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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. Effect of Lewis acid on the structure of a diiron dithiolate complex based on the active site of [FeFe]-hydrogenase assessed by density functional theory.

    PubMed

    Lee, Jin Woo; Jo, Won Ho

    2009-10-28

    The effect of Lewis acid on the structure and H2 productivity of a diiron dithiolate complex was investigated by using density functional theory (DFT) calculations. When a model molecule of [(CH3SH)(CO)2Fe(p)(mu-SCH2NHCH2S)Fe(d)(CO)3] was geometrically optimized, two isomers were found: one is the unrotated structure (1) with no ligand between two Fe atoms and the other is the rotated structure (1*) with one CO ligand between two Fe atoms. The energy of 1* was higher than 1 by 6.4 kcal/mol in a vacuum. DFT calculations also revealed that all Lewis acids bound to the rotated structure more strongly than to the unrotated structure, leading to the stabilization of the rotated structure. In particular, when AlCl3 is used, the rotated structure (1*/AlCl3) is more stable than the unrotated one (1/AlCl3) by 1.2 kcal/mol in a vacuum. The stabilization of the rotated structure arises from both the stronger basicity of the mu-CO ligand than the axial CO ligand and the increase of the bond strength between the mu-CO ligand and Fe(p) atom upon binding of Lewis acid to 1*. Calculation of energy barriers during electrocatalytic H2 production revealed that 1*/AlCl3 could efficiently produce H2via a chemical-electrochemical-chemical-electrochemical mechanism. The analysis of the energy level of the lowest unoccupied molecular orbital showed that 1*/AlCl3 may produce H2 at significantly lower reduction potential as compared with 1*. It is also found that the catalytic activity decreases with increasing polarity of the medium. PMID:19809728

  3. Brønsted acid sites in gmelinite

    NASA Astrophysics Data System (ADS)

    Benco, Łubomír; Demuth, Thomas; Hafner, Jürgen; Hutschka, François

    1999-10-01

    The structural properties of purely siliceous and Al-substituted protonated gmelinite, a zeolite with a medium-sized unit cell, are investigated by means of first-principles local-density functional calculations. For acid sites introduced into an Al-free structure, optimized geometries are compared with experimental data. The substitution of a Si-O fragment by Al-O-H induces a pronounced local deformation of the structure. Four symmetrically distinct O sites (O1-O4) are classified, according to the pattern of the deformation, into two categories showing rather localized (sites 2 and 3), and mostly delocalized (sites 1 and 4) distortions. Relative stabilities of protonated structures are shown to depend on the initial geometry of the site. Larger Si-O-Si angles lead to a higher stability of the acid site. Two approaches, a static and a dynamical one, are used to derive OH stretching frequencies. Both of them prove a rather complex relation between the infrared (IR) frequency, the acidity, and the local environment of the Bro/nsted acid site. The lowest OH stretching frequency is assigned to the O2 site as distinguished in the dynamical calculations. The shift occurs due to attractive interactions of H to the framework oxygen atoms.

  4. 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.

  5. Structural and electronic features of a Broensted acid site in H-ZSM-5

    SciTech Connect

    Cook, S.J.; Chakraborty, A.K.; Bell, A.T.; Theodorou, D.N. Univ. of California, Berkeley )

    1993-06-24

    The authors report the results of local density functional theory calculations on a Broensted acid site of the zeolite H-ZSM-5. They have investigated the structural and electronic properties of the site. Comparison is made between their results and existing experimental data. It is shown that structural relaxation around an acid site must be performed to obtain accurate energetics for substitution of aluminum into the zeolite framework. The effects of cluster termination are studied by comparing results obtained for both isolated clusters and clusters embedded in a Madelung field generated by the zeolite framework. The properties of the electron density distribution in the region around an acidic proton indicate that the acidic moiety may be characterized as a rather soft acid. 47 refs., 5 figs., 4 tabs.

  6. On the binding mode of urease active site inhibitors: A density functional study

    NASA Astrophysics Data System (ADS)

    Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M.

    The way with which boric acid, a rapid reversible competitive inhibitor, binds the urease active site was explored at density functional B3LYP level of theory. The catalytic core of the enzyme was simulated by two models of different size. In both cases, amino acid residues belonging to the inner and to the outer coordination spheres of nickel ions were replaced by smaller molecular species. Contrary to the experimental indication that attributes the inhibitory ability of this acid to the lack of a nucleophilic attack by the enzyme to the boron atom, we instead found that another possibility exists based on the presence of a strong covalent sigma bond between boron and urease that we think can be hardly broken to allow any course of the reaction.

  7. 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.

  8. Determination of the acidic sites of purified single-walled carbon nanotubes by acid base titration

    NASA Astrophysics Data System (ADS)

    Hu, H.; Bhowmik, P.; Zhao, B.; Hamon, M. A.; Itkis, M. E.; Haddon, R. C.

    2001-09-01

    We report the measurement of the acidic sites in three different samples of commercially available full-length purified single-walled carbon nanotubes (SWNTs) - as obtained from CarboLex (CLI), Carbon Solutions (CSI) and Tubes@Rice (TAR) - by simple acid-base titration methods. Titration of the purified SWNTs with NaOH and NaHCO 3 solutions was used to determine the total percentage of acidic sites and carboxylic acid groups, respectively. The total percentage of acidic sites in full length purified SWNTs from TAR, CLI and CSI are about 1-3%.

  9. 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

  10. SITE PROGRAM EVALUATION OF INNOVATIVE ACID MINE DRAINAGE TREATMENT TECHNOLOGIES AT THE LEVIATHAN MINE SITE, CA

    EPA Science Inventory

    The EPA SITE Program is conducting a detailed sampling and evaluation of several innovative acid mine drainage treatment technologies at the Leviathan Mine Superfund site in California. Technologies include BiPhasic Lime Treatment Plant, an alkaline lagoon, and an innovative bio...

  11. Density functional theory and phytochemical study of Pistagremic acid

    NASA Astrophysics Data System (ADS)

    Ullah, Habib; Rauf, Abdur; Ullah, Zakir; Fazl-i-Sattar; Anwar, Muhammad; Shah, Anwar-ul-Haq Ali; Uddin, Ghias; Ayub, Khurshid

    2014-01-01

    We report here for the first time a comparative theoretical and experimental study of Pistagremic acid (P.A). We have developed a theoretical model for obtaining the electronic and spectroscopic properties of P.A. The simulated data showed nice correlation with the experimental data. The geometric and electronic properties were simulated at B3LYP/6-31 G (d, p) level of density functional theory (DFT). The optimized geometric parameters of P.A were found consistent with those from X-ray crystal structure. Differences of about 0.01 and 0.15 Å in bond length and 0.19-1.30° degree in the angles, respectively; were observed between the experimental and theoretical data. The theoretical vibrational bands of P.A were found to correlate with the experimental IR spectrum after a common scaling factor of 0.963. The experimental and predicted UV-Vis spectra (at B3LYP/6-31+G (d, p)) have 36 nm differences. This difference from experimental results is because of the condensed phase nature of P.A. Electronic properties such as Ionization Potential (I.P), Electron Affinities (E.A), co-efficient of highest occupied molecular orbital (HOMO), co-efficient of lowest unoccupied molecular orbital (LUMO) of P.A were estimated for the first time however, no correlation can be made with experiment. Inter-molecular interaction and its effect on vibrational (IR), electronic and geometric parameters were simulated by using Formic acid as model for hydrogen bonding in P.A.

  12. Density functional theory and phytochemical study of Pistagremic acid.

    PubMed

    Ullah, Habib; Rauf, Abdur; Ullah, Zakir; Fazl-i-Sattar; Anwar, Muhammad; Shah, Anwar-ul-Haq Ali; Uddin, Ghias; Ayub, Khurshid

    2014-01-24

    We report here for the first time a comparative theoretical and experimental study of Pistagremic acid (P.A). We have developed a theoretical model for obtaining the electronic and spectroscopic properties of P.A. The simulated data showed nice correlation with the experimental data. The geometric and electronic properties were simulated at B3LYP/6-31 G (d, p) level of density functional theory (DFT). The optimized geometric parameters of P.A were found consistent with those from X-ray crystal structure. Differences of about 0.01 and 0.15 Å in bond length and 0.19-1.30° degree in the angles, respectively; were observed between the experimental and theoretical data. The theoretical vibrational bands of P.A were found to correlate with the experimental IR spectrum after a common scaling factor of 0.963. The experimental and predicted UV-Vis spectra (at B3LYP/6-31+G (d, p)) have 36 nm differences. This difference from experimental results is because of the condensed phase nature of P.A. Electronic properties such as Ionization Potential (I.P), Electron Affinities (E.A), co-efficient of highest occupied molecular orbital (HOMO), co-efficient of lowest unoccupied molecular orbital (LUMO) of P.A were estimated for the first time however, no correlation can be made with experiment. Inter-molecular interaction and its effect on vibrational (IR), electronic and geometric parameters were simulated by using Formic acid as model for hydrogen bonding in P.A. PMID:24051292

  13. A comprehensive evaluation of the density of neat fatty acids and esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Density is one of the most important physical properties of a chemical compound, affecting numerous applications. An application in the case of fatty acid esters (biodiesel) is that density is specified in some biodiesel standards. In the present work, the density of fatty acid methyl, ethyl, propyl...

  14. Luminescence and IR characterization of acid sites on alumina

    SciTech Connect

    Shen, Yan-Fei; Suib, S.L. ); Deeba, M.; Koermer, G.S. )

    1994-04-01

    Luminescence and infrared (IR) spectroscopies of pyridine and ammonia adsorption have been used to measure acidities of [gamma]-alumina. Neither luminescence nor IR spectra of pyridine adsorption show an Bronsted acidity on [gamma]-alumina pretreated to 400[degrees]C. However, luminescence emission data reveal four weak OH bands even when pretreatment is done at 600[degrees]C. Pyridine and subsequent water adsorption yield six luminescence emission bands. A red shift of the pyridine emission band is found when pretreatment or desorption temperature is increased. IR spectra of ammonia on alumina pretreated at 400[degrees]C show three deformation bands at 1452, 1465, and 1485 cm[sup [minus]1]. The first band is also observed together with a band at 1554 cm[sup [minus]1] even for pretreatment at 950[degrees]C, and it corresponds to NH[sup +][sub 4] formed from dissociative adsorption of ammonia, while the other two bands are assigned to ammonia adsorbed on Bronsted acid sites. These two bands disappear along with the appearance of a new band at 1429 cm[sup [minus]1], when deuterated alumina is pretreated at 400[degrees]C and subsequently subjected to ammonia. This new band at 1429 cm[sup [minus]1] is due to NH[sub 3]D[sup +] formed from ammonia adsorbed on acidic OD sites. Consequently, ammonia IR results demonstrate the existence of Bronsted acid sites on alumina pretreated at 400[degrees]C. 38 refs., 9 figs., 2 tabs.

  15. 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

  16. Controlling the density and site of attachment of gold nanoparticles onto the surface of carbon nanotubes.

    PubMed

    Kumar, Suresh; Kaur, Inderpreet; Dharamvir, Keya; Bharadwaj, Lalit M

    2012-03-01

    A facile method for controlling the density and site of attachment of gold nanoparticles onto the surface of carbon nanotubes is demonstrated. Nitric acid based oxidation was carried out to create carboxylic groups exclusively at the ends of carbon nanotubes, whereas oxidation using a mixture of nitric and sulfuric acid with varied reaction time was carried out to control the population of carboxylic groups on the side walls of nanotubes. In turn, 4-aminothiophenol modified gold nanoparticles were covalently interfaced to these carboxylated multi-walled carbon nanotubes in the presence of a zero length cross-linker, 1-ethylene-3-(3-dimethylaminopropyl) carbodiimide. Raman spectroscopic results showed increase in height of disorder band with each of these successive steps, indicating the increase in degree of functionalization of the carbon nanotubes. Fourier transformed infrared spectroscopic analysis affirmed the functionalization of nanostructures and the formation of nanohybrid. Transmission electron and field emission scanning electron microscopic analysis ascertained the attachment of gold nanoparticles to the ends and side walls of the multi-walled carbon nanotubes. The new hybrid nanostructures may find applications in electronic, optoelectronic, and sensing devices. PMID:22218340

  17. Electrophysiological evidence for acidic, basic, and neutral amino acid olfactory receptor sites in the catfish.

    PubMed

    Caprio, J; Byrd, R P

    1984-09-01

    Electrophysiological experiments indicate that olfactory receptors of the channel catfish, Ictalurus punctatus, contain different receptor sites for the acidic (A), basic (B), and neutral amino acids; further, at least two partially interacting neutral sites exist, one for the hydrophilic neutral amino acids containing short side chains (SCN), and the second for the hydrophobic amino acids containing long side chains (LCN). The extent of cross-adaptation was determined by comparing the electro-olfactogram (EOG) responses to 20 "test" amino acids during continuous bathing of the olfactory mucosa with water only (control) to those during each of the eight "adapting" amino acid regimes. Both the adapting and test amino acids were adjusted in concentrations to provide approximately equal response magnitudes in the unadapted state. Under all eight adapting regimes, the test EOG responses were reduced from those obtained in the unadapted state, but substantial quantitative differences resulted, depending upon the molecular structure of the adapting stimulus. Analyses of the patterns of EOG responses to the test stimuli identified and characterized the respective "transduction processes," a term used to describe membrane events initiated by a particular subset of amino acid stimuli that are intricately linked to the origin of the olfactory receptor potential. Only when the stimulus compounds interact with different transduction processes are the stimuli assumed to bind to different membrane "sites." Four relatively independent L-alpha-amino acid transduction processes (and thus at least four binding sites) identified in this report include: (a) the A process for aspartic and glutamic acids; (b) the B process for arginine and lysine; (c) the SCN process for glycine, alanine, serine, glutamine, and possibly cysteine; (d) the LCN process for methionine, ethionine, valine, norvaline, leucine, norleucine, glutamic acid-gamma-methyl ester, histidine, phenylalanine, and also

  18. 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.

  19. 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

  20. Inorganic Nitrogen Cycling in an Extreme Acid Mine Drainage Site

    NASA Astrophysics Data System (ADS)

    Kalnejais, L. H.; Smith, R. L.; Nordstrom, D. K.; Banfield, J. F.

    2006-12-01

    Weathering of the massive sulfide ore body at Iron Mountain, northern California has generated sulfuric acid solutions with pH values ranging from 0.5 to 1, temperatures up to 50°C and high concentrations of toxic metals. Communities of microorganisms catalyze the oxidation of iron and sulfur that generates this extreme environment. The nitrogen requirements of these organisms and the nitrogen cycling within these waters are not understood. By adapting the chemiluminescence detection method of Baeseman (2004) we have constrained the stability of nitrate and nitrite species in acidic, high ferrous iron solutions and have measured a time series of the nitrate concentrations at sites within Iron Mountain. The half-life of nitrite is less than an hour due to reactions with ferrous ions, while nitrate is found at concentrations of up to 10 μM within the mine. By coupling this information with geochemical and microbial community information at each site together with culture enrichment studies using various nitrogen sources we hope to gain insight into the pathways of nitrogen utilization in this extreme environment. References Baeseman, J.L. (2004) Denitrification in acid-impacted mountain stream sediments. Ph.D. Dissertation, University of Colorado, Department of Civil, Environmental, and Architectural Engineering.

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

    PubMed

    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 (57)Fe 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  3. 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

  4. Comparative density functional theory and density functional tight binding study of 2-anthroic acid on TiO2

    NASA Astrophysics Data System (ADS)

    Manzhos, Sergei

    2016-01-01

    A comparative DFTB (density functional tight binding)-DFT (density functional theory) study of several adsorption modes of 2-anthroic acid on titania is presented. Two parameterizations of DFTB previously used for dye-TiO2 interfaces are tested. DFTB predicts adsorption energies which differ from those computed by DFT not only in magnitude (by up to 0.5 eV) but also in the order among different configurations. The band alignment computed with DFTB is not consistent with DFT results and with experimental data. The strategy of geometry optimization with DFTB followed by single-point DFT calculations also does not necessarily result in plausible adsorption energies.

  5. Density functional theoretical and NMR study of Hammett bases in acidic zeolites

    SciTech Connect

    Nicholas, J.B.; Haw, J.F.; Beck, L.W.; Krawietz, T.R.; Ferguson, D.B.

    1995-12-13

    We demonstrate here that theoretical calculations using density functional theory (DFT) accurately model proton transfer reactions between Bronsted sites in zeolites (the archetypal solid acids) and Hammett bases. The validity of the theoretical results is verified by NMR measurements of key nuclei of the same Hammett bases in zeolites HZSM-5 (MFI) and HY (FAU), the first such experiments. The accuracy of the predictions of the DFT calculations for the HZSM-5 zeolite model suggests that they may be extended to other zeolite cluster models, including those which have not yet been realized experimentally and hence are not available for NMR study. We optimized the adsorbate zeolite complexes with this angle constrained to larger values; to our surprise, the SVWN/DNP calculations resulted in the proton being transferred from p-fluoronitrobenzene back to the zeolite, even if the Si-O-Al angle was held fixed at 180{degree}. Further tests at higher levels of theory are in progress. This investigation used a choice of indicators that necessarily resulted in wide limits on zeolite acid strength, but the theoretical and experimental methodologies have been established. 21 refs., 3 figs.

  6. 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.

  7. Investigation of prototypal MOFs consisting of polyhedral cages with accessible Lewis-acid sites for quinoline synthesis.

    PubMed

    Gao, Wen-Yang; Leng, Kunyue; Cash, Lindsay; Chrzanowski, Matthew; Stackhouse, Chavis A; Sun, Yinyong; Ma, Shengqian

    2015-03-21

    A series of prototypal metal-organic frameworks (MOFs) consisting of polyhedral cages with accessible Lewis-acid sites, have been systematically investigated for Friedländer annulation reaction, a straightforward approach to synthesizing quinoline and its derivatives. Amongst them MMCF-2 demonstrates significantly enhanced catalytic activity compared with the benchmark MOFs, HKUST-1 and MOF-505, as a result of a high-density of accessible Cu(II) Lewis acid sites and large window size in the cuboctahedral cage-based nanoreactor of MMCF-2. PMID:25693429

  8. Equine Endometrial Gland Density and Endometrial Thickness Vary among Sampling Sites in Thoroughbred Mares

    PubMed Central

    HANADA, Michiko; MAEDA, Yousuke; OIKAWA, Masa-aki

    2012-01-01

    The secretions of the equine endometrial glands are essential for the survival, growth, and development of the conceptus in early pregnancy, and endometrial gland density is directly related to successful pregnancy outcome. Endometrial biopsy is routinely used to assess the reproductive potential of broodmares. Some previous studies have shown that equine endometrial glands are uniformly distributed throughout the uterus; however, other work has shown variation of the endometrial architecture between biopsy sites, suggesting that a single biopsy is not representative of the entire endometrium. The aims of this study were to assess and compare the endometrial gland density and thickness at four sampling sites in the uterus (the central segment of each uterine horn, the uterine horn-body junction, and the caudal portion of the uterine body). Endometrial samples from five nulliparous Thoroughbred mares in diestrus were obtained at necropsy and used for subsequent histomorphometric analysis. The caudal uterine body had a significantly lower endometrial gland density and endometrial thickness than the other sites. This may result in nutrient deprivation and reduced survival of embryos or fetuses in this region of the uterus. The endometrial gland density and endometrial thickness did not significantly differ between the other regions sampled, indicating that they are similarly suitable for embryonic implantation and fetal development. Our results suggest that the endometrial structure of the caudal uterine body of the mare is not representative of the endometrial morphology at other sites. Thus, the caudal uterine body is not a suitable site for routine endometrial biopsy. PMID:24833993

  9. 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

  10. Gas phase acidity measurement of local acidic groups in multifunctional species: controlling the binding sites in hydroxycinnamic acids.

    PubMed

    Guerrero, Andres; Baer, Tomas; Chana, Antonio; González, Javier; Dávalos, Juan Z

    2013-07-01

    The applicability of the extended kinetic method (EKM) to determine the gas phase acidities (GA) of different deprotonable groups within the same molecule was tested by measuring the acidities of cinnamic, coumaric, and caffeic acids. These molecules differ not only in the number of acidic groups but in their nature, intramolecular distances, and calculated GAs. In order to determine independently the GA of groups within the same molecule using the EKM, it is necessary to selectively prepare pure forms of the hydrogen-bound heterodimer. In this work, the selectivity was achieved by the use of solvents of different vapor pressure (water and acetonitrile), as well as by variation of the drying temperature in the ESI source, which affected the production of heterodimers with different solvation energies and gas-phase dissociation energies. A particularly surprising finding is that the calculated solvation enthalpies of water and the aprotic acetonitrile are essentially identical, and that the different gas-phase products generated are apparently the result of their different vapor pressures, which affects the drying mechanism. This approach for the selective preparation of heterodimers, which is based on the energetics, appears to be quite general and should prove useful for other studies that require the selective production of heterodimers in ESI sources. The experimental results were supported by density functional theory (DFT) calculations of both gas-phase and solvated species. The experimental thermochemical parameters (deprotonation ΔG, ΔH, and ΔS) are in good agreement with the calculated values for the monofunctional cinnamic acid, as well as the multifunctional coumaric and caffeic acids. The measured GA for cinnamic acid is 334.5 ± 2.0 kcal/mol. The measured acidities for the COOH and OH groups of coumaric and caffeic acids are 332.7 ± 2.0, 318.7 ± 2.1, 332.2 ± 2.0, and 317.3 ± 2.2 kcal/mol, respectively. PMID:23799241

  11. 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

  12. 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

  13. ASIAN/PACIFIC ISLANDER POPULATION DENSITY AND EPA REGULATED SITES IN THE SEATTLE/TACOMA AREA

    EPA Science Inventory

    Shaded density polygons of 1990 Census Block Data for the Asian/Pacific Islander population group plotted with locations of EPA regulated sites (CERCLA, RCRA, NPDES (majors), and TRI) for the Seattle/Tacoma geographic area. Source scale of map is based on the 1990 Census tigerlin...

  14. AFRICAN AMERICAN POPULATION DENSITY AND EPA REGULATED SITES IN THE SEATTLE/TACOMA AREA

    EPA Science Inventory

    Shaded density polygons of 1990 Census Block Data for the African American population group plotted with locations of EPA regulated sites (CERCLA, RCRA, NPDES (majors), and TRI) for the Seattle/Tacoma geographic area. Source scale of map is based on the 1990 Census tigerline data...

  15. AMERICAN INDIAN POPULATION DENSITY AND EPA REGULATED SITES IN THE SEATTLE/TACOMA AREA

    EPA Science Inventory

    Shaded density polygons of 1990 Census Block Data for the American Indian population group plotted with locations of EPA regulated sites (CERCLA, RCRA, NPDES (majors), and TRI) for the Seattle/Tacoma geographic area. Source scale of map is based on the 1990 Cenesus tigerline data...

  16. HISPANIC ORIGIN POPULATION DENSITY AND EPA REGULATED SITES IN THE SEATTLE/TACOMA AREA

    EPA Science Inventory

    Shaded density polygons of 1990 Census Block Data for the Hispanic Origin population group plotted with locations of EPA regulated sites (CERCLA, RCRA, NPDES (majors), and TRI) for the Seattle/Tacoma geographic area. Source scale of map is based on the 1990 Cenesus tigerline data...

  17. 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.

  18. 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. PMID:26331764

  19. Possible intermolecular interaction between quinolones and biphenylacetic acid inhibits gamma-aminobutyric acid receptor sites.

    PubMed

    Akahane, K; Kimura, Y; Tsutomi, Y; Hayakawa, I

    1994-10-01

    The combination of some new quinolone antibacterial agents with 4-biphenylacetic acid (BPAA), a metabolite of fenbufen, is known to specifically induce functional blockade of the gamma-aminobutyric acid (GABA) receptors. The mechanisms of these drug interactions were further examined. Scatchard analysis of [3H]muscimol binding to rat brain plasma membranes in the presence of enoxacin and BPAA revealed that a significant decrease in the number of muscimol binding sites was produced without affecting the affinity of binding to the receptors. In the presence of norfloxacin, BPAA inhibited muscimol binding the most potently of the six BPAA-related compounds tested. Fenbufen and 9,10-dihydro-gamma-oxo-2-phenanthrenebutyric acid also inhibited the binding, and 4-biphenylcarboxylic acid and methyl 4-biphenylacetate inhibited it slightly, but 3-benzoylpropionic acid exhibited no competitive inhibition. Accordingly, hybrid molecules of norfloxacin and BPAA were synthesized for stereochemical analysis of these drug interactions. A hybrid with a -CONH(CH2)3- chain between norfloxacin and BPAA (flexible structure) inhibited muscimol binding, and intracisternal injection of this hybrid caused clonic convulsions in mice more potently than the combination of norfloxacin and BPAA did. In contrast, a hybrid linked by -CONH- (stretched structure) showed almost no such inhibitory effect. 1H NMR analysis indicated the presence of intramolecular attraction at the quinoline ring of the hybrid exhibiting the antagonistic activity. These results suggest the possibility that quinolones and BPAA interact with the GABA receptor at nearby sites and that the binding affinity of quinolones to the GABA receptors is largely enhanced by the intermolecular interaction with BPAA. PMID:7840564

  20. Possible intermolecular interaction between quinolones and biphenylacetic acid inhibits gamma-aminobutyric acid receptor sites.

    PubMed Central

    Akahane, K; Kimura, Y; Tsutomi, Y; Hayakawa, I

    1994-01-01

    The combination of some new quinolone antibacterial agents with 4-biphenylacetic acid (BPAA), a metabolite of fenbufen, is known to specifically induce functional blockade of the gamma-aminobutyric acid (GABA) receptors. The mechanisms of these drug interactions were further examined. Scatchard analysis of [3H]muscimol binding to rat brain plasma membranes in the presence of enoxacin and BPAA revealed that a significant decrease in the number of muscimol binding sites was produced without affecting the affinity of binding to the receptors. In the presence of norfloxacin, BPAA inhibited muscimol binding the most potently of the six BPAA-related compounds tested. Fenbufen and 9,10-dihydro-gamma-oxo-2-phenanthrenebutyric acid also inhibited the binding, and 4-biphenylcarboxylic acid and methyl 4-biphenylacetate inhibited it slightly, but 3-benzoylpropionic acid exhibited no competitive inhibition. Accordingly, hybrid molecules of norfloxacin and BPAA were synthesized for stereochemical analysis of these drug interactions. A hybrid with a -CONH(CH2)3- chain between norfloxacin and BPAA (flexible structure) inhibited muscimol binding, and intracisternal injection of this hybrid caused clonic convulsions in mice more potently than the combination of norfloxacin and BPAA did. In contrast, a hybrid linked by -CONH- (stretched structure) showed almost no such inhibitory effect. 1H NMR analysis indicated the presence of intramolecular attraction at the quinoline ring of the hybrid exhibiting the antagonistic activity. These results suggest the possibility that quinolones and BPAA interact with the GABA receptor at nearby sites and that the binding affinity of quinolones to the GABA receptors is largely enhanced by the intermolecular interaction with BPAA. PMID:7840564

  1. Acid-sensing ion channel 1a is a postsynaptic proton receptor that affects the density of dendritic spines

    PubMed Central

    Zha, Xiang-ming; Wemmie, John A.; Green, Steven H.; Welsh, Michael J.

