they played in the true history and geography of acid rain in the United States. Continuing with this theme, a connection is established between acid rain and turn-of-the-century smelter smoke problems. Literature on the latter subject is discussed, and American and German examples are given. A beginning is then made on writing acid rain's neglected chapter, focusing on Tennessee's Copper Basin (Ducktown District) where copper smelting dates back to the 1850s. A short historical overview of this area's smelting operations is given, with particular attention to the air pollution and other environmental problems resulting from large emissions of sulfur dioxide. Five additional early smelter sites for potential study are mentioned as well. The paper concludes with some observations regarding the way in which expanded research of early smelter sites could affect the general perception of acid rain in the U.S. It is also suggested that such research might contribute to a better atmosphere for making decisions and policies pertaining to the phenomenon as it exists today.

  9. CHARACTERIZATION OF INDIVIDUAL CHEMICAL REACTIONS CONSUMING ACID DURING NUCLEAR WASTE PROCESSING AT THE SAVANNAH RIVER SITE - 136B

    SciTech Connect

    Koopman, D.; Pickenheim, B.; Lambert, D.; Newell, J.; Stone, M.

    2009-09-02

    Conversion of legacy radioactive high-level waste at the Savannah River Site into a stable glass waste form involves a chemical pretreatment process to prepare the waste for vitrification. Waste slurry is treated with nitric and formic acids to achieve certain goals. The total quantity of acid added to a batch of waste slurry is constrained by the catalytic activity of trace noble metal fission products in the waste that can convert formic acid into hydrogen gas at many hundreds of times the radiolytic hydrogen generation rate. A large block of experimental process simulations were performed to characterize the chemical reactions that consume acid prior to hydrogen generation. The analysis led to a new equation for predicting the quantity of acid required to process a given volume of waste slurry.

  10. Myeloperoxidase-derived oxidants modify apolipoprotein A-I and generate dysfunctional high-density lipoproteins: comparison of hypothiocyanous acid (HOSCN) with hypochlorous acid (HOCl).

    PubMed

    Hadfield, Katrina A; Pattison, David I; Brown, Bronwyn E; Hou, Liming; Rye, Kerry-Anne; Davies, Michael J; Hawkins, Clare L

    2013-01-15

    Oxidative modification of HDLs (high-density lipoproteins) by MPO (myeloperoxidase) compromises its anti-atherogenic properties, which may contribute to the development of atherosclerosis. Although it has been established that HOCl (hypochlorous acid) produced by MPO targets apoA-I (apolipoprotein A-I), the major apolipoprotein of HDLs, the role of the other major oxidant generated by MPO, HOSCN (hypothiocyanous acid), in the generation of dysfunctional HDLs has not been examined. In the present study, we characterize the structural and functional modifications of lipid-free apoA-I and rHDL (reconstituted discoidal HDL) containing apoA-I complexed with phospholipid, induced by HOSCN and its decomposition product, OCN- (cyanate). Treatment of apoA-I with HOSCN resulted in the oxidation of tryptophan residues, whereas OCN- induced carbamylation of lysine residues to yield homocitrulline. Tryptophan residues were more readily oxidized on apoA-I contained in rHDLs. Exposure of lipid-free apoA-I to HOSCN and OCN- significantly reduced the extent of cholesterol efflux from cholesterol-loaded macrophages when compared with unmodified apoA-I. In contrast, HOSCN did not affect the anti-inflammatory properties of rHDL. The ability of HOSCN to impair apoA-I-mediated cholesterol efflux may contribute to the development of atherosclerosis, particularly in smokers who have high plasma levels of SCN- (thiocyanate). PMID:23088652

  11. Vibrational spectra, NLO analysis, and HOMO-LUMO studies of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid by density functional method.

    PubMed

    Senthil Kumar, J; Arivazhagan, M; Thangaraju, P

    2015-08-01

    The FTIR and FT-Raman spectra of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of fundamental modes of the compounds were carried out. The optimized molecular geometries, vibrational frequencies, thermodynamic properties and atomic charge of the compounds were calculated by using density functional theory (B3LYP) method with 6-311+G and 6-311++G basis sets. The difference between the observed and scaled wave number values of most of fundamentals is very small. Unambiguous vibration assignment of all the fundamentals is made up the total energy distribution (TED). The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules. Besides, molecular electro static potential (MESP), Mulliken's charge analysis, first order hyper polarizability and several thermodynamic properties were performed by the DFT method. PMID:25847785

  12. Vibrational spectra, NLO analysis, and HOMO-LUMO studies of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid by density functional method

    NASA Astrophysics Data System (ADS)

    Senthil kumar, J.; Arivazhagan, M.; Thangaraju, P.

    2015-08-01

    The FTIR and FT-Raman spectra of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid have been recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of fundamental modes of the compounds were carried out. The optimized molecular geometries, vibrational frequencies, thermodynamic properties and atomic charge of the compounds were calculated by using density functional theory (B3LYP) method with 6-311+G and 6-311++G basis sets. The difference between the observed and scaled wave number values of most of fundamentals is very small. Unambiguous vibration assignment of all the fundamentals is made up the total energy distribution (TED). The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules. Besides, molecular electro static potential (MESP), Mulliken's charge analysis, first order hyper polarizability and several thermodynamic properties were performed by the DFT method.

  13. Vibrational spectra, NLO analysis, and HOMO-LUMO studies of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid by density functional method.

    PubMed

    Senthil Kumar, J; Arivazhagan, M; Thangaraju, P

    2015-08-01

    The FTIR and FT-Raman spectra of 2-chloro-6-fluorobenzoic acid and 3,4-dichlorobenzoic acid have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of fundamental modes of the compounds were carried out. The optimized molecular geometries, vibrational frequencies, thermodynamic properties and atomic charge of the compounds were calculated by using density functional theory (B3LYP) method with 6-311+G and 6-311++G basis sets. The difference between the observed and scaled wave number values of most of fundamentals is very small. Unambiguous vibration assignment of all the fundamentals is made up the total energy distribution (TED). The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules. Besides, molecular electro static potential (MESP), Mulliken's charge analysis, first order hyper polarizability and several thermodynamic properties were performed by the DFT method.

  14. The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism.

    PubMed

    Li, Jun; Machius, Mischa; Chuang, Jacinta L; Wynn, R Max; Chuang, David T

    2007-04-20

    A long standing controversy is whether an alternating activesite mechanism occurs during catalysis in thiamine diphosphate (ThDP)-dependent enzymes. We address this question by investigating the ThDP-dependent decarboxylase/dehydrogenase (E1b) component of the mitochondrial branched-chain alpha-keto acid dehydrogenase complex (BCKDC). Our crystal structure reveals that conformations of the two active sites in the human E1b heterotetramer harboring the reaction intermediate are identical. Acidic residues in the core of the E1b heterotetramer, which align with the proton-wire residues proposed to participate in active-site communication in the related pyruvate dehydrogenase from Bacillus stearothermophilus, are mutated. Enzyme kinetic data show that, except in a few cases because of protein misfolding, these alterations are largely without effect on overall activity of BCKDC, ruling out the requirement of a proton-relay mechanism in E1b. BCKDC overall activity is nullified at 50% phosphorylation of E1b, but it is restored to nearly half of the pre-phosphorylation level after dissociation and reconstitution of BCKDC with the same phosphorylated E1b. The results suggest that the abolition of overall activity likely results from the specific geometry of the half-phosphorylated E1b in the BCKDC assembly and not due to a disruption of the alternating active-site mechanism. Finally, we show that a mutant E1b containing only one functional active site exhibits half of the wild-type BCKDC activity, which directly argues against the obligatory communication between active sites. The above results provide evidence that the two active sites in the E1b heterotetramer operate independently during the ThDP-dependent decarboxylation reaction. PMID:17329260

  15. Identification of gamma-aminobutyric acid and its binding sites in Caenorhabditis elegans

    SciTech Connect

    Schaeffer, J.M.; Bergstrom, A.R.

    1988-01-01

    Gamma-aminobutyric acid (GABA), glutamate decarboxylase and GABA-transaminase were identified in the nematode Caenorhabditis elegans. The concentration of GABA in C. elegans is approximately 10-fold lower than the concentration of GABA in rat brain. Glutamate decarboxylase and GABA-transaminase, the GABA anabolic and catabolic enzymes, are also present in C. elegans. Crude membrane fractions were prepared from C. elegans and used to study specific (/sup 3/H) GABA binding sites. GABA binds to C. elegans membranes with high affinity and low capacity. Muscimol is a competitive inhibitor of specific GABA binding with a K/sub I/ value of 120 nM. None of the other GABA agonists or antagonists inhibited greater than 40% of the specific GABA binding at concentrations up to 10/sup -4/M. Thirteen spider venoms were examined as possible GABA agonists or antagonists, the venom from Calilena agelenidae inhibits specific GABA binding with a K/sub I/ value of 6 nl/ml. These results suggest that GABA has a physiological role as a neurotransmitter in C. elegans.

  16. Interaction of pseudolaric acid B with the colchicine site of tubulin.

    PubMed

    Sarkar, Taradas; Nguyen, Tam Luong; Su, Zhi-Wei; Hao, Jun; Bai, Ruoli; Gussio, Rick; Qiu, Samuel X; Hamel, Ernest

    2012-08-15

    We purified pseudolaric acid B (PAB) from the root and stem bark of Pseudolarix kaempferi (Lindl.) Gorden. Confirming previous findings, we found that the compound had high nanomolar IC₅₀ antiproliferative effects in several cultured cell lines, causing mitotic arrest and the disappearance of intracellular microtubules. PAB strongly inhibited tubulin assembly (IC₅₀, 1.1 μM) but weakly inhibited the binding of colchicine to tubulin, as demonstrated by fluorescence and with [³H]colchicine. Kinetic analysis demonstrated that the mechanism of inhibition was competitive, with an apparent K(i) of 12-15 μM. Indirect studies demonstrated that PAB bound rapidly to tubulin and dissociated more rapidly from tubulin than the colchicine analog 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone, whose complex with tubulin is known to have a half-life of 17s at 37 °C. We modeled PAB into the colchicine site of tubulin, using the crystal structure 1SA0 that contains two αβ-tubulin heterodimers, both bound to a colchicinoid and to a stathmin fragment. The binding model of PAB revealed common pharmacophoric features between PAB and colchicinoids, not readily apparent from their chemical structures. PMID:22634405

  17. High-Temperature Decomposition of Brønsted Acid Sites in Gallium-Substituted Zeolites

    SciTech Connect

    K Al-majnouni; N Hould; W Lonergan; D Vlachos; R Lobo

    2011-12-31

    The dehydroxylation of Broensted acid sites (BAS) in Ga-substituted zeolites was investigated at temperatures up to 850 C using X-ray absorption spectroscopy (XAS), Fourier transform infrared spectroscopy (FTIR), and mass spectrometry-temperature programmed desorption (MS-TPD). X-ray absorption near-edge spectroscopy (XANES) revealed that the majority of gallium has tetrahedral coordination even after complete dehydroxylation. The interatomic gallium-oxygen distance and gallium coordination number determined by extended X-ray absorption fine structure (EXAFS) are consistent with gallium in tetrahedral coordination at low T (< 550 C). Upon heating Ga-Beta and Ga-ZSM5 to 850 C, analysis of the EXAFS showed that 70 and 80% of the gallium was still in tetrahedral coordination. The remainder of the gallium was found to be in octahedral coordination. No trigonal Ga atoms were observed. FTIR measurements carried out at similar temperatures show that the intensity of the OH vibration due to BAS has been eliminated. MS-TPD revealed that hydrogen in addition to water evolved from the samples during dehydroxylation. This shows that dehydrogenation in addition to dehydration is a mechanism that contributes to BAS decomposition. Dehydrogenation was further confirmed by exposing the sample to hydrogen to regenerate some of the BAS as monitored by FTIR and MS-TPD.

  18. Compromised Osseous Healing of Dental Extraction Sites in Zoledronic Acid-Treated Dogs

    PubMed Central

    Allen, Matthew R.; Kubek, Daniel J.; Burr, David B.; Ruggiero, Salvatore L.; Chu, Tien-Min Gabriel

    2010-01-01

    PURPOSE The goal of this study was to document how treatment with a bisphosphonate affects the bone tissue following dental extraction. METHODS Skeletally mature female beagle dogs were either untreated controls (CON) or treated with intravenous zoledronic acid (ZOL). Following the extraction of the 4th premolars, healing was allowed for 4 or 8 weeks. Properties of the extraction site were assessed using micro-computed tomography (micro-CT) and dynamic histomorphometry. RESULTS The initial infilling of the extraction socket with bone was not affected by ZOL but subsequent removal of this bone was significantly suppressed compared to CON. After 8-weeks of healing, the alveolar cortical bone adjacent to the extraction socket had a remodeling rate of ~50%/year in CON animals while ZOL-treated animals had a rate of < 1%/year. One ZOL-treated animal developed exposed bone post-extraction which eventually led to the formation of a sequestrum. Assessment of the sequestrum with micro-CT and histology showed that it had features consistent with those reported in humans with osteonecrosis of the jaw. CONCLUSIONS These results, showing significantly compromised post-extraction osseous healing as well as presence of exposed bone and development of a sequestrum in one ZOL animal, provide a building block toward understanding the pathophysiology of osteonecrosis of the jaw. PMID:20458574

  19. Dose Calculation on KV Cone Beam CT Images: An Investigation of the Hu-Density Conversion Stability and Dose Accuracy Using the Site-Specific Calibration

    SciTech Connect

    Rong Yi

    2010-10-01

    Precise calibration of Hounsfield units (HU) to electron density (HU-density) is essential to dose calculation. On-board kV cone beam computed tomography (CBCT) imaging is used predominantly for patients' positioning, but will potentially be used for dose calculation. The impacts of varying 3 imaging parameters (mAs, source-imager distance [SID], and cone angle) and phantom size on the HU number accuracy and HU-density calibrations for CBCT imaging were studied. We proposed a site-specific calibration method to achieve higher accuracy in CBCT image-based dose calculation. Three configurations of the Computerized Imaging Reference Systems (CIRS) water equivalent electron density phantom were used to simulate sites including head, lungs, and lower body (abdomen/pelvis). The planning computed tomography (CT) scan was used as the baseline for comparisons. CBCT scans of these phantom configurations were performed using Varian Trilogy{sup TM} system in a precalibrated mode with fixed tube voltage (125 kVp), but varied mAs, SID, and cone angle. An HU-density curve was generated and evaluated for each set of scan parameters. Three HU-density tables generated using different phantom configurations with the same imaging parameter settings were selected for dose calculation on CBCT images for an accuracy comparison. Changing mAs or SID had small impact on HU numbers. For adipose tissue, the HU discrepancy from the baseline was 20 HU in a small phantom, but 5 times lager in a large phantom. Yet, reducing the cone angle significantly decreases the HU discrepancy. The HU-density table was also affected accordingly. By performing dose comparison between CT and CBCT image-based plans, results showed that using the site-specific HU-density tables to calibrate CBCT images of different sites improves the dose accuracy to {approx}2%. Our phantom study showed that CBCT imaging can be a feasible option for dose computation in adaptive radiotherapy approach if the site

  20. ESTIMATES OF CLOUD WATER DEPOSITION AT MOUNTAIN DEPOSITION AT MOUNTAIN ACID DEPOSITION PROGRAM SITES IN THE APPALACHIAN MOUNTAINS

    EPA Science Inventory

    Cloud water deposition was estimated at three high elevation sites in the Appalachian Mountains of the eastern United States (Whiteface Mountain, NY, Whitetop Mountain, VA, and Clingrnan's Dome, TN) from 1994 through 1999 as part of the Mountain Acid Deposition Program (MADPro). ...

  1. Non-thermal plasma-assisted NOx reduction over Na-Y zeolites: The promotional effect of acid sites

    SciTech Connect

    Kwak, Ja Hun; Peden, Charles HF; Szanyi, Janos

    2006-06-01

    The effect of acid sites on the catalytic activities of a series of H+-modified Na-Y zeolites was investigated in the non-thermal plasma assisted NOx reduction reaction using a simulated diesel engine exhaust gas mixture. The acid sites were formed by NH4+ ion exchange and subsequent heat treatment of a NaY zeolite. The catalytic activities of these H+-modified NaY zeolites significantly increased with the number of acid sites. This NOx conversion increase was correlated with the decrease in the amount of unreacted NO2. The increase in the number of acid sites did not change the NO level, it stayed constant. Temperature programmed desorption following NO2 adsorption showed the appearance of a high temperature desorption peak at 453 K in addition to the main desorption feature of 343 K observed for the base Na-Y. The results of both the IR and TPD experiments revealed the formation of crotonaldehyde, resulting from condensation reaction of adsorbed acetaldehyde. Strong adsorptions of both NOx and hydrocarbon species are proposed to be responsible for the higher catalytic activity of H+-modified Na-Y zeolites in comparison to the base NaY material

  2. Uptake of gamma-aminobutyric acid and L-glutamic acid by synaptosomes from postmortem human cerebral cortex: multiple sites, sodium dependence and effect of tissue preparation.

    PubMed

    Dodd, P R; Watson, W E; Morrison, M M; Johnston, G A; Bird, E D; Cowburn, R F; Hardy, J A

    1989-06-26

    The uptake of gamma-aminobutyric acid (GABA) and L-glutamic acid by synaptosomes prepared from frozen postmortem human brain was shown to be effected via distinct high and low affinity sites. At approximately 17 h postmortem delay, the kinetic parameters for GABA uptake were: high affinity site, Km 7.1 +/- 2.5 microM, Vmax 18.7 +/- 4.8 nmol.min-1 per 100 mg protein; low affinity site, Km 2 +/- 1 mM, Vmax 425 +/- 250 nmol.min-1 per 100 mg protein (means +/- S.E.M., n = 13). Kinetic parameters for L-glutamate uptake were: high affinity site, Km 7.5 +/- 1.0 microM, Vmax 85 +/- 8 nmol.min-1 per 100 mg protein; low affinity site, Km 1.8 +/- 1.2 mM. Vmax 780 +/- 175 nmol.min-1 per 100 mg protein (n = 11). A detailed kinetic analysis of high affinity GABA uptake was performed over a range of sodium ion concentrations. The results were consistent with a coupling ratio of one Na+ ion to one GABA molecule; a similar result was found with rat brain synaptosomes. However, rat and human synaptosomes differed in the degree to which the substrate affinity of the high affinity GABA uptake site varied with decreasing Na+ ion concentration. High affinity GABA uptake was markedly affected by the method used to freeze and divide the tissue, but did not vary greatly in different cortical regions. There was some decline of high affinity GABA uptake activity with postmortem delay, apparently due to a loss of sites rather than a change in site affinity.

  3. Treatment with orthophosphoric acid enhances the thermal stability of the piezoelectricity in low-density polyethylene ferroelectrets

    NASA Astrophysics Data System (ADS)

    Rychkov, Dmitry; Alberto Pisani Altafim, Ruy; Qiu, Xunlin; Gerhard, Reimund

    2012-06-01

    Ferroelectrets have been fabricated from low-density polyethylene (LDPE) films by means of a template-based lamination. The temperature dependence of the piezoelectric d33 coefficient has been investigated. It was found that low-density polyethylene ferroelectrets have rather low thermal stability with the piezoelectric coefficient decaying almost to zero already at 100 °C. This behavior is attributed to the poor electret properties of the polyethylene films used for the fabrication of the ferroelectrets. In order to improve the charge trapping and the thermal stability of electret charge and piezoelectricity, LDPE ferroelectrets were treated with orthophosphoric acid. The treatment resulted in considerable improvements of the charge stability in LDPE films and in ferroelectret systems made from them. For example, the charge and piezoelectric-coefficient decay curves shifted to higher temperatures by 60 K and 40 K, respectively. It is shown that the decay of the piezoelectric coefficient in LDPE ferroelectrets is governed by the relaxation of less stable positive charges. The treatment also leads to noticeable changes in the chemical composition of the LDPE surface. Infrared spectroscopy reveals absorption bands attributed to phosphorus-containing structures, while scanning electron microscopy shows new island-like structures, 50-200 nm in diameter, on the modified surface.

  4. Histopathological Analysis from Gallic Acid Administration on Hippocampal Cell Density, Depression, and Anxiety Related Behaviors in A Trimethyltin Intoxication Model

    PubMed Central

    Moghadas, Marzieh; Edalatmanesh, Mohammad Amin; Robati, Reza

    2016-01-01

    Objective The present study investigated the effects of gallic acid (GA) administration on trimethyltin chloride (TMT) induced anxiety, depression, and hippocampal neurodegen- eration in rats. Materials and Methods In this experimental study, the rats received intraperitoneal (i.p.) injections of TMT (8 mg/kg). The animals received either GA (50, 100 and 150 mg/kg) or saline as the vehicle for 14 consecutive days. We measured depression and anxiety levels of the rats by conducting the behavioral tail suspension (TST), elevatedplusmaze (EPM), and novelty suppressed feeding (NSF) tests. Histological analyses were then used to de- termine the cell densities of different hippocampal subdivisions. The data were analyzed with ANOVA and Tukey’s post hoc test. Results GA administration ameliorated anxiety and depression in the behavioral tests. The cell densities in the CA1, CA2, CA3 and DG hippocampal subdivisionsfrom GA-treat- ed rats were higher than saline treated rats. Conclusion GA treatment against TMT-induced hippocampal degeneration altered cellular loss in the hippocampus and ameliorated the depression-anxiety state in rats. PMID:26862525

  5. Acid Hydrolysis and Molecular Density of Phytoglycogen and Liver Glycogen Helps Understand the Bonding in Glycogen α (Composite) Particles

    PubMed Central

    Powell, Prudence O.; Sullivan, Mitchell A.; Sheehy, Joshua J.; Schulz, Benjamin L.; Warren, Frederick J.; Gilbert, Robert G.

    2015-01-01

    Phytoglycogen (from certain mutant plants) and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired. PMID:25799321

  6. Acid hydrolysis and molecular density of phytoglycogen and liver glycogen helps understand the bonding in glycogen α (composite) particles.

    PubMed

    Powell, Prudence O; Sullivan, Mitchell A; Sheehy, Joshua J; Schulz, Benjamin L; Warren, Frederick J; Gilbert, Robert G

    2015-01-01

    Phytoglycogen (from certain mutant plants) and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired.

  7. Hydrogen transfer in vibrationally relaxing benzoic acid dimers: Time-dependent density matrix dynamics and infrared spectra

    NASA Astrophysics Data System (ADS)

    Scheurer, Christoph; Saalfrank, Peter

    1996-02-01

    We employ time-dependent density matrix theory to characterize the concerted double-hydrogen transfer in benzoic acid dimers—the ``system''—embedded in their crystalline environment—the ``bath.'' The Liouville-von Neumann equation for the time evolution of the reduced nuclear density matrix is solved numerically, employing one- and two-dimensional models [R. Meyer and R. R. Ernst, J. Chem. Phys. 93, 5528 (1990)], the state representation for all operators and a matrix propagator based on Newton's polynomials [M. Berman, R. Kosloff, and H. Tal-Ezer, J. Phys. A 25, 1283 (1992)]. Dissipative processes such as environment-induced vibrational energy and phase relaxation, are accounted for within the Lindblad dynamical semigroup approach. The calculation of temperature-dependent relaxation matrix elements is based on a microscopic, perturbative theory proposed earlier [R. Meyer and R. R. Ernst, J. Chem. Phys. 93, 5528 (1990)]. For the evaluation of the dissipative system dynamics, we compute (i) time-dependent state populations, (ii) energy and entropy flow between system and bath, (iii) expectation values for the hydrogen transfer coordinate, (iv) characteristic dephasing times and (v) temperature-dependent infrared spectra, determined with a recently proposed method by Neugebauer et al. Various ``pure'' and ``thermal'' nonequilibrium initial states are considered, and their equilibration with the bath followed in time.

  8. Influence of Obesity on Breast Density Reduction by Omega-3 Fatty Acids: Evidence from a Randomized Clinical Trial.

    PubMed

    Sandhu, Narinder; Schetter, Susann E; Liao, Jason; Hartman, Terryl J; Richie, John P; McGinley, John; Thompson, Henry J; Prokopczyk, Bogdan; DuBrock, Cynthia; Signori, Carina; Hamilton, Christopher; Calcagnotto, Ana; Trushin, Neil; Aliaga, Cesar; Demers, Laurence M; El-Bayoumy, Karam; Manni, Andrea

    2016-04-01

    Preclinical data indicate that omega-3 fatty acids (n-3FA) potentiate the chemopreventive effect of the antiestrogen (AE) tamoxifen against mammary carcinogenesis. The role of n-3FA in breast cancer prevention in humans is controversial. Preclinical and epidemiologic data suggest that n-3FA may be preferentially protective in obese subjects. To directly test the protective effect of n-3FA against breast cancer, we conducted a 2-year, open-label randomized clinical trial in 266 healthy postmenopausal women (50% normal weight, 30% overweight, 20% obese) with high breast density (BD; ≥25%) detected on their routine screening mammograms. Eligible women were randomized to one of the following five groups (i) no treatment, control; (ii) raloxifene 60 mg; (iii) raloxifene 30 mg; (iv) n-3FA lovaza 4 g; and (v) lovaza 4 g plus raloxifene 30 mg. The 2-year change in BD, a validated biomarker of breast cancer risk, was the primary endpoint of the study. In subset analysis, we tested the prespecified hypothesis that body mass index (BMI) influences the relationship between plasma n-3FA on BD. While none of the interventions affected BD in the intention-to-treat analysis, increase in plasma DHA was associated with a decrease in absolute breast density but only in participants with BMI >29. Our results suggest that obese women may preferentially experience breast cancer risk reduction from n-3FA administration. PMID:26714774

  9. Correlation of film density and wet etch rate in hydrofluoric acid of plasma enhanced atomic layer deposited silicon nitride

    NASA Astrophysics Data System (ADS)

    Provine, J.; Schindler, Peter; Kim, Yongmin; Walch, Steve P.; Kim, Hyo Jin; Kim, Ki-Hyun; Prinz, Fritz B.

    2016-06-01

    The continued scaling in transistors and memory elements has necessitated the development of atomic layer deposition (ALD) of silicon nitride (SiNx), particularly for use a low k dielectric spacer. One of the key material properties needed for SiNx films is a low wet etch rate (WER) in hydrofluoric (HF) acid. In this work, we report on the evaluation of multiple precursors for plasma enhanced atomic layer deposition (PEALD) of SiNx and evaluate the film's WER in 100:1 dilutions of HF in H2O. The remote plasma capability available in PEALD, enabled controlling the density of the SiNx film. Namely, prolonged plasma exposure made films denser which corresponded to lower WER in a systematic fashion. We determined that there is a strong correlation between WER and the density of the film that extends across multiple precursors, PEALD reactors, and a variety of process conditions. Limiting all steps in the deposition to a maximum temperature of 350 °C, it was shown to be possible to achieve a WER in PEALD SiNx of 6.1 Å/min, which is similar to WER of SiNx from LPCVD reactions at 850 °C.

  10. Densities of L-Glutamic Acid HCl Drug in Aqueous NaCl and KCl Solutions at Different Temperatures

    NASA Astrophysics Data System (ADS)

    Ryshetti, Suresh; Raghuram, Noothi; Rani, Emmadi Jayanthi; Tangeda, Savitha Jyostna

    2016-04-01

    Densities (ρ ) of (0.01 to 0.07) {mol}{\\cdot } {kg}^{-1} L-Glutamic acid HCl (L-HCl) drug in water, and in aqueous NaCl and KCl (0.5 and 1.0) {mol}{\\cdot } {kg}^{-1} solutions have been reported as a function of temperature at T = (298.15, 303.15, 308.15, and 313.15) K and atmospheric pressure. The accurate density (ρ ) values are used to estimate the various parameters such as the apparent molar volume (V_{2,{\\upphi }}), the partial molar volume (V2^{∞}), the isobaric thermal expansion coefficient (α 2), the partial molar expansion (E2^{∞}), and Hepler's constant (partial 2V2^{∞}/partial T2)P. The Cosphere overlap model is used to understand the solute-solvent interactions in a ternary mixture (L-HCl drug + NaCl or KCl + water). Hepler's constant (partial 2V2^{∞}/partial T2)_P is utilized to interpret the structure-making or -breaking ability of L-HCl drug in aqueous NaCl and KCl solutions, and the results are inferred that L-HCl drug acts as a structure maker, i.e., kosmotrope in aqueous NaCl solutions and performs as a structure breaker, i.e., chaotrope in aqueous KCl solutions.