    2006-01-01

    Extracellular proton concentrations in the brain may be an important signal for neuron function. Proton concentrations change both acutely when synaptic vesicles release their acidic contents into the synaptic cleft and chronically during ischemia and seizures. However, the brain receptors that detect protons and their physiologic importance remain uncertain. Using organotypic hippocampal slices and biolistic transfection, we found the acid-sensing ion channel 1a (ASIC1a), localized in dendritic spines where it functioned as a proton receptor. ASIC1a also affected the density of spines, the postsynaptic site of most excitatory synapses. Decreasing ASIC1a reduced the number of spines, whereas overexpressing ASIC1a had the opposite effect. Ca2+-mediated Ca2+/calmodulin-dependent protein kinase II (CaMKII) signaling was probably responsible, because acid evoked an ASIC1a-dependent elevation of spine intracellular Ca2+ concentration, and reducing or increasing ASIC1a levels caused parallel changes in CaMKII phosphorylation in vivo. Moreover, inhibiting CaMKII prevented ASIC1a from increasing spine density. These data indicate that ASIC1a functions as a postsynaptic proton receptor that influences intracellular Ca2+ concentration and CaMKII phosphorylation and thereby the density of dendritic spines. The results provide insight into how protons influence brain function and how they may contribute to pathophysiology. PMID:17060608

  2. A density functional theory for colloids with two multiple bonding associating sites.

    PubMed

    Haghmoradi, Amin; Wang, Le; Chapman, Walter G

    2016-06-22

    Wertheim's multi-density formalism is extended for patchy colloidal fluids with two multiple bonding patches. The theory is developed as a density functional theory to predict the properties of an associating inhomogeneous fluid. The equation of state developed for this fluid depends on the size of the patch, and includes formation of cyclic, branched and linear clusters of associated species. The theory predicts the density profile and the fractions of colloids in different bonding states versus the distance from one wall as a function of bulk density and temperature. The predictions from our theory are compared with previous results for a confined fluid with four single bonding association sites. Also, comparison between the present theory and Monte Carlo simulation indicates a good agreement. PMID:27115237

  3. A density functional theory for colloids with two multiple bonding associating sites

    NASA Astrophysics Data System (ADS)

    Haghmoradi, Amin; Wang, Le; Chapman, Walter G.

    2016-06-01

    Wertheim’s multi-density formalism is extended for patchy colloidal fluids with two multiple bonding patches. The theory is developed as a density functional theory to predict the properties of an associating inhomogeneous fluid. The equation of state developed for this fluid depends on the size of the patch, and includes formation of cyclic, branched and linear clusters of associated species. The theory predicts the density profile and the fractions of colloids in different bonding states versus the distance from one wall as a function of bulk density and temperature. The predictions from our theory are compared with previous results for a confined fluid with four single bonding association sites. Also, comparison between the present theory and Monte Carlo simulation indicates a good agreement.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. Serum Paraoxonase 1 Activity Is Associated with Fatty Acid Composition of High Density Lipoprotein

    PubMed Central

    Boshtam, Maryam; Pourfarzam, Morteza; Ani, Mohsen; Naderi, Gholam Ali; Basati, Gholam; Mansourian, Marjan; Dinani, Narges Jafari; Asgary, Seddigheh; Abdi, Soheila

    2013-01-01

    Introduction. Cardioprotective effect of high density lipoprotein (HDL) is, in part, dependent on its related enzyme, paraoxonase 1 (PON1). Fatty acid composition of HDL could affect its size and structure. On the other hand, PON1 activity is directly related to the structure of HDL. This study was designed to investigate the association between serum PON1 activity and fatty acid composition of HDL in healthy men. Methods. One hundred and forty healthy men participated in this research. HDL was separated by sequential ultracentrifugation, and its fatty acid composition was analyzed by gas chromatography. PON1 activity was measured spectrophotometrically using paraxon as substrate. Results. Serum PON1 activity was directly correlated with the amount of stearic acid and dihomo-gamma-linolenic acid (DGLA). PON1/HDL-C was directly correlated with the amount of miristic acid, stearic acid, and DGLA and was inversely correlated with total amount of ω6 fatty acids of HDL. Conclusion. The fatty acid composition of HDL could affect the activity of its associated enzyme, PON1. As dietary fats are the major determinants of serum lipids and lipoprotein composition, consuming some special dietary fatty acids may improve the activity of PON1 and thereby have beneficial effects on health. PMID:24167374

  9. 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

  10. 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.

  11. Comparison of the autoradiographic binding distribution of [3H]-gabapentin with excitatory amino acid receptor and amino acid uptake site distributions in rat brain.

    PubMed Central

    Thurlow, R. J.; Hill, D. R.; Woodruff, G. N.

    1996-01-01

    1. Gabapentin is a novel anticonvulsant with an unknown mechanism of action. Recent homogenate binding studies with [3H]-gabapentin have suggested a structure-activity relationship similar to that shown for the amino acid transport system responsible for the uptake of large neutral amino acids (LNAA). 2. The autoradiographic binding distribution of [3H]-gabapentin in rat brain was compared with the distributions for excitatory amino acid receptor subtypes and the uptake sites for excitatory and large neutral amino acids in consecutive rat brain sections. 3. Densitometric measurement of the autoradiographic images followed by normalisation with respect to the hippocampus CA1 stratum radiatum, was carried out before comparison of each binding distribution with that of [3H]-gabapentin by linear regression analysis. The correlation coefficients observed showed no absolute correlation was observed between the binding distributions of [3H]-gabapentin and those of the excitatory amino acid receptor subtypes. The acidic and large neutral amino acid uptake site distributions demonstrated a much closer correlation to the [3H]-gabapentin binding site distribution. The correlation coefficients for D-[3H]-aspartate, L-[3H]-leucine and L-[3H]-isoleucine binding site distributions were 0.76, 0.90 and 0.88 respectively. 4. Concentration-dependent inhibition by unlabelled gabapentin of autoradiographic binding of L-[3H]-leucine and L-[3H]-isoleucine was observed, with non-specific binding levels being reached at concentrations between 10 and 100 microM. 5. Excitotoxic quinolinic acid lesion studies in rat brain caudate putamen and autoradiography were carried out for the amino acid uptake sites mentioned above. The resulting glial infiltration of the lesioned areas was visualized by autoradiography using the peripheral benzodiazepine receptor specific ligand [3H]-PK11195. A significant decrease in binding density in the lesioned area compared with sham-operated animals was observed

  12. 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.

  13. 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

  14. Erythrocyte Omega-6 and Omega-3 Fatty Acids and Mammographic Breast Density

    PubMed Central

    Hudson, Alana G.; Reeves, Katherine W.; Modugno, Francesmary; Wilson, John W.; Evans, Rhobert W.; Vogel, Victor G.; Gierach, Gretchen L.; Simpson, Jennifer; Weissfeld, Joel L.

    2013-01-01

    Diets low in omega-6 (n-6) polyunsaturated fatty acids (PUFAs) and high in omega-3 (n-3) PUFAs may protect against breast cancer development. Associations of PUFA intake with mammographic density, an intermediate marker of breast cancer risk, have been inconsistent; however, prior studies have relied on self-reported dietary PUFA intake. We examined the association between circulating erythrocyte n-6 and n-3 PUFAs with mammographic density in 248 postmenopausal women who were not taking exogenous hormones. PUFAs in erythrocytes were measured by gas-liquid chromatography, and mammographic density was assessed quantitatively by planimetry. Spearman’s correlation coefficients and generalized linear models were used to evaluate the relationships between PUFA measures and mammographic density. None of the erythrocyte n-6 or n-3 PUFA measures were associated with percent density or dense breast area. PMID:23530640

  15. 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).

  16. Nitrous Acid at Concordia (Inland Site) and Dumont d'Urville (Costal Site), East Antarctica

    NASA Astrophysics Data System (ADS)

    Kerbrat, M.; Legrand, M.; Preunkert, S.; Gallée, H.; Kleffman, J.

    2012-04-01

    One of the most recent important finding made in Antarctica after the discovery of the appearance of the Antarctic ozone hole in the early 80's was the discovery of a very oxidizing canopy over the South Pole region in relation with unexpected high levels of NO. There is a strong need however to extend investigations of the oxidation capacity of the lower atmosphere at the scale of the whole Antarctic continent, and in particular, over East Antarctica. That motivated the OPALE (Oxidant Production over Antarctic Land and its Export) project. Indeed the limited data gained by using aircraft sampling during ANTCI 2003 suggest that over the East Antarctic plateau even higher NO emissions persist. Among several not yet resolved questions related to the high level of oxidants over Antarctica is the role of nitrous acid (HONO). During the austral summer 2010/2011 the levels of nitrous acid (HONO) were for the first time investigated at Concordia (75°06'S, 123°33'E) and Dumont D'Urville (66°40'S, 140°01'E), two stations located in East Antarctica. Also for the first time in Antarctica, HONO was measured by deploying a long path absorption photometer (LOPAP). At Concordia, from the end of December 2010 to mid January 2011 HONO mixing ratios at 1 m above the snow surface ranged between 5 and 60 pptv. Diurnal cycles were observed with levels peaking in the morning (06:30 to 07:30) and the evening (19:00 to 20:00). At Dumont d'Urville, background mixing ratios close to 2 pptv were observed in February 2011. No clear diurnal cycles were observed at that site but several events of air masses export from inland Antarctica were encountered with enhanced HONO levels reaching 10 pptv at night. These first HONO data gained in East Antarctica are discussed in terms of sources and sinks along with synoptic weather conditions.

  17. 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.

  18. 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.

  19. 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).

  20. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    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.

  1. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    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.

  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

    DOEpatents

    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

    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.

  5. 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.

  6. 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

  7. In-site interaction evaluation of Tn density by inhibition/competition assays.

    PubMed

    Robles, Ana; Medeiros, Andrea; Berois, Nora; Balter, Henia S; Pauwels, Ernest K; Osinaga, Eduardo

    2010-05-01

    The tumor-associated structure N-acetyl-galactosamine-O-Ser/Thr (Tn antigen), which is overexpressed in various tumor cell types, notably of the breast, ovary and colon, is an interesting determinant that is useful for cancer diagnosis and follow-up. The aim of this research was to study different assay strategies in order to determine the most sensitive system for further application in epitope characterization and binding assessment. The tetrameric isolectin obtained from Vicia villosa seeds (VVLB(4)) shows high affinity for the tumor-associated structure. A monoclonal antibody against VVLB(4), MabVV(34), was generated, and the interaction between MabVV(34) and VVLB(4) was studied by means of binding and inhibition assays. Several synthetic peptides (10 amino acid sequences) designed from the amino acid sequence of VVLB(4) and obtained from trypsin digestion were tested to determine which amino acids were involved in the interaction between MabVV(34) and VVLB(4). The further unraveling of this epitope was investigated by inhibition using designed synthetic peptides as well as mixtures mimicking variable density effect. Under the experimental circumstances, MabVV(34) was able to inhibit the binding of VVLB(4) to Tn. Two of the four peptide sequences assayed showed better inhibition properties. Finally, mixtures containing these selected sequences allowed the evaluation of binding and inhibition as a function of Tn density. We conclude that the present study facilitates the further development of a specific Tn marker and may contribute to the development of Tn-like radiolabelled peptides or Tn-specific radiolabelled fragments providing a highly selective tool for cancer diagnosis and treatment. This strategy may contribute to characterize the new generation of radiopharmaceuticals for diagnosis and therapy based on biomolecules like antibodies, fragments or peptides, whose application is directly guided by their specific molecular recognition. PMID:20447557

  8. 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.

  9. Influence of Amino Acids on Low-Density Escherichia coli Responses to Nutrient Downshifts▿

    PubMed Central

    Bodini, Sergio; Nunziangeli, Luisa; Santori, Francesca

    2007-01-01

    A vast bibliography on nutrient effects on high-density cultures exists, while it has been overlooked that low densities of starving cells are often the rule in natural environments. By means of a novel sensitive β-galactosidase assay, we examined Escherichia coli transitions to minimal media when the cell concentration was 100 to 10,000 cells per ml. As in high-density cultures, the enzyme activity depended on amino acid availability and was subject to catabolite repression and stringent control. In all conditions tested, despite the presence of other nutrient sources, the relationship between β-galactosidase activity and the l-amino acid pool was hyperbolic. The affinity constant when the amino acid pool was the only nutrient source averaged 14 μM after 90 min and increased up to 222 μM after 4.5 h. While investigating the transition from lag phase to exponential phase, we observed that the cells did not enter into starvation mode in the presence of amino acids, even when the nutrient amount was insufficient to support full survival. Based on these premises, the switch from starvation to hunger was investigated in relation to the amino acid pools. A critical range of concentrations at which E. coli linearly synthesized β-galactosidase despite, at the same time, suffering a large decrease in cell viability was then recognized. Since both β-galactosidase production and the dilution rate were reduced by more than half in the absence of leucine, we examined the contribution of leucine to cell recovery capabilities. PMID:17293414

  10. 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.

  11. 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

  12. A density functional study on dielectric properties of acrylic acid grafted polypropylene

    NASA Astrophysics Data System (ADS)

    Ruuska, Henna; Arola, Eero; Kortelainen, Tommi; Rantala, Tapio T.; Kannus, Kari; Valkealahti, Seppo

    2011-04-01

    Influence of acrylic acid grafting of isotactic polypropylene on the dielectric properties of the polymer is investigated using density functional theory (DFT) calculations, both in the molecular modeling and three-dimensional (3D) bulk periodic system frameworks. In our molecular modeling calculations, polarizability volume, and polarizability volume per mass which reflects the permittivity of the polymer, as well as the HOMO-LUMO gap, one of the important measures indicating the electrical breakdown voltage strength, were examined for oligomers with various chain lengths and carboxyl mixture ratios. When a polypropylene oligomer is grafted with carboxyl groups (cf. acrylic acid), our calculations show that the increase of the polarizability volume α' of the oligomer is proportional to the increase of its mass m, while the ratio {{α^ ' } { α^ ' } m} decreases from the value of a pure polymer when increasing the mixture ratio. The decreasing ratio of {{α^ ' } {α^ ' } m} under carboxyl grafting indicates that the material permittivity might also decrease if the mass density of the material remains constant. Furthermore, our calculations show that the HOMO-LUMO gap energy decreases by only about 15% in grafting, but this decrease seems to be independent on the mixture ratio of carboxyl. This indicates that by doping polymers with additives better dielectric properties can be tailored. Finally, using the first-principles molecular DFT results for polarizability volume per mass in connection with the classical Clausius-Mossotti relation, we have estimated static permittivity for acrylic acid grafted polypropylene, assuming the structural density keeping constant under grafting. The computed permittivity values are in a qualitative agreement with the recent experiments, showing increasing tendency of the permittivity as a function of the grafting composition. In order to validate our molecular DFT based approach, we have also carried out extensive three

  13. A density functional study on dielectric properties of acrylic acid grafted polypropylene.

    PubMed

    Ruuska, Henna; Arola, Eero; Kortelainen, Tommi; Rantala, Tapio T; Kannus, Kari; Valkealahti, Seppo

    2011-04-01

    Influence of acrylic acid grafting of isotactic polypropylene on the dielectric properties of the polymer is investigated using density functional theory (DFT) calculations, both in the molecular modeling and three-dimensional (3D) bulk periodic system frameworks. In our molecular modeling calculations, polarizability volume, and polarizability volume per mass which reflects the permittivity of the polymer, as well as the HOMO-LUMO gap, one of the important measures indicating the electrical breakdown voltage strength, were examined for oligomers with various chain lengths and carboxyl mixture ratios. When a polypropylene oligomer is grafted with carboxyl groups (cf. acrylic acid), our calculations show that the increase of the polarizability volume α' of the oligomer is proportional to the increase of its mass m, while the ratio α'/m decreases from the value of a pure polymer when increasing the mixture ratio. The decreasing ratio of α'/m under carboxyl grafting indicates that the material permittivity might also decrease if the mass density of the material remains constant. Furthermore, our calculations show that the HOMO-LUMO gap energy decreases by only about 15% in grafting, but this decrease seems to be independent on the mixture ratio of carboxyl. This indicates that by doping polymers with additives better dielectric properties can be tailored. Finally, using the first-principles molecular DFT results for polarizability volume per mass in connection with the classical Clausius-Mossotti relation, we have estimated static permittivity for acrylic acid grafted polypropylene, assuming the structural density keeping constant under grafting. The computed permittivity values are in a qualitative agreement with the recent experiments, showing increasing tendency of the permittivity as a function of the grafting composition. In order to validate our molecular DFT based approach, we have also carried out extensive three-dimensional bulk periodic first

  14. Chain dynamics of selectively deuterated fatty acids in high-density lipoproteins studied by deuterium NMR

    SciTech Connect

    Parmar, Y.I.; Gorrissen, H.; Wassall, S.R.; Cushley, R.J.

    1985-01-01

    Deuterium order parameters have been determined for approximately 5 mol% selectively deuterated palmitic acid incorporated into the outer monolayer of high-density lipoproteins (HDL/sub 3/). The values are SCD = 0.38 for (2,2-/sup 2/H/sub 2/)palmitic acid, 0.38 for (4,4-/sup 2/H/sub 2/)palmitic acid, 0.37 for (5,5,6,6-/sup 2/H/sub 4/)palmitic acid, 0.23 for (11,11,12,12-/sup 2/H/sub 4/)palmitic acid, and 0.05 for (16,16,16-/sup 2/H/sub 3/)palmitic acid. Comparison of the acyl chain order parameters in HDL/sub 3/ with acyl chain order parameters determined recently for approximately 5 mol% deuterated palmitic acid in sonicated unilamellar vesicles, composed of the same ratio of phosphatidylcholine/sphingomyelin (85/15 w/w) found in HDL/sub 3/, shows that acyl chain order in the HDL/sub 3/ monolayer is approximately 3-5 times higher than in the vesicle bilayer. The acyl chain order in the lipoprotein monolayer is approximately 1.5-2 times higher than in the bilayer of phosphatidylcholine multilamellar dispersions. Deuterium longitudinal relaxation times have been measured for deuterated palmitic acid in HDL/sub 3/, and the values T/sub 1/ approximately 16 ms for C/sub 2/H/sub 2/ and 170 ms for C/sub 2/H/sub 3/ groups are a factor of more than 2 times smaller than found in phospholipid bilayers.

  15. 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

  16. 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

  17. A simple ligation-based method to increase the information density in sequencing reactions used to deconvolute nucleic acid selections

    PubMed Central

    Childs-Disney, Jessica L.; Disney, Matthew D.

    2008-01-01

    Herein, a method is described to increase the information density of sequencing experiments used to deconvolute nucleic acid selections. The method is facile and should be applicable to any selection experiment. A critical feature of this method is the use of biotinylated primers to amplify and encode a BamHI restriction site on both ends of a PCR product. After amplification, the PCR reaction is captured onto streptavidin resin, washed, and digested directly on the resin. Resin-based digestion affords clean product that is devoid of partially digested products and unincorporated PCR primers. The product's complementary ends are annealed and ligated together with T4 DNA ligase. Analysis of ligation products shows formation of concatemers of different length and little detectable monomer. Sequencing results produced data that routinely contained three to four copies of the library. This method allows for more efficient formulation of structure-activity relationships since multiple active sequences are identified from a single clone. PMID:18065718

  18. 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

  19. 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. PMID:23112618

  20. 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

  1. 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.

  2. 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.

  3. Density functional study of H-induced defects as nucleation sites in hybrid carbon nanomaterials.

    SciTech Connect

    Barnard, A.; Terranova, M. L.; Rossi, M.; Dip. Scienze e Tecnologie Chimiche; Dip di Energetica; INFM

    2005-01-01

    Recently we have reported on the growth of an exciting new class of hybrid nanostructured carbon materials, coupling nanosized diamond with single-walled carbon nanotubes. The inner structures were shown to be single-walled C nanotubes or bundles of single-walled nanotubes up to 15 {micro}m long, and the outer deposit consisted of faceted diamond crystallites with diameters in the range of 20-100 nm. To aid in understanding the mechanisms responsible for the formation of such materials, the present study uses density functional theory to examine the role of atomic hydrogen in creating localized sp{sup 3} hybridized defects on the outer wall of carbon nanotubes. The results illustrate that certain absorption configurations may produce defects containing dangling carbon bonds, and thus promote the formation of suitable sites for nanodiamond nucleation.

  4. 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

  5. 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.

  6. Density functional theory study on the interaction between keto-9H guanine and aspartic acid.

    PubMed

    Harris, Patrina Thompson; Hill, Glake A

    2012-05-01

    A theoretical study was performed using density functional theory (DFT) to investigate hydrogen bonding interactions in signature complexes formed between keto-9H guanine (Gua) and aspartic acid (Asp) at neutral pH. Optimized geometries, binding energies and the theoretical IR spectra of guanine, aspartic acid and their corresponding complexes (Gua-Asp) were calculated using the B3LYP method and the 6-31+G(d) basis set. Stationary points found to be at local minima on the potential energy surface were verified by second derivative harmonic vibrational frequency calculations at the same level of theory. AIM theory was used to analyze the hydrogen bonding characteristics of these DNA base complex systems. Our results show that the binding motif for the most stable complex is strikingly similar to a Watson-Crick motif observed in the guanine-cytosine base pair. We have found a range of hydrogen bonding interactions between guanine and aspartic acid in the six complexes. This was further verified by theoretical IR spectra of ω(C-H--O-H) cm(-1) stretches for the Gua-Asp complexes. The electron density plot indicates strong hydrogen bonding as shown by the 2p(z) dominant HOMO orbital character. PMID:21877157

  7. 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

  8. A new temperature- and humidity-dependent surface site density approach for deposition ice nucleation

    NASA Astrophysics Data System (ADS)

    Steinke, I.; Hoose, C.; Möhler, O.; Connolly, P.; Leisner, T.

    2015-04-01

    Deposition nucleation experiments with Arizona Test Dust (ATD) as a surrogate for mineral dusts were conducted at the AIDA cloud chamber at temperatures between 220 and 250 K. The influence of the aerosol size distribution and the cooling rate on the ice nucleation efficiencies was investigated. Ice nucleation active surface site (INAS) densities were calculated to quantify the ice nucleation efficiency as a function of temperature, humidity and the aerosol surface area concentration. Additionally, a contact angle parameterization according to classical nucleation theory was fitted to the experimental data in order to relate the ice nucleation efficiencies to contact angle distributions. From this study it can be concluded that the INAS density formulation is a very useful tool to describe the temperature- and humidity-dependent ice nucleation efficiency of ATD particles. Deposition nucleation on ATD particles can be described by a temperature- and relative-humidity-dependent INAS density function ns(T, Sice) with ns(xtherm) = 1.88 ×105 · exp(0.2659 · xtherm) [m-2] , (1) where the temperature- and saturation-dependent function xtherm is defined as xtherm = -(T-273.2)+(Sice-1) ×100, (2) with the saturation ratio with respect to ice Sice >1 and within a temperature range between 226 and 250 K. For lower temperatures, xtherm deviates from a linear behavior with temperature and relative humidity over ice. Also, two different approaches for describing the time dependence of deposition nucleation initiated by ATD particles are proposed. Box model estimates suggest that the time-dependent contribution is only relevant for small cooling rates and low number fractions of ice-active particles.

  9. High density of benzodiazepine binding sites in the substantia innominata of the rat

    SciTech Connect

    Sarter, M.; Schneider, H.H.

    1988-07-01

    In order to study the neuronal basis of the pharmacological interactions between benzodiazepine receptor ligands and cortical cholinergic turnover, we examined the regional distribution of specific benzodiazepine binding sites using in vitro autoradiography. In the basal forebrain, the substantia innominata contained a high density of (/sup 3/H)lormetazepam (LMZ) binding sites (Bmax = 277 fmol/mg tissue; Kd = 0.55 nM). The label could be displaced by diazepam (IC50 = 100 nM), the benzodiazepine receptor antagonist beta-carboline ZK 93426 (45 nM) and the partial inverse agonist beta-carboline FG 7142 (540 nM). It is hypothesized that the amnesic effects of benzodiazepine receptor agonists are exerted through benzodiazepine receptors which are situated on cholinergic neurons in the substantia innominata and are involved in a tonic inhibition of cortical acetylcholine release. The benzodiazepine receptor antagonist ZK 93426 may exert its nootropic effects via benzodiazepine receptors in the substantia innominata and, consequently, by disinhibiting cortical acetylcholine release.

  10. 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}.

  11. 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

  12. 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

  13. 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.

  14. 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. PMID:23274263

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

    NASA Astrophysics Data System (ADS)

    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.

  16. 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

  17. Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices

    PubMed Central

    Dunn, Katherine A.; Jiang, Wenyi; Field, Christopher; Bielawski, Joseph P.

    2013-01-01

    Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of mitochondrial evolution should be accommodated through lineage-specific amino-acid exchangeability matrices (e.g., mtMam for mammalian data). However, such a matrix must be applied to all sites and this implies that all sites are subject to the same, or largely similar, evolutionary constraints. This assumption is unjustified. Indeed, substantial differences are expected to arise from three-dimensional structures that impose different physiochemical environments on individual amino acid residues. The objectives of this paper are (1) to investigate the extent to which amino acid evolution varies among sites of mitochondrial proteins, and (2) to assess the potential benefits of explicitly modeling such variability. To achieve this, we developed a novel method for partitioning sites based on amino acid physiochemical properties. We apply this method to two datasets derived from complete mitochondrial genomes of mammals and fish, and use maximum likelihood to estimate amino acid exchangeabilities for the different groups of sites. Using this approach we identified large groups of sites evolving under unique physiochemical constraints. Estimates of amino acid exchangeabilities differed significantly among such groups. Moreover, we found that joint estimates of amino acid exchangeabilities do not adequately represent the natural variability in evolutionary processes among sites of mitochondrial proteins. Significant improvements in likelihood are obtained when the new matrices are employed. We also find that maximum likelihood estimates of branch lengths can be strongly impacted. We provide sets of matrices suitable for groups of sites subject to similar physiochemical constraints, and discuss how they might be used to analyze real data. We also discuss how

  18. Transport and signaling via the amino acid binding site of the yeast Gap1 amino acid transceptor.

    PubMed

    Van Zeebroeck, Griet; Bonini, Beatriz Monge; Versele, Matthias; Thevelein, Johan M

    2009-01-01

    Transporter-related nutrient sensors, called transceptors, mediate nutrient activation of signaling pathways through the plasma membrane. The mechanism of action of transporting and nontransporting transceptors is unknown. We have screened 319 amino acid analogs to identify compounds that act on Gap1, a transporting amino acid transceptor in yeast that triggers activation of the protein kinase A pathway. We identified competitive and noncompetitive inhibitors of transport, either with or without agonist action for signaling, including nontransported agonists. Using substituted cysteine accessibility method (SCAM) analysis, we identified Ser388 and Val389 as being exposed into the amino acid binding site, and we show that agonist action for signaling uses the same binding site as used for transport. Our results provide the first insight, to our knowledge, into the mechanism of action of transceptors. They indicate that signaling requires a ligand-induced specific conformational change that may be part of but does not require the complete transport cycle. PMID:19060912

  19. 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

  20. 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.

  1. The nest site lottery: how selectively neutral density dependent growth suppression induces frequency dependent selection.