  11. Forced Ambiguity of the Leucine Codons for Multiple-Site-Specific Incorporation of a Noncanonical Amino Acid

    PubMed Central

    Kwon, Inchan; Choi, Eun Sil

    2016-01-01

    Multiple-site-specific incorporation of a noncanonical amino acid into a recombinant protein would be a very useful technique to generate multiple chemical handles for bioconjugation and multivalent binding sites for the enhanced interaction. Previously combination of a mutant yeast phenylalanyl-tRNA synthetase variant and the yeast phenylalanyl-tRNA containing the AAA anticodon was used to incorporate a noncanonical amino acid into multiple UUU phenylalanine (Phe) codons in a site-specific manner. However, due to the less selective codon recognition of the AAA anticodon, there was significant misincorporation of a noncanonical amino acid into unwanted UUC Phe codons. To enhance codon selectivity, we explored degenerate leucine (Leu) codons instead of Phe degenerate codons. Combined use of the mutant yeast phenylalanyl-tRNA containing the CAA anticodon and the yPheRS_naph variant allowed incorporation of a phenylalanine analog, 2-naphthylalanine, into murine dihydrofolate reductase in response to multiple UUG Leu codons, but not to other Leu codon sites. Despite the moderate UUG codon occupancy by 2-naphthylalaine, these results successfully demonstrated that the concept of forced ambiguity of the genetic code can be achieved for the Leu codons, available for multiple-site-specific incorporation. PMID:27028506

  12. Dynamic HypA zinc site is essential for acid viability and proper urease maturation in Helicobacter pylori

    PubMed Central

    Johnson, Ryan C.; Hu, Heidi Q.; Merrell, D. Scott; Maroney, Michael J.

    2015-01-01

    Helicobacter pylori requires urease activity in order to survive in the acid environment of the human stomach. Urease is regulated in part by nickelation, a process that requires the HypA protein, which is a putative nickel metallochaperone that is generally associated with hydrogenase maturation. However, in H. pylori, HypA plays a dual role. In addition to an N-terminal nickel binding site, HypA proteins also contain a structural zinc site that is coordinated by two rigorously conserved CXXC sequences, which in H. pylori are flanked by His residues. These structural Zn sites are known to be dynamic, converting from Zn(Cys)4 centers at pH 7.2 to Zn(Cys)2(His)2 centers at pH 6.3 in the presence of Ni(II) ions. In this study, mutant strains of H. pylori that express zinc site variants of the HypA protein are used to show that the structural changes in the zinc site are important for the acid viability of the bacterium, and that a reduction in acid viability in these variants can be traced in large measure to deficient urease activity. This in turn leads to a model that connects the Zn(Cys)4 coordination to urease maturation. PMID:25608738

  13. Hydroxamic acid interactions with solvated cerium hydroxides in the flotation of monazite and bastnäsite-Experiments and DFT study

    NASA Astrophysics Data System (ADS)

    Sarvaramini, A.; Azizi, D.; Larachi, F.

    2016-11-01

    Density functional theory (DFT) simulations and experiments were performed to clarify the interaction mechanisms between hydroxamic acid collectors and cerium hydroxides during the flotation of bastnäsite and monazite minerals. These minerals showed considerable floatability at moderately alkaline pH which was related to the adsorption of hydroxamic acids on their surfaces as confirmed by vibrational spectroscopic and zeta potential measurements. DFT simulations showed that at moderately alkaline pH, the interactions between solvated Ce(OH)2+ and Ce(OH)2+ and heptyl-hydroxamic acid (HHA) anions resulted in the formation of, respectively, [Ce(OH)(HHA)x(H2O)y]2-x (x[y = ] = 1[6],2[3],3[1]) and [Ce(OH)2(HHA)x(H2O)y]1-x (x[y = ] = 1[5],2[1],3[0]) complexes. The collector anions were found to interact directly through formation of two covalent bonds between their two polar-head oxygen atoms and cerium in the hydroxide complexes. However, formation of such new bonds resulted in breakage of a few covalent/electrostatic bonds between cerium and water molecules initially present in the first hydration shell of the rare-earth metal cation. Building up in the electric double layer of the semi-soluble minerals, these complexes, and by extension, those from other rare-earth elements belonging to monazite and bastnäsite, are speculated to play a role in the interactions between rare-earth minerals and hydroxamic acid collectors.

  14. Effects of sex and site on amino acid metabolism enzyme gene expression and activity in rat white adipose tissue

    PubMed Central

    Arriarán, Sofía; Agnelli, Silvia; Remesar, Xavier; Fernández-López, José Antonio

    2015-01-01

    Background and Objectives. White adipose tissue (WAT) shows marked sex- and diet-dependent differences. However, our metabolic knowledge of WAT, especially on amino acid metabolism, is considerably limited. In the present study, we compared the influence of sex on the amino acid metabolism profile of the four main WAT sites, focused on the paths related to ammonium handling and the urea cycle, as a way to estimate the extent of WAT implication on body amino-nitrogen metabolism. Experimental Design. Adult female and male rats were maintained, undisturbed, under standard conditions for one month. After killing them under isoflurane anesthesia. WAT sites were dissected and weighed. Subcutaneous, perigonadal, retroperitoneal and mesenteric WAT were analyzed for amino acid metabolism gene expression and enzyme activities. Results. There was a considerable stability of the urea cycle activities and expressions, irrespective of sex, and with only limited influence of site. Urea cycle was more resilient to change than other site-specialized metabolic pathways. The control of WAT urea cycle was probably related to the provision of arginine/citrulline, as deduced from the enzyme activity profiles. These data support a generalized role of WAT in overall amino-N handling. In contrast, sex markedly affected WAT ammonium-centered amino acid metabolism in a site-related way, with relatively higher emphasis in males’ subcutaneous WAT. Conclusions. We found that WAT has an active amino acid metabolism. Its gene expressions were lower than those of glucose-lipid interactions, but the differences were quantitatively less important than usually reported. The effects of sex on urea cycle enzymes expression and activity were limited, in contrast with the wider variations observed in other metabolic pathways. The results agree with a centralized control of urea cycle operation affecting the adipose organ as a whole. PMID:26587356

  15. Amino acid sequences of neuropeptides in the sinus gland of the land crab Cardisoma carnifex: a novel neuropeptide proteolysis site.

    PubMed

    Newcomb, R W

    1987-08-01

    The sinus gland is a major neurosecretory structure in Crustacea. Five peptides, labeled C, D, E, F, and I, isolated from the sinus gland of the land crab have been hypothesized to arise from the incomplete proteolysis at two internal sites on a single biosynthetic intermediate peptide "H", based on amino acid composition additivities and pulse-chase radiolabeling studies. The presence of only a single major precursor for the sinus gland peptides implies that peptide H may be synthesized on a common precursor with crustacean hyperglycemic hormone forms, "J" and "L," and a peptide, "K," similar to peptides with molt inhibiting activity. Here I report amino acid sequences of these peptides. The amino terminal sequence of the parent peptide, H, (and the homologous fragments) proved refractory to Edman degradation. Data from amino acid analysis and carboxypeptidase digestion of the naturally occurring fragments and of fragments produced by endopeptidase digestion were used together with Edman degradation to obtain the sequences. Amino acid analysis of fragments of the naturally occurring "overlap" peptides (those produced by internal cleavage at one site on H) was used to obtain the sequences across the cleavage sites. The amino acid sequence of the land crab peptide H is Arg-Ser-Ala-Asp-Gly-Phe-Gly-Arg-Met-Glu-Ser-Leu-Leu-Thr-Ser-Leu-Arg-Gly- Ser-Ala-Glu- Ser-Pro-Ala-Ala-Leu-Gly-Glu-Ala-Ser-Ala-Ala-His-Pro-Leu-Glu. In vivo cleavage at one site involves excision of arginine from the sequence Leu-Arg-Gly, whereas cleavage at the other site involves excision of serine from the sequence Glu-Ser-Leu. Proteolysis at the latter sequence has not been previously reported in intact secretory granules. The aspartate at position 4 is possibly covalently modified.

  16. Comparison of Some Representative Density Functional Theory and Wave Function Theory Methods for the Studies of Amino Acids

    SciTech Connect

    Yu, Wenbo; Liang, Lei; Lin, Zijing; Ling, Sanliang; Haranczyk, Maciej; Gutowski, Maciej S.

    2009-03-01

    Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-31111G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-31111G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-31111G(d,p), aug-cc-pVDZ, 6-31111G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-31111G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds.

  17. Retinoic acid signalling centres in the avian embryo identified by sites of expression of synthesising and catabolising enzymes.

    PubMed

    Blentic, Aida; Gale, Emily; Maden, Malcolm

    2003-05-01

    Retinoic acid is an important signalling molecule in the developing embryo, but its precise distribution throughout development is very difficult to determine by available techniques. Examining the distribution of the enzymes by which it is synthesised by using in situ hybridisation is an alternative strategy. Here, we describe the distribution of three retinoic acid synthesising enzymes and one retinoic acid catabolic enzyme during the early stages of chick embryogenesis with the intention of identifying localized retinoic acid signalling regions. The enzymes involved are Raldh1, Raldh2, Raldh3, and Cyp26A1. Although some of these distributions have been described before, here we assemble them all in one species and several novel sites of enzyme expression are identified, including Hensen's node, the cardiac endoderm, the presumptive pancreatic endoderm, and the dorsal lens. This study emphasizes the dynamic pattern of expression of the enzymes that control the availability of retinoic acid as well as the role that retinoic acid plays in the development of many regions of the embryo throughout embryogenesis. This strategy provides a basis for understanding the phenotypes of retinoic acid teratology and retinoic acid-deficiency syndromes.

  18. Muon sites in Ce(Ru,Rh)2Al10 investigated by using Density Functional Theory from the view point of electronic potential

    NASA Astrophysics Data System (ADS)

    Adam, N.; Suprayoga, E.; Adiperdana, B.; Guo, H.; Tanida, H.; Mohd-Tajudin, S. S.; Kobayashi, R.; Sera, M.; Nishioka, T.; Matsumura, M.; Sulaiman, S.; Mohamed-Ibrahim, M. I.; Watanabe, I.

    2014-12-01

    Numerical investigations on muon sites in Ce-based Kondo semiconductors, Ce(Ru,Rh)2Al10 were carried out by using the Density Functional Theory. From the view point of simple electrostatic potential calculations, we found all the previously reported muon sites, suggested by different groups (Kambe S et al. 2010 J. Phys. Soc. Jpn. 79 053708 and Khalyavin D D et al., 2010 Phys. Rev. B 82 100405(R)), can be possibly chosen as muon stopping sites. We also investigated the changes in the potential of the Rh-doped case. We discovered that the electronic potential around the nearest Ru atom to the substituted Rh atom is affected and the potential becomes asymmetric around the nearest Ru ion. Although big changes in hyperfine fields at muon sites have been reported (Guo H et al. 2013 Phys. Rev. B 88 115206), the muon positions estimated from the potential calculations do not change much.

  19. Gamma-aminobutyric acid-modulated benzodiazepine binding sites in bacteria

    SciTech Connect

    Lummis, S.C.R.; Johnston, G.A.R. ); Nicoletti, G. ); Holan, G. )

    1991-01-01

    Benzodiazepine binding sites, which were once considered to exist only in higher vertebrates, are here demonstrated in the bacteria E. coli. The bacterial ({sup 3}H)diazepam binding sites are modulated by GABA; the modulation is dose dependent and is reduced at high concentrations. The most potent competitors of E.Coli ({sup 3}H)diazepam binding are those that are active in displacing ({sup 3}H)benzodiazepines from vertebrate peripheral benzodiazepine binding sites. These vertebrate sites are not modulated by GABA, in contrast to vertebrate neuronal benzodiazepine binding sites. The E.coli benzodiazepine binding sites therefore differ from both classes of vertebrate benzodiazepine binding sites; however the ligand spectrum and GABA-modulatory properties of the E.coli sites are similar to those found in insects. This intermediate type of receptor in lower species suggests a precursor for at least one class of vertebrate benzodiazepine binding sites may have existed.

  20. Aspects of Structure and Bonding in Copper-Amino Acid Complexes Revealed by Single Crystal EPR/ENDOR Spectroscopy and Density Functional Calculations

    PubMed Central

    Colaneri, Michael J.; Vitali, Jacqueline; Peisach, Jack

    2010-01-01

    This work deduces from a series of well defined copper-doped amino acid crystals, relationships between structural features of the copper complexes and ligand-bound proton hyperfine parameters. These were established by combining results from electron paramagnetic resonance (EPR)/electron-nuclear double resonance (ENDOR) studies, crystallography and were further assessed by quantum mechanical (QM) calculations. A detailed evaluation of previous studies on Cu2+-doped into α-glycine, triglycine sulfate, α-glycylglycine and l-alanine crystals reveal correlations between geometric features of the copper sites and proton hyperfine couplings from amino bound and carbon bound hydrogens. Experimental variations in proton isotropic hyperfine coupling values (aiso) could be fit to cosine-square dependences on dihedral angles, namely, for Cα-bound hydrogens, aiso = −1.09 + 8.21cos2θ MHz, and for amino hydrogens, aiso = −6.16 + 4.15cos2φ MHz. For the Cα hydrogens, this dependency suggests a hyperconjugative-like mechanism for transfer of spin density into the hydrogen 1s-orbital. In the course of this work, it was also necessary to reanalyze the ENDOR measurements from Cu2+-doped α-glycine since the initial study determined the 14N coupling parameters without holding its nuclear quadrupole tensor traceless. This new treatment of the data was needed to correctly align the 14N hyperfine tensor principal directions in the molecular complex. In order to provide a theoretical basis for the coupling variations, QM calculations performed at the Density Functional Theory (DFT) level were used to compute the proton hyperfine tensors in the four crystal complexes as well as in a geometry-optimized Cu2+(glycine)2 model. These theoretical calculations confirmed systematic changes in couplings with dihedral angles, but greatly overestimated the experimental geometric sensitivity to the amino hydrogen isotropic coupling. PMID:19378965

  1. Complexation behavior of trivalent actinides and lanthanides with 1,10-phenanthroline-2,9-dicarboxylic acid based ligands: insight from density functional theory.

    PubMed

    Manna, Debashree; Ghanty, Tapan K

    2012-08-21

    We have investigated the complexation behavior of preorganized 1,10-phenanthroline-2,9-dicarboxylic acid (PDA) based ligands with trivalent lanthanides and actinides using density functional theory with various GGA type exchange-correlation functionals and different basis sets. New ligands have been designed from PDA through functionalization with soft donor atoms such as sulfur, resulting in mono-thio-dicarboxylic acids (TCA/TCA1) and di-thio-dicarboxylic acid (THIO). It has been found that selectivity in terms of complexation energy of actinides over lanthanides is the maximum with TCA1 where the metal-ligand binding is through the O atoms. This unusual feature where a softer actinide metal ion is bonded strongly with hard donor oxygen atoms has been explained using the popular chemical concepts, viz., Pearson's Hard-Soft-Acid-Base (HSAB) principle and the frontier orbital theory of chemical reactivity as proposed by Fukui. Detailed analysis within the framework of the HSAB principle indicates that the presence of softer nitrogen atoms in the phenanthroline moiety (which also act as donors to the metal ion) has a profound influence in changing the soft nature of the actinide ion, which in turn binds with the hard oxygen atoms in a stronger way as compared to the valence isoelectronic lanthanide ion. Also, the trends in the variation of calculated values of the metal-ligand bond distances and the corresponding complex formation energies have been rationalized using the Fukui reactivity indices corresponding to the metal ions and the donor sites. All the calculations have also been done in the presence of solvent. The "intra-ligand synergistic effect" demonstrated here for PDA or TCA1 with soft and hard donor centers might be very important in designing new ligands for selective extraction of various metal ions in a competitive environment. However, for TCA and THIO ligands with only soft donor centers, "intra-ligand synergism" may not be very efficient although

  2. Observation of multiple, identical binding sites in the exchange of carboxylic acid ligands with CdS nanocrystals.

    PubMed

    Li, Xin; Nichols, Valerie M; Zhou, Dapeng; Lim, Cynthia; Pau, George Shu Heng; Bardeen, Christopher J; Tang, Ming L

    2014-06-11

    We study ligand exchange between the carboxylic acid group and 5.0 nm oleic-acid capped CdS nanocrystals (NCs) using fluorescence resonance energy transfer (FRET). This is the first measurement of the initial binding events between cadmium chalcogenide NCs and carboxylic acid groups. The binding behavior can be described as an interaction between a ligand with single binding group and a substrate with multiple, identical binding sites. Assuming Poissonian binding statistics, our model fits both steady-state and time-resolved photoluminescence (SSPL and TRPL, respectively) data well. A modified Langmuir isotherm reveals that a CdS nanoparticle has an average of 3.0 new carboxylic acid ligands and binding constant, Ka, of 3.4 × 10(5) M(-1).

  3. Supercooling capacity of Urophora affinis and U. quadrifasciata (Diptera: Tephritidae) on spotted knapweed: comparisons among plants, sites, time of season, and gall densities.

    PubMed

    Nowierski, R M.; Fitzgerald, B C.; Zeng, Z

    2001-04-01

    Larval supercooling points of Urophora affinis Frauenfeld and U. quadrifasciata (Meigen) were compared among plants, six research sites in western Montana, four fall/winter time periods, and among gall densities. These two tephritid fly species are introduced biological control agents of spotted knapweed, Centaurea maculosa Lamarck, and diffuse knapweed, Centaurea diffusa Lamarck. Few differences in larval supercooling points for U. affinis and U. quadrifasciata were found among plants, and where differences were found, they were not consistent across fall/winter time periods. Significant differences in larval supercooling points were found among sites and across fall/winter time periods. No relationship was found between larval supercooling points and site elevation. Larval supercooling points of both U. affinis and U. quadrifasciata showed no relationship with the density of Urophora galls within spotted knapweed capitula. Mean larval supercooling points of U. affinis were consistently lower than those of U. quadrifasciata across sites and fall/winter time periods. In conclusion, temporal differences in temperature over the fall/winter time periods and microclimatic differences among sites appear to be the most important abiotic factors influencing the supercooling points in U. affinis and U. quadrifasciata.

  4. Acid-Sulfate-Weathering Activity in Shergottite Sites on Mars Recorded in Grim Glasses

    NASA Technical Reports Server (NTRS)

    Rao, M. N.; Nyquist, L. E.; Ross, K.; Sutton, S. R.; Schwandt, C. S.

    2011-01-01

    Based on mass spectrometric studies of sulfur species in Shergotty and EET79001, [1] and [2] showed that sulfates and sulfides occur in different proportions in shergottites. Sulfur speciation studies in gas-rich impact-melt (GRIM) glasses in EET79001 by the XANES method [3] showed that S K-XANES spectra in GRIM glasses from Lith A indicate that S is associated with Ca and Al presumably as sulfides/sulfates whereas the XANES spectra of amorphous sulfide globules in GRIM glasses from Lith B indicate that S is associated with Fe as FeS. In these amorphous iron sulfide globules, [4] found no Ni using FE-SEM and suggested that the globules resulting from immiscible sulfide melt may not be related to the igneous iron sulfides having approximately 1-3% Ni. Furthermore, in the amorphous iron sulfides from 507 GRIM glass, [5] determined delta(sup 34)S values ranging from +3.5%o to -3.1%o using Nano-SIMS. These values plot between the delta(sup 34)S value of +5.25%o determined in the sulfate fraction in Shergotty [6] at one extreme and the value of -1.7%o obtained for igneous sulfides in EET79001 and Shergotty [7] at the other. These results suggest that the amorphous Fe-S globules likely originated by shock reduction of secondary iron sulfate phases occurring in the regolith precursor materials during impact [7]. Sulfates in the regolith materials near the basaltic shergottite sites on Mars owe their origin to surficial acid-sulfate interactions. We examine the nature of these reactions by studying the composition of the end products in altered regolith materials. For the parent material composition, we use that of the host shergottite material in which the impact glasses are situated.

  5. Effects of acidic recharge on groundwater at the St. Kevin Gulch site, Leadville, Colorado

    USGS Publications Warehouse

    Paschke, S.S.; Harrison, W.J.; Walton-Day, K.

    2001-01-01

    The acid rock drainage-affected stream of St. Kevin Gulch recharges the Quaternary sand and gravel aquifer of Tennessee Park, near Leadville, Colorado, lowering pH and contributing iron, cadmium, copper, zinc and sulphate to the ground-water system. Dissolved metal mobility is controlled by the seasonal spring runoff as well as oxidation/reduction (redox) reactions in the aquifer. Oxidizing conditions occur in the unconfined portions of the aquifer whilst sulphate-reducing conditions are found down gradient where semi-confined groundwater flow occurs beneath a natural wetland. Iron-reducing conditions occur in the transition from unconfined to semi-confined groundwater flow. Dissolved iron concentrations are low to not detectable in the alluvial fan recharge zone and increase in a down gradient direction. The effects of low-pH, metal-rich recharge are pronounced during low-flow in the fall when there is a defined area of low pH groundwater with elevated concentrations of dissolved zinc, cadmium, copper and sulphate adjacent to St. Kevin Gulch. Dissolved metal and sulphate concentrations in the recharge zone are diluted during spring runoff, although the maximum concentrations of dissolved zinc, cadmium, copper and sulphate occur at selected down gradient locations during high flow. Dissolved zinc, cadmium and copper concentrations are low to not detectable, whereas dissolved iron concentrations are greatest, in groundwater samples from the sulphate-reducing zone. Attenuation of zinc, cadmium and copper beneath the wetland suggests sulphide mineral precipitation is occurring in the semi-confined aquifer, in agreement with previous site investigations and saturation index calculations. Adsorption of dissolved zinc, cadmium and copper onto iron hydroxides is a minor attenuation process due to the low pH of the groundwater system.

  6. Trace metal biogeochemistry in mangrove ecosystems: a comparative assessment of acidified (by acid sulfate soils) and non-acidified sites.

    PubMed

    Nath, Bibhash; Birch, Gavin; Chaudhuri, Punarbasu

    2013-10-01

    The generation of acidity and subsequent mobilization of toxic metals induced by acid sulfate soils (ASSs) are known to cause severe environmental damage to many coastal wetlands and estuaries of Australia and worldwide. Mangrove ecosystems serve to protect coastal environments, but are increasingly threatened from such ASS-induced acidification due to variable hydrological conditions (i.e., inundation-desiccation cycles). However, the impact of such behaviors on trace metal distribution, bio-availability and accumulation in mangrove tissues, i.e., leaves and pneumatophores, are largely unknown. In this study, we examined how ASS-induced acidifications controlled trace metal distribution and bio-availability in gray mangrove (Avicennia marina) soils and in tissues in the Kooragang wetland, New South Wales, Australia. We collected mangrove soils, leaves and pneumatophores from a part of the wetland acidified from ASS (i.e., an affected site) for detailed biogeochemical studies. The results were compared with samples collected from a natural intertidal mangrove forest (i.e., a control site) located within the same wetland. Soil pH (mean: 5.90) indicated acidic conditions in the affected site, whereas pH was near-neutral (mean: 7.17) in the control site. The results did not show statistically significant differences in near-total and bio-available metal concentrations, except for Fe and Mn, between affected and control sites. Iron concentrations were significantly (p values≤0.001) greater in the affected site, whereas Mn concentrations were significantly (p values≤0.001) greater in the control site. However, large proportions of near-total metals were potentially bio-available in control sites. Concentrations of Fe and Ni were significantly (p values≤0.001) greater in leaves and pneumatophores of the affected sites, whereas Mn, Cu, Pb and Zn were greater in control sites. The degree of metal bio-accumulation in leaves and pneumatophores suggest contrasting

  7. Trace metal biogeochemistry in mangrove ecosystems: a comparative assessment of acidified (by acid sulfate soils) and non-acidified sites.

    PubMed

    Nath, Bibhash; Birch, Gavin; Chaudhuri, Punarbasu

    2013-10-01

    The generation of acidity and subsequent mobilization of toxic metals induced by acid sulfate soils (ASSs) are known to cause severe environmental damage to many coastal wetlands and estuaries of Australia and worldwide. Mangrove ecosystems serve to protect coastal environments, but are increasingly threatened from such ASS-induced acidification due to variable hydrological conditions (i.e., inundation-desiccation cycles). However, the impact of such behaviors on trace metal distribution, bio-availability and accumulation in mangrove tissues, i.e., leaves and pneumatophores, are largely unknown. In this study, we examined how ASS-induced acidifications controlled trace metal distribution and bio-availability in gray mangrove (Avicennia marina) soils and in tissues in the Kooragang wetland, New South Wales, Australia. We collected mangrove soils, leaves and pneumatophores from a part of the wetland acidified from ASS (i.e., an affected site) for detailed biogeochemical studies. The results were compared with samples collected from a natural intertidal mangrove forest (i.e., a control site) located within the same wetland. Soil pH (mean: 5.90) indicated acidic conditions in the affected site, whereas pH was near-neutral (mean: 7.17) in the control site. The results did not show statistically significant differences in near-total and bio-available metal concentrations, except for Fe and Mn, between affected and control sites. Iron concentrations were significantly (p values≤0.001) greater in the affected site, whereas Mn concentrations were significantly (p values≤0.001) greater in the control site. However, large proportions of near-total metals were potentially bio-available in control sites. Concentrations of Fe and Ni were significantly (p values≤0.001) greater in leaves and pneumatophores of the affected sites, whereas Mn, Cu, Pb and Zn were greater in control sites. The degree of metal bio-accumulation in leaves and pneumatophores suggest contrasting

  8. Screening and assessment of solidification/stabilization amendments suitable for soils of lead-acid battery contaminated site.

    PubMed

    Zhang, Zhuo; Guo, Guanlin; Teng, Yanguo; Wang, Jinsheng; Rhee, Jae Seong; Wang, Sen; Li, Fasheng

    2015-05-15

    Lead exposure via ingestion of soil and dust generally occurs at lead-acid battery manufacturing and recycling sites. Screening solidification/stabilization (S/S) amendments suitable for lead contaminated soil in an abandoned lead-acid battery factory site was conducted based on its chemical forms and environmental risks. Twelve amendments were used to immobilize the Pb in soil and assess the solidification/stabilization efficiency by toxicity leaching tests. The results indicated that three amendments, KH₂PO₄ (KP), KH₂PO₄:oyster shell power=1:1 (by mass ratio; SPP), and KH₂PO₄:sintered magnesia=1:1 (by mass ratio; KPM) had higher remediation efficiencies that led to a 92% reduction in leachable Pb with the addition of 5% amendments, while the acid soluble fraction of Pb (AS-Pb) decreased by 41-46% and the residual fraction (RS-Pb) increased by 16-25%. The S/S costs of the three selected amendments KP, SPP, and KPM could be controlled to $22.3 per ton of soil when the Pb concentration in soil ranged from 2000 to 3000 mg/kg. The results of this study demonstrated that KP, SPP, and KPM can effectively decrease bioavailability of Pb. These findings could provide basis for decision-making of S/S remediation of lead-acid battery contaminated sites.

  9. Screening and assessment of solidification/stabilization amendments suitable for soils of lead-acid battery contaminated site.

    PubMed

    Zhang, Zhuo; Guo, Guanlin; Teng, Yanguo; Wang, Jinsheng; Rhee, Jae Seong; Wang, Sen; Li, Fasheng

    2015-05-15

    Lead exposure via ingestion of soil and dust generally occurs at lead-acid battery manufacturing and recycling sites. Screening solidification/stabilization (S/S) amendments suitable for lead contaminated soil in an abandoned lead-acid battery factory site was conducted based on its chemical forms and environmental risks. Twelve amendments were used to immobilize the Pb in soil and assess the solidification/stabilization efficiency by toxicity leaching tests. The results indicated that three amendments, KH₂PO₄ (KP), KH₂PO₄:oyster shell power=1:1 (by mass ratio; SPP), and KH₂PO₄:sintered magnesia=1:1 (by mass ratio; KPM) had higher remediation efficiencies that led to a 92% reduction in leachable Pb with the addition of 5% amendments, while the acid soluble fraction of Pb (AS-Pb) decreased by 41-46% and the residual fraction (RS-Pb) increased by 16-25%. The S/S costs of the three selected amendments KP, SPP, and KPM could be controlled to $22.3 per ton of soil when the Pb concentration in soil ranged from 2000 to 3000 mg/kg. The results of this study demonstrated that KP, SPP, and KPM can effectively decrease bioavailability of Pb. These findings could provide basis for decision-making of S/S remediation of lead-acid battery contaminated sites. PMID:25699676

  10. Site-specific regulation of adult neurogenesis by dietary fatty acid content, vitamin E and flight exercise in European starlings.

    PubMed

    Hall, Zachary J; Bauchinger, Ulf; Gerson, Alexander R; Price, Edwin R; Langlois, Lillie A; Boyles, Michelle; Pierce, Barbara; McWilliams, Scott R; Sherry, David F; Macdougall-Shackleton, Scott A

    2014-03-01

    Exercise is known to have a strong effect on neuroproliferation in mammals ranging from rodents to humans. Recent studies have also shown that fatty acids and other dietary supplements can cause an upregulation of neurogenesis. It is not known, however, how exercise and diet interact in their effects on adult neurogenesis. We examined neuronal recruitment in multiple telencephalic sites in adult male European starlings (Sturnus vulgaris) exposed to a factorial combination of flight exercise, dietary fatty acids and antioxidants. Experimental birds were flown in a wind tunnel following a training regime that mimicked the bird's natural flight behaviour. In addition to flight exercise, we manipulated the composition of dietary fatty acids and the level of enrichment with vitamin E, an antioxidant reported to enhance neuronal recruitment. We found that all three factors - flight exercise, fatty acid composition and vitamin E enrichment - regulate neuronal recruitment in a site-specific manner. We also found a robust interaction between flight training and vitamin E enrichment at multiple sites of neuronal recruitment. Specifically, flight training was found to enhance neuronal recruitment across the telencephalon, but only in birds fed a diet with a low level of vitamin E. Conversely, dietary enrichment with vitamin E upregulated neuronal recruitment, but only in birds not flown in the wind tunnel. These findings indicate conserved modulation of adult neurogenesis by exercise and diet across vertebrate taxa and indicate possible therapeutic interventions in disorders characterized by reduced adult neurogenesis.