    PubMed

    Argasinski, K; Broom, M

    2013-12-01

    Modern developments in population dynamics emphasize the role of the turnover of individuals. In the new approaches stable population size is a dynamic equilibrium between different mortality and fecundity factors instead of an arbitrary fixed carrying capacity. The latest replicator dynamics models assume that regulation of the population size acts through feedback driven by density dependent juvenile mortality. Here, we consider a simplified model to extract the properties of this approach. We show that at the stable population size, the structure of the frequency dependent evolutionary game emerges. Turnover of individuals induces a lottery mechanism where for each nest site released by a dead adult individual a single newborn is drawn from the pool of newborn candidates. This frequency dependent selection leads towards the strategy maximizing the number of newborns per adult death. However, multiple strategies can maximize this value. Among them, the strategy with the greatest mortality (which implies the greatest instantaneous growth rate) is selected. This result is important for the discussion about universal fitness measures and which parameters are maximized by natural selection. This is related to the fitness measures R0 and r, because the number of newborns per single dead individual equals the lifetime production of newborn R0 in models without aging. We thus have a two-stage procedure, instead of a single fitness measure, which is a combination of R0 and r. According to the nest site lottery mechanism, at stable population size, selection favors strategies with the greatest r, i.e. those with the highest turnover, from those with the greatest R0. PMID:24071631

  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. 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

  4. Disulfuric acid dissociated by two water molecules: ab initio and density functional theory calculations.

    PubMed

    Kim, Seong Kyu; Lee, Han Myoung; Kim, Kwang S

    2015-11-21

    We have studied geometries, energies and vibrational spectra of disulfuric acid (H2S2O7) and its anion (HS2O7(-)) hydrated by a few water molecules, using density functional theory (M062X) and ab initio theory (SCS-MP2 and CCSD(T)). The most noteworthy result is found in H2S2O7(H2O)2 in which the lowest energy conformer shows deprotonated H2S2O7. Thus, H2S2O7 requires only two water molecules, the fewest number of water molecules for deprotonation among various hydrated monomeric acids reported so far. Even the second deprotonation of the first deprotonated species HS2O7(-) needs only four water molecules. The deprotonation is supported by vibration spectra, in which acid O-H stretching peaks disappear and specific three O-H stretching peaks for H3O(+) (eigen structure) appear. We have also kept track of variations in several geometrical parameters, atomic charges, and hybrid orbital characters upon addition of water. As the number of water molecules added increases, the S-O bond weakens in the case of H2S2O7, but strengthens in the case of HS2O7(-). It implies that the decomposition leading to H2SO4 and SO3 hardly occurs prior to the 2nd deprotonation at low temperatures. PMID:26400266

  5. Ultra-high density single nanometer-scale anodic alumina nanofibers fabricated by pyrophosphoric acid anodizing.

    PubMed

    Kikuchi, Tatsuya; Nishinaga, Osamu; Nakajima, Daiki; Kawashima, Jun; Natsui, Shungo; Sakaguchi, Norihito; Suzuki, Ryosuke O

    2014-01-01

    Anodic oxide fabricated by anodizing has been widely used for nanostructural engineering, but the nanomorphology is limited to only two oxides: anodic barrier and porous oxides. Therefore, the discovery of an additional anodic oxide with a unique nanofeature would expand the applicability of anodizing. Here we demonstrate the fabrication of a third-generation anodic oxide, specifically, anodic alumina nanofibers, by anodizing in a new electrolyte, pyrophosphoric acid. Ultra-high density single nanometer-scale anodic alumina nanofibers (10(10) nanofibers/cm(2)) consisting of an amorphous, pure aluminum oxide were successfully fabricated via pyrophosphoric acid anodizing. The nanomorphologies of the anodic nanofibers can be controlled by the electrochemical conditions. Anodic tungsten oxide nanofibers can also be fabricated by pyrophosphoric acid anodizing. The aluminum surface covered by the anodic alumina nanofibers exhibited ultra-fast superhydrophilic behavior, with a contact angle of less than 1°, within 1 second. Such ultra-narrow nanofibers can be used for various nanoapplications including catalysts, wettability control, and electronic devices. PMID:25491282

  6. Ultra-High Density Single Nanometer-Scale Anodic Alumina Nanofibers Fabricated by Pyrophosphoric Acid Anodizing

    NASA Astrophysics Data System (ADS)

    Kikuchi, Tatsuya; Nishinaga, Osamu; Nakajima, Daiki; Kawashima, Jun; Natsui, Shungo; Sakaguchi, Norihito; Suzuki, Ryosuke O.

    2014-12-01

    Anodic oxide fabricated by anodizing has been widely used for nanostructural engineering, but the nanomorphology is limited to only two oxides: anodic barrier and porous oxides. Therefore, the discovery of an additional anodic oxide with a unique nanofeature would expand the applicability of anodizing. Here we demonstrate the fabrication of a third-generation anodic oxide, specifically, anodic alumina nanofibers, by anodizing in a new electrolyte, pyrophosphoric acid. Ultra-high density single nanometer-scale anodic alumina nanofibers (1010 nanofibers/cm2) consisting of an amorphous, pure aluminum oxide were successfully fabricated via pyrophosphoric acid anodizing. The nanomorphologies of the anodic nanofibers can be controlled by the electrochemical conditions. Anodic tungsten oxide nanofibers can also be fabricated by pyrophosphoric acid anodizing. The aluminum surface covered by the anodic alumina nanofibers exhibited ultra-fast superhydrophilic behavior, with a contact angle of less than 1°, within 1 second. Such ultra-narrow nanofibers can be used for various nanoapplications including catalysts, wettability control, and electronic devices.

  7. Ultra-High Density Single Nanometer-Scale Anodic Alumina Nanofibers Fabricated by Pyrophosphoric Acid Anodizing

    PubMed Central

    Kikuchi, Tatsuya; Nishinaga, Osamu; Nakajima, Daiki; Kawashima, Jun; Natsui, Shungo; Sakaguchi, Norihito; Suzuki, Ryosuke O.

    2014-01-01

    Anodic oxide fabricated by anodizing has been widely used for nanostructural engineering, but the nanomorphology is limited to only two oxides: anodic barrier and porous oxides. Therefore, the discovery of an additional anodic oxide with a unique nanofeature would expand the applicability of anodizing. Here we demonstrate the fabrication of a third-generation anodic oxide, specifically, anodic alumina nanofibers, by anodizing in a new electrolyte, pyrophosphoric acid. Ultra-high density single nanometer-scale anodic alumina nanofibers (1010 nanofibers/cm2) consisting of an amorphous, pure aluminum oxide were successfully fabricated via pyrophosphoric acid anodizing. The nanomorphologies of the anodic nanofibers can be controlled by the electrochemical conditions. Anodic tungsten oxide nanofibers can also be fabricated by pyrophosphoric acid anodizing. The aluminum surface covered by the anodic alumina nanofibers exhibited ultra-fast superhydrophilic behavior, with a contact angle of less than 1°, within 1 second. Such ultra-narrow nanofibers can be used for various nanoapplications including catalysts, wettability control, and electronic devices. PMID:25491282

  8. 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.

  9. Low density lipoprotein aged in plasma forms clusters resembling subendothelial droplets: aggregation via surface sites.

    PubMed

    De Spirito, Marco; Brunelli, Roberto; Mei, Giampiero; Bertani, Francesca R; Ciasca, Gabriele; Greco, Giulia; Papi, Massimiliano; Arcovito, Giuseppe; Ursini, Fulvio; Parasassi, Tiziana

    2006-06-01

    In early phases of atherogenesis, droplets and vesicles accumulate in the subendothelial extracellular space of arterial intima. There is much evidence to suggest that these droplets, ranging between 100 and 400 nm, derive from modified low-density lipoprotein (LDL). In investigations of the formation mechanism of these droplets, LDL fusion was previously induced in vitro by proteolysis, lipolysis, oxidation, and vigorous shaking, but all treatments failed to reproduce the size distribution range of in vivo droplets, mostly resulting, instead, in particles with a diameter intermediate between that of one and two LDL. Our approach was meant to mimic LDL aging in plasma. LDL isolated from plasma that was incubated overnight at 37 degrees C is slightly modified in the secondary structure of its protein component and is primed to form very large aggregates according to a reaction-limited mechanism. This mechanism requires interactions between selected surface sites, whereas massive fusion is ruled out. In the frame of the general theory for colloids, the aggregation of LDL aged in plasma fulfills all the requirements of the reaction-limited mechanism, encompassing 1), exponential growth; 2), fractal structure, with the dimension of elementary constituent still consistent with a single LDL; and 3), extreme polydispersity of aggregates, with shape and dimension very close to that of droplets observed in vivo. PMID:16533854

  10. Low Density Lipoprotein Aged in Plasma Forms Clusters Resembling Subendothelial Droplets: Aggregation via Surface Sites

    PubMed Central

    De Spirito, Marco; Brunelli, Roberto; Mei, Giampiero; Bertani, Francesca R.; Ciasca, Gabriele; Greco, Giulia; Papi, Massimiliano; Arcovito, Giuseppe; Ursini, Fulvio; Parasassi, Tiziana

    2006-01-01

    In early phases of atherogenesis, droplets and vesicles accumulate in the subendothelial extracellular space of arterial intima. There is much evidence to suggest that these droplets, ranging between 100 and 400 nm, derive from modified low-density lipoprotein (LDL). In investigations of the formation mechanism of these droplets, LDL fusion was previously induced in vitro by proteolysis, lipolysis, oxidation, and vigorous shaking, but all treatments failed to reproduce the size distribution range of in vivo droplets, mostly resulting, instead, in particles with a diameter intermediate between that of one and two LDL. Our approach was meant to mimic LDL aging in plasma. LDL isolated from plasma that was incubated overnight at 37°C is slightly modified in the secondary structure of its protein component and is primed to form very large aggregates according to a reaction-limited mechanism. This mechanism requires interactions between selected surface sites, whereas massive fusion is ruled out. In the frame of the general theory for colloids, the aggregation of LDL aged in plasma fulfills all the requirements of the reaction-limited mechanism, encompassing 1), exponential growth; 2), fractal structure, with the dimension of elementary constituent still consistent with a single LDL; and 3), extreme polydispersity of aggregates, with shape and dimension very close to that of droplets observed in vivo. PMID:16533854

  11. 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.

  12. 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.

  13. Evolution of HLA class II molecules: Allelic and amino acid site variability across populations.

    PubMed Central

    Salamon, H; Klitz, W; Easteal, S; Gao, X; Erlich, H A; Fernandez-Viña, M; Trachtenberg, E A; McWeeney, S K; Nelson, M P; Thomson, G

    1999-01-01

    Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations. PMID:10224269

  14. Decreased GABA(A) benzodiazepine binding site densities in postmortem brains of Cloninger type 1 and 2 alcoholics.

    PubMed

    Laukkanen, Virpi; Storvik, Markus; Häkkinen, Merja; Akamine, Yumiko; Tupala, Erkki; Virkkunen, Matti; Tiihonen, Jari

    2013-03-01

    Ethanol modulates the GABA(A) receptor to cause sedative, anxiolytic and hypnotic effects that are qualitatively similar to benzodiazepines and barbiturates. The aim of this study was to explore if GABA(A) receptor density is altered in post-mortem brains of anxiety-prone Cloninger type 1 and socially hostile type 2 alcoholic subtypes when compared to controls. The GABA(A) binding site density was measured by whole-hemisphere autoradiography with tritium labeled flunitrazepam ([(3)H]flunitrazepam) from 17 alcoholic (nine type 1, eight type 2) and 10 non-alcoholic post-mortem brains, using cold flumazepam as a competitive ligand. A total of eight specific brain areas were examined. Alcoholics displayed a significantly (p < 0.001, bootstrap type generalizing estimating equations model) reduced [(3)H]flunitrazepam binding site density when compared to controls. When localized, type 2 alcoholics displayed a significantly (p ≤ 0.05) reduced [(3)H]flunitrazepam binding site density in the internal globus pallidus, the gyrus dentatus and the hippocampus, whereas type 1 alcoholics differed from controls in the internal globus pallidus and the hippocampus. While previous reports have demonstrated significant alterations in dopaminergic and serotonergic receptors between type 1 and type 2 alcoholics among these same subjects, we observed no statistically significant difference in [(3)H]flunitrazepam binding site densities between the Cloninger type 1 and type 2 alcoholics. PMID:23332316

  15. 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.

  16. 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

  17. [THE BECOMING IN PHYLOGENESIS OF TRANSFER IN INTERCELLULAR MEDIUM AND ACTIVE ABSORPTION OF POLYENOIC FATTY ACIDS BY CELLS SEQUENTIALLY OF HIGH DENSITY LIPOPROTEINS, LOW DENSITY LIPOPROTEINS AND HIGH DENSITY APOE-LIPOPROTEINS].

    PubMed

    Titov, V N

    2015-06-01

    After more than half-century of different conceptions, the theory of general pathology was used to substantiate that all lipoproteins are bi-layer:lipid by their structure. The main function of high density lipoproteins as of all lipoproteins is transfer of fatty acids to cells and only in second turn taking away of spirit cholesterol from cells. At the stages of phylogenesis high density lipoproteins, low density lipoproteins and very low density lipoproteins began to function in a subsequent way. The fatty acids were transferred by low density lipoproteins in polar lipids at passive absorption by cells. Later on, lipoproteins transfer fatty acids in non-polar ethers with spirits glycerin and spirit cholesterol. The cells absorb them by receptor endocytosis. The hepatocytes secret in blood palmitic, oleic, linoleic and linoleic very low density lipoproteins. The palmitic and oleic very low density lipoproteins absorb physiologically insulin-dependent cells apoE/B-100 = endocytosis. The linoleic and linoleic very low density lipoproteins after transition of polyethers cholesterol from high density lipoproteins turn into low density lipoproteins. The cells absorb them by apoB-100 = endocytosis. The formation of chylomicrons occurs in blood and hepatocytes absorb them by the way of apoB/E-48 = endocytosis. The absorption of poly-unsaturated fatty acids by cells with apoB-100 = endocytosis form sensitivity of animals to exogenous hyper spirit cholesterol and absorption of poly-unsaturated fatty acids by apoE/A-I = receptors form corresponding resistance. The ApoE in lipoproteins form cooperative ligands--apoE/B-48 for chylomicrons, apoE/B-100 for very low density lipoproteins and apoE/A-I for high density lipoproteins. The chylomicrons in blood form apoB-48 from complexes of triglycerides secreted by enterocytes. These views change conceptions of pathogenesis and prevention of atherosclerosis, metabolic syndrome and resistance to insulin whose pathogenesis is unified

  18. Critical Current Density Performance of Malic Acid Doped Magnesium Diboride Wires at Different Operating Temperatures

    NASA Astrophysics Data System (ADS)

    Xu, X.; Kim, J. H.; Zhang, Y.; Jercinovic, M.; Babic, E.

    We investigated the effects of different operating temperatures on the performance of transport critical current density, Jc, for MgB2 + 10 wt% C4H6O5 MgB2/Fe wires. It was shown that the Jc values of the malic acid doped wires sintered at 900°C reached 104 Acm-2 at 20 K and 5 T. The Jc value extrapolated to 2 T and 20 K exceeds the practical level of 105 Acm-2. According to the Kramer plots, the pinning force, FK = Jc1/2 x B1/4, is expected to be a linear function of magnetic field B. The irreversibility field, Birr, at which extrapolated FK reaches zero, was 1.8 T at 32.8 K, 2.8 T at 30 K, 5.7 T at 25 K, 8.6 T at 20 K, and 12.5 T at 15 K, respectively.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Spectroscopic and density functional theory studies of trans-3-(trans-4-imidazolyl)acrylic acid.

    PubMed

    Arjunan, V; Remya, P; Sathish, U; Rani, T; Mohan, S

    2014-08-14

    The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry of trans-3-(trans-4-imidazolyl)acrylic acid have been determined from B3LYP methods with 6-311++G(**) and cc-pVTZ basis sets. The effects of substituents (acrylyl group) on the imidazole vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of trans-3-(trans-4-imidazolyl)acrylic acid have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. (1)H and (13)C NMR isotropic chemical shifts are calculated and the assignments made are compared with the experimental values. The energies of important MO's of the compound are also determined from DFT method. The total electron density and electrostatic potential of the compound are determined by natural bond orbital analysis. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities employing natural population analysis (NPA) are calculated. PMID:24755636

  4. Spectroscopic and density functional theory studies of trans-3-(trans-4-imidazolyl)acrylic acid

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Remya, P.; Sathish, U.; Rani, T.; Mohan, S.

    2014-08-01

    The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry of trans-3-(trans-4-imidazolyl)acrylic acid have been determined from B3LYP methods with 6-311++G** and cc-pVTZ basis sets. The effects of substituents (acrylyl group) on the imidazole vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of trans-3-(trans-4-imidazolyl)acrylic acid have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. 1H and 13C NMR isotropic chemical shifts are calculated and the assignments made are compared with the experimental values. The energies of important MO’s of the compound are also determined from DFT method. The total electron density and electrostatic potential of the compound are determined by natural bond orbital analysis. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities employing natural population analysis (NPA) are calculated.

  5. 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.

  6. Low-density lipoprotein-mediated delivery of docosahexaenoic acid selectively kills murine liver cancer cells

    PubMed Central

    Reynolds, Lacy; Mulik, Rohit S.; Wen, Xiaodong; Dilip, Archana; Corbin, Ian R.

    2014-01-01

    Aim The natural omega-3 polyunsaturated fatty acid, docosahexaenoic acid (DHA), has recently been credited for possessing anticancer properties. Herein, we investigate the cytotoxic actions of DHA-loaded low-density lipoprotein (LDL) nanoparticles in normal and liver cancer cells. Materials & methods LDL-DHA nanoparticles were prepared and subjected to extensive biophysical characterization. The therapeutic utility of LDL-DHA nanoparticles was evaluated in normal and malignant murine hepatocyte cell lines, TIB-73 and TIB-75, respectively. Results & discussion The engineered LDL-DHA nanoparticles possessed enhanced physical and oxidative stabilities over native LDL and free DHA. Dose–response studies showed that therapeutic doses of LDL-DHA nanoparticles that completely killed TIB-75 were innocuous to TIB-73. The selective induction of lipid peroxidation and reactive oxygen species in the cancer cells was shown to play a central role in LDL-DHA nanoparticle-mediated cytotoxicity. Conclusion In summary, these findings indicate that LDL-DHA nanoparticles show great promise as a selective anticancer agent against hepatocellular carcinoma. PMID:24397600

  7. 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

  8. Effect of sun elevation upon remote sensing of ocean color over an acid waste dump site

    NASA Technical Reports Server (NTRS)

    Bressette, W. E.

    1978-01-01

    Photographic flights were made over an ocean acid waste dump site while dumping was in progress. The flights resulted in wide angle, broadband, spectral radiance film exposure data between the wavelengths of 500 to 900 nanometers for sun elevation angles ranging from 26 to 42 degrees. It is shown from densitometer data that the spectral signature of acid waste discharged into ocean water can be observed photographically, the influence of sun elevation upon remotely sensed apparent color can be normalized by using a single spectral band ratioing technique, and photographic quantification and mapping of acid waste through its suspended iron precipitate appears possible.

  9. 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.

  10. Identification and Pharmacological Characterization of Multiple Allosteric Binding Sites on the Free Fatty Acid 1 Receptor

    PubMed Central

    Lin, Daniel C.-H.; Guo, Qi; Luo, Jian; Zhang, Jane; Nguyen, Kathy; Chen, Michael; Tran, Thanh; Dransfield, Paul J.; Brown, Sean P.; Houze, Jonathan; Vimolratana, Marc; Jiao, Xian Yun; Wang, Yingcai; Birdsall, Nigel J. M.

    2012-01-01

    Activation of FFA1 (GPR40), a member of G protein-coupling receptor family A, is mediated by medium- and long-chain fatty acids and leads to amplification of glucose-stimulated insulin secretion, suggesting a potential role for free fatty acid 1 (FFA1) as a target for type 2 diabetes. It was assumed previously that there is a single binding site for fatty acids and synthetic FFA1 agonists. However, using members of two chemical series of partial and full agonists that have been identified, radioligand binding interaction studies revealed that the full agonists do not bind to the same site as the partial agonists but exhibit positive heterotropic cooperativity. Analysis of functional data reveals positive functional cooperativity between the full agonists and partial agonists in various functional assays (in vitro and ex vivo) and also in vivo. Furthermore, the endogenous fatty acid docosahexaenoic acid (DHA) shows negative or neutral cooperativity with members of both series of agonists in binding assays but displays positive cooperativity in functional assays. Another synthetic agonist is allosteric with members of both agonist series, but apparently competitive with DHA. Therefore, there appear to be three allosterically linked binding sites on FFA1 with agonists specific for each of these sites. Activation of free fatty acid 1 receptor (FFAR1) by each of these agonists is differentially affected by mutations of two arginine residues, previously found to be important for FFAR1 binding and activation. These ligands with their high potencies and strong positive functional cooperativity with endogenous fatty acids, demonstrated in vitro and in vivo, have the potential to deliver therapeutic benefits. PMID:22859723

  11. Identification and pharmacological characterization of multiple allosteric binding sites on the free fatty acid 1 receptor.

    PubMed

    Lin, Daniel C-H; Guo, Qi; Luo, Jian; Zhang, Jane; Nguyen, Kathy; Chen, Michael; Tran, Thanh; Dransfield, Paul J; Brown, Sean P; Houze, Jonathan; Vimolratana, Marc; Jiao, Xian Yun; Wang, Yingcai; Birdsall, Nigel J M; Swaminath, Gayathri

    2012-11-01

    Activation of FFA1 (GPR40), a member of G protein-coupling receptor family A, is mediated by medium- and long-chain fatty acids and leads to amplification of glucose-stimulated insulin secretion, suggesting a potential role for free fatty acid 1 (FFA1) as a target for type 2 diabetes. It was assumed previously that there is a single binding site for fatty acids and synthetic FFA1 agonists. However, using members of two chemical series of partial and full agonists that have been identified, radioligand binding interaction studies revealed that the full agonists do not bind to the same site as the partial agonists but exhibit positive heterotropic cooperativity. Analysis of functional data reveals positive functional cooperativity between the full agonists and partial agonists in various functional assays (in vitro and ex vivo) and also in vivo. Furthermore, the endogenous fatty acid docosahexaenoic acid (DHA) shows negative or neutral cooperativity with members of both series of agonists in binding assays but displays positive cooperativity in functional assays. Another synthetic agonist is allosteric with members of both agonist series, but apparently competitive with DHA. Therefore, there appear to be three allosterically linked binding sites on FFA1 with agonists specific for each of these sites. Activation of free fatty acid 1 receptor (FFAR1) by each of these agonists is differentially affected by mutations of two arginine residues, previously found to be important for FFAR1 binding and activation. These ligands with their high potencies and strong positive functional cooperativity with endogenous fatty acids, demonstrated in vitro and in vivo, have the potential to deliver therapeutic benefits. PMID:22859723

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

    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.

  14. Modification of low-density lipoprotein by myeloperoxidase-derived oxidants and reagent hypochlorous acid.

    PubMed

    Malle, Ernst; Marsche, Gunther; Arnhold, Jürgen; Davies, Michael J

    2006-04-01

    Substantial evidence supports the notion that oxidative processes contribute to the pathogenesis of atherosclerosis and coronary heart disease. The nature of the oxidants that give rise to the elevated levels of oxidised lipids and proteins, and decreased levels of antioxidants, detected in human atherosclerotic lesions are, however, unclear, with multiple species having been invoked. Over the last few years, considerable data have been obtained in support of the hypothesis that oxidants generated by the heme enzyme myeloperoxidase play a key role in oxidation reactions in the artery wall. In this article, the evidence for a role of myeloperoxidase, and oxidants generated therefrom, in the modification of low-density lipoprotein, the major source of lipids in atherosclerotic lesions, is reviewed. Particular emphasis is placed on the reactions of the reactive species generated by this enzyme, the mechanisms and sites of damage, the role of modification of the different components of low-density lipoprotein, and the biological consequences of such oxidation on cell types present in the artery wall and in the circulation, respectively. PMID:16698314

  15. 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...

  16. 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...

  17. Site-specific growth and density control of carbon nanotubes by direct deposition of catalytic nanoparticles generated by spark discharge

    PubMed Central

    2013-01-01

    Catalytic iron nanoparticles generated by spark discharge were used to site-selectively grow carbon nanotubes (CNTs) and control their density. The generated aerosol nanoparticles were deposited on a cooled substrate by thermophoresis. The shadow mask on top of the cooled substrate enabled patterning of the catalytic nanoparticles and, thereby, patterning of CNTs synthesized by chemical vapor deposition. The density of CNTs could be controlled by varying the catalytic nanoparticle deposition time. It was also demonstrated that the density could be adjusted by changing the gap between the shadow mask and the substrate, taking advantage of the blurring effect of the deposited nanoparticles, for an identical deposition time. As all the processing steps for the patterned growth and density control of CNTs can be performed under dry conditions, we also demonstrated the integration of CNTs on fully processed, movable silicon microelectromechanical system (MEMS) structures. PMID:24090218

  18. Proton-Binding Sites of Acid-Sensing Ion Channel 1

    PubMed Central

    Ishikita, Hiroshi

    2011-01-01

    Acid-sensing ion channels (ASICs) are proton-gated cation channels that exist throughout the mammalian central and peripheral nervous systems. ASIC1 is the most abundant of all the ASICs and is likely to modulate synaptic transmission. Identifying the proton-binding sites of ASCI1 is required to elucidate its pH-sensing mechanism. By using the crystal structure of ASIC1, the protonation states of each titratable site of ASIC1 were calculated by solving the Poisson-Boltzmann equation under conditions wherein the protonation states of all these sites are simultaneously in equilibrium. Four acidic-acidic residue pairs—Asp238-Asp350, Glu220-Asp408, Glu239-Asp346, and Glu80-Glu417—were found to be highly protonated. In particular, the Glu80-Glu417 pair in the inner pore was completely protonated and possessed 2 H+, implying its possible importance as a proton-binding site. The pKa of Glu239, which forms a pair with a possible pH-sensing site Asp346, differs among each homo-trimer subunit due to the different H-bond pattern of Thr237 in the different protein conformations of the subunits. His74 possessed a pKa of ≈6–7. Conservation of His74 in the proton-sensitive ASIC3 that lacks a residue corresponding to Asp346 may suggest its possible pH-sensing role in proton-sensitive ASICs. PMID:21340031

  19. 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.

  20. 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.

  1. Density Functional Theory Study on the Interactions of Metal Ions with Long Chain Deprotonated Carboxylic Acids.

    PubMed

    Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Koch, Henrik; Åstrand, Per-Olof; Trinh, Thuat T; Grimes, Brian A

    2015-10-01

    In this work, interactions between carboxylate ions and calcium or sodium ions are investigated via density functional theory (DFT). Despite the ubiquitous presence of these interactions in natural and industrial chemical processes, few DFT studies on these systems exist in the literature. Special focus has been placed on determining the influence of the multibody interactions (with up to 4 carboxylates and one metal ion) on an effective pair-interaction potential, such as those used in molecular mechanics (MM). Specifically, DFT calculations are employed to quantify an effective pair-potential that implicitly includes multibody interactions to construct potential energy curves for carboxylate-metal ion pairs. The DFT calculated potential curves are compared to a widely used molecular mechanics force field (OPLS-AA). The calculations indicate that multibody effects do influence the energetic behavior of these ionic pairs and the extent of this influence is determined by a balance between (a) charge transfer from the carboxylate to the metal ions which stabilizes the complex and (b) repulsion between carboxylates, which destabilizes the complex. Additionally, the potential curves of the complexes with 1 and 2 carboxylates and one counterion have been examined to higher separation distance (20 Å) by the use of relaxed scan optimization and constrained density functional theory (CDFT). The results from the relaxed scan optimization indicate that near the equilibrium distance, the charge transfer between the metal ion and the deprotonated carboxylic acid group is significant and leads to non-negligible differences between the DFT and MM potential curves, especially for calcium. However, at longer separation distances the MM calculated interaction potential functions converge to those calculated with CDFT, effectively indicating the approximate domain of the separation distance coordinate where charge transfer between the ions is occurring. PMID:26331433

  2. Perfluorinated carboxylic acids in directly fluorinated high-density polyethylene material.

    PubMed

    Rand, Amy A; Mabury, Scott A

    2011-10-01

    Perfluorinated carboxylic acids (PFCAs) are ubiquitous in the environment and have been detected in human blood worldwide. One potential route is direct exposure to PFCAs through contact with polymers that have been fluorinated through a process referred to as direct fluorination. PFCAs are hypothesized to be reaction byproducts of direct fluorination when trace amounts of oxygen are present. The objective of this research was to investigate whether PFCAs could be measured in directly fluorinated high-density polyethylene (HDPE) bottles. PFCAs were quantified using Soxhlet extraction with methanol, followed by LC-MS/MS analysis. Total concentrations of PFCAs ranged from 8.5 ± 0.53 to 113 ± 2.5 ng/bottle (1 L), with the short-chain PFCAs, perfluoropropanoic, perfluorobutanoic, perfluoropentanoic, and perfluorohexanoic acids, being the dominant congeners observed. Relative PFCA concentrations varied depending on fluorination level. Structural isomers were detected using (19)F NMR and are hypothesized to have formed during the fluorination process; NMR data revealed the linear isomer typically comprised 55% of the examined sample. Internally branched, isopropyl branched, and t-butyl PFCA isomers of varying chain length were also identified. Electrochemical fluorination was previously thought to be the only source of branched PFCA isomers. The observation here of branched isomers suggests direct fluorination may be an additional source of exposure to these chemicals. The purpose of this study was to measure PFCAs in directly fluorinated material, serving as a previously unidentified source contributing to the environmental load of PFCAs, with potential for human exposure. PMID:21688793

  3. CD36 Binds Oxidized Low Density Lipoprotein (LDL) in a Mechanism Dependent upon Fatty Acid Binding*

    PubMed Central

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

    2015-01-01

    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. PMID:25555908

  4. Dopaminergic control of 125I-labeled neurotensin binding site density in corticolimbic structures of the rat brain.

    PubMed Central

    Herve, D; Tassin, J P; Studler, J M; Dana, C; Kitabgi, P; Vincent, J P; Glowinski, J; Rostene, W

    1986-01-01

    In the rat brain, destruction of dopaminergic cell groups by injections of 6-hydroxydopamine into the ventral mesencephalic tegmentum results in large decreases in the number of neurotensin binding sites in the mesencephalon and the striatum. In contrast, these lesions produce an increase in the number of 125I-labeled neurotensin binding sites in the lateral part of the prefrontal cortex despite a large decrease in cortical dopamine levels. Increases in the number of 125I-labeled neurotensin binding sites in this cortical area as well as in the entorhinal cortex, the nucleus accumbens, and the central part of the striatum were also obtained after chronic blockade of dopamine neurotransmission by a long-acting neuroleptic pipotiazine palmitic ester. We propose that dopamine inputs regulate the density of postsynaptic neurotensin binding sites through cortical and subcortical dopamine receptors. Therefore, some of the clinical effects of neuroleptics in schizophrenic patients could be partly related to changes in neurotensin neurotransmission. Images PMID:3016745

  5. Site-Specific Radiofluorination of Biomolecules with 8-[(18)F]-Fluorooctanoic Acid Catalyzed by Lipoic Acid Ligase.

    PubMed

    Drake, Christopher R; Sevillano, Natalia; Truillet, Charles; Craik, Charles S; VanBrocklin, Henry F; Evans, Michael J

    2016-06-17

    New methodologies for site-specifically radiolabeling proteins with (18)F are required to generate high quality radiotracers for preclinical and clinical applications with positron emission tomography. Herein, we report an approach by which we use lipoic acid ligase (LplA) to conjugate [(18)F]-fluorooctanoic acid to an antibody fragment bearing the peptide substrate of LplA. The mild conditions of the reaction preserve antibody immunoreactivity, and the efficiency of LplA allows for >90% yield even with very small amounts of peptidic precursor (1-10 nmol). These features are advantageous compared to the current gold standard in the field. Moreover, the methodology introduces a new application for an important tool in chemical biology. PMID:27008570

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Reexamination of the Association Between Melting Point, Buoyant Density, and Chemical Base Composition of Deoxyribonucleic Acid

    PubMed Central

    De Ley, J.