  11. Adsorption of formic acid on rutile TiO{sub 2} (110) revisited: An infrared reflection-absorption spectroscopy and density functional theory study

    SciTech Connect

    Mattsson, A.; Österlund, L.; Hu, Shuanglin Hermansson, K.

    2014-01-21

    Formic acid (HCOOH) adsorption on rutile TiO{sub 2} (110) has been studied by s- and p-polarized infrared reflection-absorption spectroscopy (IRRAS) and spin-polarized density functional theory together with Hubbard U contributions (DFT+U) calculations. To compare with IRRAS spectra, the results from the DFT+U calculations were used to simulate IR spectra by employing a three-layer model, where the adsorbate layer was modelled using Lorentz oscillators with calculated dielectric constants. To account for the experimental observations, four possible formate adsorption geometries were calculated, describing both the perfect (110) surface, and surfaces with defects; either O vacancies or hydroxyls. The majority species seen in IRRAS was confirmed to be the bridging bidentate formate species with associated symmetric and asymmetric frequencies of the ν(OCO) modes measured to be at 1359 cm{sup −1} and 1534 cm{sup −1}, respectively. The in-plane δ(C–H) wagging mode of this species couples to both the tangential and the normal component of the incident p-polarized light, which results in absorption and emission bands at 1374 cm{sup −1} and 1388 cm{sup −1}. IRRAS spectra measured on surfaces prepared to be either reduced, stoichiometric, or to contain surplus O adatoms, were found to be very similar. By comparisons with computed spectra, it is proposed that in our experiments, formate binds as a minority species to an in-plane Ti{sub 5c} atom and a hydroxyl, rather than to O vacancy sites, the latter to a large extent being healed even at our UHV conditions. Excellent agreement between calculated and experimental IRRAS spectra is obtained. The results emphasize the importance of protonation and reactive surface hydroxyls – even under UHV conditions – as reactive sites in e.g., catalytic applications.

  12. Comparison on Response and Dissolution Rates Between Ursodeoxycholic Acid Alone or in Combination With Chenodeoxycholic Acid for Gallstone Dissolution According to Stone Density on CT Scan

    PubMed Central

    Lee, Jae Min; Hyun, Jong Jin; Choi, In Young; Yeom, Suk Keu; Kim, Seung Young; Jung, Sung Woo; Jung, Young Kul; Koo, Ja Seol; Yim, Hyung Joon; Lee, Hong Sik; Lee, Sang Woo; Kim, Chang Duck

    2015-01-01

    Abstract Medical dissolution of gallstone is usually performed on radiolucent gallstones in a functioning gallbladder. However, absence of visible gallstone on plain abdominal x-ray does not always preclude calcification. This study aims to compare the response and dissolution rates between ursodeoxycholic acid (UDCA) alone or in combination with chenodeoxycholic acid (CDCA) according to stone density on computed tomography (CT) scan. A total of 126 patients underwent dissolution therapy with either UDCA alone or combination of CDCA and UDCA (CNU) from December 2010 to March 2014 at Korea University Ansan Hospital. In the end, 81 patients (CNU group = 44, UDCA group = 37) completed dissolution therapy for 6 months. Dissolution rate (percentage reduction in the gallstone volume) and response to therapy (complete dissolution or partial dissolution defined as reduction in stone volume of >50%) were compared between the 2 groups. Dissolution and response rates of sludge was also compared between the 2 groups. The overall response rate was 50.6% (CNU group 43.2% vs UDCA group 59.5%, P = 0.14), and the overall dissolution rate was 48.34% (CNU group 41.5% vs UDCA group 56.5%, P = 0.13). When analyzed according to stone density, response rate was 33.3%, 87.1%, 30.0%, and 6.2% for hypodense, isodense, hyperdense, and calcified stones, respectively. Response rate (85.7% vs 88.2%, P = 0.83) and dissolution rate (81.01% vs 85.38%, P = 0.17) of isodense stones were similar between CNU and UDCA group. When only sludge was considered, the overall response rate was 87.5% (CNU group 71.4% vs UDCA group 94.1%, P = 0.19), and the overall dissolution rate was 85.42% (CNU group 67.9% vs UDCA group 92.7%, P = 0.23). Patients with isodense gallstones and sludge showed much better response to dissolution therapy with CNU and UDCA showing comparable efficacy. Therefore, CT scan should be performed before medication therapy if stone dissolution is intended

  13. Effective catalytic media using graphitic nitrogen-doped site in graphene for a non-aqueous Li-O2 battery: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Yun, Kyung-Han; Hwang, Yubin; Chung, Yong-Chae

    2015-03-01

    The cell performance of lithium-oxygen batteries using nitrogen doped graphene as a catalytic cathode has been validated in recent research, but the cathode reaction mechanism of lithium and oxygen still remains unclear. Since the oxygen reduction reaction (ORR) mechanism by ionic lithium and catalytic surface is predicted to be distinct for different defective sites such as graphitic, pyridinic, and pyrrolic, it is necessary to observe the behavior of ionic lithium and oxygen gas at each defective site in nitrogen doped graphene. In this study, density functional theory (DFT) calculations are adopted to analyze at an atomic scale how effectively each defective site acts as a catalytic cathode. Interestingly, unlike pyridinic or pyrrolic N is known to be the most effective catalytic site for ORR in fuel cells. Among the other defective sites, it is found that the graphitic N site is the most effective catalytic media activating ORR by ionic lithium in lithium-oxygen batteries due to the electron accepting the reaction of Li-O formation by the graphitic N site.

  14. Areal power density: A preliminary examination of underground heat transfer in a potential Yucca Mountain repository and recommendations for thermal design approaches; Yucca Mountain Site Characterization Project

    SciTech Connect

    Hertel, E.S. Jr.; Ryder, E.E.

    1991-11-01

    The design of the potential Yucca Mountain repository is subject to many thermal goals related to the compliance of the site with federal regulations. This report summarizes a series of sensitivity studies that determined the expected temperatures near the potential repository. These sensitivity studies were used to establish an efficient loading scheme for the spent fuel canisters and a maximum areal power density based strictly on thermal goals. Given the current knowledge of the site, a design-basis areal power density of 80 kW/acre can be justified based on thermal goals only. Further analyses to investigate the impacts of this design-basis APD on mechanical and operational aspects of the potential repository must be undertaken before a final decision is made.

  15. A Mutational Analysis of the Active Site Loop Residues in cis-3-Chloroacrylic Acid Dehalogenase

    PubMed Central

    Schroeder, Gottfried K.; Huddleston, Jamison P.; Johnson, William H.; Whitman, Christian P.

    2013-01-01

    cis -3-Chloroacrylic acid dehalogenase (cis-CaaD) from Pseudomonas pavonaceae 170 and a homologue from Corynebacterium glutamicum designated Cg10062 share 34% sequence identity (54% similarity). The former catalyzes a key step in a bacterial catabolic pathway for the nematocide 1,3-dichloropropene, whereas the latter has no known biological activity. Although Cg10062 has the six active site residues (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114) that are critical for cis-CaaD activity, it shows only a low level cis-CaaD activity and lacks the specificity of cis-CaaD: Cg10062 processes both isomers of 3-chloroacrylate with a preference for the cis-isomer. Although the basis for these differences is unknown, a comparison of the crystal structures of the enzymes covalently modified by an adduct resulting from their incubation with the same inhibitor offers a possible explanation. A 6-residue active site loop in cis-CaaD shows a strikingly different conformation from that observed in Cg10062: the loop closes down on the active site of cis-CaaD, but not on that of Cg10062. In order to examine what this loop might contribute to cis-CaaD catalysis and specificity, the residues were changed individually to those found in Cg10062. Subsequent kinetic and mechanistic analysis suggests that the T34A mutant of cis-CaaD is more Cg10062-like. The mutant enzyme shows a 4-fold increase in Km (using cis-3-bromoacrylate), but not to the degree observed for Cg10062 (687-fold). The mutation also causes a 4-fold decrease in the burst rate (compared to the wild type cis-CaaD), whereas Cg10062 shows no burst rate. More telling is the reaction of the T34A mutant of cis-CaaD with the alternate substrate, 2,3-butadienoate. In the presence of NaBH4 and the allene, cis-CaaD is completely inactivated after one turnover due to the covalent modification of Pro-1. The same experiment with Cg10062 does not result in the covalent modification of Pro-1. The different outcomes are attributed to

  16. On-site monitoring of atomic density number for an all-optical atomic magnetometer based on atomic spin exchange relaxation.

    PubMed

    Zhang, Hong; Zou, Sheng; Chen, Xiyuan; Ding, Ming; Shan, Guangcun; Hu, Zhaohui; Quan, Wei

    2016-07-25

    We present a method for monitoring the atomic density number on site based on atomic spin exchange relaxation. When the spin polarization P ≪ 1, the atomic density numbers could be estimated by measuring magnetic resonance linewidth in an applied DC magnetic field by using an all-optical atomic magnetometer. The density measurement results showed that the experimental results the theoretical predictions had a good consistency in the investigated temperature range from 413 K to 463 K, while, the experimental results were approximately 1.5 ∼ 2 times less than the theoretical predictions estimated from the saturated vapor pressure curve. These deviations were mainly induced by the radiative heat transfer efficiency, which inevitably leaded to a lower temperature in cell than the setting temperature. PMID:27464172

  17. On-site monitoring of atomic density number for an all-optical atomic magnetometer based on atomic spin exchange relaxation.

    PubMed

    Zhang, Hong; Zou, Sheng; Chen, Xiyuan; Ding, Ming; Shan, Guangcun; Hu, Zhaohui; Quan, Wei

    2016-07-25

    We present a method for monitoring the atomic density number on site based on atomic spin exchange relaxation. When the spin polarization P ≪ 1, the atomic density numbers could be estimated by measuring magnetic resonance linewidth in an applied DC magnetic field by using an all-optical atomic magnetometer. The density measurement results showed that the experimental results the theoretical predictions had a good consistency in the investigated temperature range from 413 K to 463 K, while, the experimental results were approximately 1.5 ∼ 2 times less than the theoretical predictions estimated from the saturated vapor pressure curve. These deviations were mainly induced by the radiative heat transfer efficiency, which inevitably leaded to a lower temperature in cell than the setting temperature.

  18. Encapsulating Metal Clusters and Acid Sites within Small Voids: Synthetic Strategies and Catalytic Consequences

    NASA Astrophysics Data System (ADS)

    Goel, Sarika

    active sites. We have demonstrated the selectivity of the encapsulation processes by combining transmission electron microscopy and chemisorptive titrations with rigorous catalytic assessments of the ability of these materials to catalyze reactions of small molecules, which can access the intracrystalline voids, but not of larger molecules that cannot access the metal clusters within such voids. The selective confinement of clusters also prevented their contact with sulfur compounds (e.g., thiophene and H2S), thus allowing reactions to occur at conditions that otherwise render unconfined clusters unreactive. We have also developed synthetic protocols and guiding principles, inspired by mechanistic considerations, for the synthesis of zeolites via interzeolite transformations without the use of organic structure-directing agents (OSDA). More specifically, we have synthesized high-silica MFI (ZSM-5), CHA (chabazite), STF (SSZ-35) and MTW (ZSM-12) zeolites from FAU (faujasite) or BEA (beta) parent materials. Structures with lower framework densities (FAU or BEA) were successfully transformed into thermodynamically-favored, more stable structures with higher framework densities (MFI, CHA, STF, and MTW); to date, target materials with higher Si/Al ratios (Si/Al >10) have not been synthesized via interzeolite transformations without the aid of the OSDA species used to discover these zeolite structures and deemed essential up until now for their successful synthesis. Overcoming kinetic hurdles in such transformations required either the presence of common composite building units (CBU) between parent and target structures or, in their absence, the introduction of small amount of seeds of the daughter structures. The NaOH/SiO2 ratio, H2O/SiO2 ratio and Al content in reagents are used to enforce synchronization between the swelling and local restructuring within parent zeolite domains with the spalling of fragments or building units from seeds of the target structure. The

  19. Omega-3 fatty acid ethyl ester supplementation decreases very-low-density lipoprotein triacylglycerol secretion in obese men.

    PubMed

    Wong, Annette T Y; Chan, Dick C; Ooi, Esther M M; Ng, Theodore W K; Watts, Gerald F; Barrett, P Hugh R

    2013-07-01

    Dysregulated VLDL-TAG (very-low-density lipoprotein triacylglycerol) metabolism in obesity may account for hypertriacylglycerolaemia and increased cardiovascular disease. ω-3 FAEEs (omega-3 fatty acid ethyl esters) decrease plasma TAG and VLDL concentrations, but the mechanisms are not fully understood. In the present study, we carried out a 6-week randomized, placebo-controlled study to examine the effect of high-dose ω-3 FAEE supplementation (3.2 g/day) on the metabolism of VLDL-TAG in obese men using intravenous administration of d5-glycerol. We also explored the relationship of VLDL-TAG kinetics with the metabolism of VLDL-apo (apolipoprotein) B-100 and HDL (high-density lipoprotein)-apoA-I. VLDL-TAG isotopic enrichment was measured using gas chromatography-mass spectrometry. Kinetic parameters were derived using a multicompartmental model. Compared with placebo, ω-3 FAEE supplementation significantly lowered plasma concentrations of total (-14%, P<0.05) and VLDL-TAG (-32%, P<0.05), as well as hepatic secretion of VLDL-TAG (-32%, P<0.03). The FCR (fractional catabolic rate) of VLDL-TAG was not altered by ω-3 FAEEs. There was a significant association between the change in secretion rates of VLDL-TAG and VLDL-apoB-100 (r=0.706, P<0.05). However, the change in VLDL-TAG secretion rate was not associated with change in HDL-apoA-I FCR (r=0.139, P>0.05). Our results suggest that the TAG-lowering effect of ω-3 FAEEs is associated with the decreased VLDL-TAG secretion rate and hence lower plasma VLDL-TAG concentration in obesity. The changes in VLDL-TAG and apoB-100 kinetics are closely coupled. PMID:23356247

  20. Periodic density functional theory study of the high-pressure behavior of crystalline L-serine-L-ascorbic acid.

    PubMed

    Chen, Limin; Liu, Chunsheng; Fang, Henan; Xie, Qiyun; Kong, Chengkai; Ji, Guanghan; Xiang, Ziyue

    2016-01-01

    A detailed study of the structural, electronic and absorption properties of crystalline L-serine-L-ascorbic acid (SAA) in the pressure range of 0-300 GPa was performed by density-functional theory (DFT) calculations in this work. Our results show that the compressible crystal of SAA is anisotropic. Furthermore, specific analysis of the variation tendencies of bond lengths and bond angles under different pressures show that the main structural transformations occur at pressures of 40, 50, 70, 100, 130 and 150 GPa, accompanied by repeated formations and disconnections of covalent bonds between O2(P1) and C2(P2) as well as C3(P1) and O1(P2), and a newly formed five-atom ring at 100 GPa. In addition, from 40 to 230 GPa, complex hydrogen bond transformations occur in SAA under compression, while from 240 to 300 GPa, the curve of lattice constants, bond lengths and bond angles of SAA barely changes, suggesting structural stability after 230 GPa. Then, by analyzing the band gap and density of states of SAA, it was found that the crystal undergoes a phase transformation from insulator to semiconductor at 150 GPa and it becomes more sensitive under compression. In addition, a relatively high optical activity with the pressure increases of SAA was seen from the absorption spectra, and two obvious changes of absorption coefficients were also observed at 50 GPa and 130 GPa, respectively, indicating that structural transformations occur here. Graphical abstract Structural formation and breaking of the five-atom ring O1(P2)-C2(P2)-O2(P1)-C2(P1)-C3(P1) with increasing pressure.

  1. Behavior of Surface-Anchored Poly(acrylic acid) Brushes with Grafting Density Gradients on Solid Substrates: 1. Experiment

    SciTech Connect

    Wu,T.; Gong, P.; Szleifer, I.; Vicek, P.; Subr, V.; Genzer, J.

    2007-01-01

    We describe experiments pertaining to the formation of surface-anchored poly(acrylic acid) (PAA) brushes with a gradual variation of the PAA grafting densities on flat surfaces and provide detailed analysis of their properties. The PAA brush gradients are generated by first covering the substrate with a molecular gradient of the polymerization initiator, followed by the 'grafting from' polymerization of tert-butyl acrylate (tBA) from these substrate-bound initiator centers, and finally converting the PtBA into PAA. We use spectroscopic ellipsometry to measure the wet thickness of the grafted PAA chains in aqueous solutions at three different pH values (4, 5.8, and 10) and a series of ionic strengths (IS). Our measurements reveal that at low grafting densities, s, the wet thickness of the PAA brush (H) remains relatively constant, the polymers are in the mushroom regime. Beyond a certain value of s, the macromolecules enter the brush regime, where H increases with increasing s. For a given s, H exhibits a nonmonotonic behavior as a function of the IS. At large IS, the H is small because the charges along PAA are completely screened by the excess of the external salt. As IS decreases, the PAA enters the so-called salt brush (SB) regime, where H increases. At a certain value of IS, H reaches a maximum and then decreases again. The latter is a typical brush behavior in so-called osmotic brush (OB) regime. We provide detailed discussion of the behavior of the grafted PAA chains in the SB and OB regimes.

  2. Immersion freezing of supermicron mineral dust particles: freezing results, testing different schemes for describing ice nucleation, and ice nucleation active site densities.

    PubMed

    Wheeler, M J; Mason, R H; Steunenberg, K; Wagstaff, M; Chou, C; Bertram, A K

    2015-05-14

    Ice nucleation on mineral dust particles is known to be an important process in the atmosphere. To accurately implement ice nucleation on mineral dust particles in atmospheric simulations, a suitable theory or scheme is desirable to describe laboratory freezing data in atmospheric models. In the following, we investigated ice nucleation by supermicron mineral dust particles [kaolinite and Arizona Test Dust (ATD)] in the immersion mode. The median freezing temperature for ATD was measured to be approximately -30 °C compared with approximately -36 °C for kaolinite. The freezing results were then used to test four different schemes previously used to describe ice nucleation in atmospheric models. In terms of ability to fit the data (quantified by calculating the reduced chi-squared values), the following order was found for ATD (from best to worst): active site, pdf-α, deterministic, single-α. For kaolinite, the following order was found (from best to worst): active site, deterministic, pdf-α, single-α. The variation in the predicted median freezing temperature per decade change in the cooling rate for each of the schemes was also compared with experimental results from other studies. The deterministic model predicts the median freezing temperature to be independent of cooling rate, while experimental results show a weak dependence on cooling rate. The single-α, pdf-α, and active site schemes all agree with the experimental results within roughly a factor of 2. On the basis of our results and previous results where different schemes were tested, the active site scheme is recommended for describing the freezing of ATD and kaolinite particles. We also used our ice nucleation results to determine the ice nucleation active site (INAS) density for the supermicron dust particles tested. Using the data, we show that the INAS densities of supermicron kaolinite and ATD particles studied here are smaller than the INAS densities of submicron kaolinite and ATD particles

  3. Immersion freezing of supermicron mineral dust particles: freezing results, testing different schemes for describing ice nucleation, and ice nucleation active site densities.

    PubMed

    Wheeler, M J; Mason, R H; Steunenberg, K; Wagstaff, M; Chou, C; Bertram, A K

    2015-05-14

    Ice nucleation on mineral dust particles is known to be an important process in the atmosphere. To accurately implement ice nucleation on mineral dust particles in atmospheric simulations, a suitable theory or scheme is desirable to describe laboratory freezing data in atmospheric models. In the following, we investigated ice nucleation by supermicron mineral dust particles [kaolinite and Arizona Test Dust (ATD)] in the immersion mode. The median freezing temperature for ATD was measured to be approximately -30 °C compared with approximately -36 °C for kaolinite. The freezing results were then used to test four different schemes previously used to describe ice nucleation in atmospheric models. In terms of ability to fit the data (quantified by calculating the reduced chi-squared values), the following order was found for ATD (from best to worst): active site, pdf-α, deterministic, single-α. For kaolinite, the following order was found (from best to worst): active site, deterministic, pdf-α, single-α. The variation in the predicted median freezing temperature per decade change in the cooling rate for each of the schemes was also compared with experimental results from other studies. The deterministic model predicts the median freezing temperature to be independent of cooling rate, while experimental results show a weak dependence on cooling rate. The single-α, pdf-α, and active site schemes all agree with the experimental results within roughly a factor of 2. On the basis of our results and previous results where different schemes were tested, the active site scheme is recommended for describing the freezing of ATD and kaolinite particles. We also used our ice nucleation results to determine the ice nucleation active site (INAS) density for the supermicron dust particles tested. Using the data, we show that the INAS densities of supermicron kaolinite and ATD particles studied here are smaller than the INAS densities of submicron kaolinite and ATD particles

  4. The Relationship Between Dietary Intakes of Amino Acids and Bone Mineral Density Among Individuals with Spinal Cord Injury

    PubMed Central

    Sabour, Hadis; Nazari, Maryam; Latifi, Sahar; Soltani, Zahra; Shakeri, Hania; Larijani, Bagher; Ghodsi, Seyed-Mohammad; Razavi, Seyed-Hassan Emami

    2016-01-01

    Objectives The effect of dietary protein intake on bone mineral density (BMD) has not been explained in patients with spinal cord injury (SCI). In this study, we looked at the relationship between BMD and higher protein intake in patients with SCI while controlling for possible confounders. Methods Patients with SCI, who were referred to the Brain and Spinal Cord Injury Research Center between November 2010 and April 2012, were included in the study. In total, the dietary intakes of 103 patients were assessed by 24–hour dietary recall interviews. We used dual-energy X-ray absorptiometry to measure BMD in the femoral neck, trochanter, intertrochanteric zone, hip, and lumbar vertebras. Results Eighty-six men and 17 women participated in this study. Protein intake was negatively associated with the BMD of lumbar vertebrae (p = 0.001, r = –0.37 for T-score and p = 0.030, r = –0.24 for Z-score). The BMD of lumbar vertebrae were negatively associated with intake of tryptophan, isoleucine, lysine, cysteine, and tyrosine (p = 0.007, 0.005, 0.009, 0.008, and 0.008 for T-score, respectively). Higher intakes of threonine, leucine, methionine, phenylalanine, valine, and histidine were related to a lower BMD of lumbar vertebrae (p = 0.006, 0.010, 0.009, 0.010, 0.009, and 0.008 respectively for T-scores). Conclusions We found that high protein intake led to a lower BMD of lumbar vertebrae in patients with SCI after controlling for confounders including demographic and injury-related characteristics and calcium intake. No relationship between higher amino acids intake and BMD of the femur and hip was detected. Intake of alanine, arginine, and aspartic acid were not related to BMD. PMID:26816565

  5. Remotely operable compact instruments for measuring atmospheric CO2 and CH4 column densities at surface monitoring sites

    NASA Astrophysics Data System (ADS)

    Kobayashi, N.; Inoue, G.; Kawasaki, M.; Yoshioka, H.; Minomura, M.; Murata, I.; Nagahama, T.; Matsumi, Y.; Ibuki, T.

    2010-04-01

    Remotely operable compact instruments for measuring atmospheric CO2 and CH4 column densities were developed in two independent systems: one utilizing a grating-based desktop optical spectrum analyzer (OSA) with a resolution enough to resolve rotational lines of CO2 and CH4 in the region of 1565-1585 and 1674-1682 nm, respectively; the other is an application of an optical fiber Fabry-Perot interferometer (FFPI) to the CO2 column density. Direct sunlight was collimated via a small telescope installed on a portable sun tracker and then transmitted through an optical fiber into the OSA or the FFPI for optical analysis. The near infrared spectra of the OSA were retrieved by a least squares spectral fitting algorithm. The CO2 and CH4 column densities deduced were in excellent agreement with those measured by a Fourier transform spectrometer with high resolution. The rovibronic lines in the wavelength region of 1570-1575 nm were analyzed by the FFPI. The I0 and I values in the Beer-Lambert law equation to obtain CO2 column density were deduced by modulating temperature of the FFPI, which offered column CO2 with the statistical error less than 0.2% for six hours measurement.

  6. Remotely operable compact instruments for measuring atmospheric CO2 and CH4 column densities at surface monitoring sites

    NASA Astrophysics Data System (ADS)

    Kobayashi, N.; Inoue, G.; Kawasaki, M.; Yoshioka, H.; Minomura, M.; Murata, I.; Nagahama, T.; Matsumi, Y.; Tanaka, T.; Morino, I.; Ibuki, T.

    2010-08-01

    Remotely operable compact instruments for measuring atmospheric CO2 and CH4 column densities were developed in two independent systems: one utilizing a grating-based desktop optical spectrum analyzer (OSA) with a resolution enough to resolve rotational lines of CO2 and CH4 in the regions of 1565-1585 and 1674-1682 nm, respectively; the other is an application of an optical fiber Fabry-Perot interferometer (FFPI) to obtain the CO2 column density. Direct sunlight was collimated via a small telescope installed on a portable sun tracker and then transmitted through an optical fiber into the OSA or the FFPI for optical analysis. The near infrared spectra of the OSA were retrieved by a least squares spectral fitting algorithm. The CO2 and CH4 column densities deduced were in excellent agreement with those measured by a Fourier transform spectrometer with high resolution. The rovibronic lines in the wavelength region of 1570-1575 nm were analyzed by the FFPI. The I0 and I values in the Beer-Lambert law equation to obtain CO2 column density were deduced by modulating temperature of the FFPI, which offered column CO2 with the statistical error less than 0.2% for six hours measurement.

  7. Methyl Acetate Synthesis by Esterification on the Modified Ferrierite: Correlation of Acid Sites Measured by Pyridine IR and NH3-TPD for Steady-State Activity.

    PubMed

    Park, Jae Hyun; Pang, Changhyun; Chung, Chan-Hwa; Bae, Jong Wook

    2016-05-01

    The amounts of Brønsted acid sites on K, P, and Zr-modified microporous Ferrierite zeolite were investigated through pyridine FT-IR and NH3-TPD analyses. P-modified Ferrierite showed a superior catalytic activity for methyl acetate synthesis by esterification of methanol and acetic acid. The catalytic activity at steady-state with the acidic properties of as-prepared catalysts was well correlated with the results of pyridine FT-IR (intensity ratio of Brønsted acid sites to total acid sites) compared with that of NH3-TPD. The results can suggest the proper and simple method to estimate the esterification activity at steady-state using the measured acid sites on the as-prepared zeolites. PMID:27483801

  8. Modulation of infant formula fat profile alters the low-density lipoprotein/high-density lipoprotein ratio and plasma fatty acid distribution relative to those with breast-feeding.

    PubMed

    Hayes, K C; Pronczuk, A; Wood, R A; Guy, D G

    1992-04-01

    The effect of breast-feeding was compared with that of two fat-modified milk formulas in 45 infants (15 per group) studied by assessing body weight gain for 4 months and plasma lipids, lipoprotein profiles, fatty acid profiles of plasma and red blood cells, and plasma tocopherol status 3 months after birth. A saturated fat formula with coconut oil/soybean oil (COCO/SOY) had a fatty acid content and polyunsaturated/saturated ratio (P/S, 0.55) comparable with that of human milk fat (P/S, 0.39) and had the same fat energy content (50% kcal). The second formula, with corn oil/soybean oil (CORN/SOY), was highly unsaturated (P/S, 4.6), with only 35% kcal from fat. Energy intake and body weight gain were similar for all groups. Plasma total cholesterol, triglyceride, and phospholipid levels were significantly lower (greater than 20% on average) in infants fed the CORN/SOY formula than in infants fed either the COCO/SOY formula or human milk. Infants fed the CORN/SOY formula also had lower (25% to 35%) plasma low-density lipoprotein cholesterol and apolipoprotein B levels and low-density lipoprotein/high-density lipoprotein and apolipoprotein B/apolipoprotein A-I ratios. Plasma, red blood cell, and cholesteryl ester fatty acids from infants fed COCO/SOY contained less 18:1 and more 18:2; cholesterol esters in plasma from breast-fed infants had the highest 20:4n-6 levels. Plasma tocopherol levels were higher in infants consuming formulas. The presence of cholesterol in human milk appeared to expand the low-density lipoprotein pool and exert an "unfavorable" increase in the low-density lipoprotein/high-density lipoprotein ratio. Thus modulation of infant lipoproteins by changing dietary fat and cholesterol is feasible and in keeping with the known response in adults. PMID:1560323

  9. Effect of stearic acid-grafted starch compatibilizer on properties of linear low density polyethylene/thermoplastic starch blown film.

    PubMed

    Khanoonkon, Nattaporn; Yoksan, Rangrong; Ogale, Amod A

    2016-02-10

    The present work aims to investigate the effect of stearic acid-grafted starch (ST-SA) on the rheological, thermal, optical, dynamic mechanical thermal, and tensile properties of linear low density polyethylene/thermoplastic starch (LLDPE/TPS) blends, as well as on their water vapor and oxygen barrier properties. Blends consisting of LLDPE and TPS in a weight ratio of 60:40 and ST-SA at different concentrations, i.e. 1, 3 and 5%, were prepared using a twin-screw extruder. The obtained resins were subsequently converted into films via blown film extrusion. Incorporation of ST-SA resulted in a decreased degree of shear thinning, reduced ambient temperature elasticity, and improved tensile strength, secant modulus, extensibility, and UV absorption, as well as diminished water vapor and oxygen permeabilities of the LLDPE/TPS blend. These effects are attributed to the enhanced interfacial adhesion between LLDPE and TPS phases through the compatibilizing effect induced by ST-SA, and the good dispersion of the TPS phase in the LLDPE matrix. The results confirmed that ST-SA could potentially be used as a compatibilizer for the LLDPE/TPS blend system.

  10. Tartaric Acid-based Amphiphilic Macromolecules with Ether Linkages Exhibit Enhanced Repression of Oxidized Low Density Lipoprotein Uptake

    PubMed Central

    Abdelhamid, Dalia; Zhang, Yingue; Lewis, Daniel R.; Moghe, Prabhas V.; Welsh, William J.; Uhrich, Kathryn E.

    2015-01-01

    Cardiovascular disease initiates with the atherogenic cascade of scavenger receptor- (SR-) mediated oxidized low-density lipoprotein (oxLDL) uptake. Resulting foam cell formation leads to lipid-rich lesions within arteries. We designed amphiphilic macromolecules (AMs) to inhibit these processes by competitively blocking oxLDL uptake via SRs, potentially arresting atherosclerotic development. In this study, we investigated the impact of replacing ester linkages with ether linkages in the AM hydrophobic domain. We hypothesized that ether linkages would impart flexibility for orientation to improve binding to SR binding pockets, enhancing anti-atherogenic activity. A series of tartaric acid-based AMs with varying hydrophobic chain lengths and conjugation chemistries were synthesized, characterized, and evaluated for bioactivity. 3-D conformations of AMs in aqueous conditions may have significant effects on anti-atherogenic potency and were simulated by molecular modeling. Notably, ether-linked AMs exhibited significantly higher levels of inhibition of oxLDL uptake than their corresponding ester analogues, indicating a dominant effect of linkage flexibility on pharmacological activity. The degradation stability was also enhanced for ether-linked AMs. These studies further suggested that alkyl chain length (i.e., relative hydrophobicity), conformation (i.e., orientation), and chemical stability play a critical role in modulating oxLDL uptake, and guide the design of innovative cardiovascular therapies. PMID:25890704

  11. Glucuronic acid epimerase is associated with plasma triglyceride and high-density lipoprotein cholesterol levels in Turks.

    PubMed

    Hodoğlugil, Uğur; Williamson, David W; Yu, Yi; Farrer, Lindsay A; Mahley, Robert W

    2011-05-01

    We narrowed chromosome 15q21-23 linkage to plasma high-density lipoprotein cholesterol (HDL-C) levels in Turkish families by fine mapping, then focused on glucuronic acid epimerase (GLCE), a heparan sulfate proteoglycan (HSPG) biosynthesis enzyme. HSPGs participate in lipid metabolism along with apolipoprotein (apo) E. Of 31 SNPs in the GLCE locus, nine analyzed by haplotype were associated with HDL-C and triglyceride levels (permuted p = 0.006 and 0.013, respectively) in families. Of five tagging GLCE SNPs in two cohorts of unrelated subjects, three (rs16952868, rs11631403, and rs3865014) were associated with triglyceride and HDL-C levels in males (nonpermuted p < 0.05). The association was stronger in APOE 2/3 subjects (apoE2 has reduced binding to HSPGs) and reached multiple-testing significance (p < 0.05) in both males and females (n= 2612). Similar results were obtained in the second cohort (n= 1164). Interestingly, at the GLCE locus, bounded by recombination hotspots, Turks had a minor allele frequency of SNPs resembling Chinese more than European ancestry; adjoining regions resembled the European pattern. Studies of glce(+/-) apoe(-/-) mice fed a chow or high-fat diet supported a role for GLCE in lipid metabolism. Thus, SNPs in GLCE are associated with triglyceride and HDL-C levels in Turks, and mouse studies support a role for glce in lipid metabolism.

  12. Enhancement in the critical current density of C-doped MgB2 wire using a polyacrylic acid dopant.

    PubMed

    Lee, Seung Muk; Hwang, Soo Min; Lee, Chang Min; Kim, Won; Joo, Jinho; Lim, Jun Hyung; Kim, Chan-Joong; Hong, Gye-Won

    2012-02-01

    C-doped MgB2 wires were fabricated from a polyacrylic acid (PAA) using a conventional in-situ PIT technique. The effects of the PAA content on the lattice parameter, microstructure, critical temperature (Tc) and critical current density (Jc) were examined. With increasing PAA content, the amount of MgO in the sample increased but the crystallinity, a-axis lattice parameter, and Tc of MgB2 wires decreased, indicating that the C that decomposed from PAA during heat treatment had substituted for B. All doped samples exhibited a higher Jc than the undoped sample at high magnetic field, and the Jc(B) property improved with increasing PAA content: for the 7 wt% doped sample, the Jc was approximately 3-times higher than that of the pristine sample (1.28 kA/cm2 vs. 3.43 kA/cm2) at 5 K and 6.6 T. The improved Jc(B) of the doped sample was attributed to the decreased grain size, enlarged lattice distortion and increased C doping level.

  13. An experimental and density functional study on conformational and spectroscopic analysis of 5-methoxyindole-2-carboxylic acid.

    PubMed

    Cinar, Mehmet; Karabacak, Mehmet; Asiri, Abdullah M

    2015-02-25

    In this article, a brief conformational and spectroscopic characterization of 5-methoxyindole-2-carboxylic acid (5-MeOICA) via experimental techniques and applications of quantum chemical methods is presented. The conformational analysis of the studied molecule was determined theoretically using density functional computations for ground state, and compared with previously reported experimental findings. The vibrational transitions were examined by measured FT-IR and FT-Raman spectroscopic data, and also results obtained from B3LYP and CAM-B3LYP functionals in combination with 6-311++G(d,p) basis set. The recorded proton and carbon NMR spectra in DMSO solution were analyzed to obtain the exact conformation. Due to intermolecular hydrogen bondings, NMR calculations were performed for the dimeric form of 5-MeOICA and so chemical shifts of those protons were predicted more accurately. Finally, electronic properties of steady compound were identified by a comparative study of UV absorption spectra in ethanol and water solution and TD-DFT calculations. PMID:25255480

  14. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2009-02-24

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  15. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    Alfonta; Lital , Schultz; Peter G. , Zhang; Zhiwen

    2010-10-12

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  16. Site-specific incorporation of redox active amino acids into proteins

    SciTech Connect

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2012-02-14

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  17. Site-specific incorporation of redox active amino acids into proteins

    SciTech Connect

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2011-08-30

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  18. Coupling acidic organelles with the ER through Ca²⁺ microdomains at membrane contact sites.

    PubMed

    Penny, Christopher J; Kilpatrick, Bethan S; Eden, Emily R; Patel, Sandip

    2015-10-01

    Acidic organelles such as lysosomes serve as non-canonical Ca(2+) stores. The Ca(2+) mobilising messenger NAADP is thought to trigger local Ca(2+) release from such stores. These events are then amplified by Ca(2+) channels on canonical ER Ca(2+) stores to generate physiologically relevant global Ca(2+) signals. Coupling likely occurs at microdomains formed at membrane contact sites between acidic organelles and the ER. Molecular analyses and computational modelling suggest heterogeneity in the composition of these contacts and predicted Ca(2+) microdomain behaviour. Conversely, acidic organelles might also locally amplify and temper ER-evoked Ca(2+) signals. Ca(2+) microdomains between distinct Ca(2+) stores are thus likely to be integral to the genesis of complex Ca(2+) signals. PMID:25866010

  19. Role of arginine 285 in the active site of Rhodotorula gracilis D-amino acid oxidase. A site-directed mutagenesis study.

    PubMed

    Molla, G; Porrini, D; Job, V; Motteran, L; Vegezzi, C; Campaner, S; Pilone, M S; Pollegioni, L

    2000-08-11

    Arg(285), one of the very few conserved residues in the active site of d-amino acid oxidases, has been mutated to lysine, glutamine, aspartate, and alanine in the enzyme from the yeast Rhodotorula gracilis (RgDAAO). The mutated proteins are all catalytically competent. Mutations of Arg(285) result in an increase ( approximately 300-fold) of K(m) for the d-amino acid and in a large decrease ( approximately 500-fold) of turnover number. Stopped-flow analysis shows that the decrease in turnover is paralleled by a similar decrease in the rate of flavin reduction (k(2)), the latter still being the rate-limiting step of the reaction. In agreement with data from the protein crystal structure, loss of the guanidinium group of Arg(285) in the mutated DAAOs drastically reduces the binding of several carboxylic acids (e.g. benzoate). These results highlight the importance of this active site residue in the precise substrate orientation, a main factor in this redox reaction. Furthermore, Arg(285) DAAO mutants have spectral properties similar to those of the wild-type enzyme, but show a low degree of stabilization of the flavin semiquinone and a change in the redox properties of the free enzyme. From this, we can unexpectedly conclude that Arg(285) in the free enzyme form is involved in the stabilization of the negative charge on the N(1)-C(2)=O locus of the isoalloxazine ring of the flavin. We also suggest that the residue undergoes a conformational change in order to bind the carboxylate portion of the substrate/ligand in the complexed enzyme. PMID:10821840

  20. Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation

    PubMed Central

    Terry-Lorenzo, Ryan T.; Chun, Lawrence E.; Brown, Scott P.; Heffernan, Michele L. R.; Fang, Q. Kevin; Orsini, Michael A.; Pollegioni, Loredano; Hardy, Larry W.; Spear, Kerry L.; Large, Thomas H.

    2014-01-01

    The NMDAR (N-methyl-D-aspartate receptor) is a central regulator of synaptic plasticity and learning and memory. hDAAO (human D-amino acid oxidase) indirectly reduces NMDAR activity by degrading the NMDAR co-agonist D-serine. Since NMDAR hypofunction is thought to be a foundational defect in schizophrenia, hDAAO inhibitors have potential as treatments for schizophrenia and other nervous system disorders. Here, we sought to identify novel chemicals that inhibit hDAAO activity. We used computational tools to design a focused, purchasable library of compounds. After screening this library for hDAAO inhibition, we identified the structurally novel compound, ‘compound 2’ [3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid], which displayed low nM hDAAO inhibitory potency (Ki=7 nM). Although the library was expected to enrich for compounds that were competitive for both D-serine and FAD, compound 2 actually was FAD uncompetitive, much like canonical hDAAO inhibitors such as benzoic acid. Compound 2 and an analog were independently co-crystalized with hDAAO. These compounds stabilized a novel conformation of hDAAO in which the active-site lid was in an open position. These results confirm previous hypotheses regarding active-site lid flexibility of mammalian D-amino acid oxidases and could assist in the design of the next generation of hDAAO inhibitors. PMID:25001371

  1. Demographics and density estimates of two three-toed box turtle (Terrapene carolina triunguis) populations within forest and restored prairie sites in central Missouri

    PubMed Central

    Rittenhouse, Chadwick D.; Millspaugh, Joshua J.; Rittenhouse, Tracy A.G.

    2015-01-01

    Box turtles (Terrapene carolina) are widely distributed but vulnerable to population decline across their range. Using distance sampling, morphometric data, and an index of carapace damage, we surveyed three-toed box turtles (Terrapene carolina triunguis) at 2 sites in central Missouri, and compared differences in detection probabilities when transects were walked by one or two observers. Our estimated turtle densities within forested cover was less at the Thomas S. Baskett Wildlife Research and Education Center, a site dominated by eastern hardwood forest (d = 1.85 turtles/ha, 95% CI [1.13, 3.03]) than at the Prairie Fork Conservation Area, a site containing a mix of open field and hardwood forest (d = 4.14 turtles/ha, 95% CI [1.99, 8.62]). Turtles at Baskett were significantly older and larger than turtles at Prairie Fork. Damage to the carapace did not differ significantly between the 2 populations despite the more prevalent habitat management including mowing and prescribed fire at Prairie Fork. We achieved improved estimates of density using two rather than one observer at Prairie Fork, but negligible differences in density estimates between the two methods at Baskett. Error associated with probability of detection decreased at both sites with the addition of a second observer. We provide demographic data on three-toed box turtles that suggest the use of a range of habitat conditions by three-toed box turtles. This case study suggests that habitat management practices and their impacts on habitat composition may be a cause of the differences observed in our focal populations of turtles. PMID:26417539

  2. Properties of the single-site reduced density matrix in the Bose-Bose resonance model in the ground state and in quantum quenches

    NASA Astrophysics Data System (ADS)

    Dorfner, F.; Heidrich-Meisner, F.

    2016-06-01

    We study properties of the single-site reduced density matrix in the Bose-Bose resonance model as a function of system parameters. This model describes a single-component Bose gas with a resonant coupling to a diatomic molecular state, here defined on a lattice. A main goal is to demonstrate that the eigenstates of the single-site reduced density matrix have structures that are characteristic for the various quantum phases of this system. Since the Hamiltonian conserves only the global particle number but not the number of bosons and molecules individually, these eigenstates, referred to as optimal modes, can be nontrivial linear combinations of bare eigenstates of the molecular and boson particle number. We numerically analyze the optimal modes and their weights, the latter giving the importance of the corresponding state, in the ground state of the Bose-Bose resonance model. We find that the single-site von Neumann entropy is sensitive to the location of the phase boundaries. We explain the structure of the optimal modes and their weight spectra using perturbation theory and via a comparison to results for the single-component Bose-Hubbard model. We further study the dynamical evolution of the optimal modes and of the single-site entanglement entropy in two quantum quenches that cross phase boundaries of the model and show that these quantities are thermal in the steady state. For our numerical calculations, we use the density-matrix renormalization group method for ground-state calculations and time evolution in a Krylov subspace for the quench dynamics as well as exact diagonalization.

  3. Plasma phosphatidylcholine concentrations of polyunsaturated fatty acids are differentially associated with hop bone mineral density and hip fracture in older adults: The Framingham Osteoporosis Study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polyunsaturated fatty acids (PUFA) may influence bone health. Our objective was to examine associations between plasma phosphatidylcholine (PC) PUFA concentrations and hip measures: 1) femoral neck bone mineral density (FN-BMD) (n=765); 2) 4-y change in FN-BMD (n=556); and 3) hip fracture risk (n=76...

  4. Exercise raises high-density lipoprotein cholesterol in men after consumption of ground beef with a high but not low monounsaturated fatty acid-saturated fatty acid ratio.

    PubMed

    Crouse, Stephen F; Green, John S; Meade, Thomas H; Smith, Dana R; Smith, Stephen B

    2016-09-01

    Exercise and diets with higher monounsaturated fatty acid (MUFA):saturated fatty acid (SFA) ratios are independently linked to improved blood lipid profiles, yet interactive effects in men have not been studied. We hypothesized that dietary ground beef with a high MUFA:SFA ratio (HR = 1.1) would augment the beneficial changes in the lipid profile induced by exercise compared to dietary ground beef with a lower MUFA:SFA ratio (LR = 0.71). Untrained men (n = 13, age = 35 ± 12 y, weight = 91.4 ± 14.2 kg, body mass index = 27.8 ± 3.3kg/m(2)) consumed 5 HR or LR 114 g ground beef patties weekly for 5 weeks (random order) interspersed with a 4-week self-selected (SS) washout diet. One session of exercise (70% VO2max, 1675 kJ) was completed at the end of HR and LR diets, and again after a 5-week SS diet. Diets and physical activity were otherwise not controlled. Fasting blood samples for lipid and lipoprotein analyses were obtained 30 min before and 24 h after exercise. Subjects reported no other changes in diets or physical activity patterns, and body weight and body mass index did not change over the study duration. Diet (3) × Exercise Time (2) repeated measures analysis of variance (α = .05) and follow-up analyses revealed that blood concentrations (mmol/L ± SD) of total cholesterol (5.07 ± 1.16 to 5.73 ± 1.36), high-density lipoprotein cholesterol (HDL-C) (1.19 ± 0.20 to 1.36 ± 0.29), HDL2-C (0.24 ± 0.08 to 0.28 ± 0.11), HDL3-C (0.94 ± 0.14 to 1.08 ± 0.20), and non-HDL-C (3.88 ± 1.24 to 4.37 ± 1.38) were significantly elevated with exercise after the HR beef diet, but not after LR and SS diets. Thus, in healthy, untrained men the dietary beef MUFA:SFA ratio affects the blood lipid response to a single session of aerobic exercise. PMID:27632917

  5. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids

    PubMed Central

    Kim, Ki-Hyun; Nielsen, Peter E.; Glazer, Peter M.

    2007-01-01

    Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in mammalian cells. However, the utility of TFOs is limited by the requirement for homopurine stretches in the target duplex DNA. Here, we report the use of pseudo-complementary peptide nucleic acids (pcPNAs) for intracellular gene targeting at mixed sequence sites. Due to steric hindrance, pcPNAs are unable to form pcPNA–pcPNA duplexes but can bind to complementary DNA sequences by Watson–Crick pairing via double duplex-invasion complex formation. We show that psoralen-conjugated pcPNAs can deliver site-specific photoadducts and mediate targeted gene modification within both episomal and chromosomal DNA in mammalian cells without detectable off-target effects. Most of the induced psoralen-pcPNA mutations were single-base substitutions and deletions at the predicted pcPNA-binding sites. The pcPNA-directed mutagenesis was found to be dependent on PNA concentration and UVA dose and required matched pairs of pcPNAs. Neither of the individual pcPNAs alone had any effect nor did complementary PNA pairs of the same sequence. These results identify pcPNAs as new tools for site-specific gene modification in mammalian cells without purine sequence restriction, thereby providing a general strategy for designing gene targeting molecules. PMID:17977869

  6. Conceptual Model of Uranium in the Vadose Zone for Acidic and Alkaline Wastes Discharged at the Hanford Site Central Plateau

    SciTech Connect

    Truex, Michael J.; Szecsody, James E.; Qafoku, Nikolla; Serne, R. Jeffrey

    2014-09-01

    Historically, uranium was disposed in waste solutions of varying waste chemistry at the Hanford Site Central Plateau. The character of how uranium was distributed in the vadose zone during disposal, how it has continued to migrate through the vadose zone, and the magnitude of potential impacts on groundwater are strongly influenced by geochemical reactions in the vadose zone. These geochemical reactions can be significantly influenced by the disposed-waste chemistry near the disposal location. This report provides conceptual models and supporting information to describe uranium fate and transport in the vadose zone for both acidic and alkaline wastes discharged at a substantial number of waste sites in the Hanford Site Central Plateau. The conceptual models include consideration of how co-disposed acidic or alkaline fluids influence uranium mobility in terms of induced dissolution/precipitation reactions and changes in uranium sorption with a focus on the conditions near the disposal site. This information, when combined with the extensive information describing uranium fate and transport at near background pH conditions, enables focused characterization to support effective fate and transport estimates for uranium in the subsurface.

  7. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  8. Analysis of the five glycosylation sites of human alpha 1-acid glycoprotein.

    PubMed Central

    Treuheit, M J; Costello, C E; Halsall, H B

    1992-01-01

    Orosomucoid (OMD) contains complex bi-, tri- and tetra-antennary glycan chains. Subfractionation of OMD into three molecular variants using concanavalin A lectin chromatography is based on variations in these complex structures. Standard h.p.l.c. profiles have been developed to analyse the percentage and distribution of the glycoforms present at each glycosylation site in OMD and its molecular variants. The ability to quantify the glycoforms present at each site allows us to extend the earlier results of others and resolve the remaining questions concerning the glycan structures of these variants. Most significantly, the proportions of bi-, tri- and tetra-antennary chains differ at each site for the three molecular variants. The most strongly retained variant from concanavalin A is uniquely capable of possessing biantennary chains at all five sites, whereas the unretained variant is completely devoid of biantennary chains. Only glycosylation site II of the five present is 100% biantennary in the retained and weakly retained variants. In addition, the two gene products of OMD were differentially glycosylated. Molecular masses of the glycoforms were verified by matrix-assisted u.v. laser desorption mass spectrometry. On the basis of the site distribution of oligosaccharides in the variants, efforts were made to understand the factors that control the processing of the carbohydrate chains in OMD. The results indicate that the 'site-directed' model of processing offers the most consistent explanation for the structures seen at the individual glycosylation sites of OMD. PMID:1567356

  9. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations.

    PubMed

    Poongavanam, Vasanthanathan; Madala, Praveen K; Højland, Torben; Veedu, Rakesh N

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  10. Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules

    SciTech Connect

    Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

    2015-08-07

    Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.

  11. [Identification of rat and human hemoglobin acetilation sites after its interaction with acetylsalicylic acid].

    PubMed

    Shreĭner, E V; Murashko, E A; Dubrovskiĭ, Ia D; Krasnov, N V; Podol'skaia, E P; Babakov, V N

    2012-01-01

    The possibility of interaction of 0.1 mg/mL acetylsalicylic acid with purified human and rat globin in vitro during 24 h at 37 degrees C was investigated. The rat globin can be modified with acetylsalicylic acid on aminoacid residues K-17, K-57, K-91, K-140 in alpha subunit as well as on K-18, K-77 in beta subunit. The human globin can be modified with acetylsalicylic acid on aminoacid residues K-17, K-41, K-57 and K-91 in alpha subunit as well as on K-18, K-96 and K- 133 in beta subunit. We identified of acetetylated lysines K-17 and K-57 in alpha subunit of human hemoglobin after incubation whole blood with 0.1 mg/mL acetylsalicylic acid during 3 h.

  12. Investigation into the use of cement kiln dust in high density sludge (HDS) treatment of acid mine water.

    PubMed

    Mackie, Allison L; Walsh, Margaret E

    2015-11-15

    The purpose of this study was to investigate the potential to replace lime with cement kiln dust (CKD) in high density sludge (HDS) treatment of acid mine drainage (AMD). The bench-scale study used two water samples: AMD sampled from a lead-zinc mine with high concentrations of iron (Fe), zinc (Zn), and arsenic (As) (Fe/Zn-AMD) and a synthetic AMD solution (Syn-AMD) spiked with ferric sulfate (Fe2(SO4)3). Arsenic was found to be significantly reduced with CKD-HDS treatment of Fe/Zn-AMD compared to lime-HDS treatment, to concentrations below the stringent mine effluent discharge regulation of 0.10 mg As/L (i.e., 0.04 ± 0.02 mg/L). Both CKD- and lime-HDS treatment of the two AMD samples resulted in settled water Fe concentrations above the stringent discharge guideline of 0.3 mg Fe/L. CKD addition in the HDS process also resulted in high settled water turbidity, above typical discharge guidelines of 15 mg TSS/L. CKD-HDS treatment was found to result in significantly improved settled solids (i.e., sludge) quality compared to that generated in the lime-HDS process. HDS treatment with CKD resulted in 25-88% lower sludge volume indices, 2 to 9 times higher % wet solids, and 10 to 20 times higher % dry solids compared to lime addition. XRD and XPS testing indicated that CKD-HDS sludge consisted of mainly CaCO3 and SiO2 with Fe(3+) precipitates attached at particle surfaces. XRD and XPS testing of the lime-HDS generated sludge showed that it consisted of non-crystalline Fe oxides typical of sludge formed from precipitates with a high water concentration. Increased sedimentation rates were also found for CKD (1.3 cm/s) compared to lime (0.3 cm/s). The increased solids loading with CKD addition compared to lime addition in the HDS process was suggested to both promote surface complexation of metal precipitates with insoluble CKD particles and increase compression effects during Type IV sedimentation. These mechanisms collectively contributed to the reduced water content of

  13. Investigation into the use of cement kiln dust in high density sludge (HDS) treatment of acid mine water.

    PubMed

    Mackie, Allison L; Walsh, Margaret E

    2015-11-15

    The purpose of this study was to investigate the potential to replace lime with cement kiln dust (CKD) in high density sludge (HDS) treatment of acid mine drainage (AMD). The bench-scale study used two water samples: AMD sampled from a lead-zinc mine with high concentrations of iron (Fe), zinc (Zn), and arsenic (As) (Fe/Zn-AMD) and a synthetic AMD solution (Syn-AMD) spiked with ferric sulfate (Fe2(SO4)3). Arsenic was found to be significantly reduced with CKD-HDS treatment of Fe/Zn-AMD compared to lime-HDS treatment, to concentrations below the stringent mine effluent discharge regulation of 0.10 mg As/L (i.e., 0.04 ± 0.02 mg/L). Both CKD- and lime-HDS treatment of the two AMD samples resulted in settled water Fe concentrations above the stringent discharge guideline of 0.3 mg Fe/L. CKD addition in the HDS process also resulted in high settled water turbidity, above typical discharge guidelines of 15 mg TSS/L. CKD-HDS treatment was found to result in significantly improved settled solids (i.e., sludge) quality compared to that generated in the lime-HDS process. HDS treatment with CKD resulted in 25-88% lower sludge volume indices, 2 to 9 times higher % wet solids, and 10 to 20 times higher % dry solids compared to lime addition. XRD and XPS testing indicated that CKD-HDS sludge consisted of mainly CaCO3 and SiO2 with Fe(3+) precipitates attached at particle surfaces. XRD and XPS testing of the lime-HDS generated sludge showed that it consisted of non-crystalline Fe oxides typical of sludge formed from precipitates with a high water concentration. Increased sedimentation rates were also found for CKD (1.3 cm/s) compared to lime (0.3 cm/s). The increased solids loading with CKD addition compared to lime addition in the HDS process was suggested to both promote surface complexation of metal precipitates with insoluble CKD particles and increase compression effects during Type IV sedimentation. These mechanisms collectively contributed to the reduced water content of

  14. High-Resolution Sedimentation Rates at IODP Sites U1424 and U1427 since the late Pliocene from spectral-analyzing GRA Bulk Density and RGB Color Profiles

    NASA Astrophysics Data System (ADS)

    Gorgas, Thomas; Irino, Tomohisa; Tada, Ryuji

    2016-04-01

    Sedimentation Rates (SRs) for IODP Sites U1424 (lat/lon coordinates: 40o11.40'N, 138o13.90'E; water depth: 2808 mbsl) and U1427 (lat/lon coordinates: 35o57.92'N, 134o26.06'E; water depth: 330 mbsl) were calculated by performing spectral analysis in the depth domain on both RGB color and Gamma-Ray-Attenuation (GRA) bulk density data. Inversion and integration of SRs versus depth from spectral analysis yielded detailed SR profiles in both time and depth domains. Our results show a greater variability in calculated SRs and differed from those established through coarse-scaled biostratigraphy and paleo-magnetic data. Our data analyses produces pulses of distinct high SRs for certain depth/age intervals at both sites, with time lags for such features possibly due to variable oceanographic conditions near-shore for Site U1427 versus those at Site U1424 further offshore. Both GRA and RGB profiles reveal a distinct periodicity in the waveband of Milankovitch cycles and other prominent periodicities in the 10-to-1ky period range. This observation suggests climate variabilities and trends in SRs responding to insolation patterns during the past 1 Myr at both sites and extending to 4.5 Myr for Site U1424. With only few identified eccentricity (100ky) cycle segments throughout the entire normalized spectral amplitude profile, our high-resolution Age-Depth model was tuned to obliquity (41ky) and precessional (19-23ky) cycles to achieving a strong fit with corresponding low-resolution models based on biostratigraphy, paleo-magnetic and, at least for Site U1424, augmenting volcanostratigraphy data. According to our Age-Depth models, relatively low SRs occur when evolutive amplitude spectra are dominated by periods in the range of obliquity and eccentricity. In contrast, significant SR peaks at both sites often occur when strong precessional amplitudes coexist with all other cycles. Lower SRs at Site U1424 have been interpreted to reflect a decrease in diatom flux and relative

  15. The impact of acid treatment on soilwater chemistry at the Humex site

    SciTech Connect

    Vogt, R.D.; Ranneklev, S.B.; Mykkelbost, T.C. )

    1994-01-01

    The effects of acid treatment on soil water dissolved organic carbon (DOC) and inorganic chemistry are being monitored at the Humic Lake Acidification Experiment (HUMEX) in western Norway. The HUMEX project involves artificial acidification of half of a dystrophic lake and the corresponding drainage basin. Soil water chemistry data were collected from 30 monitoring lysimeters and 130 grid lysimeters. The samples from the monitoring lysimeters were collected before and, for a period of two years, after the onset of acid treatment. Operationally-defined functional fractions of DOC showed that hydrophilic (HPI) and hydrophobic (HPO) acids account for 60% to 90% of the DOC. In soils rich in DOC, the HPO acids were dominant, whereas in mineral soil horizons low in DOC, the HPI acid fractions were highest. The amount of DOC relative to labile aluminum and iron may determine the HPO/HPI acid ratio. The sulphate concentration has increased more in the treated than in the reference side. Coincident decreases in DOC and organically complexes aluminum (Al[sub 0]) concentrations were observed for surface histosol locations. The temporal and spatial variations in c(Al[sub 0]) were mainly explained by variation in c(DOC). 26 refs., 5 figs., 3 tabs.