    1970-01-01

    The equations currently used for the calculation of the chemical base composition of deoxyribonucleic acid (DNA), expressed as moles per cent guanine plus cytosine (% GC), from either buoyant density (ρ) or midpoint of thermal denaturation (Tm) were recalculated by using only sets of data on DNA determined with the same strains. All available information from the literature was screened and supplemented by unpublished data. The results were calculated by regression and correlation analysis and treated statistically. From the data on 96 strains of bacteria, it was calculated that% GC = 2.44 (Tm – 69.4). Tm appears to be unaffected by the substitution of cytosine by hydroxymethylcytosine. This equation is also valid for nonbacterial DNA. From the data on 84 strains of bacteria, the relation% GC = 1038.47 (–1.6616) was calculated. The constants in this equation are slightly modified when data on nonbacterial DNA are included. Both correlations differ only slightly from those currently used, but now they lean on a statistically sound basis. As a control, the relation between ρ and Tm was calculated from data of 197 strains; it agrees excellently with the above two equations. PMID:5438045

  11. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Takahashi, Ohgi; Kirikoshi, Ryota

    2014-01-01

    Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.

  12. 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. PMID:26487699

  13. 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

  14. Biomass, productivity and density of the seagrass Thalassia testudinum at three sites in Cahuita National Park, Costa Rica.

    PubMed

    Paynter, C K; Cortés, J; Engels, M

    2001-12-01

    The basic ecology of seagrass beds was investigated by comparing biomass, productivity and density of Thalassia testudinum (turtle grass) at three sites: Puerto Vargas, Punta Cahuita and Rio Perezoso, in Cahuita National Park, Limón, Costa Rica, over a two month period (March-April 1999). Above ground biomass, density, and productivity were highest in the Puerto Vargas site while Punta Cahuita had the least non-green above ground biomass was significantly lower in total biomass than Puerto Vargas. Punta Cahuita was distinguished by the largest grain size, a very hard substrate, and shallower water. Rio Perezoso, on the other hand, had extremely fine sediment and lower salinity, while Puerto Vargas was intermediate both in sediment size and environmental conditions. It appears, therefore, that higher biomass and productivity result from a combination of moderate environmental characteristics and an intermediate sediment size. PMID:15264540

  15. 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.

  16. 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

  17. Site-Specific Characterization of d-Amino Acid Containing Peptide Epimers by Ion Mobility Spectrometry

    PubMed Central

    2013-01-01

    Traditionally, the d-amino acid containing peptide (DAACP) candidate can be discovered by observing the differences of biological activity and chromatographic retention time between the synthetic peptides and naturally occurring peptides. However, it is difficult to determine the exact position of d-amino acid in the DAACP candidates. Herein, we developed a novel site-specific strategy to rapidly and precisely localize d-amino acids in peptides by ion mobility spectrometry (IMS) analysis of mass spectrometry (MS)-generated epimeric fragment ions. Briefly, the d/l-peptide epimers were separated by online reversed-phase liquid chromatography and fragmented by collision-induced dissociation (CID), followed by IMS analysis. The epimeric fragment ions resulting from d/l-peptide epimers exhibit conformational differences, thus showing different mobilities in IMS. The arrival time shift between the epimeric fragment ions was used as criteria to localize the d-amino acid substitution. The utility of this strategy was demonstrated by analysis of peptide epimers with different molecular sizes, [d-Trp]-melanocyte-stimulating hormone, [d-Ala]-deltorphin, [d-Phe]-achatin-I, and their counterparts that contain all-l amino acids. Furthermore, the crustacean hyperglycemia hormones (CHHs, 8.5 kDa) were isolated from the American lobster Homarus americanus and identified by integration of MS-based bottom-up and top-down sequencing approaches. The IMS data acquired using our novel site-specific strategy localized the site of isomerization of l- to d-Phe at the third residue of the CHHs from the N-terminus. Collectively, this study demonstrates a new method for discovery of DAACPs using IMS technique with the ability to localize d-amino acid residues. PMID:24328107

  18. 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.

  19. beta-Hydroxyaspartic acid or beta-hydroxyasparagine in bovine low density lipoprotein receptor and in bovine thrombomodulin.

    PubMed

    Stenflo, J; Ohlin, A K; Owen, W G; Schneider, W J

    1988-01-01

    All of the vitamin K-dependent plasma proteins with domains that are homologous to the epidermal growth factor (EGF) precursor have 1 hydroxylated aspartic acid residue in the NH2-terminal EGF-homology region. In addition, protein S has 1 hydroxylated asparagine residue in each of the three COOH-terminal EGF-homology regions. All of these proteins have been found to have the amino acid sequence, CX(D or N)XXXX(F or Y)XCXC (corresponding to residues 20 to 33 in EGF), where the Asp or Asn residue is hydroxylated. This sequence also appears in two of the three EGF-homology regions of the human low density lipoprotein receptor and in two of the six EGF-homology regions of bovine thrombomodulin so far identified, suggesting that they may have the modified amino acid. We have now identified beta-hydroxyaspartic acid in acid hydrolysates of both these proteins. PMID:2826439

  20. 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.

  1. FT-IR characterization of the acidic and basic sites on a nanostructured aluminum nitride surface

    SciTech Connect

    Baraton, M.I.; Chen, X.; Gonsalves, K.E.

    1997-12-31

    A nanostructured aluminum nitride powder prepared by sol-gel type chemical synthesis is analyzed by Fourier transform infrared spectrometry. The surface acidic and basic sites are probed out by adsorption of several organic molecules. Resulting from the unavoidable presence of oxygen, the aluminum nitride surface is an oxinitride layer in fact, and its surface chemistry should present some analogies with alumina. Therefore, a thorough comparison between the acido-basicity of aluminum nitride and aluminum oxide is discussed. The remaining nitrogen atoms in the first atomic layer modify the acidity-basicity relative balance and reveals the specificity of the aluminum nitride surface.

  2. 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. PMID:24509720

  3. 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.

  4. 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

  5. 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.

  6. Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

    PubMed Central

    Martín, M. Cruz; Alonso, Juan C.; Suárez, Juan E.; Alvarez, Miguel A.

    2000-01-01

    The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation. PMID:10831443

  7. 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. PMID:12661689

  8. 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…

  9. Prevalence of Osteoporosis and Low Bone Mass in Older Chinese Population Based on Bone Mineral Density at Multiple Skeletal Sites.

    PubMed

    Lu, Yi-Chien; Lin, Ying Chin; Lin, Yen-Kuang; Liu, Yi-Jui; Chang, Kwang-Hwa; Chieng, Poon-Ung; Chan, Wing P

    2016-01-01

    Diagnosis of osteoporosis is based on bone mineral density (BMD) measurement, which is site dependent and commonly discordant between measurement sites. We aimed to determine the prevalence of osteoporosis diagnosed based on BMD T-scores measured by dual-energy x-ray absorptiometry (DXA) at different sites: the lumbar spine (LS) alone, femoral neck (FN) alone, or both. A total of 1712 women and 2028 men with LS and FN BMD measurements were enrolled. Over 50% discordance was found between osteoporosis classifications based on T-scores measured at the LS and FN. Use of the lowest T-scores measured at both the LS and right and left FN (rather than one site) significantly increased the prevalence of osteoporosis from 4.03 to 10.75% in postmenopausal women and 1.82 to 4.29% in men aged ≧50 years (p < 0.001). The trends of overall and age-adjusted prevalence of osteoporosis were similar in women and men. Osteoporosis was diagnosed at a higher rate if the USA reference rather than the Asia reference was used to calculate the T-score (26.64% vs. 10.75%). In conclusion, diagnosis based on the lowest T-score from multiple site BMD measurement can increase the prevalence of osteoporosis, demonstrating the higher sensitivity of the multiple site measurement strategy. PMID:27143609

  10. Prevalence of Osteoporosis and Low Bone Mass in Older Chinese Population Based on Bone Mineral Density at Multiple Skeletal Sites

    PubMed Central

    Lu, Yi-Chien; Lin, Ying Chin; Lin, Yen-Kuang; Liu, Yi-Jui; Chang, Kwang-Hwa; Chieng, Poon-Ung; Chan, Wing P.

    2016-01-01

    Diagnosis of osteoporosis is based on bone mineral density (BMD) measurement, which is site dependent and commonly discordant between measurement sites. We aimed to determine the prevalence of osteoporosis diagnosed based on BMD T-scores measured by dual-energy x-ray absorptiometry (DXA) at different sites: the lumbar spine (LS) alone, femoral neck (FN) alone, or both. A total of 1712 women and 2028 men with LS and FN BMD measurements were enrolled. Over 50% discordance was found between osteoporosis classifications based on T-scores measured at the LS and FN. Use of the lowest T-scores measured at both the LS and right and left FN (rather than one site) significantly increased the prevalence of osteoporosis from 4.03 to 10.75% in postmenopausal women and 1.82 to 4.29% in men aged ≧50 years (p < 0.001). The trends of overall and age-adjusted prevalence of osteoporosis were similar in women and men. Osteoporosis was diagnosed at a higher rate if the USA reference rather than the Asia reference was used to calculate the T-score (26.64% vs. 10.75%). In conclusion, diagnosis based on the lowest T-score from multiple site BMD measurement can increase the prevalence of osteoporosis, demonstrating the higher sensitivity of the multiple site measurement strategy. PMID:27143609

  11. 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

  12. Site-specific analysis of protein hydration based on unnatural amino acid fluorescence.

    PubMed

    Amaro, Mariana; Brezovský, Jan; Kováčová, Silvia; Sýkora, Jan; Bednář, David; Němec, Václav; Lišková, Veronika; Kurumbang, Nagendra Prasad; Beerens, Koen; Chaloupková, Radka; Paruch, Kamil; Hof, Martin; Damborský, Jiří

    2015-04-22

    Hydration of proteins profoundly affects their functions. We describe a simple and general method for site-specific analysis of protein hydration based on the in vivo incorporation of fluorescent unnatural amino acids and their analysis by steady-state fluorescence spectroscopy. Using this method, we investigate the hydration of functionally important regions of dehalogenases. The experimental results are compared to findings from molecular dynamics simulations. PMID:25815779

  13. Subgroup Variations in Bone Mineral Density Response to Zoledronic Acid After Hip Fracture

    PubMed Central

    Magaziner, Jay S; Orwig, Denise L; Lyles, Kenneth W; Nordsletten, Lars; Boonen, Steven; Adachi, Jonathan D; Recknor, Chris; Colón-Emeric, Cathleen S; Mesenbrink, Peter; Bucci-Rechtweg, Christina; Su, Guoqin; Johnson, Rasheeda; Pieper, Carl F

    2014-01-01

    Minimizing post-fracture bone loss is an important aspect of recovery from hip fracture, and determination of factors that affect bone mineral density (BMD) response to treatment after hip fracture may assist in the development of targeted therapeutic interventions. A post hoc analysis of the HORIZON Recurrent Fracture Trial was done to determine the effect of zoledronic acid (ZOL) on total hip (TH) and femoral neck (FN) BMD in subgroups with low-trauma hip fracture. A total of 2127 patients were randomized (1:1) to yearly infusions of ZOL 5 mg (n = 1065) or placebo (n = 1062) within 90 days of operation for low-trauma hip fracture. The 1486 patients with a baseline and at least one post-baseline BMD assessment at TH or FN (ZOL = 745, placebo = 741) were included in the analyses. Percentage change from baseline in TH and FN BMD was assessed at months 12 and 24 and compared across subgroups of hip fracture patients. Percentage change from baseline in TH and FN BMD at months 12 and 24 was greater (p < 0.05) in ZOL-treated patients compared with placebo in most subgroups. Treatment-by-subgroup interactions (p < 0.05) indicated that a greater effect on BMD was observed for TH BMD at month 12 in females, in patients in the lower tertile body mass index at baseline (≤22.6 kg/m2), and in patients with baseline FN BMD T-score of ≤ –2.5; for FN BMD in patients who received ZOL for >6 weeks post-surgery; and for TH and FN BMD in patients with a history of one or more prior fractures. All interactions were limited to the first 12 months after treatment with none observed for the 24-month comparisons. (Clinical trial registration number NCT00046254.) PMID:24839241

  14. 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

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

    USGS Publications Warehouse

    Robinson, G.R., Jr.; 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

  16. 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.

  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. 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.

  19. 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.

  20. 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.

  1. 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.

  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. 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

  4. 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 .

  5. 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.

  6. 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.

  7. Influence of adipic acid on tensile and morphology properties of linear low density polyethylene/rambutan peels flour blends

    NASA Astrophysics Data System (ADS)

    Nadhirah, A. A.; Sam, S. T.; Noriman, N. Z.; Ragunathan, S.; Ismail, H.

    2015-07-01

    This study investigate about the tensile and morphological properties of degradable polymer produced from linear low density polyethylene/rambutan peel flour (LLDPE/RPF) blends and adipic acid (AA) was used as a compatibilizer by varying the rambutan peel flour (RPF) amount from 0-25wt%. The samples were subjected to tensile and morphological tests. AA compatibilized showed higher strength compared to uncompatibilized blends. The Young's modulus for LLDPE/RPF blends increased with increasing flour content. However, the addition of adipic acid had reduced the Young's Modulus.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from

  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. Mechanism of dehydroxylation of naturally occurring high-silica zeolites involving the formation of Lewis acid sites

    SciTech Connect

    Kazanskii, V.B.

    1987-11-01

    Using low-temperature adsorbed dihydrogen and carbon monoxide as molecular probes, the dehydroxylation of the hydrogen forms of the zeolites Y, and ZSM-5 has been studied. The high stability of the high-silica zeolites to dealumination and their difference from faujasites has been established as being due not only to the strength of their Broensted acid sites but also to the nature of their Lewis acid sites. The chemical properties of the Lewis acid sites and their possible role in catalytic reactions are discussed.

  11. Solid-state NMR investigation of acid sites in dealuminated HZSM-5 zeolite.

    PubMed

    Deng, F; Du, Y; Ye, C H

    1996-01-01

    The acid sites and the hydration behaviors of dealuminated HZSM-5 zeolites (calcined at 550, 600, 650, and 700 degrees C) were characterized by high-resolution 1H MAS, 1H{27A1} spin-echo double resonance in combination with 27A1 MAS NMR. Apart from the usually observed peaks for dealuminated zeolite HZSM-5, a narrow plus a broad peak simultaneously appears at ca. 6.9 ppm in the 1H spectra and they exhibit different decay behavior in the 1H [27A1] double-resonance experiments. The existence of the former signal indicates that Lewis acid sites may'be formed in the zeolites after calcination. By means of the spin echo double resonance technique, we observed for the first time a previously unexpected narrow signal at 5.2 ppm, which resonates on the downfield side of Bronsted acid signal (4.3 ppm) and cannot be resolved in the 1H MAS spectra. This new signal is probably due to another kind of Bronsted acid site, locating in the small cages bounded by four- and five-membered rings. Three narrow peaks at 50 ppm, 30 ppm, and 0 ppm are superimposed on a very broad signal in the 27A1 MAS NMR spectra of dried HZSM-5. The intensity of the line at 50 ppm is significantly reduced compared with that of the rehydrated sample. 27A1 MAS NMR suggests that most part of the four-coordinated framework A1 turns into a intermediate case between four- and three-coordinated A1 after the dehydration and this process is reversible upon dehydration/rehydration. While some framework A1 atoms are transformed into three-coordinated A1 species and Lewis acid sites are, thus, generated in the dealuminated zeolites. For the signal at 30 ppm, the hydration leads to a dispersion in the chemical shift or the quadrupole interaction, which broadens its linewidth in hydrated samples. PMID:8970117

  12. Site characterization and containment/remediation of acid mine drainage at an abandoned mine waste dump

    SciTech Connect

    Djahanguiri, F.; Snodgrass, J.; Koerth, J.

    1996-12-31

    This paper focuses on the preliminary results of laboratory tests to evaluate a new suspension grout consisting of a mixture of a naturally occurring lignite coal based wax {open_quotes}montan wax{close_quotes}, sodium bentonite {open_quotes}pure gold grout{close_quotes}, and water. The test program assesses the suitability of the grout for creating subsurface containment barriers in coal waste dump sites for acid mine seepage control to surface and ground waters. The laboratory activities evaluated the reduction in permeability that could be achieved in a coal waste dump site under optimum conditions and the compatibility of the grout with representative waste from the test site. Information on geological, geochemical and geophysical about the test site is presented. Laboratory formulation of the grout is complete and simulation of field condition is in progress. Pregrout geophysical surveys for determination of hydrogeologic conditions at the site are also completed. Based on geophysical surveys, a grout curtain is proposed which will consist of two rows of grout placement holes in an array across the seepage area toward Belt Creek in Montana, Post-grout geophysical survey will be carried out immediately after grouting work. Performance of the grout curtain will be monitored by collection of water samples from monitoring wells in the Belt Creek and seepage area.

  13. 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.

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

    DOE PAGESBeta

    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

  15. 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

  16. 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

  17. 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

  18. 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...

  19. 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...

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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., Jr.; 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.

  5. In situ detection of salicylic acid binding sites in plant tissues.

    PubMed

    Liu, Jing-Wen; Deng, Da-Yi; Yu, Ying; Liu, Fang-Fei; Lin, Bi-Xia; Cao, Yu-Juan; Hu, Xiao-Gang; Wu, Jian-Zhong

    2015-02-01

    The determination of hormone-binding sites in plants is essential in understanding the mechanisms behind hormone function. Salicylic acid (SA) is an important plant hormone that regulates responses to biotic and abiotic stresses. In order to label SA-binding sites in plant tissues, a quantum dots (QDs) probe functionalized with a SA moiety was successfully synthesized by coupling CdSe QDs capped with 3-mercaptopropionic acid (MPA) to 4-amino-2-hydroxybenzoic acid (PAS), using 1-ethyl-3-(3-dimethyllaminopropyl) carbodiimide (EDC) as the coupling agent. The probe was then characterized by dynamic light scattering and transmission electron microscopy, as well as UV/vis and fluorescence spectrophotometry. The results confirmed the successful conjugation of PAS to CdSe QDs and revealed that the conjugates maintained the properties of the original QDs, with small core diameters and adequate dispersal in solution. The PAS-CdSe QDs were used to detect SA-binding sites in mung bean and Arabidopsis thaliana seedlings in vitro and in vivo. The PAS-CdSe QDs were effectively transported into plant tissues and specifically bound to SA receptors in vivo. In addition, the effects of the PAS-CdSe QDs on cytosolic Ca(2+) levels in the tips of A. thaliana seedlings were investigated. Both SA and PAS-CdSe QDs had similar effects on the trend in cytosolic-free Ca(2+) concentrations, suggesting that the PAS-CdSe QDs maintained the bioactivity of SA. To summarize, PAS-CdSe QDs have high potential as a fluorescent probe for the in vitro/in vivo labeling and imaging of SA receptors in plants. PMID:24833131

  6. Studies on the acidity of mordenite and ZSM-5. 1. Determination of Broensted acid site concentrations in mordenite and ZSM-5 by conductometric titration

    SciTech Connect

    Crocker, M.; Herold, R.H.M.; Sonnemans, M.H.W.; Emeis, C.A.; Wilson, A.E.; Moolen, J.N. van der )

    1993-01-14

    The Broensted acidity of H-mordenite and H-ZSM-5 samples of varying proton concentration has been studied using aqueous conductometric titration, IR spectroscopy, and aqueous potentiometric titration. Good agreement is observed between Broensted acid site concentrations determined by conductometric titration and IR measurements, while indirect potentiometric titration affords acid site concentrations consistently lower than those measured using the conductometric technique. This finding is rationalized on the basis that, in a conductometric titration, all the accessible Broensted acid sites are direct;y titrated, whereas in the potentiometric procedure utilized, only those protons which can be ion-exchanged out of the zeolite are titrated. After allowing for the presence of extraframework aluminum in the zeolites (determined by [sup 27]Al NMR), the measured acidity for H-mordenite is found to increase linearly with increasing Al content within the range 0-1.5 mmol Al/g but appears to reach a limiting value at higher Al concentrations. For H-ZSM-5, the experimentally determined number of Broensted acid sites is also found to be linearly dependent on the Al molar fraction within the range measured (0-1.20 mmol Al/g). For both series of zeolite samples, the measured acidity is generally found to be less than the theoretical maximum calculated on the basis of an H[sup +]/Al ratio of 1. 43 refs., 10 figs., 4 tabs.

  7. 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

  8. Enhanced concentrations of citric acid in spring aerosols collected at the Gosan background site in East Asia

    NASA Astrophysics Data System (ADS)

    Jung, Jinsang; Kawamura, Kimitaka

    2011-09-01

    In order to investigate water-soluble dicarboxylic acids and related compounds in the aerosol samples under the Asian continent outflow, total suspended particle (TSP) samples ( n = 32) were collected at the Gosan site in Jeju Island over 2-5 days integration during 23 March-1 June 2007 and 16-24 April 2008. The samples were analyzed for water-soluble dicarboxylic acids, ketocarboxylic acids, and α-dicarbonyls using a capillary gas chromatography technique. We found elevated concentrations of atmospheric citric acid (range: 20-320 ng m -3) in the TSP samples during mid- to late April of 2007 and 2008. To specify the sources of citric acid, dicarboxylic acids and related compounds were measured in the pollen sample collected at the Gosan site (Pollen_Gosan), authentic pollen samples from Japanese cedar ( Cryptomeria) (Pollen_cedar) and Japanese cypress ( Chamaecyparis obtusa) (Pollen_cypress), and tangerine fruit produced from Jeju Island. Citric acid (2790 ng in unit mg of pollen mass) was found as most abundant species in the Pollen_Gosan, followed by oxalic acid (2390 ng mg -1). Although citric acid was not detected in the Pollen_cedar and Pollen_cypress as major species, it was found as a dominant species in the tangerine juice while malic acid was detected as major species in the tangerine peel, followed by oxalic and citric acids. Since Japanese cedar trees are planted around tangerine farms to prevent strong winds from the Pacific Ocean, citric acid that may be directly emitted from tangerine is likely adsorbed on pollens emitted from Japanese cedar and then transported to the Gosan site. Much lower malic/citric acid ratios obtained under cloudy condition than clear condition suggest that malic acid may rapidly decompose to lower molecular weight compounds such as oxalic and malonic acids (

  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. 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

  11. 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

  12. Site-Specific Mapping of Sialic Acid Linkage Isomers by Ion Mobility Spectrometry.

    PubMed

    Guttman, Miklos; Lee, Kelly K

    2016-05-17

    Detailed structural elucidation of protein glycosylation is a tedious process often involving several techniques. Glycomics and glycoproteomics approaches with mass spectrometry offer a rapid platform for glycan profiling but are limited by the inability to resolve isobaric species such as linkage and positional isomers. Recently, ion mobility spectrometry (IMS) has been shown to effectively resolve isobaric oligosaccharides, but the utility of IMS to obtain glycan structural information on a site-specific level with proteomic analyses has yet to be investigated. Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. With further development IMS may hold the potential for rapid and complete structural elucidation of glycan chains at a site-specific level. PMID:27089023

  13. Chronic caffeine or theophylline exposure reduces gamma-aminobutyric acid/benzodiazepine receptor site interactions.

    PubMed

    Roca, D J; Schiller, G D; Farb, D H

    1988-05-01

    Methylxanthines, such as caffeine and theophylline, are adenosine receptor antagonists that exert dramatic effects upon the behavior of vertebrate animals by increasing attentiveness, anxiety, and convulsive activity. Benzodiazepines, such as flunitrazepam, generally exert behavioral effects that are opposite to those of methylxanthines. We report the finding that chronic exposure of embryonic brain neurons to caffeine or theophylline reduces the ability of gamma-aminobutyric acid (GABA) to potentiate the binding of [3H]flunitrazepam to the GABA/benzodiazepine receptor. This theophylline-induced "uncoupling" of GABA- and benzodiazepine-binding site allosteric interactions is blocked by chloroadenosine, an adenosine receptor agonist, indicating that the chronic effects of theophylline are mediated by a site that resembles an adenosine receptor. We speculate that adverse central nervous system effects of long-term exposure to methylxanthines such as in caffeine-containing beverages or theophylline-containing medications may be exerted by a cell-mediated modification of the GABAA receptor. PMID:2835648

  14. 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.

  15. 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

  16. Heavy metal binding to heparin disaccharides. I. Iduronic acid is the main binding site.

    PubMed

    Whitfield, D M; Choay, J; Sarkar, B

    1992-06-01

    As model compounds for Ni(II)-binding heparin-like compounds isolated from human kidneys (Templeton, D.M. & Sarkar, B. (1985) Biochem. J. 230 35-42.), we investigated two disaccharides--4-O-(2-O-sulfo-alpha-L-idopyranosyluronic acid)-2,5-anhydro- D-mannitol, disodium salt (1a), and 4-O-(2-O-sulfo-alpha-L-idopyranosyluronic acid)-6-O- sulfo-2,5-anhydro-D-mannitol, trisodium salt (1b)--that were isolated from heparin after nitrous acid hydrolysis and reduction. The monosulfate (1a) was active whereas the disulfate (1b) was inactive in a high-performance liquid chromatography (HPLC) binding assay with the tracer ions 63Ni(II) 54Mn(II), 65Zn(II), and 109Cd(II). This result is in accord with the isolation of two 67Cu(II) and 63Ni(II) binding fractions from a complete pool of nitrous-acid-derived heparin disaccharides using sulfate gradients and a MonoQ anion exchange column on an FPLC system. One was identified as compound (1a) and the other as a tetrasulfated trisaccharide by high resolution FAB-MS, NMR and HPLC-PAD. Similarly, two synthetic disaccharides-methyl, 2-O-sulfo-4-O-(alpha-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-alpha-D-glucosamine, trisodium salt [IdopA2S(alpha 1,4)GlcNS alpha Me, 2a], and 2-O-sulfo-4-O-(alpha-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-6-O-sulfo- alpha-D-glucosamine, tetrasodium salt [IdopA2S (alpha 1,4)GlcNS6S alpha Me, 2b]--were shown to bind tracer amounts of 63Ni and 67Cu using chromatographic assays. Subsequently, 1H NMR titrations of 1a, 1b, 2a, and 2b with Zn (OAc)2 were analyzed to yield 1:1 Zn(II)-binding constants of 472 +/- 59, 698 +/- 120, 8,758 +/- 2,237 and 20,100 +/- 5,598 M-1, respectively. The values for 2a and 2b suggest chelation. It is suggested that the idopyranosiduronic acid residue is the major metal binding site. NMR evidence for this hypothesis comes from marked 1H and 13C chemical shift changes to the iduronic acid resonances after addition of diamagnetic Zn(II) ions. PMID:1643264

  17. Minodronic acid ameliorates vertebral bone strength by increasing bone mineral density in 9-month treatment of ovariectomized cynomolgus monkeys.