  16. Low-cost silica, calcite and metal sulfide scale control through on-site production of sulfurous acid from H{sub 2}S or elemental sulfur

    SciTech Connect

    Gallup, D.L.; Kitz, K.

    1997-12-31

    UNOCAL Corporation currently utilizes brine pH modification technology to control scale deposition. Acids utilized in commercial operations include, sulfuric and hydrochloric. A new process reduces costs by producing acid on-site by burning hydrogen sulfide or elemental sulfur. Hydrogen sulfide in non-condensible gas emissions is reduced by oxidization to sulfurous acid. Brine or condensate is treated with sulfurous acid to control scale deposition, mitigate corrosion and improve gas partitioning in condensers.

  17. Specificity of the antibody receptor site to D-lysergamide: model of a physiological receptor for lysergic acid diethylamide.

    PubMed

    Van Vunakis, H; Farrow, J T; Gjika, H B; Levine, L

    1971-07-01

    Antibodies to D-lysergic acid have been produced in rabbits and guinea pigs and a radioimmunoassay for the hapten was developed. The specificity of this lysergamide-antilysergamide reaction was determined by competitive binding with unlabeled lysergic acid diethylamide (LSD), psychotomimetic drugs, neurotransmitters, and other compounds with diverse structures. LSD and several related ergot alkaloids were potent competitors, three to seven times more potent than lysergic acid itself. The N,N-dimethyl derivatives of several compounds, including tryptamine, 5-hydroxytryptamine, 4-hydroxytryptamine, 5-methoxytryptamine, tyramine, and mescaline, were only about ten times less effective than lysergic acid, even though these compounds lack some of the ring systems of lysergic acid. The pattern of inhibition by related compounds with various substituents suggests that the antibody receptor site recognizes structural features resembling the LSD molecule. In particular, the aromatic nucleus and the dimethylated ethylamine side chain in phenylethylamine and tryptamine derivatives may assume in solution a conformation resembling ring A and the methylated nitrogen in ring C of LSD. Among the tryptamine derivatives, a large percentage of the most potent competitors are also psychotomimetic compounds.

  18. Runoff of acidic substances that originated from atmospheric deposition on Yakushima Island, a world natural heritage site.

    PubMed

    Nagafuchi, O; Kakimoto, H; Ebise, S; Inoue, T; Koga, M

    2001-01-01

    In this paper we present monitoring data of stream waters that may reflect acidic impacts on the island as well as the rainwater qualities. The pH ranges of the river water in the Kawara streams in the western part of the island and the Yodogo stream in the central part of the island were 5.71-6.35 and 5.85-6.12 during 1992-1999, respectively. The concentrations of SO4(2-) and NO3- in the river water were lower than those in the rainwater. Many differences were observed among the sampling sites. Higher concentrations of acid substances are found in the stream waters of the western area compared to the other areas. On the other hand, sulfuric acid is the major acid in the rainwater, snow and rime ice. No differences were observed in the ion constituents of the rainwater collected in the areas. These results suggested that the densely growing canopy may play a role in holding air pollutants, and acidic substances deposited on the canopy would be discharged as a through-fall and a stem flow. Furthermore, the water mass containing high ionic substances in the western area has been held in the groundwater layer, continuously supplying the stream waters during dry weather days. On the other hand, part of the basic runoff will be diluted with a surface runoff during the rainy days. As a result, the concentrations of the ionic substances in the stream waters during rainy days decreased.

  19. A study of the source-receptor relationships influencing the acidity of precipitation collected at a rural site in France

    NASA Astrophysics Data System (ADS)

    Charron, Aurélie; Plaisance, Hervé; Sauvage, Stéphane; Coddeville, Patrice; Galloo, Jean-Claude; Guillermo, René

    In order to examine the qualitative and quantitative source-receptor relationships responsible for acid rains at a background site in France, a receptor-oriented model was applied to the precipitation data collected from 1992 to 1995. Origins of acidic and alkaline species in precipitations have been investigated. The methodology combines precipitation chemical data with air parcel backward trajectories to establish concentration field maps of likely contributing sources. Highest acidities and concentrations of sulfate and nitrate in precipitation were associated with transport from the high emission areas of central Europe. Alkaline events were associated with air masses originating from Mediterranean basin or northern Africa. The quantitative relationships between the maps of potential sources and the European emissions of SO 2 and NO x were examined performing a correlation analysis. Good correlations were found between computed concentrations of acidic species and emissions of SO 2 and NO x. Substantial seasonal variations of acidic species were revealed. The highest concentrations occurred during the warm season. These seasonal variations are the effect of change of meteorological conditions and of the strength atmospheric processes according to the season.

  20. Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico.

    PubMed

    Pompa-García, Marín; Venegas-González, Alejandro

    2016-01-01

    Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass) was estimated from a specific allometric equation for this species based on: (i) variation of intra-annual wood density and (ii) diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries. PMID:27272519

  1. Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico.

    PubMed

    Pompa-García, Marín; Venegas-González, Alejandro

    2016-01-01

    Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass) was estimated from a specific allometric equation for this species based on: (i) variation of intra-annual wood density and (ii) diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries.

  2. Temporal Variation of Wood Density and Carbon in Two Elevational Sites of Pinus cooperi in Relation to Climate Response in Northern Mexico

    PubMed Central

    Pompa-García, Marín; Venegas-González, Alejandro

    2016-01-01

    Forest ecosystems play an important role in the global carbon cycle. Therefore, understanding the dynamics of carbon uptake in forest ecosystems is much needed. Pinus cooperi is a widely distributed species in the Sierra Madre Occidental in northern Mexico and future climatic variations could impact these ecosystems. Here, we analyze the variations of trunk carbon in two populations of P. cooperi situated at different elevational gradients, combining dendrochronological techniques and allometry. Carbon sequestration (50% biomass) was estimated from a specific allometric equation for this species based on: (i) variation of intra-annual wood density and (ii) diameter reconstruction. The results show that the population at a higher elevation had greater wood density, basal area, and hence, carbon accumulation. This finding can be explained by an ecological response of trees to adverse weather conditions, which would cause a change in the cellular structure affecting the within-ring wood density profile. The influence of variations in climate on the maximum density of chronologies showed a positive correlation with precipitation and the Multivariate El Niño Southern Oscillation Index during the winter season, and a negative correlation with maximum temperature during the spring season. Monitoring previous conditions to growth is crucial due to the increased vulnerability to extreme climatic variations on higher elevational sites. We concluded that temporal variability of wood density contributes to a better understanding of environmental historical changes and forest carbon dynamics in Northern Mexico, representing a significant improvement over previous studies on carbon sequestration. Assuming a uniform density according to tree age is incorrect, so this method can be used for environmental mitigation strategies, such as for managing P. cooperi, a dominant species of great ecological amplitude and widely used in forest industries. PMID:27272519

  3. Inhibition of triacylglycerol and apoprotein B secretion and of low density lipoprotein binding in Hep G2 cells by eicosapentaenoic acid

    SciTech Connect

    Wong, S.H.; Nestel, P.J.

    1987-05-01

    The consumption of long chain polyunsaturated fatty acids of fish oils leads to profound lowering of plasma triacylglyercol (TAG) but not of plasma cholesterol. Reasons for this were investigated with the human hepatoma cell line, the Hep G2 cell. Incubations with oleic acid (OA), linoleic acid (LA) and the characteristic marine fatty acid eicosapentaenoic acid (EPA) enriched cellular TAG mass, though least with EPA. However, secretion of very low density lipoprotein (VLDL)-TAG and apoprotein B (apo B), measured from (/sup 3/H)-glycerol and (/sup 3/H)-leucine was markedly inhibited by EPA. Preincubation with LA reduced VLDL-TAG but not apo B secretion in comparison with OA which stimulated both. A possible effect on low density lipoprotein (LDL) removal was studied by measuring (/sup 125/I)-LDL binding. Preincubation with either EPA or LA inhibited the saturable binding of LDL, observed with OA and control incubations. The binding of lipoproteins containing chylomicron remnants was not affected by any of the fatty acids.

  4. CD44 Binding to Hyaluronic Acid Is Redox Regulated by a Labile Disulfide Bond in the Hyaluronic Acid Binding Site

    PubMed Central

    Kellett-Clarke, Helena; Stegmann, Monika; Barclay, A. Neil; Metcalfe, Clive

    2015-01-01

    CD44 is the primary leukocyte cell surface receptor for hyaluronic acid (HA), a component of the extracellular matrix. Enzymatic post translational cleavage of labile disulfide bonds is a mechanism by which proteins are structurally regulated by imparting an allosteric change and altering activity. We have identified one such disulfide bond in CD44 formed by Cys77 and Cys97 that stabilises the HA binding groove. This bond is labile on the surface of leukocytes treated with chemical and enzymatic reducing agents. Analysis of CD44 crystal structures reveal the disulfide bond to be solvent accessible and in the–LH hook configuration characteristic of labile disulfide bonds. Kinetic trapping and binding experiments on CD44-Fc chimeric proteins show the bond is preferentially reduced over the other disulfide bonds in CD44 and reduction inhibits the CD44-HA interaction. Furthermore cells transfected with CD44 no longer adhere to HA coated surfaces after pre-treatment with reducing agents. The implications of CD44 redox regulation are discussed in the context of immune function, disease and therapeutic strategies. PMID:26379032

  5. Site and chirality selective chemical modifications of boron nitride nanotubes (BNNTs) via Lewis acid-base interactions.

    PubMed

    Sundaram, Rajashabala; Scheiner, Steve; Roy, Ajit K; Kar, Tapas

    2015-02-01

    The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their surface. Interactions of ammonia and borane molecules, representatives of Lewis base and acid as adsorbates respectively, with matching sites at the surface of BNNTs, have been explored in the present DFT study. Adsorption energies suggest stronger chemisorption (about 15-20 kcal mol(-1)) of borane than ammonia (about 5-10 kcal mol(-1)) in both armchair (4,4) and zigzag (8,0) variants of the tube. NH3 favors (8,0) over the (4,4) tube, whereas BH3 exhibits the opposite preference, indicating some chirality dependence on acid-base interactions. A new feature of bonding is found in BH3/AlH3-BNNTs (at the edge site) complexes, where one hydrogen of the guest molecule is involved in three-center two-electron bonding, in addition to dative covalent bond (N: → B). This interaction causes a reversal of electron flow from borane/alane to BNNT, making the tube an electron acceptor, suggesting tailoring of electronic properties could be possible by varying strength of incoming Lewis acids. On the contrary, BNNTs always behave as electron acceptor in ammonia complexes. IR, XPS and NMR spectra show some characteristic features of complexes and can help experimentalists to identify not only structures of such complexes but also the location of the guest molecules and design second functionalizations. Interaction with several other neutral BF3, BCl3, BH2CH3 and ionic CH3(+) acids as well as amino group (CH3NH2 and NH2COOH) were also studied. The strongest interaction (>100 kcal mol(-1)) is found in BNNT-CH3(+) complexes and H-bonds are the only source of stability of NH2COOH-BNNT complexes. PMID:25559141

  6. Mu-opioid receptor densities are depleted in regions implicated in agonistic and sexual behavior in male European starlings (Sturnus vulgaris) defending nest sites and courting females

    PubMed Central

    Kelm, Cynthia A.; Forbes-Lorman, Robin M.; Auger, Catherine J.; Riters, Lauren V.

    2010-01-01

    Social status and resource availability can strongly influence individual behavioral responses to conspecifics. In European starlings, males that acquire nest sites sing in response to females and dominate other males. Males without nest sites sing, but not to females, and they do not interact agonistically with other males. Little is known about the neural regulation of status- or resource-appropriate behavioral responses to conspecifics. Opioid neuropeptides are implicated in birdsong and agonistic behavior, suggesting that opioids may underlie differences in the production of these behaviors in males with and without nest sites. Here, we examined densities of immunolabeled mu-opioid receptors in groups of male starlings. Males that defended nest boxes dominated other males and sang at higher rates when presented with a female than males without nest boxes, independent of testosterone concentrations. Multiple regression analyses showed nest box ownership (not agonistic behavior or singing) predicted the optical density of receptor labeling in the medial bed nucleus of stria terminalis, paraventricular nucleus, ventral tegmental area and the medial preoptic nucleus. Compared to males without nest boxes, males with nest boxes had lower densities of immunolabeled mu-opioid receptors in these regions. Singing additionally predicted the area covered by labeling in the ventral tegmental area. The results suggest that elevated opioid activity in these regions suppresses courtship and agonistic behavioral responses to conspecifics in males without nest boxes. The findings are consistent with a dynamic role for opioid receptors in adjusting social behavior so that it is appropriate given the resources available to an individual. PMID:21147175

  7. Mu-opioid receptor densities are depleted in regions implicated in agonistic and sexual behavior in male European starlings (Sturnus vulgaris) defending nest sites and courting females.

    PubMed

    Kelm, Cynthia A; Forbes-Lorman, Robin M; Auger, Catherine J; Riters, Lauren V

    2011-05-16

    Social status and resource availability can strongly influence individual behavioral responses to conspecifics. In European starlings, males that acquire nest sites sing in response to females and dominate other males. Males without nest sites sing, but not to females, and they do not interact agonistically with other males. Little is known about the neural regulation of status- or resource-appropriate behavioral responses to conspecifics. Opioid neuropeptides are implicated in birdsong and agonistic behavior, suggesting that opioids may underlie differences in the production of these behaviors in males with and without nest sites. Here, we examined densities of immunolabeled mu-opioid receptors in groups of male starlings. Males that defended nest boxes dominated other males and sang at higher rates when presented with a female than males without nest boxes, independent of testosterone concentrations. Multiple regression analyses showed nest box ownership (not agonistic behavior or singing) predicted the optical density of receptor labeling in the medial bed nucleus of stria terminalis, paraventricular nucleus, ventral tegmental area and the medial preoptic nucleus. Compared to males without nest boxes, males with nest boxes had lower densities of immunolabeled mu-opioid receptors in these regions. Singing additionally predicted the area covered by labeling in the ventral tegmental area. The results suggest that elevated opioid activity in these regions suppresses courtship and agonistic behavioral responses to conspecifics in males without nest boxes. The findings are consistent with a dynamic role for opioid receptors in adjusting social behavior so that it is appropriate given the resources available to an individual. PMID:21147175

  8. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

    PubMed

    Hasan, Md Mehedi; Zhou, Yuan; Lu, Xiaotian; Li, Jinyan; Song, Jiangning; Zhang, Ziding

    2015-01-01

    Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup) tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP)] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM) classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/.

  9. Interaction of P-aminobenzoic acid with normal and sickel erythrocyte membrane: photoaffinity labelling of the binding sites

    SciTech Connect

    Premachandra, B.R.

    1986-03-05

    Electron microscopic studies revealed that P-Amino benzoic acid (PABA) could prevent eichinocytosis of red cells in vitro. Equilibrium binding studies with right side out membrane vesicles (ROV) revealed a similar number of binding sites (1.2-1.4 ..mu..mol/mg) and Kd (1.4-1.6 mM) values for both normal and sickle cell membranes. /sup 14/C-Azide analogue of PABA was synthesized as a photoaffinity label to probe its sites of interaction on the erythrocyte membranes. Competitive binding studies of PABA with its azide indicated that both the compounds share common binding sites on the membrane surface since a 20 fold excess of azide inhibited PABA binding in a linear fashion. The azide was covalently incorporated into the membrane components only upon irradiation (52-35% of the label found in the proteins and the rest in lipids). Electrophoretic analysis of photolabelled ROV revealed that the azide interacts chiefly with Band 3 protein. PABA inhibited both high and low affinity calcium (Ca) binding sites situated on either surface of the membrane in a non-competitive manner; however, Ca binding stimulated by Mg-ATP was not affected. Ca transport into inside out vesicles was inhibited by PABA; but it did not affect the calcium ATP-ase activity. The authors studies suggest that the mechanism of action of PABA is mediated by its interaction with Band 3 protein (anion channel), calcium channel and calcium binding sites of erythrocyte membrane.

  10. An active site mutant of Escherichia coli cyclopropane fatty acid synthase forms new non-natural fatty acids providing insights on the mechanism of the enzymatic reaction.

    PubMed

    E, Guangqi; Drujon, Thierry; Correia, Isabelle; Ploux, Olivier; Guianvarc'h, Dominique

    2013-12-01

    We have produced and purified an active site mutant of the Escherichia coli cyclopropane fatty acid synthase (CFAS) by replacing the strictly conserved G236 within cyclopropane synthases, by a glutamate residue, which corresponds to E146 of the homologous mycolic acid methyltransferase, Hma, producing hydroxymethyl mycolic acids. The G236E CFAS mutant had less than 1% of the in vitro activity of the wild type enzyme. We expressed the G236E CFAS mutant in an E. coli (DE3) strain in which the chromosomal cfa gene had been deleted. After extraction of phospholipids and conversion into the corresponding fatty acid methyl esters (FAMEs), we observed the formation of cyclopropanated FAMEs suggesting that the mutant retained some of the normal activity in vivo. However, we also observed the formation of new C17 methyl-branched unsaturated FAMEs whose structures were determined using GC/MS and NMR analyses. The double bond was located at different positions 8, 9 or 10, and the methyl group at position 10 or 9. Thus, this new FAMEs are likely arising from a 16:1 acyl chain of a phospholipid that had been transformed by the G236E CFAS mutant in vivo. The reaction catalyzed by this G236E CFAS mutant thus starts by the methylation of the unsaturated acyl chain at position 10 or 9 yielding a carbocation at position 9 or 10 respectively. It follows then two competing steps, a normal cyclopropanation or hydride shift/elimination events giving different combinations of alkenes. This study not only provides further evidence that cyclopropane synthases (CSs) form a carbocationic intermediate but also opens the way to CSs engineering for the synthesis of non-natural fatty acids.

  11. Benzene on Cu(111): I. Application of van der Waals-Density Functional Formalism to Determine Binding Sites and Energy Contour Map

    NASA Astrophysics Data System (ADS)

    Berland, Kristian; Einstein, T. L.; Hyldgaard, Per

    2010-03-01

    With a recently developed van der Waals density functional (vdW-DF)footnotetextM. Dion et al., Phys. Rev. Lett. 92 (2004) 246401 we study the adsorption of benzene on Cu(111).footnotetextKB, TLE, and PH, Phys. Rev. B 80 (2009) 155431 The vdW-DF inclusion of nonlocal correlations changes the relative stability of 8 high-symmetry binding-position options and increases the adsorption energy by over an order of magnitude, achieving good agreement with experiment. The metallic surface state survives benzene adsorption. From a contour plot of the potential energy, we find that benzene can move almost freely along a honeycomb web of ``corridors" linking fcc and hcp sites via bridge sites, consistent with the low diffusion barrier in experiment.

  12. Analysis of a nucleotide-binding site of 5-lipoxygenase by affinity labelling: binding characteristics and amino acid sequences.

    PubMed Central

    Zhang, Y Y; Hammarberg, T; Radmark, O; Samuelsson, B; Ng, C F; Funk, C D; Loscalzo, J

    2000-01-01

    5-Lipoxygenase (5LO) catalyses the first two steps in the biosynthesis of leukotrienes, which are inflammatory mediators derived from arachidonic acid. 5LO activity is stimulated by ATP; however, a consensus ATP-binding site or nucleotide-binding site has not been found in its protein sequence. In the present study, affinity and photoaffinity labelling of 5LO with 5'-p-fluorosulphonylbenzoyladenosine (FSBA) and 2-azido-ATP showed that 5LO bound to the ATP analogues quantitatively and specifically and that the incorporation of either analogue inhibited ATP stimulation of 5LO activity. The stoichiometry of the labelling was 1.4 mol of FSBA/mol of 5LO (of which ATP competed with 1 mol/mol) or 0.94 mol of 2-azido-ATP/mol of 5LO (of which ATP competed with 0.77 mol/mol). Labelling with FSBA prevented further labelling with 2-azido-ATP, indicating that the same binding site was occupied by both analogues. Other nucleotides (ADP, AMP, GTP, CTP and UTP) also competed with 2-azido-ATP labelling, suggesting that the site was a general nucleotide-binding site rather than a strict ATP-binding site. Ca(2+), which also stimulates 5LO activity, had no effect on the labelling of the nucleotide-binding site. Digestion with trypsin and peptide sequencing showed that two fragments of 5LO were labelled by 2-azido-ATP. These fragments correspond to residues 73-83 (KYWLNDDWYLK, in single-letter amino acid code) and 193-209 (FMHMFQSSWNDFADFEK) in the 5LO sequence. Trp-75 and Trp-201 in these peptides were modified by the labelling, suggesting that they were immediately adjacent to the C-2 position of the adenine ring of ATP. Given the stoichiometry of the labelling, the two peptide sequences of 5LO were probably near each other in the enzyme's tertiary structure, composing or surrounding the ATP-binding site of 5LO. PMID:11042125

  13. Effective atomic numbers and electron densities of bacteriorhodopsin and its comprising amino acids in the energy range 1 keV-100 GeV

    NASA Astrophysics Data System (ADS)

    Ahmadi, Morteza; Lunscher, Nolan; Yeow, John T. W.

    2013-04-01

    Recently, there has been an interest in fabrication of X-ray sensors based on bacteriorhodopsin, a proton pump protein in cell membrane of Halobacterium salinarium. Therefore, a better understanding of interaction of X-ray photons with bacteriorhodopsin is required. We use WinXCom program to calculate the mass attenuation coefficient of bacteriorhodopsin and its comprising amino acids for photon energies from 1 keV to 100 GeV. These amino acids include alanine, arginine, asparagine, aspartic acid, glutamine, glutamic acid, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, Asx1, Asx2, Glx1 and Glx2. We then use that data to calculate effective atomic number and electron densities for the same range of energy. We also emphasize on two ranges of energies (10-200 keV and 1-20 MeV) in which X-ray imaging and radiotherapy machines work.

  14. Mosquito control in Dar es Salaam. II. Impact of expanded polystyrene beads and pyriproxyfen treatment of breeding sites on Culex quinquefasciatus densities.

    PubMed

    Chavasse, D C; Lines, J D; Ichimori, K; Majala, A R; Minjas, J N; Marijani, J

    1995-04-01

    In two contrasting areas of Dar es Salaam (Ilala and Mikocheni) all enclosed breeding sites of Culex quinquefasciatus, such as latrines and septic tanks, were treated with a floating layer of expanded polystyrene beads. 7 months later checks in both study areas revealed only one site (from which the polystyrene had been removed during emptying) containing immature stages of Cx quinquefasciatus. Open breeding sites such as areas of flooded land and blocked drains were treated with pyriproxyfen (an insect growth regulator) at a concentration of 0.1 ppm. Emergence of Cx quinquefasciatus adults from these sites was inhibited for 4 weeks during the rainy season and for up to 11 weeks during the dry season. The problem of mosquito breeding sites caused by bathroom sullage water was addressed through a combination of health education and indirect pressure from the Urban Malaria Control Project (UMCP) via local community leaders. Households responsible for these sites were encouraged to eliminate them by diverting the water into an enclosed drainage structure, usually a pit latrine. After two weekly visits 64.7% of households had complied and 93.4% had complied after five visits. 5 months later, only 15.7% had reverted to allowing sullage water to collect into puddles. Densities of Cx quinquefasciatus adults dropped by 76.7% in Mikocheni and by 46.2% in Ilala following intervention, but increased by 84.9% and 25.6% in two untreated comparison areas. The reasons for differential success of the combined interventions in the two treated areas are discussed.

  15. Identification of Rosmarinic Acid-Adducted Sites in Meat Proteins in a Gel Model under Oxidative Stress by Triple TOF MS/MS.

    PubMed

    Tang, Chang-Bo; Zhang, Wan-Gang; Wang, Yao-Song; Xing, Lu-Juan; Xu, Xing-Lian; Zhou, Guang-Hong

    2016-08-24

    Triple TOF MS/MS was used to identify adducts between rosmarinic acid (RosA)-derived quinones and meat proteins in a gel model under oxidative stress. Seventy-five RosA-modified peptides responded to 67 proteins with adduction of RosA. RosA conjugated with different amino acids in proteins, and His, Arg, and Lys adducts with RosA were identified for the first time in meat. A total of 8 peptides containing Cys, 14 peptides containing His, 48 peptides containing Arg, 64 peptides containing Lys, and 5 peptides containing N-termini that which participated in adduction reaction with RosA were identified, respectively. Seventy-seven adduction sites were subdivided into all adducted proteins including 2 N-terminal adduction sites, 3 Cys adduction sites, 4 His adduction sites, 29 Arg adduction sites, and 39 Lys adduction sites. Site occupancy analyses showed that approximately 80.597% of the proteins carried a single RosA-modified site, 14.925% retained two sites, 1.492% contained three sites, and the rest 2.985% had four or more sites. Large-scale triple TOF MS/MS mapping of RosA-adducted sites reveals the adduction regulations of quinone and different amino acids as well as the adduction ratios, which clarify phenol-protein adductions and pave the way for industrial meat processing and preservation. PMID:27486909

  16. Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment

    PubMed Central

    Estrada, Karol; St Pourcain, Beate; Heppe, Denise H. M.; Warrington, Nicole M.; Oei, Ling; Ring, Susan M.; Kruithof, Claudia J.; Timpson, Nicholas J.; Wolber, Lisa E.; Reppe, Sjur; Gautvik, Kaare; Grundberg, Elin; Ge, Bing; van der Eerden, Bram; van de Peppel, Jeroen; Hibbs, Matthew A.; Ackert-Bicknell, Cheryl L.; Choi, Kwangbom; Koller, Daniel L.; Econs, Michael J.; Williams, Frances M. K.; Foroud, Tatiana; Carola Zillikens, M.; Ohlsson, Claes; Hofman, Albert; Uitterlinden, André G.; Davey Smith, George; Jaddoe, Vincent W. V.; Tobias, Jonathan H.; Rivadeneira, Fernando; Evans, David M.

    2014-01-01

    Heritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (rg) and residual (re) correlations between BMD measured at the upper limbs (UL-BMD), lower limbs (LL-BMD) and skull (SK-BMD), using total-body DXA scans of ∼4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC). Point estimates of rg indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD rg = 0.78) between them, than with the skull (UL-/SK-BMD rg = 0.58 and LL-/SK-BMD rg = 0.43). Likewise, the residual correlation between BMD at appendicular sites (re = 0.55) was higher than the residual correlation between SK-BMD and BMD at appendicular sites (re = 0.20–0.24). To explore the basis for the observed differences in rg and re, genome-wide association meta-analyses were performed (n∼9,395), combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites). In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01×10−37), whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31×10−14). In addition, we report a novel association between RIN3 (previously associated with Paget's disease) and LL-BMD (rs754388: β = 0.13, SE = 0.02, P = 1.4×10−10). Our results suggest that BMD at different skeletal sites is

  17. Density functional study of electronic, charge density, and chemical bonding properties of 9-methyl-3-Thiophen-2-YI-Thieno [3,2-e] [1, 2, 4] Thriazolo [4,3-c] pyrimidine-8-Carboxylic acid ethyl ester crystals

    NASA Astrophysics Data System (ADS)

    Reshak, A. H.; Kamarudin, H.; Alahmed, Z. A.; Auluck, S.; Chyský, Jan

    2014-06-01

    A comprehensive theoretical density functional investigation of the electronic crystal structure, chemical bonding, and the electron charge densities of 9-Methyl-3-Thiophen-2-YI-Thieno [3, 2-e] [1, 2, 4] Thriazolo [4,3-c] Pyrimidine-8-Carboxylic Acid Ethyl Ester (C15H12N4O2S2) is performed. The density of states at Fermi level equal to 5.50 (3.45) states/Ry cell, and the calculated bare electronic specific heat coefficient is found to be 0.95 (0.59) mJ/mole-K2 for the local density approximation (Engel-Vosko generalized gradient approximation). The electronic charge density space distribution contours in (1 0 0) and (1 1 0) planes were calculated. We find that there are two independent molecules (A and B) in the asymmetric unit exhibit intramolecular C-H…O, C-H…N interactions. This intramolecular interaction is different in molecules A and B, where A molecule show C-H…O interaction while B molecule exhibit C-H…N interaction. We should emphasis that there is π-π interaction between the pyrimidine rings of the two neighbors B molecules gives extra strengths and stabilizations to the superamolecular structure. The calculated distance between the two neighbors pyrimidine rings found to be 3.345 Å, in good agreement with the measured one (3.424(1) Å).

  18. Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density

    PubMed Central

    Richards, Neil; Parker, David S.; Johnson, Lisa A.; Allen, Benjamin L.; Barolo, Scott; Gumucio, Deborah L.

    2015-01-01

    The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting us to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. We therefore developed a computational algorithm to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. We conclude that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci. PMID:26710299

  19. Gas/particle partitioning of low-molecular-weight dicarboxylic acids at a suburban site in Saitama, Japan

    NASA Astrophysics Data System (ADS)

    Bao, Linfa; Matsumoto, Mariko; Kubota, Tsutomu; Sekiguchi, Kazuhiko; Wang, Qingyue; Sakamoto, Kazuhiko

    2012-02-01

    Low-molecular-weight dicarboxylic acids (diacids) exhibit semivolatile behavior in the atmosphere, but their partitioning between the gaseous and particulate phases is still unclear. An annular denuder-filter pack system with a cyclone PM 2.5 was employed to investigate the gaseous and particulate phase concentrations of diacids, with high collection efficiency of most target compounds. Saturated diacids, unsaturated diacids, ketocarboxylic acids, and dicarbonyls were determined in gaseous and particulate samples collected from a suburban site in Japan, during 2007 summer, 2008 late-winter and early-winter. The concentrations of gaseous and particulate diacids in early-winter were lower than those in summer, but higher than those in late-winter. Individual diacid in gaseous phase showed a relatively good correlation with ambient oxidants, but a low correlation with NO gas (a primary pollutant). Particulate fraction to the total amount ( FP) of individual acid was larger in winter than in summer, and also was larger at night than in the daytime. In the same sample, individual diacid and ketocarboxylic acid had higher particulate phase occurrence ( FP > 56% in summer), whereas unsaturated diacid had higher gaseous phase occurrence ( FP < 18% in summer). In summer, gas/particle partitioning of diacids varied diurnally; FP values of oxalic and glyoxylic acids increased from their lowest values in the morning to their highest values at night, exhibiting the similar diurnal variation of relative humidity in the atmosphere. The higher humidity at night may lead to the formation of droplets in which water-soluble gaseous phases can dissolve, thus promoting gas-to-particle conversion. These results suggest that gas/particle partitioning of diacids depends not only on the concentrations in the gaseous phase by photochemical oxidation, but also on the characteristics of the atmosphere (e.g., temperature, sunlight, and relative humidity) and the aerosols (e.g., acidity

  20. Boron and calcium sites involved in indole-3-acetic Acid transport in sunflower hypocotyl segments.

    PubMed

    Tang, P M; Dela Fuente, R K

    1986-06-01

    Sunflower (Helianthus annuus L. cv Russian Mammoth) hypocotyl segments deficient in either B or Ca exhibited a higher rate of potassium leakage, compared to nondeficient segments. Potassium leakage, used here as an indication of membrane integrity, was completely reversed by the addition of H(3)BO(3) or Ca(NO(3))(2) to the incubation medium of the B-deficient or Ca-deficient hypocotyl segments, respectively. This role of B and Ca in membrane integrity, which may be important in the entry and exit of auxin in cells, is identified as the first site of action for each of these two essential elements in the basipetal secretion of auxin. A second site for B is postulated because auxin transport was not restored, even when K(+) leakage has been completely reversed to the nondeficient level, when B-deficient hypocotyls were incubated in B solution. This lack of reversibility of auxin transport implied that the incubation for 2 h in B solution was not enough to restore the auxin transport process. However, since the transfer of B-deficient seedlings to B solutions prevented further deterioration of auxin transport, these observations suggest that: (a) either an intact seedling, or a longer period of incubation of the hypocotyl in B solution, is required for the synthesis or maintenance of the functional second site for B; (b) B is probably essential in the synthesis of a ligand, which may or may not be needed to bind B, but which is essential in the basipetal transport of auxin. The second site for Ca in auxin transport, is indicated by the complete reversal of its inhibition in Ca-deficient hypocotyl, when incubated in Ca solution. The second site for Ca is thought to be directly involved in the secretion of auxin, in which Ca probably plays the role of a second messenger, as in stimulus-response coupling. The two sites for Ca can be distinguished from each other by their cation specificity. The requirement for Ca in the first site can be substituted by other divalent

  1. Histomorphological researches on large porous hydroxyapatite cylinder tubes with polylactic acid surface coating in different nonskeletal sites in vivo.

    PubMed

    Zhang, Cong; Huang, Peng; Weng, Jie; Zhi, Wei; Hu, Yonghe; Feng, Huaizhi; Yao, Yimin; Li, Shuo; Xia, Tian

    2012-05-01

    Porous hydroxyapatite (HA) ceramic cylinder tubes coated with polylactic acid on the exposed surfaces were implanted in four nonskeletal sites (omentum, peritoneum, vastus lateralis, and side of femur). Six months postoperatively, proper amount of Chinese ink was injected to dye the implanting areas. Decalcified and nondecalcified sections were observed under inverted microscope. The results showed that the soft tissues around the HA cylinder tubes in peritoneum, vastus lateralis, and side of femur groups appeared visible black. Some small blacked vascular architectures were also discernible. However in omentum group, only small number of blacked vessels existed. Histological observations indicated that vascularization and ossification occurred in peritoneum, vastus lateralis, and side of femur groups. In omentum group, there was no any sign of vascularization and ossification. A conclusion could be made in this study that excepting bones and muscles, parietal peritoneum could serve as a potential spot for culturing histoengineering hydroxyapatite (HA)-polylactic acid (PLA) ceramic bone substitutes.

  2. Histomorphological researches on large porous hydroxyapatite cylinder tubes with polylactic acid surface coating in different nonskeletal sites in vivo.

    PubMed

    Zhang, Cong; Huang, Peng; Weng, Jie; Zhi, Wei; Hu, Yonghe; Feng, Huaizhi; Yao, Yimin; Li, Shuo; Xia, Tian

    2012-05-01

    Porous hydroxyapatite (HA) ceramic cylinder tubes coated with polylactic acid on the exposed surfaces were implanted in four nonskeletal sites (omentum, peritoneum, vastus lateralis, and side of femur). Six months postoperatively, proper amount of Chinese ink was injected to dye the implanting areas. Decalcified and nondecalcified sections were observed under inverted microscope. The results showed that the soft tissues around the HA cylinder tubes in peritoneum, vastus lateralis, and side of femur groups appeared visible black. Some small blacked vascular architectures were also discernible. However in omentum group, only small number of blacked vessels existed. Histological observations indicated that vascularization and ossification occurred in peritoneum, vastus lateralis, and side of femur groups. In omentum group, there was no any sign of vascularization and ossification. A conclusion could be made in this study that excepting bones and muscles, parietal peritoneum could serve as a potential spot for culturing histoengineering hydroxyapatite (HA)-polylactic acid (PLA) ceramic bone substitutes. PMID:22344718

  3. Hydrogenation of biofuels with formic acid over a palladium-based ternary catalyst with two types of active sites.

    PubMed

    Wang, Liang; Zhang, Bingsen; Meng, Xiangju; Su, Dang Sheng; Xiao, Feng-Shou

    2014-06-01

    A composite catalyst including palladium nanoparticles on titania (TiO2) and on nitrogen-modified porous carbon (Pd/TiO2@N-C) is synthesized from palladium salts, tetrabutyl titanate, and chitosan. N2 sorption isotherms show that the catalyst has a high BET surface area (229 m(2)  g(-1)) and large porosity. XPS and TEM characterization of the catalyst shows that palladium species with different chemical states are well dispersed across the TiO2 and nitrogen-modified porous carbon, respectively. The Pd/TiO2@N-C catalyst is very active and shows excellent stability towards hydrogenation of vanillin to 2-methoxy-4-methylphenol using formic acid as hydrogen source. This activity can be attributed to a synergistic effect between the Pd/TiO2 (a catalyst for dehydrogenation of formic acid) and Pd/N-C (a catalyst for hydrogenation of vanillin) sites.

  4. Chicoric acid binds to two sites and decreases the activity of the YopH bacterial virulence factor

    PubMed Central

    Kuban-Jankowska, Alicja; Sahu, Kamlesh K.; Gorska, Magdalena; Tuszynski, Jack A.; Wozniak, Michal

    2016-01-01

    Chicoric acid (CA) is a phenolic compound present in dietary supplements with a large spectrum of biological properties reported ranging from antioxidant, to antiviral, to immunostimulatory properties. Due to the fact that chicoric acid promotes phagocytic activity and was reported as an allosteric inhibitor of the PTP1B phosphatase, we examined the effect of CA on YopH phosphatase from pathogenic bacteria, which block phagocytic processes of a host cell. We performed computational studies of chicoric acid binding to YopH as well as validation experiments with recombinant enzymes. In addition, we performed similar studies for caffeic and chlorogenic acids to compare the results. Docking experiments demonstrated that, from the tested compounds, only CA binds to both catalytic and secondary binding sites of YopH. Our experimental results showed that CA reduces activity of recombinant YopH phosphatase from Yersinia enterocolitica and human CD45 phosphatase. The inhibition caused by CA was irreversible and did not induce oxidation of catalytic cysteine. We proposed that inactivation of YopH induced by CA is involved with allosteric inhibition by interacting with essential regions responsible for ligand binding. PMID:26735581

  5. Equivalent Energy Density concept: A preliminary reexamination of a technique for equating thermal loads; Yucca Mountain Site Characterization Project

    SciTech Connect

    Ryder, E.E.

    1992-08-01

    Historical and projected inventories of spent fuel from commercial light-water nuclear reactors exhibit diverse decay characteristics and ages. This report summarizes a preliminary reexamination of a method for determining equivalent thermal loads for the range of spent fuel expected at a potential underground repository. The method, known at the Equivalent Energy Density (EED) concept, bases its equivalence criteria on the assumption that a given waste will produce worst-case thermomechanical effects equal to worst-case thermomechanical effects produced by a baseline waste, provided that the thermal energy deposited in the host rock over a specified deposition period is the same for both waste descriptions. To test this assumption, temperature histories at representative locations within the host rock were calculated using layouts defined by the EED concept and four deposition periods (20, 50, 100, and 300 years). It was found that the peak temperatures at near-field locations were best matched by the shorter deposition periods of 20 and 50 years. However, due to the sensitivity of the near-field environment to short-term canister-to-canister interactions, caution,should be used when choosing a near-field deposition period. At the location chosen to represent the far-field, a 300-year deposition period provided reasonable correspondence of peak temperature responses for all waste descriptions examined.

  6. Photochemiluminescent detection of antiradical activity. VI. Antioxidant characteristics of human blood plasma, low density lipoprotein, serum albumin and amino acids during in vitro oxidation.

    PubMed

    Popov, I; Lewin, G

    1999-01-01

    During investigation of the mechanism of therapeutic efficacy of UV (254 nm)-irradiated autologous blood, the antioxidant capacity (AC) of plasma, serum albumin, 20 amino acids, uric acid, ascorbic acid and alpha-tocopherol was measured after irradiation in vitro. AC of plasma demonstrated a biphasic time course (decrease to in a minimum (greater zero) followed by an increase). AC of uric acid, ascorbic acid and alpha-tocopherol diminished under irradiation to zero. In contrast, albumin and seven amino acids developed AC following irradiation. During the Cu(+2)-induced oxidation of low-density lipoprotein (LDL), the AC measured in a system for water-soluble substances appeared, after a lag-phase, to be comparable to that of the conjugated diene formation; AC of LDL measured in a system for lipid-soluble substances demonstrated a biphasic course. Our results suggest that: (a) the oxidized products of some amino acids and proteins acquire antiradical properties at the same time that they are being produced; (b) the biphasic character of changes of antioxidant properties of blood plasma during UV irradiation represents the overlapping of two processes: disappearing of antioxidants and acquisition of AC by (lipo)proteins; and (c) the measurement of AC of blood plasma (lipo)proteins can possibly serve to detect the existence and extent of oxidative stress in human organism.

  7. Remediation of acid mine drainage at the friendship hill national historic site with a pulsed limestone bed process

    USGS Publications Warehouse

    Sibrell, P.L.; Watten, B.; Boone, T.; ,

    2003-01-01

    A new process utilizing pulsed fluidized limestone beds was tested for the remediation of acid mine drainage at the Friendship Hill National Historic Site, in southwestern Pennsylvania. A 230 liter-per-minute treatment system was constructed and operated over a fourteen-month period from June 2000 through September 2001. Over this period of time, 50,000 metric tons of limestone were used to treat 50 million liters of water. The influent water pH was 2.5 and acidity was 1000 mg/L as CaCO3. Despite the high potential for armoring at the site, effluent pH during normal plant operation ranged from 5.7 to 7.8 and averaged 6.8. As a result of the high influent acidity, sufficient CO2 was generated and recycled to provide a net alkaline discharge with about 50 mg/L as CaCO3 alkalinity. Additions of commercial CO2 increased effluent alkalinity to as high as 300 mg/L, and could be a useful process management tool for transient high flows or acidities. Metal removal rates were 95% for aluminum (60 mg/L in influent), 50 to 90% for iron (Fe), depending on the ratio of ferrous to ferric iron, which varied seasonally (200 mg/L in influent), and <10% of manganese (Mn) (10 mg/L in influent). Ferrous iron and Mn removal was incomplete because of the high pH required for precipitation of these species. Iron removal could be improved by increased aeration following neutralization, and Mn removal could be effected by a post treatment passive settling/oxidation pond. Metal hydroxide sludges were settled in settling tanks, and then hauled from the site for aesthetic purposes. Over 450 metric tons of sludge were removed from the water over the life of the project. The dried sludge was tested by the Toxicity Characteristics Leaching Protocol (TCLP) and was found to be non-hazardous. Treatment costs were $43,000 per year and $1.08 per m 3, but could be decreased to $22,000 and $0.51 per m3 by decreasing labor use and by onsite sludge handling. These results confirm the utility of the new

  8. Technology development for phosphoric acid fuel cell powerplant (phase 2). [on site integrated energy systems

    NASA Technical Reports Server (NTRS)

    Christner, L.

    1980-01-01

    Progress is reported in the development of material, cell components, and reformers for on site integrated energy systems. Internal resistance and contact resistance were improved. Dissolved gases (O2, N2, and CO2) were found to have no effect on the electrochemical corrosion of phenolic composites. Stack performance was increased by 100 mV over the average 1979 level.

  9. Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 2: Peptide Tags and Unnatural Amino Acids.

    PubMed

    Adumeau, Pierre; Sharma, Sai Kiran; Brent, Colleen; Zeglis, Brian M

    2016-04-01

    Molecular imaging using radioisotope- or fluorophore-labeled antibodies is increasingly becoming a critical component of modern precision medicine. Yet despite this promise, the vast majority of these immunoconjugates are synthesized via the random coupling of amine-reactive bifunctional probes to lysines within the antibody, a process that can result in heterogeneous and poorly defined constructs with suboptimal pharmacological properties. In an effort to circumvent these issues, the last 5 years have played witness to a great deal of research focused on the creation of effective strategies for the site-specific attachment of payloads to antibodies. These chemoselective modification methods yield immunoconjugates that are more homogenous and better defined than constructs created using traditional synthetic approaches. Moreover, site-specifically labeled immunoconjugates have also been shown to exhibit superior in vivo behavior compared to their randomly modified cousins. The over-arching goal of this two-part review is to provide a broad yet detailed account of the various site-specific bioconjugation approaches that have been used to create immunoconjugates for positron emission tomography (PET), single photon emission computed tomography (SPECT), and fluorescence imaging. In Part 1, we covered site-specific bioconjugation techniques based on the modification of cysteine residues and the chemoenzymatic manipulation of glycans. In Part 2, we will detail two families of bioconjugation approaches that leverage biochemical tools to achieve site-specificity. First, we will discuss modification methods that employ peptide tags either as sites for enzyme-catalyzed ligations or as radiometal coordination architectures. And second, we will examine bioconjugation strategies predicated on the incorporation of unnatural or non-canonical amino acids into antibodies via genetic engineering. Finally, we will compare the advantages and disadvantages of the modification

  10. Site-Specifically Labeled Immunoconjugates for Molecular Imaging—Part 2: Peptide Tags and Unnatural Amino Acids

    PubMed Central

    Adumeau, Pierre; Sharma, Sai Kiran; Brent, Colleen; Zeglis, Brian M.

    2016-01-01

    Molecular imaging using radioisotope- or fluorophore-labeled antibodies is increasingly becoming a critical component of modern precision medicine. Yet despite this promise, the vast majority of these immunoconjugates are synthesized via the random coupling of amine-reactive bifunctional probes to lysines within the antibody, a process that can result in heterogeneous and poorly defined constructs with suboptimal pharmacological properties. In an effort to circumvent these issues, the last 5 years have played witness to a great deal of research focused on the creation of effective strategies for the site-specific attachment of payloads to antibodies. These chemoselective modification methods yield immunoconjugates that are more homogenous and better defined than constructs created using traditional synthetic approaches. Moreover, site-specifically labeled immunoconjugates have also been shown to exhibit superior in vivo behavior compared to their randomly modified cousins. The over-arching goal of this two-part review is to provide a broad yet detailed account of the various site-specific bioconjugation approaches that have been used to create immunoconjugates for positron emission tomography (PET), single photon emission computed tomography (SPECT), and fluorescence imaging. In Part 1, we covered site-specific bioconjugation techniques based on the modification of cysteine residues and the chemoenzymatic manipulation of glycans. In Part 2, we will detail two families of bioconjugation approaches that leverage biochemical tools to achieve site-specificity. First, we will discuss modification methods that employ peptide tags either as sites for enzyme-catalyzed ligations or as radiometal coordination architectures. And second, we will examine bioconjugation strategies predicated on the incorporation of unnatural or non-canonical amino acids into antibodies via genetic engineering. Finally, we will compare the advantages and disadvantages of the modification

  11. The Significance of Lewis Acid Sites for the Selective Catalytic Reduction of Nitric Oxide on Vanadium-Based Catalysts.

    PubMed

    Marberger, Adrian; Ferri, Davide; Elsener, Martin; Kröcher, Oliver

    2016-09-19

    The long debated reaction mechanisms of the selective catalytic reduction (SCR) of nitric oxide with ammonia (NH3 ) on vanadium-based catalysts rely on the involvement of Brønsted or Lewis acid sites. This issue has been clearly elucidated using a combination of transient perturbations of the catalyst environment with operando time-resolved spectroscopy to obtain unique molecular level insights. Nitric oxide reacts predominantly with NH3 coordinated to Lewis sites on vanadia on tungsta-titania (V2 O5 -WO3 -TiO2 ), while Brønsted sites are not involved in the catalytic cycle. The Lewis site is a mono-oxo vanadyl group that reduces only in the presence of both nitric oxide and NH3 . We were also able to verify the formation of the nitrosamide (NH2 NO) intermediate, which forms in tandem with vanadium reduction, and thus the entire mechanism of SCR. Our experimental approach, demonstrated in the specific case of SCR, promises to progress the understanding of chemical reactions of technological relevance.

  12. Structure and Mutagenesis of Neural Cell Adhesion Molecule Domains Evidence for Flexibility in the Placement of Polysialic Acid Attachment Sites

    SciTech Connect

    Foley, Deirdre A.; Swartzentruber, Kristin G.; Lavie, Arnon; Colley, Karen J.

    2010-11-09

    The addition of {alpha}2,8-polysialic acid to the N-glycans of the neural cell adhesion molecule, NCAM, is critical for brain development and plays roles in synaptic plasticity, learning and memory, neuronal regeneration, and the growth and invasiveness of cancer cells. Our previous work indicates that the polysialylation of two N-glycans located on the fifth immunoglobulin domain (Ig5) of NCAM requires the presence of specific sequences in the adjacent fibronectin type III repeat (FN1). To understand the relationship of these two domains, we have solved the crystal structure of the NCAM Ig5-FN1 tandem. Unexpectedly, the structure reveals that the sites of Ig5 polysialylation are on the opposite face from the FN1 residues previously found to be critical for N-glycan polysialylation, suggesting that the Ig5-FN1 domain relationship may be flexible and/or that there is flexibility in the placement of Ig5 glycosylation sites for polysialylation. To test the latter possibility, new Ig5 glycosylation sites were engineered and their polysialylation tested. We observed some flexibility in glycosylation site location for polysialylation and demonstrate that the lack of polysialylation of a glycan attached to Asn-423 may be in part related to a lack of terminal processing. The data also suggest that, although the polysialyltransferases do not require the Ig5 domain for NCAM recognition, their ability to engage with this domain is necessary for polysialylation to occur on Ig5 N-glycans.

  13. The Significance of Lewis Acid Sites for the Selective Catalytic Reduction of Nitric Oxide on Vanadium-Based Catalysts.

    PubMed

    Marberger, Adrian; Ferri, Davide; Elsener, Martin; Kröcher, Oliver

    2016-09-19

    The long debated reaction mechanisms of the selective catalytic reduction (SCR) of nitric oxide with ammonia (NH3 ) on vanadium-based catalysts rely on the involvement of Brønsted or Lewis acid sites. This issue has been clearly elucidated using a combination of transient perturbations of the catalyst environment with operando time-resolved spectroscopy to obtain unique molecular level insights. Nitric oxide reacts predominantly with NH3 coordinated to Lewis sites on vanadia on tungsta-titania (V2 O5 -WO3 -TiO2 ), while Brønsted sites are not involved in the catalytic cycle. The Lewis site is a mono-oxo vanadyl group that reduces only in the presence of both nitric oxide and NH3 . We were also able to verify the formation of the nitrosamide (NH2 NO) intermediate, which forms in tandem with vanadium reduction, and thus the entire mechanism of SCR. Our experimental approach, demonstrated in the specific case of SCR, promises to progress the understanding of chemical reactions of technological relevance. PMID:27553251

  14. Tailoring p- and n- type semiconductor through site selective oxygen doping in Cu3N: density functional studies

    NASA Astrophysics Data System (ADS)

    Sahoo, Guruprasad; Kashikar, Ravi; Jain, Mahaveer K.; Nanda, B. R. K.

    2016-06-01

    Using ab initio density functional calculations, we have investigated the stability and electronic structure of pure and oxygen doped semiconducting Cu3N. The oxygen can be accommodated in the system without structural instability as the formation energy either decreases when oxygen substitutes nitrogen, or remains nearly same when oxygen occupies the interstitial position. The interstitial oxygen (OI) prefers to stabilize in the unusual charge neutral state and acts as an acceptor to make the system a p-type degenerate semiconductor. In this case the hole pockets are formed by the partially occupied OI-p states. On the other hand, oxygen substituting nitrogen (OS) stabilizes in its usual -2 charge state and acts as a donor to make the system an n-type degenerate semiconductor. The electron pockets are formed by the conducting Cu-p states. In the case of mixed doping, holes are gradually compensated by the donor electrons and an intrinsic gap is obtained for {{{Cu}}}3{{{N}}}{1-2{x}}{{{{O}}}{{S}}}2{x}{{{{O}}}{{I}}}{x} stoichiometry. Our calculations predict the nature of doping as well as optical band gap ({{E}{{g}}}{{o}{{p}}{{t}}}) variation in experimentally synthesized copper oxynitride. While interstitial doping contracts the lattice and increases the {{E}{{g}}}{{o}{{p}}{{t}}}, substitutional doping increases both lattice size and {{E}{{g}}}{{o}{{p}}{{t}}}. Mixed doping reduces {{E}{{g}}}{{o}{{p}}{{t}}}. Additionally we show that a rare intra-atomic d-p optical absorption can be realized in the pristine Cu3N as the Fermi level lies in the gap between the Cu-d dominated anti-bonding valence state and Cu-p conducting state.

  15. Tailoring p- and n- type semiconductor through site selective oxygen doping in Cu3N: density functional studies

    NASA Astrophysics Data System (ADS)

    Sahoo, Guruprasad; Kashikar, Ravi; Jain, Mahaveer K.; Nanda, B. R. K.

    2016-06-01

    Using ab initio density functional calculations, we have investigated the stability and electronic structure of pure and oxygen doped semiconducting Cu3N. The oxygen can be accommodated in the system without structural instability as the formation energy either decreases when oxygen substitutes nitrogen, or remains nearly same when oxygen occupies the interstitial position. The interstitial oxygen (OI) prefers to stabilize in the unusual charge neutral state and acts as an acceptor to make the system a p-type degenerate semiconductor. In this case the hole pockets are formed by the partially occupied OI-p states. On the other hand, oxygen substituting nitrogen (OS) stabilizes in its usual ‑2 charge state and acts as a donor to make the system an n-type degenerate semiconductor. The electron pockets are formed by the conducting Cu-p states. In the case of mixed doping, holes are gradually compensated by the donor electrons and an intrinsic gap is obtained for {{{Cu}}}3{{{N}}}{1-2{x}}{{{{O}}}{{S}}}2{x}{{{{O}}}{{I}}}{x} stoichiometry. Our calculations predict the nature of doping as well as optical band gap ({{E}{{g}}}{{o}{{p}}{{t}}}) variation in experimentally synthesized copper oxynitride. While interstitial doping contracts the lattice and increases the {{E}{{g}}}{{o}{{p}}{{t}}}, substitutional doping increases both lattice size and {{E}{{g}}}{{o}{{p}}{{t}}}. Mixed doping reduces {{E}{{g}}}{{o}{{p}}{{t}}}. Additionally we show that a rare intra-atomic d–p optical absorption can be realized in the pristine Cu3N as the Fermi level lies in the gap between the Cu-d dominated anti-bonding valence state and Cu-p conducting state.

  16. Capture and Recycling of Sortase A through Site-Specific Labeling with Lithocholic Acid.

    PubMed

    Rosen, Christian B; Kwant, Richard L; MacDonald, James I; Rao, Meera; Francis, Matthew B

    2016-07-18

    Enzyme-mediated protein modification often requires large amounts of biocatalyst, adding significant costs to the process and limiting industrial applications. Herein, we demonstrate a scalable and straightforward strategy for the efficient capture and recycling of enzymes using a small-molecule affinity tag. A proline variant of an evolved sortase A (SrtA 7M) was N-terminally labeled with lithocholic acid (LA)-an inexpensive bile acid that exhibits strong binding to β-cyclodextrin (βCD). Capture and recycling of the LA-Pro-SrtA 7M conjugate was achieved using βCD-modified sepharose resin. The LA-Pro-SrtA 7M conjugate retained full enzymatic activity, even after multiple rounds of recycling. PMID:27239057

  17. Fixed-site ion exchanger for liquid chromatographic determination of multifunctional carboxylic acids

    SciTech Connect

    Cassidy, R.M.; Elchuk, S.

    1985-03-01

    Reversed phases coated with a permanently sorbed ion exchanger and indirect UV detection have been investigated for the determination of simple and multifunctional carboxylic acids in chemical cleaning solutions. The advantages of being able to vary both the ion-exchange capacity and the hydrophobic interactions on these types of ion exchangers for the optimization of resolution and detection are illustrated, and the selection of optimum separation conditions is discussed. Dissolved iron interferes with the analysis due to photochemical, redox, and kinetic effects but good recoveries can be obtained after reduction of the iron with hydroxylamine and complexation with 1,2-diaminocyclohexanetetraacetic acid. Detection limits (3 x base line noise) for oxalate, citrate, ethylenediaminetetraacetate, and hydroxyethylenediaminetriacetate are 0.6-20 ..mu..g x mL/sup -1/ for a 20-..mu..L sample, and relative standard deviations are 3 to % in the 75-350 ..mu..g x mL/sup -1/ range. Analysis results for reactor decontamination solutions containing up to 250 ..mu..g x mL/sup -1/ of iron agree with results obtained by other techniques, and it is shown that this technique should also be useful for determination of metal ions in the samples. A determination of the above reagents in the presence of Fe(II) and Ni(II) takes 7 to 12 min after a 5 to 10 min reduction step. Cr(III) forms nonlabile complexes with ethylenediaminetetraacetic acid, and its presence will cause low results for this acid. 17 references, 4 figures, 6 tables.

  18. One site is enough: a theoretical investigation of iron-catalyzed dehydrogenation of formic Acid.

    PubMed

    Sánchez-de-Armas, Rocío; Xue, Liqin; Ahlquist, Mårten S G

    2013-09-01

    Dehydrogenation of HCO2H: The reaction mechanism for the dehydrogenation of formic acid catalyzed by a highly active and selective iron complex has been studied by DFT. The most favorable pathway shows the hydride in Fe-H complexes acting as a spectator ligand throughout the catalytic cycle. This result opens up the Fe complex for modification in order to achieve more efficient and selective catalysts. PMID:23907850

  19. Effect of Initial Population Density of Criconemella xenoplax on Reducing Sugars, Free Amino Acids, and Survival of Peach Seedlings over Time.