    PubMed

    Tanaka, Makoto; Mori, Hiroshi; Kawabata, Kazuhito; Mashiba, Tasuku

    2016-07-01

    The effect of treatment for 9months with minodronic acid, a nitrogen-containing bisphosphonate, on vertebral mechanical strength was examined in ovariectomized (OVX) cynomolgus monkeys. Forty skeletally mature female monkeys were randomized into four OVX groups and one sham group (n=8) based on lumbar bone mineral density (BMD). OVX animals were treated orally with 15 and 150μg/kg QD of minodronic acid or 500μg/kg QD alendronate as a reference drug. Measurements of bone turnover markers and lumbar BMD were conducted at 0, 4 and 8months. Measurements of bone mechanical strength and minodronic acid concentration in vertebral bodies were also performed. OVX resulted in a decrease in lumbar BMD and an increase in bone turnover markers at 4 and 8months, compared to the sham group, and the ultimate load on the lumbar vertebra was decreased in OVX animals. Minodronic acid and alendronate prevented the OVX-induced increase in bone turnover markers and decrease in lumbar BMD. Minodronic acid at 150μg/kg increased the ultimate load on lumbar vertebra compared to untreated OVX animals. Regression analysis revealed that the ultimate load was correlated with lumbar BMD and bone mineral content (BMC), and most strongly with the increase in lumbar BMD and BMC over 8months. In a separate analysis within the sham-OVX controls and minodronic acid and alendronate treatment groups, the ultimate loads were also correlated with BMD and BMC. The load-BMD (BMC) correlation in the minodronic acid group showed a trend for a shift to a higher load from the basal relationship in the sham-OVX controls. These results indicate that treatment with minodronic acid for 9months increases vertebral mechanical strength in OVX monkeys, mainly by increasing BMD and BMC. PMID:27155564

  18. 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.

  19. SuccinSite: a computational tool for the prediction of protein succinylation sites by exploiting the amino acid patterns and properties.

    PubMed

    Hasan, Md Mehedi; Yang, Shiping; Zhou, Yuan; Mollah, Md Nurul Haque

    2016-03-01

    Lysine succinylation is an emerging protein post-translational modification, which plays an important role in regulating the cellular processes in both eukaryotic and prokaryotic cells. However, the succinylation modification site is particularly difficult to detect because the experimental technologies used are often time-consuming and costly. Thus, an accurate computational method for predicting succinylation sites may help researchers towards designing their experiments and to understand the molecular mechanism of succinylation. In this study, a novel computational tool termed SuccinSite has been developed to predict protein succinylation sites by incorporating three sequence encodings, i.e., k-spaced amino acid pairs, binary and amino acid index properties. Then, the random forest classifier was trained with these encodings to build the predictor. The SuccinSite predictor achieves an AUC score of 0.802 in the 5-fold cross-validation set and performs significantly better than existing predictors on a comprehensive independent test set. Furthermore, informative features and predominant rules (i.e. feature combinations) were extracted from the trained random forest model for an improved interpretation of the predictor. Finally, we also compiled a database covering 4411 experimentally verified succinylation proteins with 12 456 lysine succinylation sites. Taken together, these results suggest that SuccinSite would be a helpful computational resource for succinylation sites prediction. The web-server, datasets, source code and database are freely available at http://systbio.cau.edu.cn/SuccinSite/. PMID:26739209

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

    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 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.

  2. 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.

  3. Progression of changes in dopamine transporter binding site density as a result of cocaine self-administration in rhesus monkeys.

    PubMed

    Letchworth, S R; Nader, M A; Smith, H R; Friedman, D P; Porrino, L J

    2001-04-15

    The present study examined the time course of alterations in levels of dopamine transporter (DAT) binding sites that accompany cocaine self-administration using quantitative in vitro receptor autoradiography with [(3)H]WIN 35,428. The density of dopamine transporter binding sites in the striatum of rhesus monkeys with 5 d, 3.3 months, or 1.5 years of cocaine self-administration experience was compared with DAT levels in cocaine-naive control monkeys. Animals in the long-term (1.5 years) exposure group self-administered cocaine at 0.03 mg/kg per injection, whereas the initial (5 d) and chronic (3.3 months) treatment groups were each divided into lower dose (0.03 mg/kg per injection) and higher dose (0.3 mg/kg per injection) groups. Initial cocaine exposure led to moderate decreases in [(3)H]WIN 35,428 binding sites, with significant changes in the dorsolateral caudate (-25%) and central putamen (-19%) at the lower dose. Longer exposure, in contrast, resulted in elevated levels of striatal binding sites. The increases were most pronounced in the ventral striatum at the level of the nucleus accumbens shell. At the lower dose of the chronic phase, for example, significant increases of 21-42% were measured at the caudal level of the ventral caudate, ventral putamen, olfactory tubercle, and accumbens core and shell. Systematic variation of cocaine dose and drug exposure time demonstrated the importance of these factors in determining the intensity of increased DAT levels. With self-administration of higher doses especially, increases were more intense and included dorsal portions of the striatum so that every region at the caudal level exhibited a significant increase in DAT binding sites (20-54%). The similarity of these findings to previous studies in human cocaine addicts strongly suggest that the increased density of dopamine transporters observed in studies of human drug abusers are the result of the neurobiological effects of cocaine, ruling out confounds such as

  4. Mixed valency and site-preference chemistry for cerium and its compounds: A predictive density-functional theory study

    SciTech Connect

    Alam, Aftab; Johnson, Duane D.

    2014-06-01

    Cerium and its technologically relevant compounds are examples of anomalous mixed valency, originating from two competing oxidation states—itinerant Ce4+ and localized Ce3+. Under applied stress, anomalous transitions are observed but not well understood. Here we treat mixed valency as an “alloy” problem involving two valences with competing and numerous site-occupancy configurations. We use density-functional theory with Hubbard U (i.e., DFT+U) to evaluate the effective valence and predict properties, including controlling the valence by pseudoternary alloying. For Ce and its compounds, such as (Ce,La)2(Fe,Co)14B permanent magnets, we find a stable mixed-valent α state near the spectroscopic value of νs=3.53. Ce valency in compounds depends on its steric volume and local chemistry. For La doping, Ce valency shifts towards γ-like Ce3+, as expected from steric volume; for Co doping, valency depends on local Ce-site chemistry and steric volume. Our approach captures the key origins of anomalous valency and site-preference chemistry in complex compounds.

  5. Mixed valency and site-preference chemistry for cerium and its compounds: A predictive density-functional theory study

    NASA Astrophysics Data System (ADS)

    Alam, Aftab; Johnson, D. D.

    2014-06-01

    Cerium and its technologically relevant compounds are examples of anomalous mixed valency, originating from two competing oxidation states—itinerant Ce4+ and localized Ce3+. Under applied stress, anomalous transitions are observed but not well understood. Here we treat mixed valency as an "alloy" problem involving two valences with competing and numerous site-occupancy configurations. We use density-functional theory with Hubbard U (i.e., DFT+U) to evaluate the effective valence and predict properties, including controlling the valence by pseudoternary alloying. For Ce and its compounds, such as (Ce,La)2(Fe,Co)14B permanent magnets, we find a stable mixed-valent α state near the spectroscopic value of νs=3.53. Ce valency in compounds depends on its steric volume and local chemistry. For La doping, Ce valency shifts towards γ-like Ce3+, as expected from steric volume; for Co doping, valency depends on local Ce-site chemistry and steric volume. Our approach captures the key origins of anomalous valency and site-preference chemistry in complex compounds.

  6. Pseudomonas aeruginosa Cytotoxicity Is Attenuated at High Cell Density and Associated with the Accumulation of Phenylacetic Acid

    PubMed Central

    Wang, Jianhe; Dong, Yihu; Zhou, Tielin; Liu, Xiaoling; Deng, Yinyue; Wang, Chao; Lee, Jasmine; Zhang, Lian-Hui

    2013-01-01

    Background P. aeruginosa is known to cause acute cytotoxicity against various human and animal cells and tissues. Methodology/Findings Intriguingly, however, in this study we noticed that while a low cell density inoculum of P. aeruginosa caused severe cytotoxicity against human lung tissue cell line A549, increasing the cell density of bacterial inoculum led to decreased cytotoxicity. Addition of the supernatants from high density bacterial culture to low cell density inoculum protected the human cells from bacterial cytotoxic damage, suggesting that P. aeruginosa may produce and accumulate an inhibitory molecule(s) counteracting its pathogenic infection. The inhibitor was purified from the stationary-phase culture supernatants of P. aeruginosa strain PAO1 using bioassay-guided high performance liquid chromatography (HPLC), and characterized to be phenylacetic acid (PAA) by mass spectrometry and nuclear magnetic resonance spectroscopy. Microarray analysis revealed that treatment of P. aeruginosa with PAA down-regulated the transcriptional expression of Type III secretion system (T3SS) genes and related regulatory genes including rsmA and vfr, which were confirmed by transcriptional and translational analysis. Conclusions Identification of bacterial metabolite PAA as a T3SS-specific inhibitor explains this intriguing inverse cell-density-dependent-cytotoxicity phenomenon as T3SS is known to be a key virulence factor associated with cytotoxicity and acute infection. The findings may provide useful clues for design and development of new strategies to combat this formidable bacterial pathogen. PMID:23555919

  7. 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.

  8. 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.

  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. The effect of glutamic acid side chain on acidity constant of lysine in beta-sheet: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Sargolzaei, M.; Afshar, M.; Sadeghi, M. S.; Kavee, M.

    2014-07-01

    In this work, the possibility of proton transfer between side chain of lysine and glutamic acid in peptide of Glu--Ala-Lys+ was demonstrated using density functional theory (DFT). We have shown that the proton transfer takes place between side chain of glutamic and lysine residues through the hydrogen bond formation. The structures of transition state for proton transfer reaction were detected in gas and solution phases. Our kinetic studies show that the proton transfer reaction rate in gas phase is higher than solution phase. The ionization constant (p K a) value of lysine residue in peptide was estimated 1.039 which is lower than intrinsic p K a of lysine amino acid.

  11. Lysine residues direct the chlorination of tyrosines in YXXK motifs of apolipoprotein A-I when hypochlorous acid oxidizes high density lipoprotein.

    PubMed

    Bergt, Constanze; Fu, Xiaoyun; Huq, Nabiha P; Kao, Jeff; Heinecke, Jay W

    2004-02-27

    Oxidized lipoproteins may play an important role in the pathogenesis of atherosclerosis. Elevated levels of 3-chlorotyrosine, a specific end product of the reaction between hypochlorous acid (HOCl) and tyrosine residues of proteins, have been detected in atherosclerotic tissue. Thus, HOCl generated by the phagocyte enzyme myeloperoxidase represents one pathway for protein oxidation in humans. One important target of the myeloperoxidase pathway may be high density lipoprotein (HDL), which mobilizes cholesterol from artery wall cells. To determine whether activated phagocytes preferentially chlorinate specific sites in HDL, we used tandem mass spectrometry (MS/MS) to analyze apolipoprotein A-I that had been oxidized by HOCl. The major site of chlorination was a single tyrosine residue located in one of the protein's YXXK motifs (where X represents a nonreactive amino acid). To investigate the mechanism of chlorination, we exposed synthetic peptides to HOCl. The peptides encompassed the amino acid sequences YKXXY, YXXKY, or YXXXY. MS/MS analysis demonstrated that chlorination of tyrosine in the peptides that contained lysine was regioselective and occurred in high yield if the substrate was KXXY or YXXK. NMR and MS analyses revealed that the N(epsilon) amino group of lysine was initially chlorinated, which suggests that chloramine formation is the first step in tyrosine chlorination. Molecular modeling of the YXXK motif in apolipoprotein A-I demonstrated that these tyrosine and lysine residues are adjacent on the same face of an amphipathic alpha-helix. Our observations suggest that HOCl selectively targets tyrosine residues that are suitably juxtaposed to primary amino groups in proteins. This mechanism might enable phagocytes to efficiently damage proteins when they destroy microbial proteins during infection or damage host tissue during inflammation. PMID:14660678

  12. 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). PMID:24552064

  13. SITE EVALUATION OF INNOVATIVE SEMI-PASSIVE ACID MINE DRAINAGE TREATMENT TECHNOLOGIES AT THE SUMMITVILLE SUPERFUND SITE, COLORADO

    EPA Science Inventory

    The EPA SITE Program is conducting a detailed sampling and evaluation of two innovative passive mine drainage treatment technologies at the Summitville Superfund Mining site in Southern Colorado. The technologies evaluated include the Aquafix automatic hydraulic lime dispensing s...

  14. 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.

  15. 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 ...

  16. 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.

  17. 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.

  18. 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

  19. Generation of Broensted and Lewis acid sites on the surface of silica by addition of dopant cations

    SciTech Connect

    Connell, G.; Dumesic, J.A.

    1987-06-01

    Pyridine adsorption was used to study the acidic properties of silica doped with the following cations: Sc/sup 3 +/, Mg/sup 2 +/, Fe/sup 2 +/, Fe/sup 3 +/, Zn/sup 2 +/, Al/sup 3 +/, and Ga/sup 3 +/. All samples were exposed to pyridine at 423 K and subsequently evacuated at successively higher temperatures to 723 K. Infrared spectra of the adsorbed pyridine indicated that all of these cations generated Lewis acid sites. This can be explained by the presence of coordinatively unsaturated dopant cations on the surface of silica, in accord with a model based on Pauling's electrostatic bond strength rules. The infrared frequency of the 19b band of pyridine adsorbed on these Lewis acid sites was found to increase with increasing electronegativity of the dopant cation. It is suggested that both of these quantities are related to the strength of the Lewis acid sites. Broensted acid sites were also observed by infrared spectroscopy for Sc/sup 3 +/, Al/sup 3 +/, and Ga/sup 3 +/ on silica. These dopant cations are believed to be bonded tetrahedrally on the surface of silica, generating bridging hydroxyl groups between the dopant cation and Si/sup 4 +/. As for zeolite catalysts, the proton associated with these groups and required for charge neutrality is the Broensted acid site. Finally, Broensted acid sites can also be generated on silica by highly electronegative anions, such as HPO/sub 4//sup 2 -/, which generate Broensted acidity in a different manner. 55 references.

  20. Fabrication of hydrophobic polymer foams with double acid sites on surface of macropore for conversion of carbohydrate.

    PubMed

    Pan, Jianming; Mao, Yanli; Gao, Heping; Xiong, Qingang; Qiu, Fengxian; Zhang, Tao; Niu, Xiangheng

    2016-06-01

    Herein we reported a simple and novel synthetic strategy for the fabrication of two kinds of hydrophobic polymer foam catalysts (i.e. Cr(3+)-HPFs-1-H(+) and HPFs-1-H(+)) with hierarchical porous structure, inhomogeneous acidic composition and Lewis-Brønsted double acid sites distributed on the surface, which was used to one-pot conversion of carbohydrate (such as cellulose, glucose and fructose) to a key chemical platform (i.e. 5-hydroxymethylfurfural, HMF). The water-in-oil (W/O) high internal phase emulsions (HIPEs), stabilized by both Span 80 and acidic prepolymers as analogous particles offered the acidic actives, were used as the template for simultaneous polymerization of oil phase in the presence of divinylbenzene (DVB) and styrene (St). After subsequent ion-exchange process, Lewis and Brønsted acid sites derived from exchanged Cr(3+) and H(+) ion were both fixed on the surface of cell of the catalysts. The HPFs-1-H(+) and Cr(3+)-HPFs-1-H(+) had similar hierarchical porous, hydrophobic surface and acid sites (HPFs-1-H(+) with macropores ranging from 0.1 μm to 20 μm, uniform mesopores in 14.4 nm, water contact angle of 122° and 0.614 mmolg(-1) of Brønsted acid sites, as well as Cr(3+)-HPFs-1-H(+) with macropores ranging from 0.1 μm to 20 μm, uniform mesopores in 13.3 nm, water contact angle of 136° and 0.638 mmolg(-1) of Lewis-Brønsted acid sites). It was confirmed that Lewis acid sites of catalyst had a slight influence on the HMF yield of fructose came from the function of Brønsted acid sites, and Lewis acid sites were in favor of improving the HMF yield from cellulose and glucose. This work opens up a simple and novel route to synthesize multifunctional polymeric catalysts for efficient one-pot conversion of carbohydrate to HMF. PMID:27083362

  1. Dansyl labeling to modulate the relative affinity of bile acids for the binding sites of human serum albumin.

    PubMed

    Rohacova, Jana; Sastre, German; Marin, M Luisa; Miranda, Miguel A

    2011-09-01

    Binding of natural bile acids to human serum albumin (HSA) is an important step in enterohepatic circulation and provides a measure of liver function. In this article, we report on the use of four dansyl (Dns) derivatives of cholic acid (ChA) to demonstrate a regiodifferentiation in their relative affinity for the two binding sites of HSA. Using both steady-state and time-resolved fluorescence, formation of Dns-ChA@HSA complexes was confirmed; the corresponding binding constants were determined, and their distribution between bulk solution and HSA microenvironment was estimated. By means of energy transfer from Trp to the Dns moiety, donor-acceptor distances were estimated (21-25 Å) and found to be compatible with both site 1 and site 2 occupancies. Nevertheless, titration using warfarin and ibuprofen as specific displacement probes clearly indicated that 3α- and 3β-Dns-ChA bind to HSA at site 2, whereas their C-7 regioisomers bind to HSA at site 1. Furthermore, the C-3-labeled compounds are displaced by lithocholic acid, whereas they are insensitive to ChA, confirming the assumption that the former binds to HSA at site 2. Thus, Dns labeling provides a useful tool to modulate the relative affinity of ChA to the major binding sites of HSA and, in combination with other fluorescent ChA analogs, to mimic the binding behavior of natural bile acids. PMID:21797258

  2. Phase stability of Fe and Mn within density-functional theory plus on-site Coulomb interaction approaches

    NASA Astrophysics Data System (ADS)

    Stojić, N. L.; Binggeli, N. L.

    Approaches based on the density-functional theory and including the on-site Coulomb interaction U have been extensively used to describe strongly correlated systems. Moreover, it has been shown that even in the case of moderate correlations, present for example in some of the 3d transition metals, this and similar methods can improve upon the local-density and generalized-gradient approximation (LDA and GGA) results. We investigate, by means of the LDA+U and GGA+U approaches, the phase stability of Fe and Mn, for which it is known that the LDA predicts a wrong ground state. In particular, we compare two different double-counting corrections, the so called "fully-localized limit" (FLL) and "around mean-field" (AMF). We find that the LDA and the LDA+UAMF do not yield the correct ground state, while the LDA+UFLL, GGA+UAMF and GGA+UFLL for specific ranges of effective U values, typically around 1 eV, give the correct phase stability, and in general, an improved description of the equilibrium volume and magnetic moment, compared to the GGA values.

  3. The influence of hyaluronic acid hydrogel crosslinking density and macromolecular diffusivity on human MSC chondrogenesis and hypertrophy

    PubMed Central

    Bian, Liming; Hou, Chieh; Tous, Elena; Rai, Reena; Mauck, Robert L.; Burdick, Jason A.

    2012-01-01

    Hyaluronic acid (HA) hydrogels formed via photocrosslinking provide stable 3D hydrogel environments that support the chondrogenesis of mesenchymal stem cells (MSCs). Crosslinking density has a significant impact on the physical properties of hydrogels, including their mechanical stiffness and macromolecular diffusivity. Variations in the HA hydrogel crosslinking density can be obtained by either changes in the HA macromer concentration (1, 3, or 5% w/v at 15 min exposure) or the extent of reaction through light exposure time (5% w/v at 5, 10, or 15 min). In this work, increased crosslinking by either method resulted in an overall decrease in cartilage matrix content and more restricted matrix distribution. Increased crosslinking also promoted hypertrophic differentiation of the chondrogenically induced MSCs, resulting in more matrix calcification in vitro. For example, type X collagen expression in the high crosslinking density 5% 15 min group was ~156 and 285% higher when compared to the low crosslinking density 1% 15 min and 5% 5 min groups on day 42, respectively. Supplementation with inhibitors of the small GTPase pathway involved in cytoskeletal tension or myosin II had no effect on hypertrophic differentiation and matrix calcification, indicating that the differential response is unlikely to be related to force-sensing mechanotransduction mechanisms. When implanted subcutaneously in nude mice, higher crosslinking density again resulted in reduced cartilage matrix content, restricted matrix distribution, and increased matrix calcification. This study demonstrates that hydrogel properties mediated through alterations in crosslinking density must be considered in the context of the hypertrophic differentiation of chondrogenically induced MSCs. PMID:23084553

  4. The influence of hyaluronic acid hydrogel crosslinking density and macromolecular diffusivity on human MSC chondrogenesis and hypertrophy.

    PubMed

    Bian, Liming; Hou, Chieh; Tous, Elena; Rai, Reena; Mauck, Robert L; Burdick, Jason A

    2013-01-01

    Hyaluronic acid (HA) hydrogels formed via photocrosslinking provide stable 3D hydrogel environments that support the chondrogenesis of mesenchymal stem cells (MSCs). Crosslinking density has a significant impact on the physical properties of hydrogels, including their mechanical stiffness and macromolecular diffusivity. Variations in the HA hydrogel crosslinking density can be obtained by either changes in the HA macromer concentration (1, 3, or 5% w/v at 15 min exposure) or the extent of reaction through light exposure time (5% w/v at 5, 10, or 15 min). In this work, increased crosslinking by either method resulted in an overall decrease in cartilage matrix content and more restricted matrix distribution. Increased crosslinking also promoted hypertrophic differentiation of the chondrogenically induced MSCs, resulting in more matrix calcification in vitro. For example, type X collagen expression in the high crosslinking density 5% 15 min group was ~156 and 285% higher when compared to the low crosslinking density 1% 15 min and 5% 5 min groups on day 42, respectively. Supplementation with inhibitors of the small GTPase pathway involved in cytoskeletal tension or myosin II had no effect on hypertrophic differentiation and matrix calcification, indicating that the differential response is unlikely to be related to force-sensing mechanotransduction mechanisms. When implanted subcutaneously in nude mice, higher crosslinking density again resulted in reduced cartilage matrix content, restricted matrix distribution, and increased matrix calcification. This study demonstrates that hydrogel properties mediated through alterations in crosslinking density must be considered in the context of the hypertrophic differentiation of chondrogenically induced MSCs. PMID:23084553

  5. 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.

  6. Study on the mechanism of platinum-assisted hydrofluoric acid etching of SiC using density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Bui, P. V.; Isohashi, A.; Kizaki, H.; Sano, Y.; Yamauchi, K.; Morikawa, Y.; Inagaki, K.

    2015-11-01

    Hydrofluoric acid (HF) etching of the SiC surface assisted by Pt as a catalyst is investigated using density functional theory. Etching is initiated by the dissociative adsorption of HF on step-edge Si, forming a five-fold coordinated Si moiety as a metastable state. This is followed by breaking of the Si-C back-bond by a H-transfer process. The gross activation barrier strongly correlates with the stability of the metastable state and is reduced by the formation of Pt-O chemical bonds, leading to an enhancement of the etching reaction.

  7. Reconstituted high-density lipoprotein infusion modulates fatty acid metabolism in patients with type 2 diabetes mellitus

    PubMed Central

    Drew, Brian G.; Carey, Andrew L.; Natoli, Alaina K.; Formosa, Melissa F.; Vizi, Donna; Reddy-Luthmoodoo, Medini; Weir, Jacquelyn M.; Barlow, Christopher K.; van Hall, Gerrit; Meikle, Peter J.; Duffy, Stephen J.; Kingwell, Bronwyn A.

    2011-01-01

    We recently demonstrated that reconstituted high-density lipoprotein (rHDL) modulates glucose metabolism in humans via both AMP-activated protein kinase (AMPK) in muscle and by increasing plasma insulin. Given the key roles of both AMPK and insulin in fatty acid metabolism, the current study investigated the effect of rHDL infusion on fatty acid oxidation and lipolysis. Thirteen patients with type 2 diabetes received separate infusions of rHDL and placebo in a randomized, cross-over study. Fatty acid metabolism was assessed using steady-state tracer methodology, and plasma lipids were measured by mass spectrometry (lipidomics). In vitro studies were undertaken in 3T3-L1 adipocytes. rHDL infusion inhibited fasting-induced lipolysis (P = 0.03), fatty acid oxidation (P < 0.01), and circulating glycerol (P = 0.04). In vitro, HDL inhibited adipocyte lipolysis in part via activation of AMPK, providing a possible mechanistic link for the apparent reductions in lipolysis observed in vivo. In contrast, circulating NEFA increased after rHDL infusion (P < 0.01). Lipidomic analyses implicated phospholipase hydrolysis of rHDL-associated phosphatidylcholine as the cause, rather than lipolysis of endogenous fat stores. rHDL infusion inhibits fasting-induced lipolysis and oxidation in patients with type 2 diabetes, potentially through both AMPK activation in adipose tissue and elevation of plasma insulin. The phospholipid component of rHDL also has the potentially undesirable effect of increasing circulating NEFA. PMID:21224289

  8. Role of Criegee Intermediates in Formation of Sulfuric Acid at BVOCs-rich Cape Corsica Site

    NASA Astrophysics Data System (ADS)

    Kukui, A.; Dusanter, S.; Sauvage, S.; Gros, V.; Bourrianne, T.; Sellegri, K.; Wang, J.; Colomb, A.; Pichon, J. M.; Chen, H.; Kalogridis, C.; Zannoni, N.; Bonsang, B.; Michoud, V.; Locoge, N.; Leonardis, T.

    2015-12-01

    Oxidation of SO2 in reactions with stabilised Criegee Intermediates (sCI) was suggested as an additional source of gaseous sulfuric acid (H2SO4) in the atmosphere, complementary to the conventional H2SO4 formation in reaction of SO2 with OH radicals. Evaluation of the importance of this additional source is complicated due to large uncertainty in the mechanism and rate constants for the reactions of different sCI with SO2, water vapor and other atmospheric species. Here we present an evaluation of the role of sCI in H2SO4 production at remote site on Cape Corsica near the North tip of Corsica Island (Ersa station, Western Mediterranean). In July 2013 comprehensive field observations including gas phase (OH and RO2 radicals, H2SO4, VOCs, NOx, SO2, others) and aerosol measurements were conducted at this site in the frame of ChArMEx project. During the field campaign the site was strongly influenced by local emissions of biogenic volatile compounds (BVOCs), including isoprene and terpenes, forming different sCI in reactions with ozone and, hence, presenting additional source of H2SO4 via sCI+SO2. However, this additional source of H2SO4 at the Ersa site was found to be insignificant. The observed concentrations of H2SO4 were found to be in good agreement with those estimated from the H2SO4 condensation sink and the production of H2SO4 only in the reaction of OH with SO2, without accounting for any additional H2SO4 source. Using the BVOCs observations we present estimation of the upper limit for the rate constants of H2SO4 production via reactions of different sCI with SO2.