    PubMed

    Nyczepir, A P; Reilly, C C; Okie, W R

    1987-07-01

    Percentage of mortality, growth suppression, and changes in free amino acid and reducing sugar content in root and (or) stem tissue of Nemaguard peach seedlings were studied in the greenhouse in relation to time and eight different initial population densities (Pi) of Criconemella xenoplax. After 90 and 180 days, free amino acid content in root tissue significantly increased with increasing nematode numbers. Suppression of root volume, dry root and stem weight, height increase, plant survival, and content of reducing sugars in root tissue were detected at 180 and 270 days and following pruning. All criteria were negatively correlated with nematode Pi. Changes in growth, metabolic parameters, and survival percentage were attributed to Pi density of C. xenoplax, duration of the experiment, and nematode reproduction rate.

  20. Metal ion blockage of tritium incorporation into gamma-carboxyglutamic acid of prothrombin. Stoichiometry of gamma-carboxyglutamic acid to Gd3+ for the high affinity sites

    SciTech Connect

    Bajaj, S.P.; Saini, R.; Katz, A.; Cai, G.Z.; Maki, S.L.; Brodsky, G.L.

    1988-07-15

    Prothrombin possesses two high affinity and four low affinity gamma-carboxyglutamic acid (Gla)-dependent gadolinium binding sites. Earlier work has shown that tritium can be specifically incorporated at the gamma-carbon of Gla in proteins at pH 5. In the present work we show that inclusion of saturating concentrations of Ca2+ in nondenaturing buffer systems ranging from pH 5.5 to 8.5 prevents the exchange of tritium into all 10 Gla residues of prothrombin. Similarly, saturating concentrations of Gd3+ prevent tritium incorporation into Gla at pH 5.5. Positive cooperativity was observed for the binding of Gd3+ to human prothrombin (at pH 5.5) for the two high affinity sites (Kd congruent to 35 nM). The four low affinity sites bind Gd3+ with a Kd congruent to 5 microM. Incubation of prothrombin ranging in concentrations from 10 to 40 microM with 2 eq of Gd3+ at pH 5.5 prevents 5.7 (average of seven determinations) Gla residues from tritium incorporation. Sedimentation velocity experiments conducted at pH 5.5 indicate that prothrombin in the presence of saturating concentrations of Gd3+ polymerizes, most likely, to a trimer. Further, in the presence of 2 eq of Gd3+, calculated percent weight average concentration of monomer prothrombin is congruent to 100% at 10 microM, approximately equal to 95% at 20 microM, and congruento to 80% at 40 microM protein concentration. Thus, it appears that under conditions in which prothrombin primarily exists as a monomer, occupancy of the initial two metal binding sites by Gd3+ involves six Gla residues.

  1. Pericoronary Adipose Tissue as Storage and Supply Site for Oxidized Low-Density Lipoprotein in Human Coronary Plaques

    PubMed Central

    Uchida, Yasumi; Uchida, Yasuto; Shimoyama, Ei; Hiruta, Nobuyuki; Kishimoto, Toshihiko; Watanabe, Soichiro

    2016-01-01

    Objectives It is generally believed that low-density lipoprotein enters the vascular wall from its lumen and oxidized (oxLDL), after which it plays an important role in atherosclerosis. Because voluminous epicardial adipose tissue is a risk factor for coronary events, there is a possibility that the pericoronary adipose tissue (PCAT), which is a part of epicardial adipose tissue, acts as a risk factor by supplying oxLDL to the coronary arterial wall. The present study was performed whether PCAT stores and supplies oxLDL to the coronary wall. Methods Localization of oxLDL in PCAT and its relation to plaque morphology were examined by immunohistochemical techniques in 27 epicardial coronary arteries excised from 9 human autopsy cases. Results OxLDL deposited in all PCAT of the studied cases. The percent (%) incidence of oxLDL in the intima of 25 normal segment, 19 white plaques, 15 yellow plaques without necrotic core (NC) and 10 yellow plaques with NC, was 32, 84, 93 (p<0.05 vs normal segments and yellow plaques with NC), and 30, respectively. OxLDL deposited either in dotted or diffuse pattern. Double immunohistochemical staining revealed that the dotted oxLDL was that contained in CD68(+)-macrophages. The oxLDL-containing macrophages were observed in the interstitial space but not inside of the vasa vasorum, and they traversed PCAT, adventitia, external and internal elastic laminae, suggesting their migration towards the intima. Diffuse oxLDL deposits were observed in 17 preparations, the majority of which were co-localized with the vasa vasorum in outer or in both inner and outer halves of intima, and rarely in the inner half alone. Conclusions The results suggested that PCAT is a supply source of oxLDL to coronary intima and acts as a risk factor for coronary events, that oxLDL increasingly deposits in the intima with plaque growth and decreases after plaque maturation, and therefore molecular therapies targeting the PCAT before plaque growth could be effective

  2. A self-assembling peptide matrix used to control stiffness and binding site density supports the formation of microvascular networks in three dimensions

    PubMed Central

    Stevenson, M.D.; Piristine, H.; Hogrebe, N.J.; Nocera, T.M.; Boehm, M.W.; Reen, R.K.; Koelling, K.W.; Agarwal, G.; Sarang-Sieminski, A.L.; Gooch, K.J.

    2015-01-01

    A three-dimensional (3-D) cell culture system that allows control of both substrate stiffness and integrin binding density was created and characterized. This system consisted of two self-assembling peptide (SAP) sequences that were mixed in different ratios to achieve the desired gel stiffness and adhesiveness. The specific peptides used were KFE ((acetyl)-FKFEFKFE-CONH2), which has previously been reported not to support cell adhesion or MVN formation, and KFE-RGD ((acetyl)-GRGDSP-GG-FKFEFKFE-CONH2), which is a similar sequence that incorporates the RGD integrin binding site. Storage modulus for these gels ranged from ~60 to 6000 Pa, depending on their composition and concentration. Atomic force microscopy revealed ECM-like fiber microarchitecture of gels consisting of both pure KFE and pure KFE-RGD as well as mixtures of the two peptides. This system was used to study the contributions of both matrix stiffness and adhesiveness on microvascular network (MVN) formation of endothelial cells and the morphology of human mesenchymal stem cells (hMSC). When endothelial cells were encapsulated within 3-D gel matrices without binding sites, little cell elongation and no network formation occurred, regardless of the stiffness. In contrast, matrices containing the RGD binding site facilitated robust MVN formation, and the extent of this MVN formation was inversely proportional to matrix stiffness. Compared with a matrix of the same stiffness with no binding sites, a matrix containing RGD-functionalized peptides resulted in a ~2.5-fold increase in the average length of network structure, which was used as a quantitative measure of MVN formation. Matrices with hMSC facilitated an increased number and length of cellular projections at higher stiffness when RGD was present, but induced a round morphology at every stiffness when RGD was absent. Taken together, these results demonstrate the ability to control both substrate stiffness and binding site density within 3-D cell

  3. Experimental (FT-IR, FT-Raman, UV-Vis, 1H and 13C NMR) and computational (density functional theory) studies on 3-bromophenylboronic acid

    NASA Astrophysics Data System (ADS)

    Karabacak, M.; Kose, E.; Atac, A.; Sas, E. B.; Asiri, A. M.; Kurt, M.

    2014-11-01

    Structurally, boronic acids are trivalent boron-containing organic compounds that possess one alkyl substituent (i.e., C-Br bond) and two hydroxyl groups to fill the remaining valences on the boron atom. We studied 3-bromophenylboronic acid (3BrPBA); a derivative of boronic acid. This study includes the experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV-Vis) techniques and theoretical (DFT-density functional theory) calculations. The experimental data are recorded, FT-IR (4000-400 cm-1) and FT-Raman spectra (3500-10 cm-1) in the solid phase. 1H and 13C NMR spectra are recorded in DMSO solution. UV-Vis spectrum is recorded in the range of 200-400 nm for each solution (in ethanol and water). The theoretical calculations are computed DFT/B3LYP/6-311++G(d,p) basis set. The optimum geometry is also obtained from inside for possible four conformers using according to position of hydrogen atoms after the scan coordinate of these structures. The fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and parallel quantum solutions (PQS) program. 1H and 13C NMR chemical shifts are racked on by using the gauge-invariant atomic orbital (GIAO) method. The time-dependent density functional theory (TD-DFT) is used to find HOMO and LUMO energies, excitation energies, oscillator strengths. The density of state of the studied molecule is investigated as total and partial density of state (TDOS and PDOS) and overlap population density of state (OPDOS or COOP) diagrams have been presented. Besides, frontier molecular orbitals (FMOs), molecular electrostatic potential surface (MEPs) and thermodynamic properties are performed. At the end of this work, the results are ensured beneficial for the literature contribution.

  4. Heterogeneous Chemistry of Lipopolysaccharides with Gas-Phase Nitric Acid: Reactive Sites and Reaction Pathways.

    PubMed

    Trueblood, Jonathan V; Estillore, Armando D; Lee, Christopher; Dowling, Jacqueline A; Prather, Kimberly A; Grassian, Vicki H

    2016-08-18

    Recent studies have shown that sea spray aerosol (SSA) has a size-dependent, complex composition consisting of biomolecules and biologically derived organic compounds in addition to salts. This additional chemical complexity most likely influences the heterogeneous reactivity of SSA, as these other components will have different reactive sites and reaction pathways. In this study, we focus on the reactivity of a class of particles derived from some of the biological components of sea spray aerosol including lipopolysaccharides (LPS) that undergo heterogeneous chemistry within the reactive sites of the biological molecule. Examples of these reactions and the relevant reactive sites are proposed as follows: R-COONa(s) + HNO3(g) → NaNO3 + R-COOH and R-HPO4Na(s) + HNO3(g) → NaNO3 + R-H2PO4. These reactions may be a heterogeneous pathway not only for sea spray aerosol but also for a variety of other types of atmospheric aerosol as well.

  5. Definition of osteoporosis by bone density criteria in men: effect of using female instead of male young reference data depends on skeletal site and densitometer manufacturer.

    PubMed

    Schousboe, John T; Tanner, S Bobo; Leslie, William D

    2014-01-01

    Whether to use young male or young female reference data to calculate bone mineral density (BMD) T-scores in men remains controversial. The third National Health and Nutrition Examination and Survey (NHANES III) data show that the mean and standard deviation of femoral neck and total hip BMD is greater in young men than young women, and therefore differences in T-scores at these sites using NHANES III female vs male norms becomes less as BMD decreases. In contrast, manufacturer-specific reference databases generally assume similar standard deviations of BMD in men and women. Using NHANES III reference data for the femoral neck and total hip, respectively we found that men with T-scores of -2.5 when young male norms are used have T-scores of -2.4 and -2.3 when young female norms are used. Using manufacturer-specific reference data, we found that men with T-scores of -2.5 when young male norms are used at the femoral neck, total hip, lumbar spine, or one-third of the forearm would have T-scores ranging from -2.4 to -0.4 when young female norms are used, depending on skeletal site and densitometer manufacturer. The change of proportions of men diagnosed with osteoporosis when young female norms are used instead of young male reference data differs substantially according to skeletal site and densitometer manufacturer.

  6. Net Endogenous Acid Production (NEAP) and Bone Mineral Density in Men and Women: The Framingham Offspring Study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the short term, bone may buffer excess acid by releasing calcium. It has been proposed that diets high in protein, which have high potential renal acid load, may contribute to low BMD. In contrast, some evidence indicates higher protein intake may be beneficial for bone health, possibly by enhanc...

  7. Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid.

    PubMed

    Dumit, Verónica I; Cortez, Néstor; Matthias Ullmann, G

    2011-07-01

    Flavin-containing reductases are involved in a wide variety of physiological reactions such as photosynthesis, nitric oxide synthesis, and detoxification of foreign compounds, including therapeutic drugs. Ferredoxin-NADP(H)-reductase (FNR) is the prototypical enzyme of this family. The fold of this protein is highly conserved and occurs as one domain of several multidomain enzymes such as the members of the diflavin reductase family. The enzymes of this family have emerged as fusion of a FNR and a flavodoxin. Although the active sites of these enzymes are very similar, different enzymes function in opposite directions, that is, some reduce oxidized nicotinamide adenine dinucleotide phosphate (NADP(+)) and some oxidize reduced nicotinamide adenine dinucleotide phosphate (NADPH). In this work, we analyze the protonation behavior of titratable residues of these enzymes through electrostatic calculations. We find that a highly conserved carboxylic acid in the active site shows a different titration behavior in different flavin reductases. This residue is deprotonated in flavin reductases present in plastids, but protonated in bacterial counterparts and in diflavin reductases. The protonation state of the carboxylic acid may also influence substrate binding. The physiological substrate for plastidic enzymes is NADP(+), but it is NADPH for the other mentioned reductases. In this article, we discuss the relevance of the environment of this residue for its protonation and its importance in catalysis. Our results allow to reinterpret and explain experimental data. PMID:21538544

  8. Impact of acid mine drainages on surficial waters of an abandoned mining site.

    PubMed

    García-Lorenzo, M L; Marimón, J; Navarro-Hervás, M C; Pérez-Sirvent, C; Martínez-Sánchez, M J; Molina-Ruiz, José

    2016-04-01

    Weathering of sulphide minerals produces a great variety of efflorescences of soluble sulphate salts. These minerals play an important role for environmental pollution, since they can be either a sink or a source for acidity and trace elements. This paper aims to characterise surface waters affected by mining activities in the Sierra Minera of Cartagena-La Union (SE, Spain). Water samples were analysed for trace metals (Zn, Cd, Pb, Cu, As and Fe), major ions (Na(+), K(+), Ca(2+) and Mg(2+)) and anions (F(-), Cl(-), NO3 (-), CO3 (2-), SO4 (2-)) concentrations and were submitted to an "evaporation-precipitation" experiment that consisted in identifying the salts resulting from the evaporation of the water aliquots sampled onsite. Mineralogy of the salts was studied using X-ray diffraction and compared with the results of calculations using VISUAL MINTEQ. The study area is heavily polluted as a result of historical mining and processing activities that has produced large amount of wastes characterised by a high trace elements content, acidic pH and containing minerals resulting from the supergene alteration of the raw materials. The mineralogical study of the efflorescences obtained from waters shows that magnesium, zinc, iron and aluminium sulphates predominate in the acid mine drainage precipitates. Minerals of the hexahydrite group have been quantified together with minerals of the rozenite group, alunogen and other phases such as coquimbite and copiapite. Calcium sulphates correspond exclusively to gypsum. In a semiarid climate, such as that of the study area, these minerals contribute to understand the response of the system to episodic rainfall events. MINTEQ model could be used for the analysis of waters affected by mining activities but simulation of evaporation gives more realistic results considering that MINTEQ does not consider soluble hydrated salts.

  9. Impact of acid mine drainages on surficial waters of an abandoned mining site.

    PubMed

    García-Lorenzo, M L; Marimón, J; Navarro-Hervás, M C; Pérez-Sirvent, C; Martínez-Sánchez, M J; Molina-Ruiz, José

    2016-04-01

    Weathering of sulphide minerals produces a great variety of efflorescences of soluble sulphate salts. These minerals play an important role for environmental pollution, since they can be either a sink or a source for acidity and trace elements. This paper aims to characterise surface waters affected by mining activities in the Sierra Minera of Cartagena-La Union (SE, Spain). Water samples were analysed for trace metals (Zn, Cd, Pb, Cu, As and Fe), major ions (Na(+), K(+), Ca(2+) and Mg(2+)) and anions (F(-), Cl(-), NO3 (-), CO3 (2-), SO4 (2-)) concentrations and were submitted to an "evaporation-precipitation" experiment that consisted in identifying the salts resulting from the evaporation of the water aliquots sampled onsite. Mineralogy of the salts was studied using X-ray diffraction and compared with the results of calculations using VISUAL MINTEQ. The study area is heavily polluted as a result of historical mining and processing activities that has produced large amount of wastes characterised by a high trace elements content, acidic pH and containing minerals resulting from the supergene alteration of the raw materials. The mineralogical study of the efflorescences obtained from waters shows that magnesium, zinc, iron and aluminium sulphates predominate in the acid mine drainage precipitates. Minerals of the hexahydrite group have been quantified together with minerals of the rozenite group, alunogen and other phases such as coquimbite and copiapite. Calcium sulphates correspond exclusively to gypsum. In a semiarid climate, such as that of the study area, these minerals contribute to understand the response of the system to episodic rainfall events. MINTEQ model could be used for the analysis of waters affected by mining activities but simulation of evaporation gives more realistic results considering that MINTEQ does not consider soluble hydrated salts. PMID:26347422

  10. Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins

    PubMed Central

    2010-01-01

    Background While occurring enzymatically in biological systems, O-linked glycosylation affects protein folding, localization and trafficking, protein solubility, antigenicity, biological activity, as well as cell-cell interactions on membrane proteins. Catalytic enzymes involve glycotransferases, sugar-transferring enzymes and glycosidases which trim specific monosaccharides from precursors to form intermediate structures. Due to the difficulty of experimental identification, several works have used computational methods to identify glycosylation sites. Results By investigating glycosylated sites that contain various motifs between Transmembrane (TM) and non-Transmembrane (non-TM) proteins, this work presents a novel method, GlycoRBF, that implements radial basis function (RBF) networks with significant amino acid pairs (SAAPs) for identifying O-linked glycosylated serine and threonine on TM proteins and non-TM proteins. Additionally, a membrane topology is considered for reducing the false positives on glycosylated TM proteins. Based on an evaluation using five-fold cross-validation, the consideration of a membrane topology can reduce 31.4% of the false positives when identifying O-linked glycosylation sites on TM proteins. Via an independent test, GlycoRBF outperforms previous O-linked glycosylation site prediction schemes. Conclusion A case study of Cyclic AMP-dependent transcription factor ATF-6 alpha was presented to demonstrate the effectiveness of GlycoRBF. Web-based GlycoRBF, which can be accessed at http://GlycoRBF.bioinfo.tw, can identify O-linked glycosylated serine and threonine effectively and efficiently. Moreover, the structural topology of Transmembrane (TM) proteins with glycosylation sites is provided to users. The stand-alone version of GlycoRBF is also available for high throughput data analysis. PMID:21034461

  11. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling

    PubMed Central

    Evans, Eric G.B.; Millhauser, Glenn L.

    2016-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain “K1,” and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron–electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite

  12. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling.

    PubMed

    Evans, Eric G B; Millhauser, Glenn L

    2015-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents

  13. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling.

    PubMed

    Evans, Eric G B; Millhauser, Glenn L

    2015-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents

  14. Trans-9-octadecenoic acid is biologically neutral and does not regulate the low density lipoprotein receptor as the cis isomer does in the hamster.

    PubMed

    Woollett, L A; Daumerie, C M; Dietschy, J M

    1994-09-01

    The concentration of cholesterol carried in low density lipoproteins (LDL-C) is primarily determined by the rate at which LDL-C is produced (Jt) and the rate at which the liver takes up this particle through receptor-dependent transport (Jm). The accumulation of specific dietary fatty acids in the liver profoundly alters these kinetic parameters and will either increase hepatic receptor activity or further suppress Jm, depending upon the particular fatty acid that enriches the various lipid pools. This study tests the thesis that the cellular effects of each fatty acid are determined by the ability of that lipid to act as an effective substrate for cholesteryl ester formation by examining the metabolic effects of either cis-9-octadecenoic acid (18:1(9c)), the preferred substrate for esterification, or trans-9-octadecenoic acid (18:1(9t)), a poor substrate for this reaction. When fed to hamsters for 30 days, the steady-state concentration of cholesteryl esters was markedly increased by the 18:1(9c), as compared to the 18:1(9t), compound. In animals receiving the 18:1(9c) fatty acid, hepatic receptor activity was significantly increased, LDL-C production was suppressed, and the steady-state LDL-C concentration was reduced. In contrast, the 18:1(9t) fatty acid did not significantly alter Jm, Jt, or the plasma LDL-C level from those values found in the control animals fed an isocaloric amount of a biologically neutral fatty acid, octanoic acid. Despite these different effects on the parameters of LDL metabolism, neither the cis nor trans fatty acid altered net cholesterol delivery to the liver from de novo sterol synthesis in any tissue in the body or from uptake of dietary cholesterol across the intestine. Therefore, these studies provide strong support for the thesis that fatty acids exert regulatory effects on hepatic LDL receptor activity by altering the distribution of cholesterol in the hepatocyte between a putative regulatory pool and the inert pool of

  15. Beneficial Effects of Omega-3 Fatty Acids on Low Density Lipoprotein Particle Size in Patients with Type 2 Diabetes Already under Statin Therapy.

    PubMed

    Lee, Myung Won; Park, Jeong Kyung; Hong, Jae Won; Kim, Kwang Joon; Shin, Dong Yeob; Ahn, Chul Woo; Song, Young Duk; Cho, Hong Keun; Park, Seok Won; Lee, Eun Jig

    2013-06-01

    Beyond statin therapy for reducing low density lipoprotein cholesterol (LDL-C), additional therapeutic strategies are required to achieve more optimal reduction in cardiovascular risk among diabetic patients with dyslipidemia. To evaluate the effects and the safety of combined treatment with omega-3 fatty acids and statin in dyslipidemic patients with type 2 diabetes, we conducted a randomized, open-label study in Korea. Patients with persistent hypertriglyceridemia (≥200 mg/dL) while taking statin for at least 6 weeks were eligible. Fifty-one patients were randomized to receive either omega-3 fatty acid 4, 2 g, or no drug for 8 weeks while continuing statin therapy. After 8 weeks of treatment, the mean percentage change of low density lipoprotein (LDL) particle size and triglyceride (TG) level was greater in patients who were prescribed 4 g of omega-3 fatty acid with statin than in patients receiving statin monotherapy (2.8%±3.1% vs. 2.3%±3.6%, P=0.024; -41.0%±24.1% vs. -24.2%±31.9%, P=0.049). Coadministration of omega-3 fatty acids with statin increased LDL particle size and decreased TG level in dyslipidemic patients with type 2 diabetes. The therapy was well tolerated without significant adverse effects.

  16. The role of citric acid and ascorbic acid in morphology control of palladium nanocrystals: A molecular dynamics and density functional theory study

    NASA Astrophysics Data System (ADS)

    Yue, Jeffrey; Du, Zheng; Shao, Minhua

    2016-08-01

    The effect of surfactants on the synthesis of shape-controlled palladium (Pd) nanocrystals was studied using computational simulation methods. We found that the functional groups in surfactant molecules played an important role in the specific adsorption on Pd surfaces. Citric acid and ascorbic acid were found to be preferentially adsorbed onto Pd(1 1 1) and (1 0 0) planes resulting in the formation of octahedral and cubic nanocrystals, respectively.

  17. Element mobility during pyrite weathering: implications for acid and heavy metal pollution at mining-impacted sites

    NASA Astrophysics Data System (ADS)

    Lu, Long; Wang, Rucheng; Chen, Fanrong; Xue, Jiyue; Zhang, Peihua; Lu, Jianjun

    2005-11-01

    Based on back scattered electron images and electron micro-probe analysis results, four alteration layers, including a transition layer, a reticulated ferric oxide layer, a nubby ferric oxide layer and a cellular ferric oxide layer, were identified in the naturally weathering products of pyrite. These layers represent a progressive alteration sequence of pyrite under weathering conditions. The cellular ferric oxide layer correlates with the strongest weathering phase and results from the dissolution of nubby ferric oxide by acidic porewater. Leaching coefficient was introduced to better express the response of element mobility to the degree of pyrite weathering. Its variation shows that the mobility of S, Co and Bi is stronger than As, Cu and Zn. Sulfur in pyrite is oxidized to sulfuric acid and sulfate that are basically released into to porewater, and heavy metals Co and Bi are evidently released by acid dissolution. As, Cu and Zn are enriched in ferric oxide by adsorption and by co-precipitation, but they would re-release to the environment via desorption or dissolution when porewater pH becomes low enough. Consequently, Co, Bi, As, Cu and Zn may pose a substantial impact on water quality. Considering that metal mobility and its concentration in mine waste are two important factors influencing heavy metal pollution at mining-impacted sites, Bi and Co are more important pollutants in this case.

  18. DNA adducts of aristolochic acid II: total synthesis and site-specific mutagenesis studies in mammalian cells

    PubMed Central

    Attaluri, Sivaprasad; Bonala, Radha R.; Yang, In-Young; Lukin, Mark A.; Wen, Yujing; Grollman, Arthur P.; Moriya, Masaaki; Iden, Charles R.; Johnson, Francis

    2010-01-01

    Aristolochic acids I and II (AA-I, AA-II) are found in all Aristolochia species. Ingestion of these acids either in the form of herbal remedies or as contaminated wheat flour causes a dose-dependent chronic kidney failure characterized by renal tubulointerstitial fibrosis. In ∼50% of these cases, the condition is accompanied by an upper urinary tract malignancy. The disease is now termed aristolochic acid nephropathy (AAN). AA-I is largely responsible for the nephrotoxicity while both AA-I and AA-II are genotoxic. DNA adducts derived from AA-I and AA-II have been isolated from renal tissues of patients suffering from AAN. We describe the total synthesis, de novo, of the dA and dG adducts derived from AA-II, their incorporation site-specifically into DNA oligomers and the splicing of these modified oligomers into a plasmid construct followed by transfection into mouse embryonic fibroblasts. Analysis of the plasmid progeny revealed that both adducts blocked replication but were still partly processed by DNA polymerase(s). Although the majority of coding events involved insertion of correct nucleotides, substantial misincorporation of bases also was noted. The dA adduct is significantly more mutagenic than the dG adduct; both adducts give rise, almost exclusively, to misincorporation of dA, which leads to AL-II-dA→T and AL-II-dG→T transversions. PMID:19854934

  19. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site.

    PubMed

    Bond, P L; Smriga, S P; Banfield, J F

    2000-09-01

    An unusually thick ( approximately 1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at Iron Mountain, near Redding, Calif. The slime was studied over the period of 1 year. The subaerial form of the slime distinguished it from more typical submerged streamers. Phylogenetic analysis of 16S rRNA genes revealed a diversity of sequences that were mostly novel. Nearest relatives to the majority of sequences came from iron-oxidizing acidophiles, and it appears that iron oxidation is the predominant metabolic characteristic of the organisms in the slime. The most abundant of the 16S rRNA genes detected were from organisms related to Leptospirillum species. The dominant sequence (71% of clones) may represent a new genus. Sequences within the Archaea of the Thermoplasmales lineage were detected. Most of these were only distantly related to known microorganisms. Also, sequences affiliating with Acidimicrobium were detected. Some of these were closely related to "Ferromicrobium acidophilus," and others were affiliated with a lineage only represented by environmental clones. Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected. The predominant metabolic feature of bacteria of this subdivision is anaerobic sulfate or metal reduction. Thus, microenvironments of low redox potential possibly exist in the predominantly oxidizing environments of the slime. These results expand our knowledge of the biodiversity of acid mine drainage environments and extend our understanding of the ecology of extremely acidic systems. PMID:10966399

  20. Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data

    PubMed Central

    Muñoz, María; Alves, Estefânia; Corominas, Jordi; Folch, Josep María; Casellas, Joaquim; Noguera, Jose Luis; Silió, Luis; Fernández, Ana Isabel

    2012-01-01

    Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content. PMID

  1. Correlation for the estimation of the density of fatty acid esters fuels and its implications. A proposed Biodiesel Cetane Index.

    PubMed

    Lapuerta, Magín; Rodríguez-Fernández, José; Armas, Octavio

    2010-09-01

    Biodiesel fuels (methyl or ethyl esters derived from vegetables oils and animal fats) are currently being used as a means to diminish the crude oil dependency and to limit the greenhouse gas emissions of the transportation sector. However, their physical properties are different from traditional fossil fuels, this making uncertain their effect on new, electronically controlled vehicles. Density is one of those properties, and its implications go even further. First, because governments are expected to boost the use of high-biodiesel content blends, but biodiesel fuels are denser than fossil ones. In consequence, their blending proportion is indirectly restricted in order not to exceed the maximum density limit established in fuel quality standards. Second, because an accurate knowledge of biodiesel density permits the estimation of other properties such as the Cetane Number, whose direct measurement is complex and presents low repeatability and low reproducibility. In this study we compile densities of methyl and ethyl esters published in literature, and proposed equations to convert them to 15 degrees C and to predict the biodiesel density based on its chain length and unsaturation degree. Both expressions were validated for a wide range of commercial biodiesel fuels. Using the latter, we define a term called Biodiesel Cetane Index, which predicts with high accuracy the Biodiesel Cetane Number. Finally, simple calculations prove that the introduction of high-biodiesel content blends in the fuel market would force the refineries to reduce the density of their fossil fuels. PMID:20599853

  2. Correlation for the estimation of the density of fatty acid esters fuels and its implications. A proposed Biodiesel Cetane Index.