  9. 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

  10. Methane to acetic acid over Cu-exchanged zeolites: mechanistic insights from a site-specific carbonylation reaction.

    PubMed

    Narsimhan, Karthik; Michaelis, Vladimir K; Mathies, Guinevere; Gunther, William R; Griffin, Robert G; Román-Leshkov, Yuriy

    2015-02-11

    The selective low temperature oxidation of methane is an attractive yet challenging pathway to convert abundant natural gas into value added chemicals. Copper-exchanged ZSM-5 and mordenite (MOR) zeolites have received attention due to their ability to oxidize methane into methanol using molecular oxygen. In this work, the conversion of methane into acetic acid is demonstrated using Cu-MOR by coupling oxidation with carbonylation reactions. The carbonylation reaction, known to occur predominantly in the 8-membered ring (8MR) pockets of MOR, is used as a site-specific probe to gain insight into important mechanistic differences existing between Cu-MOR and Cu-ZSM-5 during methane oxidation. For the tandem reaction sequence, Cu-MOR generated drastically higher amounts of acetic acid when compared to Cu-ZSM-5 (22 vs 4 μmol/g). Preferential titration with sodium showed a direct correlation between the number of acid sites in the 8MR pockets in MOR and acetic acid yield, indicating that methoxy species present in the MOR side pockets undergo carbonylation. Coupled spectroscopic and reactivity measurements were used to identify the genesis of the oxidation sites and to validate the migration of methoxy species from the oxidation site to the carbonylation site. Our results indicate that the Cu(II)-O-Cu(II) sites previously associated with methane oxidation in both Cu-MOR and Cu-ZSM-5 are oxidation active but carbonylation inactive. In turn, combined UV-vis and EPR spectroscopic studies showed that a novel Cu(2+) site is formed at Cu/Al <0.2 in MOR. These sites oxidize methane and promote the migration of the product to a Brønsted acid site in the 8MR to undergo carbonylation. PMID:25562431

  11. 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.

  12. Volatile aromatic hydrocarbons and dicarboxylic acid concentrations in air at an urban site in the Southwestern US

    NASA Astrophysics Data System (ADS)

    Tran, Ngoc K.; Steinberg, Spencer M.; Johnson, Brian J.

    Concentrations of benzene, toluene, ethylbenzene, o-xylene, and m- and p-xylene were measured at an urban sampling site in Las Vegas, NV by sorbent sampling followed by thermal desorption and determination by GC-PID. Simultaneously, measurements of oxalic, malonic, succinic, and adipic acids were made at the same site by collection on quartz filters, extraction, esterification, and determination by GC-FID. For the period from April 7, 1997 to June 11, 1997, 201 sets of hydrocarbon measurements and 99 sets of acid measurements were made. Additional measurements of dicarboxylic acids were made on samples that represented potential direct sources, e.g. green plants and road dust. Correlations between the hydrocarbon and CO concentrations (measured by the Clark County Health District at a nearby site) were highly significant and a strong negative correlation of hydrocarbon concentration with ozone concentration (also from the county site) was observed under quiescent atmospheric conditions. In general, dicarboxylic acid concentrations were well correlated with one another (with the exception of adipic acid) but not well correlated with hydrocarbon, CO, and ozone concentrations. Multiple sources and complex formation processes are indicated for the dicarboxylic acids.

  13. [THE EFFECT OF SATINS: ACTIVATION OF LIPOLYSIS AND ABSORPTION BY INSULIN-DEPENDED CELLS LIPOPROTEINS OF VERY LOW DENSITY, INCREASING OF BIO-AVAILABILITY OF POLYENOIC FATTY ACIDS AND DECREASING OF CHOLESTEROL OF LIPOPROTEINS OF LOW DENSITY].

    PubMed

    Titov, V N; Malyshev, P P; Amelyushkina, V A; Aripovsky, A V; Smirnov, G P; Polevaya, T Yu; Kabo, S I; Kukhartchuk, V V

    2015-10-01

    The Russian cardiologic R&D production complex of Minzdrav of Russia, 121552 Moscow, Russia The statins are synthetic xenobiotics alien to animal cells. They are unlikely capable to manifest pleiotropic effect. It is feasible to evaluate effect of statins by stages: a) initially a specific inhibition of synthesis of cholesterol alcohol; b) further indirect activation of hydrolysis of triglycerides in lipoproteins of very low density; c) nonspecific activation of cells' receptor absorption of palmitic and oleic lipoproteins of very low density and then d) linoleic and linolenic lipoproteins of low density with all polyenoic fatty acids. On balance, statins activate absorption ofpolyenoic fatty acids by cells. Just they manifest physiological, specific pleiotropic effect. The statins inhibit synthesis of pool of cholesterol alcohol-lipoproteins of very low density condensed between phosphatidylcholines in polar mono-layer phosphatidylcholines+cholesterol alcohol on surface oftriglycerides. The low permeability of mono-layer separates substrate-triglycerides in lipoproteins of very low density and post-heparin lipoprotein lipase in hydrophilic blood plasma. The higher is ratio cholesterol alcohol/phosphatidylcholines in mono-layer of lipoproteins of very low density the slower is lipolysis, formation of ligand lipoproteins of very low density and their absorption by cells under apoB-100-endocytosis. The statins normalize hyperlipemia by force of a) activation of absorption oflipoproteins of very low density by insulin-depended cells and b) activation of absorption of lipoproteins of low density by all cells, increasing of bio-availability of polyenoic fatty acids, activation of apoB-100-endocytosis. The limitation in food of content of palmitic saturated fatty acid and increasing of content of ω-3 polyenoic fatty acids improve "bio-availability" of polyenoic fatty acids and their absorption by cells and also decreases cholesterol alcohol/phosphatidylcholines and

  14. 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

  15. Hybridoma antibodies to the lipid-binding site(s) in the amino-terminal region of fibronectin inhibits binding of streptococcal lipoteichoic acid.

    PubMed

    Stanislawski, L; Courtney, H S; Simpson, W A; Hasty, D L; Beachey, E H; Robert, L; Ofek, I

    1987-08-01

    In this report, we present evidence to suggest that streptococci and lipoteichoic acid (LTA) interact with a fatty acid binding site located near the NH2-terminus of fibronectin. The evidence is based on the following observations. Antibodies directed against a synthetic peptide (residues 1-30 of the amino-terminus of fibronectin) reacted with the two thermolysin-generated peptides (24 and 28 kilodaltons [kDa]) that were adsorbed by and eluted from streptococci. The adsorption of the 24- and 28-kDa peptides to streptococci was inhibited by LTA. The two monoclonal antibodies that inhibited the binding of LTA to fibronectin reacted only with the 24- and 28-kDa fragments of fibronectin. Conversely, LTA, as well as lauric acid and oleic acid, blocked the binding of the same monoclonal antibodies to fibronectin. LTA had no effect on the binding of hybridoma antibodies directed against the collagen or cell-binding domain. PMID:3298457

  16. Effects of cholestyramine on low density lipoprotein binding sites on liver membranes from rabbits with endogenous hypercholesterolemia induced by a wheat starch-casein diet.

    PubMed

    Chao, Y; Yamin, T T; Alberts, A W

    1982-04-10

    Rabbits fed a wheat starch-casein diet develop a marked hypercholesterolemia with a lipoprotein distribution similar to that of humans. Approximately 76% of the total cholesterol is carried in the low density lipoprotein (LDL) fraction (1.006 less than d less than 1.063 g/ml). Inclusion of 1% cholestyramine in the diet prevents the increase in plasma cholesterol. The cholestyramine effect is mediated through an increased fractional catabolic rate of 125I-LDL. In order to determine the potential role of hepatic LDL receptors in the removal of LDL from the plasma, binding of 125I-LDL and 125I-beta-VLDL (beta-migrating very low density lipoproteins) to hepatic membranes prepared from livers of rabbits fed the wheat starch-casein diet with or without cholestyramine supplementation was investigated. Membranes from livers of the cholestyramine-supplemented animals exhibit high levels of specific EDTA-sensitive binding of either of the 125I-labeled lipoproteins. Very little EDTA-sensitive binding occurs on liver membranes from wheat starch-casein-fed rabbits that have not been treated with cholestyramine. These results indicate that the hypercholesterolemia in rabbits associated with the wheat starch-casein diet is wholly or partially the result of a decreased number of specific hepatic LDL receptors and thus a decreased catabolism of plasma cholesterol. The response of the liver to the inclusion in the diet of the bile acid sequestrant, cholestyramine, is to maintain or increase the number of specific LDL binding sites, thus promoting catabolism of plasma cholesterol. PMID:6277940

  17. Using tandem mass spectrometry to quantify site-specific chlorination and nitration of proteins: model system studies with high-density lipoprotein oxidized by myeloperoxidase.

    PubMed

    Shao, Baohai; Heinecke, Jay W

    2008-01-01

    Protein oxidation is implicated in atherogenesis and other inflammatory conditions. Measuring levels of chlorinated and nitrated proteins in biological matrices serves as a quantitative index of oxidative stress in vivo. One potential mechanism for oxidative stress involves myeloperoxidase, a heme protein expressed by neutrophils, monocytes, and some populations of macrophages. The enzyme uses hydrogen peroxide to generate an array of cytotoxic oxidants, including hypochlorous acid (HOCl), a potent chlorinating intermediate, and nitrogen dioxide radical, a reactive nitrogen species (RNS). One important target may be high-density lipoprotein (HDL), which is implicated in atherogenesis. This chapter describes liquid chromatography-tandem mass spectrometric methods for quantifying site-specific modifications of proteins that have been oxidized by HOCl or RNS. Our studies center on apolipoprotein A-I, the major HDL protein, which provides an excellent model system for investigating factors that target specific residues for oxidative damage. Our approach is sensitive and rapid, applicable to a wide array of posttranslational modifications, and does not require peptides to be derivatized or labeled with an isotope. PMID:18423210

  18. Metal toxicity inferred from algal population density, heterotrophic substrate use, and fatty acid profile in a small stream

    SciTech Connect

    Genter, R.B.; Lehman, R.M.

    2000-04-01

    The purpose of this study was to examine relations between metal concentrations in periphyton and the abundance of algal species, heterotrophic use of 95 carbon sources, and phospholipid fatty acids (PLFA) of the periphyton in a small stream spanning a mine in Lemhi County, Idaho, USA. Two upstream two mine, and two downstream sites were examined. Elevated concentrations of As and Cu at the mine sites were associated with communities that were depleted of diatoms and filamentous blue-green algae and characterized by a low-diversity community dominated by a single blue-green alga and patchy populations of the diatom Achnanthidium minutissimum and a filamentous green alga. Carbon source use and PLFA profiles provided a rapid assessment of stream conditions that were consistent with algal taxonomy and with the hypotheses constructed from previous reports on periphyton responses to metal stress.

  19. Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of ferulic acid by density functional study.

    PubMed

    Sebastian, S; Sundaraganesan, N; Manoharan, S

    2009-10-01

    Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of ferulic acid (FA) (4-hydroxy-3-methoxycinnamic acid) were carried out by using density functional (DFT/B3LYP/BLYP) method with 6-31 G(d,p) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment (micro) and the first hyperpolarizability (beta) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the FA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of FA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title molecule have been constructed. PMID:19581124

  20. 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). PMID:25380633

  1. 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.

  2. 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.

  3. Hydrogen-bond acidity of OH groups in various molecular environments (phenols, alcohols, steroid derivatives, and amino acids structures): experimental measurements and density functional theory calculations.

    PubMed

    Graton, Jérôme; Besseau, François; Brossard, Anne-Marie; Charpentier, Eloïse; Deroche, Arnaud; Le Questel, Jean-Yves

    2013-12-12

    The hydrogen-bond (H-bond) donating strengths of a series of 36 hydroxylic H-bond donors (HBDs) with N-methylpyrrolidinone have been measured in CCl4 solution by FTIR spectrometry. These data allow the definition of a H-bond acidity scale named pKAHY covering almost three pK units, corresponding to 16 kJ mol(-1). These results are supplemented by equilibrium constants determined in CH2Cl2 for one-third of the data set to study compounds showing a poor solubility in CCl4. A systematic comparison of these experimental results with theoretical data computed in the gas phase using DFT (density functional theory) calculations has also been carried out. Quantum electrostatic parameters appear to accurately describe the H-bond acidity of the hydroxyl group, whereas partial atomic charges according to the Merz-Singh-Kollman and CHelpG schemes are not suitable for this purpose. A substantial decrease of the H-bond acidity of the OH group is pointed out when the hydroxyl moiety is involved in intramolecular H-bond interactions. In such situations, the interactions are further characterized through AIM and NBO analyses, which respectively allow localizing the corresponding bond critical point and the quantification of a significant charge transfer from the available lone pair to the σ*OH antibonding orbital. Eventually, the H-bond ability of the hydroxyl groups of steroid derivatives and of lateral chains of amino acids are evaluated on the basis of experimental and/or theoretical data. PMID:24274054

  4. Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation

    PubMed Central

    Chakraborty, Anirban; Mazumder, Abhishek; Lin, Miaoxin; Hasemeyer, Adam; Xu, Qumiao; Wang, Dongye; Ebright, Yon W.; Ebright, Richard H.

    2015-01-01

    Summary A three-step procedure comprising (i) unnatural-amino-acid mutagenesis with 4-azido-phenylalanine, (ii) Staudinger-Bertozzi ligation with a probe-phosphine derivative, and (iii) in vitro reconstitution of RNA polymerase (RNAP) enables the efficient site-specific incorporation of a fluorescent probe, a spin label, a crosslinking agent, a cleaving agent, an affinity tag, or any other biochemical or biophysical probe, at any site of interest in RNAP. Straightforward extensions of the procedure enable the efficient site-specific incorporation of two or more different probes in two or more different subunits of RNAP. We present protocols for synthesis of probe-phosphine derivatives, preparation of RNAP subunits and the transcription initiation factor σ, unnatural amino acid mutagenesis of RNAP subunits and σ, Staudinger ligation with unnatural-amino-acid-containing RNAP subunits and σ, quantitation of labelling efficiency and labelling specificity, and reconstitution of RNAP. PMID:25665560

  5. 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

  6. Human Plasma Very Low-Density Lipoproteins Are Stabilized by Electrostatic Interactions and Destabilized by Acidic pH

    PubMed Central

    Guha, Madhumita; Gursky, Olga

    2011-01-01

    Very low-density lipoproteins (VLDL) are precursors of low-density lipoproteins (LDL, or “bad cholesterol”). Factors affecting structural integrity of VLDL are important for their metabolism. To assess the role of electrostatic interactions in VLDL stability, we determined how solvent ionic conditions affect the heat-induced VLDL remodeling. This remodeling involves VLDL fusion, rupture, and fission of apolipoprotein E-containing high-density lipoprotein-(HDL-) like particles similar to those formed during VLDL-to-LDL maturation. Circular dichroism and turbidity show that increasing sodium salt concentration in millimolar range reduces VLDL stability and its enthalpic component. Consequently, favorable electrostatic interactions stabilize VLDL. Reduction in pH from 7.4 to 6.0 reduces VLDL stability, with further destabilization detected at pH < 6, which probably results from titration of the N-terminal α-amino groups and free fatty acids. This destabilization is expected to facilitate endosomal degradation of VLDL, promote their coalescence into lipid droplets in atherosclerotic plaques, and affect their potential use as drug carriers. PMID:21773050

  7. Density Functional Investigation of the Adsorption of Isooctane, Ethanol, and Acetic Acid on a Water-Covered Fe(100) Surface

    PubMed Central

    2014-01-01

    The presence of water in biofuels poses the question of how it affects the frictional performance of additives in fuels containing organic substances. To investigate the effect of water on the adsorption of molecules present in fuel and its additives we simulated within the framework of density functional theory the adsorption of ethanol, isooctane (2,2,4-trimethylpentane), and acetic acid on a bare and a water-covered Fe(100) surface. Van der Waals interactions are taken into account in our computations. In those molecules, where dispersion forces contribute significantly to the binding mechanism, the water layer has a stronger screening effect. Additionally, this effect can be enhanced by the presence of polar functional groups in the molecule. Thus, with the introduction of a water layer, the adsorption energy of isooctane and ethanol is reduced but it is increased in the case of the acetic acid. The adsorption configuration of ethanol is changed, while the one of acetic acid is moderately, and for isooctane only very slightly altered. Therefore, the effect of a water layer in the adsorption of organic molecules on an Fe(100) surface strongly depends on the type of bond and consequently, so do the tribological properties. PMID:25243045

  8. Efficacy of two acidic sanitizers for microbial reduction on metal cans and low-density polyethylene film surfaces.

    PubMed

    Lee, J; Gupta, M J; Lopes, J; Pascall, M A

    2007-10-01

    This study investigated 2 sanitizer formulations and compared them with hydrogen peroxide (H(2)O(2)). Formulation number 1 contained citric acid and sodium dodecylbenzene sulfonate (SDBS). Formulation number 2 contained SDBS, citric, lactic, phosphoric acids, and benzoic acid. Low concentration levels of the sanitizers (1.0% for formulation 1 and 0.5% for formulation 2) were compared with 35% H(2)O(2) for their efficacies on Escherichia coli, Listeria innocua, and Saccharomyces cerevisiae inoculated onto low-density polyethylene (LDPE) films and metal cans at room temperature (23 +/- 1 degrees C) and 40 degrees C. The results showed that both formulations 1 and 2 required >120 s to sanitize both materials from microbial populations at room temperature, while <15 s was needed for the H(2)O(2). Except for formulation 1 on the E. coli inoculated LDPE film surface, the sanitizers completely eliminated the bacterial populations on both materials in 60 s at 40 degrees C. In general, the formulations were more effective for reduction of the microbial numbers on the can material when compared with the LDPE film. The E. coli showed greater tolerance for the sanitizers when exposed to the process conditions in this study. All sanitizers completely eliminated the test organisms in

  9. Deoxyribonucleic acid-based hybrid thin films for potential application as high energy density capacitors

    NASA Astrophysics Data System (ADS)

    Joyce, Donna M.; Venkat, Narayanan; Ouchen, Fahima; Singh, Kristi M.; Smith, Steven R.; Grabowski, Christopher A.; Terry Murray, P.; Grote, James G.

    2014-03-01

    Deoxyribonucleic acid (DNA) based hybrid films incorporating sol-gel-derived ceramics have shown strong promise as insulating dielectrics for high voltage capacitor applications. Our studies of DNA-CTMA (cetyltrimethylammonium) complex/sol-gel ceramic hybrid thin film devices have demonstrated reproducibility and stability in temperature- and frequency-dependent dielectric properties with dielectric constant k ˜ 5.0 (1 kHz), as well as reliability in DC voltage breakdown measurements, attaining values consistently in the range of 300-350 V/μm. The electrical/dielectric characteristics of DNA-CTMA films with sol-gel-derived ceramics were examined to determine the critical energy storage parameters such as voltage breakdown and dielectric constant.

  10. 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.

  11. Effect of zoledronic acid on bone mineral density in patients of celiac disease: A prospective, randomized, pilot study

    PubMed Central

    Kumar, Mukul; Rastogi, Ashu; Bhadada, Sanjay Kumar; Bhansali, Anil; Vaiphei, Kim; Kochhar, Rakesh

    2013-01-01

    Background & objectives: The symptoms of celiac disease (CD) are varied and metabolic bone disease (MBD) is less recognized amongst all manifestations in CD patients. Bone disease in CD is attributed to secondary hyperparathyroidism, which in turn is associated with increased bone remodelling. Improvement in bone mineral density (BMD) with gluten free diet (GFD) is known, but the data on efficacy of bisphosphonates in CD patients are limited. Bisphosphonates being a potent inhibitor of bone resorption may be useful in patients with CD having low BMD. The aim of the present investigation was to study the effect of zoledronic acid on BMD in CD patients. Methods: A total of 28 CD patients were randomized to receive GFD, calcium and cholecalciferol (group A), and zoledronic acid (group B). Baseline biochemical tests and T-score by dual energy x-ray absorptiometer were done and repeated after 12 months. Results: The T-score showed improvement in the control arm (group A) from -3.31 ± 1.46 to -2.12 ± 1.44, a gain of 35.9 per cent (P<0.05) and in drug arm (group B) -2.82 ± 1.27 to -1.06 ± 1.84, registering a gain of 62.4 per cent (P<0.001). However, there was no difference in improvement of T-score in zoledronic acid group as compared to the control group. Interpretation & conclusions: Administration of zoledronic acid was not found to be better than GFD alone in increasing BMD in CD patients with low BMD in this pilot study. PMID:24521630

  12. Locating high-affinity fatty acid-binding sites on albumin by x-ray crystallography and NMR spectroscopy

    PubMed Central

    Simard, J. R.; Zunszain, P. A.; Ha, C.-E.; Yang, J. S.; Bhagavan, N. V.; Petitpas, I.; Curry, S.; Hamilton, J. A.

    2005-01-01

    Human serum albumin (HSA) is a versatile transport protein for endogenous compounds and drugs. To evaluate physiologically relevant interactions between ligands for the protein, it is necessary to determine the locations and relative affinities of different ligands for their binding site(s). We present a site-specific investigation of the relative affinities of binding sites on HSA for fatty acids (FA), the primary physiological ligand for the protein. Titration of HSA with [13C]carboxyl-labeled FA was used initially to identify three NMR chemical shifts that are associated with high-affinity binding pockets on the protein. To correlate these peaks with FA-binding sites identified from the crystal structures of FA–HSA complexes, HSA mutants were engineered with substitutions of amino acids involved in coordination of the bound FA carboxyl. Titration of [13C]palmitate into solutions of HSA mutants for either FA site four (R410A/Y411A) or site five (K525A) within domain III of HSA each revealed loss of a specific NMR peak that was present in spectra of wild-type protein. Because these peaks are among the first three to be observed on titration of HSA with palmitate, sites four and five represent two of the three high-affinity long-chain FA-binding sites on HSA. These assignments were confirmed by titration of [13C]palmitate into recombinant domain III of HSA, which contains only sites four and five. These results establish a protocol for direct probing of the relative affinities of FA-binding sites, one that may be extended to examine competition between FA and other ligands for specific binding sites. PMID:16330771

  13. Locating high-affinity fatty acid-binding sites on albumin by x-ray crystallography and NMR spectroscopy.

    PubMed

    Simard, J R; Zunszain, P A; Ha, C-E; Yang, J S; Bhagavan, N V; Petitpas, I; Curry, S; Hamilton, J A

    2005-12-13

    Human serum albumin (HSA) is a versatile transport protein for endogenous compounds and drugs. To evaluate physiologically relevant interactions between ligands for the protein, it is necessary to determine the locations and relative affinities of different ligands for their binding site(s). We present a site-specific investigation of the relative affinities of binding sites on HSA for fatty acids (FA), the primary physiological ligand for the protein. Titration of HSA with [(13)C]carboxyl-labeled FA was used initially to identify three NMR chemical shifts that are associated with high-affinity binding pockets on the protein. To correlate these peaks with FA-binding sites identified from the crystal structures of FA-HSA complexes, HSA mutants were engineered with substitutions of amino acids involved in coordination of the bound FA carboxyl. Titration of [(13)C]palmitate into solutions of HSA mutants for either FA site four (R410A/Y411A) or site five (K525A) within domain III of HSA each revealed loss of a specific NMR peak that was present in spectra of wild-type protein. Because these peaks are among the first three to be observed on titration of HSA with palmitate, sites four and five represent two of the three high-affinity long-chain FA-binding sites on HSA. These assignments were confirmed by titration of [(13)C]palmitate into recombinant domain III of HSA, which contains only sites four and five. These results establish a protocol for direct probing of the relative affinities of FA-binding sites, one that may be extended to examine competition between FA and other ligands for specific binding sites. PMID:16330771

  14. Effective on-site Coulomb interaction and electron configurations in transition-metal complexes from constraint density functional theory

    NASA Astrophysics Data System (ADS)

    Nawa, Kenji; Nakamura, Kohji; Akiyama, Toru; Ito, Tomonori; Weinert, Michael

    Effective on-site Coulomb interactions (Ueff) and electron configurations in the localized d and f orbitals of metal complexes in transition-metal oxides and organometallic molecules, play a key role in the first-principles search for the true ground-state. However, wide ranges of values in the Ueff parameter of a material, even in the same ionic state, are often reported. Here, we revisit this issue from constraint density functional theory (DFT) by using the full-potential linearized augmented plane wave method. The Ueff parameters for prototypical transition-metal oxides, TMO (TM =Mn, Fe, Co, Ni), were calculated by the second derivative of the total energy functional with respect to the d occupation numbers inside the muffin-tin (MT) spheres as a function of the sphere radius. We find that the calculated Ueff values depend significantly on the MT radius, with a variation of more than 3 eV when the MT radius changes from 2.0 to 2.7 a.u., but importantly an identical valence band structure can be produced in all the cases, with an approximate scaling of Ueff. This indicates that a simple transferability of the Ueff value among different calculation methods is not allowed. We further extend the constraint DFT to treat various electron configurations of the localized d-orbitals in organometallic molecules, TMCp2 (TM =Cr, Mn, Fe, Co, Ni), and find that the calculated Ueff values can reproduce the experimentally determined ground-state electron configurations.

  15. High density active-site MnO{sub 2} nanofibers for energy storage and conversion applications

    SciTech Connect

    Xiao, T.D.; Reisner, D.E.; Strutt, P.R.

    1998-07-01

    This investigation involves the synthesis of MnO{sub 2} nanofibrous materials, via an aqueous chemical synthesis route. A critical step in the synthesis is the extended period of the refluxing of the reactive constituents, which enables the gradual transformation of the initial amorphous nanoparticles into a random-weave nanofibrous structure, in the form of a bird's nest superstructure. The bird's nest has a diameter of approximately 10 {micro}m, which is an assemblage of many individual nanofibers with a diameter of about 15 nm, and a length up to 1 {micro}m. Partial transformation of the nanostructured MnO{sub 2} realizes a novel bimodal morphology, which combines a high density of chemically active sites with an enhanced percolation rate. Characterization of these nanofibers include SEM, TEM, surface area, and chemical analysis. High resolution TEM observations reveals that the as-synthesized MnO{sub 2} nanofibers contain lattice defects, including molecular pores, meso- and micro-pores.

  16. Direct photoaffinity labeling of cellular retinoic acid-binding protein I (CRABP-I) with all-trans-retinoic acid: identification of amino acids in the ligand binding site.

    PubMed

    Chen, G; Radominska-Pandya, A

    2000-10-17

    Cellular retinoic acid-binding proteins I and II (CRABP-I and -II, respectively) are transport proteins for all-trans-retinoic acid (RA), an active metabolite of vitamin A (retinol), and have been reported to be directly involved in the metabolism of RA. In this study, direct photoaffinity labeling with [11,12-(3)H]RA was used to identify amino acids comprising the ligand binding site of CRABP-I. Photoaffinity labeling of CRABP-I with [(3)H]RA was light- and concentration-dependent and was protected by unlabeled RA and various retinoids, indicating that the labeling was directed to the RA-binding site. Photolabeled CRABP-I was hydrolyzed with endoproteinase Lys-C to yield radioactive peptides, which were separated by reversed-phase HPLC for analysis by Edman degradation peptide sequencing. This method identified five modified amino acids from five separate HPLC fractions: Trp7, Lys20, Arg29, Lys38, and Trp109. All five amino acids are located within one side of the "barrel" structure in the area indicated by the reported crystal structure as the ligand binding site. This is the first direct identification of specific amino acids in the RA-binding site of CRABPs by photoaffinity labeling. These results provide significant information about the ligand binding site of the CRABP-I molecule in solution. PMID:11027136

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Correction: Acid-catalyzed carboxylic acid esterification and ester hydrolysis mechanism: acylium ion as a sharing active intermediate via a spontaneous trimolecular reaction based on density functional theory calculation and supported by electrospray ionization-mass spectrometry.

    PubMed

    Shi, Hongchang; Wang, Yilei; Hua, Ruimao

    2015-12-28

    Correction for 'Acid-catalyzed carboxylic acid esterification and ester hydrolysis mechanism: acylium ion as a sharing active intermediate via a spontaneous trimolecular reaction based on density functional theory calculation and supported by electrospray ionization-mass spectrometry' by Hongchang Shi et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp02914g. PMID:26583937

  4. The Elusive Metal-Free Primary Amination of Arylboronic Acids: Synthetic Studies and Mechanism by Density Functional Theory

    PubMed Central

    Zhu, Chen; Li, Gongqiang; Ess, Daniel H.; Falck, John R.; Kürti, László

    2012-01-01

    Herein, we disclose the first metal-free synthesis of primary aromatic amines from arylboronic acids, a reaction that has eluded synthetic chemists for decades. This remarkable transformation affords structurally diverse primary arylamines in good chemical yields, including a variety of halogenated primary anilines that often cannot be prepared via transition metal-catalyzed amination. The reaction is operationally simple, requires only a slight excess of aminating agent, proceeds under neutral or basic conditions and, importantly, it can be scaled up to provide multigram quantities of primary anilines. Density functional calculations reveal that the most likely mechanism involves a facile 1,2-aryl migration and that the presence of an ortho nitro group in the aminating agent plays a critical role in lowering the free energy barrier of the 1,2-aryl migration step. PMID:23082853

  5. Pathways for oxidation of low density lipoprotein by myeloperoxidase: tyrosyl radical, reactive aldehydes, hypochlorous acid and molecular chlorine.

    PubMed

    Heinecke, J W

    1997-01-01

    Many lines of evidence implicate oxidation of low density lipoprotein (LDL) in the pathogenesis of atherosclerosis, a chronic inflammatory disease. The physiologically relevant mechanisms have not been identified, but phagocytic white cells may play an important role because macrophage-rich lesions characterize the disorder. Recent studies have shown that myeloperoxidase, a heme enzyme secreted only by phagocytes, is present in human atherosclerotic tissue. The enzyme is a potent catalyst of LDL oxidation in vitro, it co-localizes with macrophages in lesions, and it generates products that are detectable in atherosclerotic plaque. These findings suggest that myeloperoxidase may promote LDL oxidation in the artery wall. This article reviews the enzyme's ability to generate a range of oxidants, including tyrosyl radical, reactive aldehydes, hypochlorous acid and molecular chlorine. These products have the potential to damage host molecules as well as microbes, suggesting a mechanism that may contribute to atherosclerotic vascular disease. PMID:9259996

  6. Quality of diet and potential renal acid load as risk factors for reduced bone density in elderly women

    PubMed Central

    Pedone, Claudio; Napoli, Nicola; Lauretani, Fulvio; Pozzilli, Paolo; Ferrucci, Luigi; Antonelli-Incalzi, Raffaele

    2010-01-01

    Background Bone mass density (BMD) may be influenced by the general dietary pattern and the potential renal acid load (PRAL). Objective To evaluate the association between PRAL and BMD. Methods We evaluated BMD using computed tomography and dietary intake using the EPIC questionnaire in 543 community-living women aged 60 years and older. We grouped the participants according to tertiles of total, trabecular and cortical BMD, and compared demographic, anthropometric and nutritional characteristics across groups. Analyses were repeated using tertiles of BMD variation over a 6-years follow-up. Results Total BMD was inversely associated with age, time since menopause, and creatinine clearance. The intake of PUFAs was slightly higher among women with the highest total BMD, none of the other nutrients taken into account nor PRAL was associated with total BMD. Similar results were found for trabecular BMD, with the exception that alcohol intake was associated with lower bone density. Cortical BMD was associated with vitamin D intake (1.6, 1.8, and 1.8 mcg/day in first, second and third tertile, respectively) and serum 25-OH vitamin D (38.8, 43.2, and 49.5 nmol/L in the first, second, and third tertile, respectively). In the longitudinal analysis, a lower BMI was associated with greater loss of total BMD, while lower serum 25-hydroxy vitamin D at baseline was associated with smaller loss of cortical BMD. Conclusions We found no relationship between dietary acid load and BMD. We also confirmed the role of well recognized risk factor for osteoporosis and found a possible protective effect of PUFA intake on BMD. PMID:20005315

  7. Terahertz Spectra of L-Ascorbic Acid and Thiamine Hydrochloride Studied by Terahertz Spectroscopy and Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Jiang, Ling; Li, Miao; Li, Chun; Sun, Haijun; Xu, Li; Jin, Biaobin; Liu, Yunfei

    2014-10-01

    We have investigated the terahertz spectra of L-ascorbic acid and thiamine hydrochloride measured by terahertz time-domain spectroscopy (THz-TDS) and Fourier transform infrared spectroscopy (FTIR). The measured absorption spectra were demonstrated to be in good agreement with the results simulated by Density Functional Theory (DFT) using hybrid functional B3LYP with basis set of 6-31G (d), except with slight frequency shift and few peaks missing. We presented the comparison of measured spectra by the FTIR spectroscopy employing low temperature silicon bolometer as detector and the TDS system. The measured spectra of the L-ascorbic acid showed shoulder bands at 0.25, 1.1, 1.5, 1.82, 2.03, 2.30, 2.44, 2.67, 2.97, 3.12, and 3.40 THz, respectively. The spectra of the thiamine hydrochloride show shoulder bands at 0.48, 1.11, 1.57, 1.75, 1.92, 2.08, 2.31, 2.53, 2.69, 2.85, 3.12, 3.22, and 3.31 THz. Most absorption peaks of the two samples agree with the results simulated by Density Function Theory (DFT) method of Gaussian 09 software. In our work, more spectral peaks based on experimental and theoretical results were found in comparison to that of other groups, since we employed higher sensitive FTIR measurement system and considered the effect of number of molecule unit in simulation. The study suggests that the effect of intermolecular vibration is stronger than intramolecular interaction on the absorption bands in THz region.

  8. Cyclic GMP-gated channels of bovine rod photoreceptors: affinity, density and stoichiometry of Ca(2+)-calmodulin binding sites.

    PubMed Central

    Bauer, P J

    1996-01-01

    1. Ca(2+)-loaded vesicles of bovine rod outer segment (ROS) membranes were used to examine the influence of Ca(2+)-calmodulin (Ca(2+)-CaM) on the activity of cGMP-gated channels. 2. In vesicles prepared from ROS membranes which were washed at zero free Ca2+, Ca(2+)-CaM reduced the Ca2+ flux to maximally 40%. The dose-response curve for activation of the cGMP-gated channel had a half-maximal value of 36.8 +/- 2 microM in the CaM-free state, and of 55.6 +/- 5.2 microM in the Ca(2+)-CaM-bound state. In both cases the Hill coefficients were 2.2 +/- 0.2. 3. In vesicles prepared from ROS membranes which were washed at 100 microM Ca2+, the dose-response curve was identical to the Ca(2+)-CaM-bound state. 4. Titration of the Ca(2+)-CaM-dependent decrease of the channel activity upon addition of 40 microM cGMP yielded half-maximal Ca(2+)-CaM concentrations (EC50CaM) which were linearly correlated with the concentration of membrane vesicles. Extrapolation of EC50CaM to infinite dilution of vesicles yielded a Ca(2+)-CaM affinity constant for the cGMP-gated channel of 1.01 +/- 0.20 nM. Hill analysis of the Ca(2+)-CaM titrations resulted in a Hill coefficient of 1.36 +/- 0.15. 5. From the slope of the linear regression of EC50CaM plotted vs. the rhodopsin concentration, the molar ratio of rhodopsin to externally accessible Ca(2+)-CaM binding sites of fused ROS membranes was determined to be 1439 +/- 109. Therefore, there are about 720 molecules of rhodopsin per Ca(2+)-CaM binding site present in ROS. 6. Based on these data, a density of 560 Ca(2+)-CaM binding sites micron-2 is estimated for the plasma membrane of bovine ROS, suggesting that there are two Ca(2+)-CaM binding sites per channel. 7. The Ca(2+)-CaM effect did not become noticeable until the ROS membranes were hypotonically washed at free [Ca2+] below 100 nM, suggesting that an endogenous Ca(2+)-binding protein was washed off in the absence of Ca2+. 8. If the endogenous Ca(2+)-binding protein of bovine ROS membranes

  9. 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.

  10. Hydrolysis of phosphodiesters by diiron complexes: design of nonequivalent iron sites in purple acid phosphatase models.

    PubMed

    Verge, François; Lebrun, Colette; Fontecave, Marc; Ménage, Stéphane

    2003-01-27

    New mu-oxo-diferric complexes have been designed for hydrolysis of phosphodiesters. To mimic the diiron active site of purple acid phosphatase, a combinatorial method has been used to select complexes containing two distinct iron coordination spheres. The introduction of a bidentate ligand, a substituted phenanthroline (L) into complex 1, [Fe2O(bipy)4(OH2)2](NO3)4, generates in solution the complex [Fe2O(bipy)3(L)(OH2)2](NO3)4 as shown by ESI/MS and 1H NMR studies. The latter complex was found to be 20-fold more active than complex 1. On the basis of kinetic studies, we demonstrated that the complex [Fe2O(bipy)3(L)(OH)(OH2)](NO3)3 was the active species and the reaction proceeded through the formation of a ternary complex in which one iron binds a hydroxide and the second, the substrate. At nonsaturating concentrations of the substrate, the increased activity with increased methyl substituents in L was due to an increased affinity of the complex for the substrate. The activity of [Fe2O(bipy)3(33'44'Me2-Phen)(OH2)2](NO3)4 [33'44'Me2Phen = 3,3',4,4'-dimethyl-1,10-phenanthroline] was found to be comparable to that reported for Co(III) or Ce(IV) complexes. PMID:12693232

  11. 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.

  12. Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models

    PubMed Central

    Maaskola, Jonas; Rajewsky, Nikolaus

    2014-01-01

    We present a discriminative learning method for pattern discovery of binding sites in nucleic acid sequences based on hidden Markov models. Sets of positive and negative example sequences are mined for sequence motifs whose occurrence frequency varies between the sets. The method offers several objective functions, but we concentrate on mutual information of condition and motif occurrence. We perform a systematic comparison of our method and numerous published motif-finding tools. Our method achieves the highest motif discovery performance, while being faster than most published methods. We present case studies of data from various technologies, including ChIP-Seq, RIP-Chip and PAR-CLIP, of embryonic stem cell transcription factors and of RNA-binding proteins, demonstrating practicality and utility of the method. For the alternative splicing factor RBM10, our analysis finds motifs known to be splicing-relevant. The motif discovery method is implemented in the free software package Discrover. It is applicable to genome- and transcriptome-scale data, makes use of available repeat experiments and aside from binary contrasts also more complex data configurations can be utilized. PMID:25389269

  13. 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). ...

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. Electrochemical oxidation of humic acid and sanitary landfill leachate: Influence of anode material, chloride concentration and current density.

    PubMed

    Fernandes, A; Santos, D; Pacheco, M J; Ciríaco, L; Lopes, A

    2016-01-15

    The influence of applied current density and chloride ion concentration on the ability of Ti/Pt/PbO2 and Ti/Pt/SnO2-Sb2O4 anodes for the electrochemical oxidation of humic acid and sanitary landfill leachate samples was assessed and compared with that of BDD anode. For the experimental conditions used, results show that both organic load and nitrogen removal rates increase with the applied current density and chloride ion concentration, although there is an optimum COD/[Cl-]0 ratio below which there is no further increase in COD removal. Metal oxide anodes present a similar performance to that of BDD, being the results obtained for Ti/Pt/PbO2 slightly better than for Ti/Pt/SnO2-Sb2O4. Contrary to BDD, Ti/Pt/PbO2 promotes lower nitrate formation and is the most suitable material for total nitrogen elimination. The importance of the optimum ratio of Cl-/COD/NH4 +initial concentrations is discussed. PMID:26410703

  1. 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

  2. Synthesis, density functional theory, molecular dynamics and electrochemical studies of 3-thiopheneacetic acid-capped gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Sosibo, Ndabenhle M.; Mdluli, Phumlane S.; Mashazi, Philani N.; Dyan, Busiswa; Revaprasadu, Neerish; Nyokong, Tebello; Tshikhudo, Robert T.; Skepu, Amanda; van der Lingen, Elma

    2011-12-01

    Gold nanoparticles capped with a bifunctional ligand, 3-thiopheneacetic acid (3-TAA) were synthesised by borohydride reduction at room temperature. The transmission electron microscopy (TEM) analysis showed that the particle aggregates and had semi-linear partial linkages that could be attributed to multi-modal binding of the ligand with various gold nanoparticles through the terminal thiolether (-S-) group and oxygen of the carboxylic (-COOH) group. This bimodal interaction led to limited stability of the resultant nanoparticles when tested using highly electrolytic media. To investigate further, density functional theory (DFT) quantum chemical and molecular dynamic calculations were conducted. The energetically favorable binding modes of the ligand to gold nanoparticle surfaces using the Gaussian program were studied. The DFT results showed kinetic stability of Au-3-TAA-Au interactions leading to inter-particle coupling or aggregation. Electrochemical analysis of the resultant nature of the capping agent revealed that 3-thiopheneacetic acid did not form a polymer during the preparation of Au-3-TAA. The cyclic voltammograms of Au-3-TAA nanoparticles coated glassy carbon electrode showed a typical gold character with the oxidation and reduction peaks at 1.4 V and 0.9 V, respectively.

  3. 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

  4. 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

  5. Effects of conjugated linoleic acid supplementation during resistance training on body composition, bone density, strength, and selected hematological markers.

    PubMed

    Kreider, Richard B; Ferreira, Maria P; Greenwood, Michael; Wilson, Michael; Almada, Anthony L

    2002-08-01

    Conjugated linoleic acids (CLA) are essential fatty acids that have been reported in animal studies to decrease catabolism, promote fat loss, increase bone density, enhance immunity, and serve as an antiatherogenic and anticarcinogenic agent. For this reason, CLA has been marketed as a supplement to promote weight loss and general health. CLA has also been heavily marketed to resistance-trained athletes as a supplement that may help lessen catabolism, decrease body fat, and promote greater gains in strength and muscle mass during training. Although basic research is promising, few studies have examined whether CLA supplementation during training enhances training adaptations and/or affects markers of health. This study evaluated whether CLA supplementation during resistance training affects body composition, strength, and/or general markers of catabolism and immunity. In a double-blind and randomized manner, 23 experienced, resistance-trained subjects were matched according to body mass and training volume and randomly assigned to supplement their diet with 9 g;pdd(-1) of an olive oil placebo or 6 g;pdd(-1) of CLA with 3 g;pdd(-1) of fatty acids for 28 days. Prior to and following supplementation, fasting blood samples, total body mass, and dual-energy X-ray absorptiometry (DEXA) determined body composition, and isotonic bench press and leg press 1 repetition maximums (1RMs) were determined. Results revealed that although some statistical trends were observed with moderate to large effect sizes, CLA supplementation did not significantly affect (p > 0.05) changes in total body mass, fat-free mass, fat mass, percent body fat, bone mass, strength, serum substrates, or general markers of catabolism and immunity during training. These findings indicate that CLA does not appear to possess significant ergogenic value for experienced resistance-trained athletes. PMID:12173945

  6. 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.

  7. 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

  8. 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

  9. 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

  10. Effects of sex and site on amino acid metabolism enzyme gene expression and activity in rat white adipose tissue.

    PubMed

    Arriarán, Sofía; Agnelli, Silvia; Remesar, Xavier; Fernández-López, José Antonio; Alemany, Marià

    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

  11. 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.

  12. A nuclear magnetic resonance-based structural rationale for contrasting stoichiometry and ligand binding site(s) in fatty acid-binding proteins.

    PubMed

    He, Yan; Estephan, Rima; Yang, Xiaomin; Vela, Adriana; Wang, Hsin; Bernard, Cédric; Stark, Ruth E

    2011-03-01

    Liver fatty acid-binding protein (LFABP) is a 14 kDa cytosolic polypeptide, differing from other family members in the number of ligand binding sites, the diversity of bound ligands, and the transfer of fatty acid(s) to membranes primarily via aqueous diffusion rather than direct collisional interactions. Distinct two-dimensional (1)H-(15)N nuclear magnetic resonance (NMR) signals indicative of slowly exchanging LFABP assemblies formed during stepwise ligand titration were exploited, without determining the protein-ligand complex structures, to yield the stoichiometries for the bound ligands, their locations within the protein binding cavity, the sequence of ligand occupation, and the corresponding protein structural accommodations. Chemical shifts were monitored for wild-type LFABP and an R122L/S124A mutant in which electrostatic interactions viewed as being essential to fatty acid binding were removed. For wild-type LFABP, the results compared favorably with the data for previous tertiary structures of oleate-bound wild-type LFABP in crystals and in solution: there are two oleates, one U-shaped ligand that positions the long hydrophobic chain deep within the cavity and another extended structure with the hydrophobic chain facing the cavity and the carboxylate group lying close to the protein surface. The NMR titration validated a prior hypothesis that the first oleate to enter the cavity occupies the internal protein site. In contrast, (1)H and (15)N chemical shift changes supported only one liganded oleate for R122L/S124A LFABP, at an intermediate location within the protein cavity. A rationale based on protein sequence and electrostatics was developed to explain the stoichiometry and binding site trends for LFABPs and to put these findings into context within the larger protein family. PMID:21226535

  13. Hump-Shaped Density-Dependent Regulation of Mosquito Oviposition Site-Selection by Conspecific Immature Stages: Theory, Field Test with Aedes albopictus, and a Meta-Analysis

    PubMed Central

    Wasserberg, Gideon; Bailes, Nicholas; Davis, Christopher; Yeoman, Kim

    2014-01-01

    Oviposition site selection by gravid females is an important determinant of the distribution, abundance, and dynamics of dipteran hematophagous insects. The presence of conspecific immature stages in a potential oviposition site could, on the one hand, indicate the suitability of that site but on the other hand could indicate the potential for intraspecific competition. In this paper, we present a graphic model suggesting that the trade-off between these two opposing forces could result in a hump-shaped density-dependent relationship between oviposition rate and conspecific immature stage density (hereafter, the “Hump-shaped regulation model”) with positive effects of aggregation prevailing at low densities and negative effect of intraspecific competition prevailing at higher densities. We field-tested the predictions of this model at both the egg- and the larval levels with Aedes albopictus and evaluated if and how these relationships are affected by resource enrichment. We found support for the hump-shaped regulation model at both the larval and the egg levels. Using oviposition cups containing varying numbers of conspecific larvae, we showed that the oviposition activity of Ae. albopictus first increases and then decreases with larvae number. Medium enrichment resulted in higher hatching rate, and demonstrated linear relations for the no-enrichment treatment where larvae density range was low and hump-shaped relationship for the enriched medium that had a wider larvae density range. Using pairs of oviposition cups, we showed that at low egg densities mosquitoes laid more eggs on substrates containing pre-existing eggs. However, at higher egg densities, mosquitoes laid more eggs on a virgin substrate. Based on our results and on a meta-analysis, we suggest that due to study design or methodological shortcomings the hump-shaped regulation model is often left undetected and that it is likely to be more common than currently thought. PMID:24681526

  14. The relationship between density of alpha-adrenoceptor binding sites and contractile responses in several porcine isolated blood vessels.

    PubMed Central

    Wright, I K; Blaylock, N A; Kendall, D A; Wilson, V G

    1995-01-01

    1. The aim of this study was to investigate constrictor alpha-adrenoceptors in three isolated blood vessels of the pig, the thoracic aorta (TA), the splenic artery (SA) and marginal ear vein (MEV) and then compare the functional response with the densities of alpha 1- and alpha 2-adrenoceptor binding sites in these and several other porcine vascular tissues, palmar common digital artery (PCDA), palmar lateral vein (PLV) and ear artery (EA). 2. Noradrenaline (NA), phenylephrine (PE) and UK14304 (all at 0.03-10 microM) elicited concentration-dependent contractions in the TA and MEV, with a rank order of potency of UK14304 > NA > PE. UK14304 produced maximal responses which were 58% (TA) and 65% (MEV) of that of NA. In the SA, UK14304 and PE produced maximal responses which were less than 10% and 50% of the NA-induced maximal response respectively, with an order of potency of NA > PE. In the SA, NA-induced contractions were competitively antagonized by prazosin (pA2 = 8.60 +/- 0.15). Further, rauwolscine (1-10 microM) antagonized NA-induced contractions with an apparent pKB of 6.09 +/- 0.11 (n = 6), indicating an action at alpha 1-adrenoceptors. The combination of the two antagonists at concentrations selective for alpha 1- (0.1 microM) and alpha 2-adrenoceptors (1 microM) had no greater effect than either antagonist alone. This suggests that the SA expresses only post-junctional alpha 1-adrenoceptors. 3. In the TA, prazosin produced non-parallel shifts in the NA-induced CRC and this was also observed with rauwolscine, where reductions in the maximal responses were also observed. In the MEV, prazosin was largely inactive in antagonizing NA-induced contractions. In both these vessels a combination of these two antagonists had a greater effect than either alone, indicating the presence of functional alpha 1- and alpha 2-adrenoceptors. The post-junctional alpha 2-adrenoceptors in all of these vessels were resistant to prazosin, suggesting the alpha 2-adrenoceptor to be

  15. Protons and Psalmotoxin-1 reveal nonproton ligand stimulatory sites in chicken acid-sensing ion channel

    PubMed Central

    Smith, Rachel N; Gonzales, Eric B

    2014-01-01

    Acid-sensing ion channels (ASICs) are proton-sensitive, sodium-selective channels expressed in the nervous system that sense changes in extracellular pH. These ion channels are sensitive to an increasing number of nonproton ligands that include natural venom peptides and guanidine compounds. In the case of chicken ASIC1, the spider toxin Psalmotoxin-1 (PcTx1) activates the channel, resulting in an inward current. Furthermore, a growing class of ligands containing a guanidine group has been identified that stimulate peripheral ASICs (ASIC3), but exert subtle influence on other ASIC subtypes. The effects of the guanidine compounds on cASIC1 have not been the focus of previous study. Here, we investigated the interaction of the guanidine compound 2-guanidine-4-methylquinazoline (GMQ) on cASIC1 proton activation and PcTx1 stimulation. Exposure of expressed cASIC1 to PcTx1 resulted in biphasic currents consisting of a transient peak followed by an irreversible cASIC1 PcTx1 persistent current. This cASIC1 PcTx1 persistent current may be the result of locking the cASIC1 protein into a desensitized transition state. The guanidine compound GMQ increased the apparent affinity of protons on cASIC1 and decreased the half-maximal constant of the cASIC1 steady-state desensitization profile. Furthermore, GMQ stimulated the cASIC1 PcTx1 persistent current in a concentration-dependent manner, which resulted in a non-desensitizing inward current. Our data suggests that GMQ may have multiple sites within cASIC1 and may act as a “molecular wedge” that forces the PcTx1-desensitized ASIC into an open state. Our findings indicate that guanidine compounds, such as GMQ, may alter acid-sensing ion channel activity in combination with other stimuli, and that additional ASIC subtypes (along with ASIC3) may serve to sense and mediate signals from multiple stimuli. PMID:24262969

  16. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites.

    PubMed

    Liang, Yuting; Zhao, Huihui; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

    2014-07-15

    To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils. PMID:24784752

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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. PMID:24372878

  3. 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.

  4. 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

  5. Site-directed mutagenesis of dicarboxylic acids near the active site of Bacillus cereus 5/B/6 beta-lactamase II.

    PubMed Central

    Lim, H M; Iyer, R K; Pène, J J

    1991-01-01

    An amino acid residue functioning as a general base has been proposed to assist in the hydrolysis of beta-lactam antibiotics by the zinc-containing Bacillus cereus beta-lactamase II [Bicknell & Waley (1985) Biochemistry 24, 6876-6887]. Oligonucleotide-directed mutagenesis of cloned Bacillus cereus 5/B/6 beta-lactamase II was used in an 'in vivo' study to investigate the role of carboxy-group-containing amino acids near the active site of the enzyme. Substitution of asparagine for the wild-type aspartic acid residue at position 81 resulted in fully functional enzyme. An aspartic acid residue at position 90 is essential for beta-lactamase II to confer any detectable ampicillin and cephalosporin C resistance to Escherichia coli. Conversion of Asp90 into Asn90 or Glu90 lead to the synthesis of inactive enzyme, suggesting that the spatial position of the beta-carboxy group of Asp90 is critical for enzyme function. Images Fig. 2. Fig. 3. PMID:1904717

  6. 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.

  7. 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. PMID:26711816

  8. 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

  9. Expression of recombinant human serum amyloid A in mammalian cells and demonstration of the region necessary for high-density lipoprotein binding and amyloid fibril formation by site-directed mutagenesis.

    PubMed Central

    Patel, H; Bramall, J; Waters, H; De Beer, M C; Woo, P

    1996-01-01

    Site-directed mutagenesis of the acute-phase human serum amyloid A (SAA1 alpha) protein was used to evaluate the importance of the N-terminal amino acid residues, namely RSFFSFLGEAF The full-length cDNA clone of SAA1 alpha (pA1.mod.) was used to create two mutations, namely Gly-8 to Asp-8 and an 11 amino acid truncation between Arg-1 and Phe-11 respectively. Wild-type and mutant cDNAs were expressed in Chinese hamster ovary (CHO) cells under the control of the human cytomegalovirus promoter, which resulted in the secretion of the processed proteins into the culture media. Wild-type recombinant human SAA (rSAA) protein was shown to have pI values of 6.0 and 6.4, similar to the human SAA isoform SAA1 alpha and SAA1 alpha desArg found in acute-phase plasma. N-terminal sequencing of 56 residues confirmed its identity with human SAA1 alpha. The total yield of wild-type rSAA measured by ELISA was between 3.5 and 30 mg/l. The two mutations resulted in reduced expression levels of the mutant SAA proteins (3-10 mg/l). Further measurements of rSAA concentration in lipid fractions of culture medium collected at a density of 1.21 g/ml (high-density liporotein; HDL) and 1.063-1.18 g/ml (very-low-density lipoprotein/low-density lipoprotein; VLDL/LDL) showed that 76% of the wild-type protein was found in the HDL fraction and the remaining 24% in the infranatant non-lipid fraction. In contrast the relative concentration of mutant rSAA in HDL and infranatant fractions was reversed. This is consistent with the previously proposed involvement of the 11 amino acid peptide in anchoring. SAA protein on to HDL3 [Turnell, Sarra, Glover, Baum, Caspi, Baltz and Pepys (1986) Mol. Biol. Med. 3, 387-407]. Wild-type rSAA protein was shown to from amyloid fibrils in vitro under acidic conditions as shown by electron microscopy, and stained positive with Congo Red and exhibited apple-green birefringence when viewed under polarized light. Under the same conditions mutSAA(G8D) and mutSAA delta 1

  10. High desolvation temperature facilitates the ESI-source H/D exchange at non-labile sites of hydroxybenzoic acids and aromatic amino acids.

    PubMed

    Zherebker, Alexander; Kostyukevich, Yury; Kononikhin, Alexey; Roznyatovsky, Vitaliy A; Popov, Igor; Grishin, Yuri K; Perminova, Irina V; Nikolaev, Eugene

    2016-04-21

    Hydrogen/deuterium exchange coupled with high-resolution mass spectrometry has become a powerful analytical approach for structural investigations of complex organic matrices. Here we report the feasibility of the site-specific H/D exchange of non-labile hydrogens directly in the electrospray ionization (ESI) source, which was facilitated by an increase in the desolvation temperature from 200 °C up to 400 °C. We have found that the exchanges at non-labile sites were observed only for the model compounds capable of keto-enol tautomeric transformations (e.g., 2,3-, 2,4-dihydroxybenzoic acids, gallic acid, DOPA), and only when water was used as a solvent. We hypothesized that the detected additional exchanges were induced by the presence of hydroxyls in the sprayed water droplets generated in the negative ESI mode. It was indicative of the exchange reactions taking place in the sprayed droplets rather than in the gas phase. To support this hypothesis, the H/D exchange experiments were run in deuterated water under base-catalyzed conditions for three model compounds, which showed the most intensive exchanges in the MS experiments: DOPA, 2,4-DHB, and 5-acetylsalicylic acid. (2)H NMR spectroscopy has confirmed keto-enolic transformations of the model compounds leading to the specific labeling of the corresponding non-labile sites. We believe that the proposed technique will be useful for structural investigations of natural complex mixtures (e.g. proteins, humic substances) using site-specific H/D exchange. PMID:27002310

  11. 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

  12. Density functional studies of the formation of nitrous acid from the reaction of nitrogen dioxide and water vapor

    SciTech Connect

    Chou, A.; Li, Z.; Tao, F.M.