    PubMed

    Lapuerta, Magín; Rodríguez-Fernández, José; Armas, Octavio

    2010-09-01

    Biodiesel fuels (methyl or ethyl esters derived from vegetables oils and animal fats) are currently being used as a means to diminish the crude oil dependency and to limit the greenhouse gas emissions of the transportation sector. However, their physical properties are different from traditional fossil fuels, this making uncertain their effect on new, electronically controlled vehicles. Density is one of those properties, and its implications go even further. First, because governments are expected to boost the use of high-biodiesel content blends, but biodiesel fuels are denser than fossil ones. In consequence, their blending proportion is indirectly restricted in order not to exceed the maximum density limit established in fuel quality standards. Second, because an accurate knowledge of biodiesel density permits the estimation of other properties such as the Cetane Number, whose direct measurement is complex and presents low repeatability and low reproducibility. In this study we compile densities of methyl and ethyl esters published in literature, and proposed equations to convert them to 15 degrees C and to predict the biodiesel density based on its chain length and unsaturation degree. Both expressions were validated for a wide range of commercial biodiesel fuels. Using the latter, we define a term called Biodiesel Cetane Index, which predicts with high accuracy the Biodiesel Cetane Number. Finally, simple calculations prove that the introduction of high-biodiesel content blends in the fuel market would force the refineries to reduce the density of their fossil fuels.

  3. Acid potentiation of the capsaicin receptor determined by a key extracellular site.

    PubMed

    Jordt, S E; Tominaga, M; Julius, D

    2000-07-01

    The capsaicin (vanilloid) receptor, VR1, is a sensory neuron-specific ion channel that serves as a polymodal detector of pain-producing chemical and physical stimuli. The response of VR1 to capsaicin or noxious heat is dynamically potentiated by extracellular protons within a pH range encountered during tissue acidosis, such as that associated with arthritis, infarction, tumor growth, and other forms of injury. A molecular determinant for this important physiological activity was localized to an extracellular Glu residue (E600) in the region linking the fifth transmembrane domain with the putative pore-forming region of the channel. We suggest that this residue serves as a key regulatory site of the receptor by setting sensitivity to other noxious stimuli in response to changes in extracellular proton concentration. We also demonstrate that protons, vanilloids, and heat promote channel opening through distinct pathways, because mutations at a second site (E648) selectively abrogate proton-evoked channel activation without diminishing responses to other noxious stimuli. Our findings provide molecular evidence for stimulus-specific steps in VR1 activation and offer strategies for the development of novel analgesic agents. PMID:10859346

  4. Protein engineering of alcohol dehydrogenase--1. Effects of two amino acid changes in the active site of yeast ADH-1.

    PubMed

    Murali, C; Creaser, E H

    1986-01-01

    One of the promises held out by protein engineering is the ability to alter predictably the properties of an enzyme to enable it to find new substrates or catalyse existing substrates more efficiently, such manipulations being of interest both enzymologically and, potentially, industrially. It has been postulated that in yeast alcohol dehydrogenase (YADH-1) certain amino acids such as Trp 93 and Thr 48 constrict the active site due to their bulky side chains and thus impede catalysis of molecules larger than ethanol. To study effects of enlarging the active site we have made two changes into YADH-1, replacing Trp 93 with Phe and Thr 48 with Ser. Kinetic experiments showed that this enzyme had marked increases in reaction velocity for the n-alcohols propanol, butanol, pentanol, hexanol, heptanol, octanol and cinnamyl alcohol compared to the parent, agreeing with the prediction that expanding the active site should facilitate the oxidation of larger alcohols. The substrate affinities were slightly reduced in the altered enzyme, possibly due to its having reduced hydrophobicity at Phe 93.

  5. Isolation and properties of the acid site-specific endonuclease from mature eggs of the sea urchin Strongylocentrotus intermedius

    SciTech Connect

    Sibirtsev, Yu.T.; Konechnyi, A.A.; Rasskazov, V.A.

    1986-01-10

    An acid site-specific endonuclease has been detected in mature sea urchin eggs and cells of embryos at early stages of differentiation. Fractionation with ammonium sulfate, followed by chromatography on columns with DEAE, phosphocellulose, and hydroxyapatite resulted in an 18,000-fold purification. The molecular weight of the enzyme was determined at approx. 29,000, the optimum pH 5.5. The activity of the enzyme does not depend on divalent metal ions, EDTA, ATP, and tRNA, but it is modulated to a substantial degree by NaCl. The maximum rate of cleavage of the DNA supercoil (form I) is observed at 100 mM NaCl. Increasing the NaCl concentration to 350 mM only slightly lowers the rate of cleavage of form I, yielding form II, but entirely suppresses the accumulation of form III. Restriction analysis of the products of enzymatic hydrolysis of Co1E1 and pBR322 DNA showed that at the early stages of hydrolysis the enzyme exhibits pronounced specificity for definite sites, the number of which is 12 for Co1 E1 DNA and 8 sites for pBR322 DNA.

  6. Computational Investigation of Locked Nucleic Acid (LNA) Nucleotides in the Active Sites of DNA Polymerases by Molecular Docking Simulations

    PubMed Central

    Poongavanam, Vasanthanathan; Madala, Praveen K.; Højland, Torben; Veedu, Rakesh N.

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5′-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3′-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  7. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections

    PubMed Central

    Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T. G.; Hendriks, Wiljan J. A. J.; Cortés, Jesús M.; Pulido, Rafael

    2016-01-01

    Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

  8. The role of amino acid residues in the active site of L-methionine γ-lyase from Pseudomonas putida.

    PubMed

    Fukumoto, Mitsuki; Kudou, Daizou; Murano, Shouko; Shiba, Tomoo; Sato, Dan; Tamura, Takashi; Harada, Shigeharu; Inagaki, Kenji

    2012-01-01

    Cys116, Lys240*, and Asp241* (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we found that substitution of Cys116 for His led to a drastic increase in activity toward L-cysteine and a decrease in that toward L-methionine. In this study, we examined some properties of the C116H mutant by kinetic analysis and 3D structural analysis. We assumed that substitution of Cys116 for His broke the original hydrogen-bond network and that this induced a significant effect of Tyr114 as a general acid catalyst, possibly due to the narrow space in the active site. The C116H mutant acquired a novel β-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. Furthermore, we suggest that Lys240* is important for substrate recognition and structural stability and that Asp241* is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240*, and Asp241* contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL_Pp.

  9. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections.

    PubMed

    Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T G; Hendriks, Wiljan J A J; Cortés, Jesús M; Pulido, Rafael

    2016-01-01

    Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

  10. Interaction of anthranilic acid with silver nanoparticles: A Raman, surface-enhanced Raman scattering and density functional theoretical study

    NASA Astrophysics Data System (ADS)

    Chadha, Ridhima; Maiti, Nandita; Kapoor, Sudhir

    2014-11-01

    Raman and surface-enhanced Raman scattering (SERS) studies of anthranilic acid have been investigated in solid, aqueous solution and on silver colloid. Anthranilic acid plays a key role in the brain in the production of quinolinic acid which is a powerful excitant and convulsant substance. Due to its medicinal importance, the surface adsorption properties of anthranilic acid have been studied. The experimental Raman and SERS data is supported with DFT calculations using B3LYP functional with aug-cc-pvdz and LANL2DZ basis sets. The comparison of experimental and theoretical results infers that anthranilate is chemisorbed to the silver surface directly through the carboxylate group with a perpendicular orientation. The time-dependent SERS spectrum of anthranilate showed no observable change indicating no structural transformation with time. The SERS spectrum recorded at different excitation wavelengths helped in understanding the origin of the SERS mechanism.

  11. Synthesis and Site-Specific Incorporation of Red-Shifted Azobenzene Amino Acids into Proteins.

    PubMed

    John, Alford A; Ramil, Carlo P; Tian, Yulin; Cheng, Gang; Lin, Qing

    2015-12-18

    A series of red-shifted azobenzene amino acids were synthesized in moderate-to-excellent yields via a two-step procedure in which tyrosine derivatives were first oxidized to the corresponding quinonoidal spirolactones followed by ceric ammonium nitrate-catalyzed azo formation with the substituted phenylhydrazines. The resulting azobenzene-alanine derivatives exhibited efficient trans/cis photoswitching upon irradiation with a blue (448 nm) or green (530 nm) LED light. Moreover, nine superfolder green fluorescent protein (sfGFP) mutants carrying the azobenzene-alanine analogues were expressed in E. coli in good yields via amber codon suppression with an orthogonal tRNA/PylRS pair, and one of the mutants showed durable photoswitching with the LED light.

  12. Magic-angle-spinning NMR studies of acid sites in zeolite H-ZSM-5

    SciTech Connect

    Brunner, E.; Ernst, H.; Freude, D.; Froehlich, T.; Hunger, M.; Pfeifer, H. )

    1991-01-01

    {sup 1}H, {sup 13}C, {sup 27}Al, and {sup 29}Si magic-angle-spinning (MAS) NMR was used to elucidate the nature of the catalytic activity of zeolite H-ZSM-5. {sup 1}H MAS NMR of sealed samples after mild hydrothermal dealumination shows that the enhanced activity for n-hexane cracking is not due to an enhanced Bronstead acidity. The concentrations of the various OH groups and aluminous species suggest that the reason for the enhanced catalytic activity is the interaction of the n-hexane molecule with a bridging hydroxyl group and with extra-framework aluminium species, which give rise to the enhanced activity, cannot be easily removed from their positions, and are therefore immobilized by the zeolitic framework.

  13. Site-Selective Binding of Nanoparticles to Double-Stranded DNA via Peptide Nucleic Acid "Invasion"

    SciTech Connect

    Stadler, A.L.; van der Lelie, D.; Sun, D.; Maye, M. M.; Gang, O.

    2011-04-01

    We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

  14. Neurologic syndrome associated with homozygous mutation at MAG sialic acid binding site.

    PubMed

    Roda, Ricardo H; FitzGibbon, Edmond J; Boucekkine, Houda; Schindler, Alice B; Blackstone, Craig

    2016-08-01

    The MAG gene encodes myelin-associated glycoprotein (MAG), an abundant protein involved in axon-glial interactions and myelination during nerve regeneration. Several members of a consanguineous family with a clinical syndrome reminiscent of Pelizaeus-Merzbacher disease and demyelinating leukodystrophy on brain MRI were recently found to harbor a homozygous missense p.Ser133Arg MAG mutation. Here, we report two brothers from a nonconsanguineous family afflicted with progressive cognitive impairment, neuropathy, ataxia, nystagmus, and gait disorder. Exome sequencing revealed the homozygous missense mutation p.Arg118His in MAG. This Arg118 residue in immunoglobulin domain 1 is critical for sialic acid binding, providing a compelling mechanistic basis for disease pathogenesis. PMID:27606346

  15. A Wood-Waste Cover Prevents Sulphide Oxidation and Treats Acid Effluents at the East-Sullivan Mine Site

    NASA Astrophysics Data System (ADS)

    Germain, D.; Tassé, N.; Cyr, J.

    2004-05-01

    At the East Sullivan site, wood wastes covering the abandoned mine tailings impoundment prevent sulphide oxidation by creating an anoxic environment. The addition of coarse ligneous wastes favours infiltration, resulting in a water table rise. This maintains most tailings saturated and thus provides an additional protection against sulphide oxidation. Moreover, high infiltration allows a more rapid flushing of acid prone groundwater generated prior to the cover placement. Finally, the pore-waters under the cover are characterized by a strong reducing potential and high alkalinity. These conditions favour sulphate reduction and base metal precipitation as sulphides and carbonates. The restoration strategy capitalized on the alkaline and reductive properties of the waters underlying the wood-waste cover. An original treatment of acid effluents, based on the recirculation of water discharging around the impoundment through the organic cover, was implemented in 1998. In 2003, the total volume of water treated was 725 000 m3. Data gathered near the dispersal zone show that despite dispersing acid water, the groundwater pH decreases by only one unit from 7 to 6, during the recirculation period: May to October. However, alkalinity decreases from 800 to 100 mg/L-CaCO3. But it is back up to 800 mg/L the following spring, thanks to sulphate reduction. Fe2+ concentrations near the dispersal zone are maintained below 2 mg/L. Evolution of the iron mass in the surface waters suggests that the contaminated groundwater flush is completed in the north and west sectors of the impoundment; the east and south ones are expected to be recovered within 3 to 4 years. A wood-waste cover, besides limiting sulphide oxidation, can fill the role of alkaline reducing barrier for the treatment of these acidogenic waters, until a balance between acidity and alkalinity in the effluent is reached.

  16. Schiff base structured acid-base cooperative dual sites in an ionic solid catalyst lead to efficient heterogeneous knoevenagel condensations.

    PubMed

    Zhang, Mingjue; Zhao, Pingping; Leng, Yan; Chen, Guojian; Wang, Jun; Huang, Jun

    2012-10-01

    An acid-base bifunctional ionic solid catalyst [PySaIm](3)PW was synthesized by the anion exchange of the ionic-liquid (IL) precursor 1-(2-salicylaldimine)pyridinium bromide ([PySaIm]Br) with the Keggin-structured sodium phosphotungstate (Na(3) PW). The catalyst was characterized by FTIR, UV/Vis, XRD, SEM, Brunauer-Emmett-Teller (BET) theory, thermogravimetric analysis, (1)H NMR spectroscopy, ESI-MS, elemental analysis, and melting points. Together with various counterparts, [PySaIm](3)PW was evaluated in Knoevenagel condensation under solvent and solvent-free conditions. The Schiff base structure attached to the IL cation of [PySaIm](3)PW involves acidic salicyl hydroxyl and basic imine, and provides a controlled nearby position for the acid-base dual sites. The high melting and insoluble properties of [PySaIm](3)PW are relative to the large volume and high valence of PW anions, as well as the intermolecular hydrogen-bonding networks among inorganic anions and IL cations. The ionic solid catalyst [PySaIm](3)PW leads to heterogeneous Knoevenagel condensations. In solvent-free condensation of benzaldehyde with ethyl cyanoacetate, it exhibits a conversion of 95.8 % and a selectivity of 100 %; the conversion is even much higher than that (78.2 %) with ethanol as a solvent. The solid catalyst has a convenient recoverability with only a slight decrease in conversion following subsequent recyclings. Furthermore, the new catalyst is highly applicable to many substrates of aromatic aldehydes with activated methylene compounds. On the basis of the characterization and reaction results, a unique acid-base cooperative mechanism within a Schiff base structure is proposed and discussed, which thoroughly explains not only the highly efficient catalytic performance of [PySaIm](3)PW, but also the lower activities of various control catalysts.

  17. Characterization of cyclo-Acetoacetyl-L-Tryptophan Dimethylallyltransferase in Cyclopiazonic Acid Biosynthesis: Substrate Promiscuity and Site Directed Mutagenesis Studies

    PubMed Central

    Liu, Xinyu; Walsh, Christopher T.

    2009-01-01

    The fungal neurotoxin α-cyclopiazonic acid (CPA), a nanomolar inhibitor of Ca2+-ATPase with a unique pentacyclic indole tetramic acid scaffold is assembled by a three enzyme pathway CpaS, CpaD and CpaO in Aspergillus sp. We recently characterized the first pathway-specific enzyme CpaS, a hybrid two module polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) that generates cyclo-acetoacetyl-L-tryptophan (cAATrp). Here we report the characterization of the second pathway-specific enzyme CpaD that regiospecifically dimethylallylates cAATrp to form β-cyclopiazonic acid. By exploring the tryptophan and tetramate moieties of cAATrp, we demonstrate that CpaD discriminates against free Trp but accepts tryptophan-containing thiohydantoins, diketopiperazines and linear peptides as substrates for C4-prenylation and also acts as regiospecific O-dimethylallyltransferase (DMAT) on a tyrosine-derived tetramic acid. Comparative evaluation of CpaDs from A. oryzae RIB40 and A. flavus NRRL3357 indicated the importance of the N-terminal region for its activity. Sequence alignment of CpaD with eleven homologous fungal Trp-DMATs revealed five regions of conservation suggesting the presense of critical motifs that could be diagonostic for discovering additional Trp-DMATs. Subsequent site-directed mutagenesis studies identified five polar/charged residues and five tyrosine residues within these motifs that are critical for CpaD activity. This motif characerization will enable a gene probe-based approach to discover additional biosynthetic Trp-DMATs. PMID:19877600

  18. Direct conversion of bio-ethanol to isobutene on nanosized Zn(x)Zr(y)O(z) mixed oxides with balanced acid-base sites.

    PubMed

    Sun, Junming; Zhu, Kake; Gao, Feng; Wang, Chongmin; Liu, Jun; Peden, Charles H F; Wang, Yong

    2011-07-27

    We report the design and synthesis of nanosized Zn(x)Zr(y)O(z) mixed oxides for direct and high-yield conversion of bio-ethanol to isobutene (~83%). ZnO is addded to ZrO(2) to selectively passivate zirconia's strong Lewis acidic sites and weaken Brönsted acidic sites, while simultaneously introducing basicity. As a result, the undesired reactions of bio-ethanol dehydration and acetone polymerization/coking are suppressed. Instead, a surface basic site-catalyzed ethanol dehydrogenation to acetaldehyde, acetaldehyde to acetone conversion via a complex pathway including aldol-condensation/dehydrogenation, and a Brönsted acidic site-catalyzed acetone-to-isobutene reaction pathway dominates on the nanosized Zn(x)Zr(y)O(z) mixed oxide catalyst, leading to a highly selective process for direct conversion of bio-ethanol to isobutene. PMID:21682296

  19. Use of the interior cavity of the P22 capsid for site-specific initiation of atom-transfer radical polymerization with high-density cargo loading.

    PubMed

    Lucon, Janice; Qazi, Shefah; Uchida, Masaki; Bedwell, Gregory J; LaFrance, Ben; Prevelige, Peter E; Douglas, Trevor

    2012-10-01

    Virus-like particles (VLPs) have emerged as important and versatile architectures for chemical manipulation in the development of functional hybrid nanostructures. Here we demonstrate a successful site-selective initiation of atom-transfer radical polymerization reactions to form an addressable polymer constrained within the interior cavity of a VLP. Potentially, this protein-polymer hybrid of P22 and cross-linked poly(2-aminoethyl methacrylate) could be useful as a new high-density delivery vehicle for the encapsulation and delivery of small-molecule cargos. In particular, the encapsulated polymer can act as a scaffold for the attachment of small functional molecules, such as fluorescein dye or the magnetic resonance imaging (MRI) contrast agent Gd-diethylenetriaminepentacetate, through reactions with its pendant primary amine groups. Using this approach, a significant increase in the labelling density of the VLP, compared to that of previous modifications of VLPs, can be achieved. These results highlight the use of multimeric protein-polymer conjugates for their potential utility in the development of VLP-based MRI contrast agents with the possibility of loading other cargos.

  20. Radical scavenging ability of gallic acid toward OH and OOH radicals. Reaction mechanism and rate constants from the density functional theory.

    PubMed

    Marino, Tiziana; Galano, Annia; Russo, Nino

    2014-09-01

    Gallic acid is a ubiquitous compound, widely distributed in the vegetal kingdom and frequently found in the human diet. In the present work, its primary antioxidant activity has been investigated using the density functional theory (DFT), and the quantum mechanics-based test for overall free radical scavenging activity (QM-ORSA) protocol. It was found that gallic acid is a better antioxidant than the reference compound, Trolox, regardless of the polarity of the environment. In addition, gallic acid is predicted to be among the best peroxyl radical scavengers identified so far in nonpolar (lipid) media. This compound is capable of scavenging hydroxyl radicals at diffusion-limited rates, and hydroperoxyl radicals with rate constants in the order of 10(5) M(-1) s(-1). The deprotonation of gallic acid, in aqueous solution, is predicted to increase the protective action of this compound against oxidative stress. Gallic acid was also identified as a versatile scavenger, capable of rapidly deactivating a wide variety of reactive oxygen species (ROS) and reactive nitrogen species (RNS) via electron transfer at physiological pH. PMID:25119432

  1. Amino Acid Intakes Are Associated With Bone Mineral Density and Prevalence of Low Bone Mass in Women: Evidence From Discordant Monozygotic Twins.

    PubMed

    Jennings, Amy; MacGregor, Alexander; Spector, Tim; Cassidy, Aedín

    2016-02-01

    Although a higher protein intake, particularly from vegetable sources, has been shown to be associated with higher bone mineral density (BMD) the relative impact of specific amino acids on BMD and risk of osteoporosis remains to be determined. Mechanistic research suggests that a number of specific amino acids, including five nonessential amino acids--alanine, arginine, glutamic acid, glycine, and proline--may play a role in bone health, principally through improved production of insulin and insulin-like growth factor 1 and the synthesis of collagen and muscle protein. However to date, no previous studies have examined the associations between habitual intake of amino acids and direct measures of BMD and prevalence of osteoporosis or osteopenia, and no studies have examined this relationship in discordant identical twin-pairs. In these analyses of female monozygotic twin-pairs discordant for amino acid intake (n = 135), twins with higher intakes of alanine and glycine had significantly higher BMD at the spine than their co-twins with within-pair differences in spine-BMD of 0.012 g/cm(2) (SE 0.01; p = 0.039) and 0.014 g/cm(2) (SE 0.01; p = 0.026), respectively. Furthermore, in cross-sectional multivariable analyses of 3160 females aged 18 to 79 years, a higher intake of total protein was significantly associated with higher DXA-measured BMD at the spine (quartile Q4 to quartile Q1: 0.017 g/cm(2), SE 0.01, p = 0.035) and forearm (Q4 to Q1: 0.010 g/cm(2), SE 0.003, p = 0.002). Intake of six amino acids (alanine, arginine, glutamic acid, leucine, lysine, and proline) were associated with higher BMD at the spine and forearm with the strongest association observed for leucine (Q4 to Q1: 0.024 g/cm(2), SE 0.01, p = 0.007). When intakes were stratified by protein source, vegetable or animal, prevalence of osteoporosis or osteopenia was 13% to 19% lower comparing extreme quartiles of vegetable intake for five amino acids (not glutamic acid or proline). These data provide

  2. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation.

  3. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation. PMID:27264846

  4. A Mutational Analysis of Active Site Residues in trans-3-Chloroacrylic Acid Dehalogenase

    PubMed Central

    Poelarends, Gerrit J.; Serrano, Hector; Huddleston, Jamison P.; Johnson, William H.; Whitman, Christian P.

    2013-01-01

    trans -3-Chloroacrylic acid dehalogenase (CaaD) catalyzes the hydrolytic dehalogenation of trans-3-haloacrylates to yield malonate semialdehyde by a mechanism utilizing βPro-1, αArg-8, αArg-11, and αGlu-52. These residues are implicated in a promiscuous hydratase activity where 2-oxo-3-pentynoate is processed to acetopyruvate. The roles of three nearby residues (βAsn-39, αPhe-39, and αPhe-50) are unexplored. Mutants were constructed at these positions (βN39A, αF39A, αF39T, αF50A and αF50Y) and kinetic parameters determined along with those of the αR8K and αR11K mutants. Analysis indicates that αArg-8, αArg-11, and βAsn-39 are critical for dehalogenase activity whereas αArg-11 and αPhe-50 are critical for hydratase activity. Docking studies suggest structural bases for these observations. PMID:23851010

  5. Lipid content and fatty acid composition of green algae Scenedesmus obliquus grown in a constant cell density apparatus

    NASA Technical Reports Server (NTRS)

    Choi, K. J.; Nakhost, Z.; Barzana, E.; Karel, M.

    1987-01-01

    The lipids of alga Scenedesmus obliquus grown under controlled conditions were separated and fractionated by column and thin-layer chromatography, and fatty acid composition of each lipid component was studied by gas-liquid chromatography (GLC). Total lipids were 11.17%, and neutral lipid, glycolipid and phospholipid fractions were 7.24%, 2.45% and 1.48% on a dry weight basis, respectively. The major neutral lipids were diglycerides, triglycerides, free sterols, hydrocarbons and sterol esters. The glycolipids were: monogalactosyl diglyceride, digalactosyl diglyceride, esterified sterol glycoside, and sterol glycoside. The phospholipids included: phosphatidyl choline, phosphatidyl glycerol and phosphatidyl ethanolamine. Fourteen fatty acids were identified in the four lipid fractions by GLC. The main fatty acids were C18:2, C16:0, C18:3(alpha), C18:1, C16:3, C16:1, and C16:4. Total unsaturated fatty acid and essential fatty acid compositions of the total algal lipids were 80% and 38%, respectively.

  6. Varying ratios of omega-6: omega-3 fatty acids on the pre-and postmortem bone mineral density, bone ash, and bone breaking strength of laying chickens.

    PubMed

    Baird, H T; Eggett, D L; Fullmer, S

    2008-02-01

    The purpose of this study was to investigate the effects of varying ratios of n-6 to n-3 fatty acids in the diets of White Leghorn chickens on tibia bone characteristics [bone mineral density, bone mineral content (BMC), ash bone mineral content, bone morphology, and cortical thickness] and tibia bone strength parameters (ultimate force, bending stress, maximum strain, Young's modulus of elasticity, area under the curve, and moment of inertia). Seventy-five 16-wk-old female White Leghorn chickens were randomly assigned to 1 of 5 dietary ratios of n-6 to n-3 fatty acids: 47.8:1, 18.0:1, 7.6:1, 5.9:1, or 4.7:1. Corn oil was the n-6 fatty acid source, whereas flax oil provided the n-3 fatty acids. Bone density was measured on the left tibia via dual-energy x-ray absorptiometry (DXA) prior to killing and after excision. Bones were ashed in a muffle furnace at 500 degrees F. Tibia bones were broken by using a 3-point bending rig. Results showed no significant effect of diet on bone characteristics. There were no significant differences among diet groups for parameters of bone strength except cortical thickness (P < or = 0.01). Bone mineral content determined by ashing was significantly different by 9.2% (P < or = 0.0001) from BMC determined in vivo by DXA; however, there were no differences in ex vivo BMC and BMC ash, although they were highly correlated (r = 0.99, P < or = 0.0001). We concluded that there was no effect of n-3 fatty acids on tibia bone in mature White Leghorn chickens. The GE Lunar Prodigy DXA instrument significantly underestimated the in vivo BMC in chickens.

  7. Varying ratios of omega-6: omega-3 fatty acids on the pre-and postmortem bone mineral density, bone ash, and bone breaking strength of laying chickens.

    PubMed

    Baird, H T; Eggett, D L; Fullmer, S

    2008-02-01

    The purpose of this study was to investigate the effects of varying ratios of n-6 to n-3 fatty acids in the diets of White Leghorn chickens on tibia bone characteristics [bone mineral density, bone mineral content (BMC), ash bone mineral content, bone morphology, and cortical thickness] and tibia bone strength parameters (ultimate force, bending stress, maximum strain, Young's modulus of elasticity, area under the curve, and moment of inertia). Seventy-five 16-wk-old female White Leghorn chickens were randomly assigned to 1 of 5 dietary ratios of n-6 to n-3 fatty acids: 47.8:1, 18.0:1, 7.6:1, 5.9:1, or 4.7:1. Corn oil was the n-6 fatty acid source, whereas flax oil provided the n-3 fatty acids. Bone density was measured on the left tibia via dual-energy x-ray absorptiometry (DXA) prior to killing and after excision. Bones were ashed in a muffle furnace at 500 degrees F. Tibia bones were broken by using a 3-point bending rig. Results showed no significant effect of diet on bone characteristics. There were no significant differences among diet groups for parameters of bone strength except cortical thickness (P < or = 0.01). Bone mineral content determined by ashing was significantly different by 9.2% (P < or = 0.0001) from BMC determined in vivo by DXA; however, there were no differences in ex vivo BMC and BMC ash, although they were highly correlated (r = 0.99, P < or = 0.0001). We concluded that there was no effect of n-3 fatty acids on tibia bone in mature White Leghorn chickens. The GE Lunar Prodigy DXA instrument significantly underestimated the in vivo BMC in chickens. PMID:18212376

  8. Ellagic acid protects endothelial cells from oxidized low-density lipoprotein-induced apoptosis by modulating the PI3K/Akt/eNOS pathway

    SciTech Connect

    Ou, Hsiu-Chung; Lee, Wen-Jane; Lee, Shin-Da; Huang, Chih-Yang; Chiu, Tsan-Hung; Tsai, Kun-Ling; Hsu, Wen-Cheng; Sheu, Wayne Huey-Herng

    2010-10-15

    Endothelial apoptosis is a driving force in atherosclerosis development. Oxidized low-density lipoprotein (oxLDL) promotes inflammatory and thrombotic processes and is highly atherogenic, as it stimulates macrophage cholesterol accumulation and foam cell formation. Previous studies have shown that the phosphatidylinositol 3-kinase/Akt/endothelial nitric oxide synthase/nitric oxide (PI3K/Akt/eNOS/NO) pathway is involved in oxLDL-induced endothelial apoptosis. Ellagic acid, a natural polyphenol found in berries and nuts, has in recent years been the subject of intense research within the fields of cancer and inflammation. However, its protective effects against oxLDL-induced injury in vascular endothelial cells have not been clarified. In the present study, we investigated the anti-apoptotic effect of ellagic acid in human umbilical vein endothelial cells (HUVECs) exposed to oxLDL and explored the possible mechanisms. Our results showed that pretreatment with ellagic acid (5-20 {mu}M) significantly attenuated oxLDL-induced cytotoxicity, apoptotic features, and