    1999-09-30

    Nitrous acid (HONO) has long been recognized as an important trace gas in the troposphere where its rapid photolysis represents a significant source of hydroxy (OH) radicals. During the night, HONO has been observed to accumulate to concentrations up to 15 ppb, and this accumulation of HONO has a profound impact on the daytime chemistry of the troposphere. Reaction mechanisms for the production of nitrous acid (HONO ) from the homogeneous gas-phase hydrolysis of nitrogen dioxide (NO{sub 2}) are examined by density functional theory calculations. The molecular structures and energies of the NO{sub 2}-(H{sub 2}O){sub n} (n = 1, 2, 3) and N{sub 2}O{sub 4}-(H{sub 2} O){sub n}(n = 1, 2) systems corresponding to the stationary points on the potential energy surface along the reaction pathways are calculated using the B3LYP method with the 6-311+G(2d,p) basis set. These reaction pathways represent the homogeneous hydrolysis of NO{sub 2} or N{sub 2}O{sub 4} with a varying number of water (H{sub 2}O) molecules. The reactions of NO{sub 2} with water produce HONO, along with the OH radical which was postulated to combine in the next step with a second NO{sub 2} to form nitric acid (HNO{sub 3}). The simple NO{sub 2} + H{sub 2}O bimolecular reaction leads to the highly unstable OH radical which reacts reversibly with HONO without an energy barrier. The introduction of single solvating H{sub 2}O molecule appears to stabilize the transition state as well as an intermediate that contains the OH radical. However, the energy barrier is found to be near 30 kcal mol{sup {minus}1} and is not affected by multiple additional H{sub 2}O molecules. On the other hand, the reaction of N{sub 2}O{sub 4} with water lead directly to HONO and HNO{sub 3}. the energy barrier for the N{sub 2}O{sub 4} reaction is above 30 kcal mol{sup {minus}1} and is also unaffected by additional H{sub 2}O molecules. The study demonstrates that the gas-phase hydrolysis of NO{sub 2} or N{sub 2}O{sub 4} is

  13. 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.

  14. 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. PMID:26686117

  15. 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

  16. 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

  17. ACIDIC EPISODES AND SURFACE WATER CHEMISTRY: A COMPARISON OF NORTHEAST AND SOUTHEAST STUDY SITES

    EPA Science Inventory

    Much of the emphasis in the National Acid Precipitation Assessment Program (NAPAP) has been on historical or longterm trends in surface water acidification. Short-term acidic episodes, however, also might have significant adverse effects on aquatic ecosystems. The U.S. EPA is pre...

  18. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    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.

  19. 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.

  20. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    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.

  1. 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.

  2. Active site density and reactivity for the photocatalytic dehydrogenation of 2-propanol on TiO 2 (110)

    NASA Astrophysics Data System (ADS)

    Brinkley, David; Engel, Thomas

    1998-10-01

    By combining molecular beam experiments at 350 K with low temperature experiments on an immobile adlayer, we determine the fraction of surface sites active for the photocatalytic dehydrogenation of 2-propanol to acetone to be 0.08 on a fully oxidized surface. We also find that the reaction probability at these sites is essentially unity. The presence of oxygen vacancies (≈0.1 monolayer) increases the fraction of active sites to 0.15 without changing the reaction probability, reaction kinetics, or product distribution. From this, we conclude that only sites which can bind O 2 strongly are active for the reaction. Candidates for such sites include steps and kinks on fully oxidized surfaces and oxygen lattice vacancies on reduced surfaces.

  3. Probing the steric requirements of the γ-aminobutyric acid aminotransferase active site with fluorinated analogues of vigabatrin

    PubMed Central

    Juncosa, Jose I.; Groves, Andrew P.; Xia, Guoyao; Silverman, Richard B.

    2012-01-01

    We have synthesized three analogues of 4-amino-5-fluorohexanoic acids as potential inactivators of γ-aminobutyric acid aminotransferase (GABA-AT), which were designed to combine the potency of their shorter chain analogue, 4-amino-5-fluoropentanoic acid (AFPA), with the greater enzyme selectivity of the antiepileptic vigabatrin (Sabril®). Unexpectedly, these compounds failed to inactivate or inhibit the enzyme, even at high concentrations. On the basis of molecular modeling studies, we propose that the GABA-AT active site has an accessory binding pocket that accommodates the vinyl group of vigabatrin and the fluoromethyl group of AFPA, but is too narrow to support the extra width of one distal methyl group in the synthesized analogues. PMID:23306054

  4. 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

  5. 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...

  6. Removal of 14 N-terminal amino acids of lactoferrin enhances its affinity for parenchymal liver cells and potentiates the inhibition of beta- very low density lipoprotein binding.

    PubMed

    Ziere, G J; Bijsterbosch, M K; van Berkel, T J

    1993-12-25

    Lactoferrin inhibits the hepatic uptake of lipoprotein remnants, and we showed earlier that arginine residues of lactoferrin are involved. In this study, lactoferrin was treated with aminopeptidase M (APM), which resulted in removal of 14 N-terminal amino acids, including 4 clustered arginine residues at positions 2-5 (APM-lactoferrin). After intravenous injection into rats, 125I-labeled APM-lactoferrin was cleared within 10 min by the liver parenchymal cells (74.7% of the dose). In contrast to native lactoferrin, APM-lactoferrin was rapidly internalized after liver association (> 80% of the liver-associated radioactivity was internalized within 10 min). Binding of APM-lactoferrin to isolated parenchymal liver cells was saturable with a Kd of 186 nM (750,000 sites/cell). This is in striking contrast to the binding of native lactoferrin (Kd 10 microM; 20 x 10(6) sites/cell). Preinjection of rats with 20 mg of APM-lactoferrin/kg of body weight reduced the liver association of beta-very low density lipoprotein (beta-VLDL) by 50%, whereas lactoferrin had no effect at this dose. With isolated parenchymal liver cells, APM-lactoferrin was a more effective competitor for beta-VLDL binding than native lactoferrin (50% inhibition at 0.5 mg/ml versus 8.0 mg/ml). Selective modification of the arginines of APM-lactoferrin with 1,2-cyclohexanedione reduced the liver association by approximately 60% and abolished the capacity of APM-lactoferrin to inhibit the binding of 125I-labeled beta-VLDL in vitro. In conclusion, our data indicate that the four-arginine cluster of lactoferrin at positions 2-5 is involved in its massive, low affinity association of lactoferrin with the liver, possibly to proteoglycans, but is not essential for the inhibition of lipoprotein remnant uptake. The Arg-Lys sequence at positions 25-31, which resembles the binding site of apolipoprotein E, may mediate the high affinity binding of lactoferrin and block the binding of beta-VLDL to the remnant receptor

  7. 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.

  8. Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand.

    PubMed

    Thielges, Megan C; Axup, Jun Y; Wong, Daryl; Lee, Hyun Soo; Chung, Jean K; Schultz, Peter G; Fayer, Michael D

    2011-09-29

    Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein. PMID:21823631

  9. Two-Dimensional IR Spectroscopy of Protein Dynamics Using Two Vibrational Labels: A Site-Specific Genetically Encoded Unnatural Amino Acid and an Active Site Ligand

    PubMed Central

    Thielges, Megan C.; Axup, Jun Y.; Wong, Daryl; Lee, Hyun Soo; Chung, Jean K.; Schultz, Peter G.; Fayer, Michael D.

    2012-01-01

    Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ~1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein. PMID:21823631

  10. 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.

  11. 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.

  12. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids.

    PubMed

    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

  13. Characterization of Fe(II) oxidizing bacterial activities and communities at two acidic Appalachian coalmine drainage-impacted sites

    SciTech Connect

    Senko, John M.; Wanjugi, Pauline; Lucas, Melanie; Bruns, Mary Ann; Burgos, William D.

    2008-06-12

    We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalminederived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O2. Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenic spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.

  14. 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

  15. In situ fluorescence labelling of jasmonic acid binding sites in plant tissues with cadmium-free quantum dots.

    PubMed

    Liao, Qiumei; Yu, Ying; Cao, Yujuan; Lin, Bixia; Wei, Jingjing

    2015-02-01

    The fluorescence labelling of plant hormone binding sites is an important analytical technique in research on the molecular mechanisms of plant hormone activities. The authors synthesised a jasmonic acid (JA)-conjugated ZnS:Mn quantum dot (QD) probe, with a cubic structure and average hydrodynamic sizes of about 17.0 nm. The maximum fluorescence emission of the probe was recorded at about 585 nm. The probe was used for fluorescence labelling of JA binding sites in mung bean seedling tissues. Analysis revealed that the probe exhibited high selectivity to JA binding sites and good performance in eliminating interference from background fluorescence in plant tissues. In addition, the probe did not exhibit any apparent biotoxicity, and is much more suitable than probes constructed from CdTe QDs for the analysis of biological samples. PMID:25650324

  16. A novel method to identify nucleic acid binding sites in proteins by scanning mutagenesis: application to iron regulatory protein.

    PubMed Central

    Neupert, B; Menotti, E; Kühn, L C

    1995-01-01

    We describe a new procedure to identify RNA or DNA binding sites in proteins, based on a combination of UV cross-linking and single-hit chemical peptide cleavage. Site-directed mutagenesis is used to create a series of mutants with single Asn-Gly sequences in the protein to be analysed. Recombinant mutant proteins are incubated with their radiolabelled target sequence and UV irradiated. Covalently linked RNA- or DNA-protein complexes are digested with hydroxylamine and labelled peptides identified by SDS-PAGE and autoradiography. The analysis requires only small amounts of protein and is achieved within a relatively short time. Using this method we mapped the site at which human iron regulatory protein (IRP) is UV cross-linked to iron responsive element RNA to amino acid residues 116-151. Images PMID:7544459

  17. 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...

  18. 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.

  19. 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

  20. Formic acid requirement for the Savannah River Site Defense Waste Processing Facility melter feed preparation

    SciTech Connect

    Hsu, C.W.

    1991-01-01

    The Westinghouse Savannah River Company (WSRC) will vitrify the high-level radioactive waste into a borosilicate glass wasteform using a slurry-fed, joule-heated melter. Formic acid is used to treat the sludge slurry for melter feed preparation. Both a minimum formate requirement and a maximum allowable formate level need to be established to adequately prepare the sludge for melter feed. The data from the Savannah River Laboratory (SRL) Scale Glass Melter (SGM), Integrated DWPF Melter System (IDMS), and research mini-melter runs were used for this purpose. The stoichiometry for major reactions during formic acid treatment was revised to reflect the more predominant chemical reactions and their yields. A minimum formic acid requirement was established according to this revised stoichiometry. Methods for determining the minimum level of formic acid were specified. An operating envelope that includes the maximum total formate level and the minimum nitrate levels, was also proposed. 5 refs., 3 figs., 4 tabs.

  1. Seasonal and diurnal cycles of ammonia, nitrous acid and nitric acid at a forest site in Finland

    NASA Astrophysics Data System (ADS)

    Virkkula, A.; Makkonen, U.; Mäntykenttä, J.; Hakola, H.

    2012-04-01

    Background In July - August 2010 a large campaign "Hyytiälä United Measurements of Photochemistry and Particles in Air - Comprehensive Organic Precursor Emission Concentration 2010 (HUMPPA - COPEC-10)", was conducted in a boreal forest at the SMEAR II station in Hyytiälä, southwestern central Finland. The general goal was to study links between gas phase oxidation chemistry and particle properties and processes. The Finnish Meteorological Institute contributed to the campaign with an on-line analyzer MARGA 2S (Ten Brink et al., 2007) for semi-continuous (1-hr time resolution) measurement of water-soluble gases and ions. Concentrations of gases (HCl, HNO3, HNO2, NH3, SO2) and major ions in particles (Cl, NO3, SO4, NH4, Na, K, Mg, Ca) were measured in two size fractions: PM2.5 and PM10. The MARGA was kept running at SMEAR II also after the campaign. Here we discuss data collected until 30 April, 2011, and restrict the analysis to the nitrogen-containing gases. Ammonia plays a key role in neutralizing acidic atmospheric compounds and in aerosol formation. The concentration of semi-volatile aerosol species such as ammonium nitrate and ammonium chloride is strongly dependent on the gas phase precursors, NH3, HNO3 and HCl. HONO is of atmospheric importance due to its expected significant contribution to the production of OH radicals. Results and discussion The median concentrations of ammonia (NH3), nitrous acid (HONO) and nitric acid (HNO3) during whole period of 21 June 2010 - 30 April 2011 were 85, 54, and 57 ppt, respectively. The seasonal cycle was such that in summer the concentrations of all of these gases were the highest, the respective medians were 356, 70, and 81 ppt in June 21 - August 12, and lowest in winter (December - February), the respective medians were 38, 54, and 52 ppt. A very clear diurnal cycle of all these gases was observed, especially in July. In December there were no cyclic diurnal variation of these but in spring, especially in April the

  2. 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

  3. Specificity of the Antibody Receptor Site to D-Lysergamide: Model of a Physiological Receptor for Lysergic Acid Diethylamide

    PubMed Central

    Vunakis, Helen Van; Farrow, John T.; Gjika, Hilda B.; Levine, Lawrence

    1971-01-01

    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. PMID:5283939

  4. Envelope Membranes from Spinach Chloroplasts Are a Site of Metabolism of Fatty Acid Hydroperoxides.

    PubMed Central

    Blee, E.; Joyard, J.

    1996-01-01

    Enzymes in envelope membranes from spinach (Spinacia oleracea L.) chloroplasts were found to catalyze the rapid breakdown of fatty acid hydroperoxides. In contrast, no such activities were detected in the stroma or in thylakoids. In preparations of envelope membranes, 9S-hydroperoxy-10(E),12(Z)-octadecadienoic acid, 13S-hydroperoxy-9(Z),11(E)-octadecadienoic acid, or 13S-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid were transformed at almost the same rates (1-2 [mu]mol min-1 mg-1 protein). The products formed were separated by reversed-phase high-pressure liquid chromatography and further characterized by gas chromatography-mass spectrometry. Fatty acid hydroperoxides were cleaved (a) into aldehydes and oxoacid fragments, corresponding to the functioning of a hydroperoxide lyase, (b) into ketols that were spontaneously formed from allene oxide synthesized by a hydroperoxide dehydratase, (c) into hydroxy compounds synthesized enzymatically by a system that has not yet been characterized, and (d) into oxoenes resulting from the hydroperoxidase activity of a lipoxygenase. Chloroplast envelope membranes therefore contain a whole set of enzymes that catalyze the synthesis of a variety of fatty acid derivatives, some of which may act as regulatory molecules. The results presented demonstrate a new role for the plastid envelope within the plant cell. PMID:12226196

  5. 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.

  6. 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

  7. Active-site amino acid residues in γ-glutamyltransferase and the nature of the γ-glutamyl-enzyme bond

    PubMed Central

    Elce, John S.

    1980-01-01

    Active-site residues in rat kidney γ-glutamyltransferase (EC 2.3.2.2) were investigated by means of chemical modification. 1. In the presence of maleate, the activity was inhibited by phenylmethanesulphonyl fluoride, and the inhibition was not reversed by β-mercaptoethanol, suggesting that a serine residue is close to the active site, but is shielded except in the presence of maleate. 2. Treatment of the enzyme with N-acetylimidazole modified an amino group, exposed a previously inaccessible cysteine residue and inhibited hydrolysis of the γ-glutamyl-enzyme intermediate, but not its formation. 3. After reaction of the enzyme successively with N-acetylimidazole and with non-radioactive iodoacetamide/serine/borate, two active-site residues reacted with iodo[14C]acetamide. One of these possessed a carboxy group, which formed a [14C]glycollamide ester, and the other was cysteine, shown by isolation of S-[14C]carboxymethylcysteine after acid hydrolysis. When N-acetylimidazole treatment was omitted, only the carboxy group reacted with iodo[14C]acetamide. 4. Isolation of the γ-[14C]glutamyl-enzyme intermediate was made easier by prior treatment of the enzyme with N-acetylimidazole. The γ-glutamyl-enzyme bond was stable to performic acid, and to hydroxylamine/urea at pH10, but was hydrolysed slowly at pH12, indicating attachment of the γ-[14C]glutamyl group in amide linkage to an amino group on the enzyme. Proteolysis of the γ-[14C]glutamyl-enzyme after performic acid oxidation gave rise to a small acidic radioactive peptide that was resistant to further proteolysis and was not identical with γ-glutamyl-ε-lysine. 5. A scheme for the catalytic mechanism is proposed. PMID:6104953

  8. A novel amino acid supplementation strategy based on a stoichiometric model to enhance human IL-2 (interleukin-2) expression in high-cell-density Escherichia coli cultures.

    PubMed

    Sarkandy, Shahin Yegane; Khalilzadeh, Rasoul; Shojaosadati, Seyed Abbas; Sadeghizadeh, Majid; Farnoud, Amir Mohammad; Babaeipour, Valiollah; Maghsoudi, Amir

    2010-12-01

    A novel amino acid supplementation strategy was developed for enhancing the production of IL-2 (interleukin-2; as a model protein) by recombinant Escherichia coli BL21 (pET21a-hil2) in fed-batch high-cell-density cultures. The amino acids most needed and their amounts were determined using a stoichiometric model, and full factorial design experiments were conducted to determine the effects of single amino acids and amino acid mixtures on production. One of the most effective amino acid mixtures was found to be leucine, aspartic acid and glycine. This amino acid mixture was utilized for the production of IL-2 in batch and fed-batch fermentations. The amount of IL-2 produced increased from 403 to 722 mg/l and from 5.15 × 10³ to 8.08 × 10³ mg/l in batch and fed-batch cultures respectively. The results also revealed that the above amino acid mixture specifically increases IL-2 concentration in the cells. PMID:21062264

  9. 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

  10. 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.

  11. 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.

  12. Chromatographic analysis of the effects of fatty acids and glycation on binding by probes for Sudlow sites I and II to human serum albumin.

    PubMed

    Anguizola, Jeanethe; Debolt, Erin; Suresh, D; Hage, David S

    2016-05-15

    The primary endogenous ligands of human serum albumin (HSA) are non-esterified fatty acids, with 0.1-2mol of fatty acids normally being bound to HSA. In type II diabetes, fatty acid levels in serum are often elevated, and the presence of high glucose results in an increase in the non-enzymatic glycation of HSA. High-performance affinity chromatography (HPAC) was used to examine the combined effects of glycation and the presence of long chain fatty acids on the binding of HSA with R-warfarin and l-tryptophan (i.e., probes for Sudlow sites I and II, the major sites for drugs on this protein). Zonal elution competition studies were used to examine the interactions of myristic acid, palmitic acid and stearic acid with these probes on HSA. It was found that all these fatty acids had direct competition with R-warfarin at Sudlow site I of normal HSA and glycated HSA, with the glycated HSA typically having stronger binding for the fatty acids at this site. At Sudlow site II, direct competition was observed for all the fatty acids with l-tryptophan when using normal HSA, while glycated HSA gave no competition or positive allosteric interactions between these fatty acids and l-tryptophan. These data indicated that glycation can alter the interactions of drugs and fatty acids at specific binding sites on HSA. The results of this study should lead to a better understanding of how these interactions may change during diabetes and demonstrate how HPAC can be used to examine drug/solute-protein interactions in complex systems. PMID:26468085

  13. Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites.

    PubMed Central

    Jiang, H; Parales, R E; Lynch, N A; Gibson, D T

    1996-01-01

    The terminal oxygenase component of toluene dioxygenase from Pseudomonas putida F1 is an iron-sulfur protein (ISP(TOL)) that requires mononuclear iron for enzyme activity. Alignment of all available predicted amino acid sequences for the large (alpha) subunits of terminal oxygenases showed a conserved cluster of potential mononuclear iron-binding residues. These were between amino acids 210 and 230 in the alpha subunit (TodC1) of ISP(TOL). The conserved amino acids, Glu-214, Asp-219, Tyr-221, His-222, and His-228, were each independently replaced with an alanine residue by site-directed mutagenesis. Tyr-266 in TodC1, which has been suggested as an iron ligand, was treated in an identical manner. To assay toluene dioxygenase activity in the presence of TodC1 and its mutant forms, conditions for the reconstitution of wild-type ISP(TOL) activity from TodC1 and purified TodC2 (beta subunit) were developed and optimized. A mutation at Glu-214, Asp-219, His-222, or His-228 completely abolished toluene dioxygenase activity. TodC1 with an alanine substitution at either Tyr-221 or Tyr-266 retained partial enzyme activity (42 and 12%, respectively). In experiments with [14C]toluene, the two Tyr-->Ala mutations caused a reduction in the amount of Cis-[14C]-toluene dihydrodiol formed, whereas a mutation at Glu-214, Asp-219, His-222, or His-228 eliminated cis-toluene dihydrodiol formation. The expression level of all of the mutated TWO proteins was equivalent to that of wild-type TodC1 as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analyses. These results, in conjunction with the predicted amino acid sequences of 22 oxygenase components, suggest that the conserved motif Glu-X3-4,-Asp-X2-His-X4-5-His is critical for catalytic function and the glutamate, aspartate, and histidine residues may act as mononuclear iron ligands at the site of oxygen activation. PMID:8655491

  14. 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/. PMID:26080082

  15. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

    PubMed Central

    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 in10-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/. PMID:26080082

  16. 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.

  17. Higher Serum Uric Acid Is Associated with Higher Bone Mineral Density in Chinese Men with Type 2 Diabetes Mellitus

    PubMed Central

    Zhao, Dian-dian; Jiao, Pei-lin; Yu, Jing-jia; Wang, Xiao-jing; Zhao, Lin; Xuan, Yan; Sun, Li-hao; Tao, Bei; Wang, Wei-qing; Ning, Guang; Liu, Jian-min; Zhao, Hong-yan

    2016-01-01

    Accumulating evidence suggests that oxidative stress is associated with osteoporosis. Serum uric acid (UA) is a strong endogenous antioxidant. Therefore, we investigated the relationship between the serum UA and BMD in Chinese men with T2DM. In this cross-sectional study of 621 men with T2DM, BMDs at lumbar spine (L2–4), femoral neck (FN), and total hip (TH) were measured by dual-energy X-ray absorptiometry (DXA). Serum levels of UA, calcium (Ca), 25-OH vitamin D3 (vitD3), parathyroid hormone (PTH), and creatinine (Cr) were also tested. Data analyses revealed that serum UA levels were positively associated with BMD at all sites (p < 0.05) in men with T2DM after adjusting for multiple confounders. The serum UA levels were positively correlated with body weight (r = 0.322), body mass index (BMI) (r = 0.331), Ca (r = 0.179), and Cr (r = 0.239) (p < 0.001) and were also positively associated with the concentrations of PTH (r = 0.10, p < 0.05). When compared with those in the lowest tertile of UA levels, men with T2DM in the highest tertile had a lower prevalence of osteoporosis or osteopenia (adjusted odds ratio 0.54, 95% confidence interval [CI] 0.31–0.95). These data suggest that higher serum levels of UA are associated with higher BMDs and lower risks of osteoporosis in Chinese men with T2DM. PMID:27022396

  18. 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.

  19. Fluorescence properties and sequestration of peripheral anionic site specific ligands in bile acid hosts: Effect on acetylcholinesterase inhibition activity.

    PubMed

    Islam, Mullah Muhaiminul; Aguan, Kripamoy; Mitra, Sivaprasad

    2016-05-01

    The increase in fluorescence intensity of model acetyl cholinesterase (AChE) inhibitors like propidium iodide (PI) and ethidium bromide (EB) is due to sequestration of the probes in primary micellar aggregates of bile acid (BA) host medium with moderate binding affinity of ca. 10(2)-10(3)M(-1). Multiple regression analysis of solvent dependent fluorescence behavior of PI indicates the decrease in total nonradiative decay rate due to partial shielding of the probe from hydrogen bond donation ability of the aqueous medium in bile acid bound fraction. Both PI and EB affects AChE activity through mixed inhibition and consistent with one site binding model; however, PI (IC50=20±1μM) shows greater inhibition in comparison with EB (IC50=40±3μM) possibly due to stronger interaction with enzyme active site. The potency of AChE inhibition for both the compounds is drastically reduced in the presence of bile acid due to the formation of BA-inhibitor complex and subsequent reduction of active inhibitor fraction in the medium. Although the inhibition mechanism still remains the same, the course of catalytic reaction critically depends on equilibrium binding among several species present in the solution; particularly at low inhibitor concentration. All the kinetic parameters for enzyme inhibition reaction are nicely correlated with the association constant for BA-inhibitor complex formation. PMID:26974580

  20. Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events

    PubMed Central

    Phatak, Prasad; Sumner, Isaiah; Iyengar, Srinivasan S.

    2012-01-01

    We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical towards maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process. PMID:22838384

  1. Cost-minimization study comparing annual infusion of zoledronic acid or weekly oral alendronate in women with low bone mineral density.

    PubMed

    Chávez-Valencia, Venice; Arce-Salinas, César Alejandro; Espinosa-Ortega, Fabricio

    2014-01-01

    Cost-minimization study to assess the annual direct costs of 2 antiresorptive strategies in postmenopausal women with low bone mineral densities (BMDs). Patients were randomly assigned to receive 70 mg of oral weekly alendronate or a 1-time 5mg of intravenous zoledronic acid. All medical and nonmedical direct costs were recorded for 1 yr. Student's t-test or the Chi-squared test was used. A total of 101 postmenopausal women were enrolled with a mean age of 58.3 ± 7.6 yr and a postmenopausal period of 13.5 ± 8.3 yr. A total of 50 patients completed 1 yr of alendronate and 51 patients received zoledronic acid. At baseline, no differences were seen between the 2 groups in anthropometric measures, comorbidities, and bone mineral density. The costs for medical attention for low bone mass were $81,532 (US Dollars) for the alendronate group and $69,251 for the zoledronic acid group; the cost per patient was $1631 in the alendronate group vs $1358 in the zoledronic acid group (p<0.0001). Therefore, zoledronic acid treatment provided an annual savings of 15% of the direct costs compared with oral alendronate treatment. Moreover, there was a significant increase in lumbar spine T-scores in the zoledronic acid group when compared with the alendronate group. Annual zoledronic acid infusion as an antiresorptive treatment in women with low BMD provides significant monetary savings when compared with weekly alendronate therapy for 1 yr. Zoledronic acid infusion is also linked to higher increase in BMD and compliance. PMID:24613450

  2. 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

  3. 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

  4. Demographics and density estimates of two three-toed box turtle (Terrapene carolina triunguis) populations within forest and restored prairie sites in central Missouri.

    PubMed

    O'Connor, Kelly M; 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

  5. 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.

  6. 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

  7. 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

  8. Identification of a Binding Site for Unsaturated Fatty Acids in the Orphan Nuclear Receptor Nurr1.

    PubMed

    de Vera, Ian Mitchelle S; Giri, Pankaj K; Munoz-Tello, Paola; Brust, Richard; Fuhrmann, Jakob; Matta-Camacho, Edna; Shang, Jinsai; Campbell, Sean; Wilson, Henry D; Granados, Juan; Gardner, William J; Creamer, Trevor P; Solt, Laura A; Kojetin, Douglas J

    2016-07-15

    Nurr1/NR4A2 is an orphan nuclear receptor, and currently there are no known natural ligands that bind Nurr1. A recent metabolomics study identified unsaturated fatty acids, including arachidonic acid and docosahexaenoic acid (DHA), that interact with the ligand-binding domain (LBD) of a related orphan receptor, Nur77/NR4A1. However, the binding location and whether these ligands bind other NR4A receptors were not defined. Here, we show that unsaturated fatty acids also interact with the Nurr1 LBD, and solution NMR spectroscopy reveals the binding epitope of DHA at its putative ligand-binding pocket. Biochemical assays reveal that DHA-bound Nurr1 interacts with high affinity with a peptide derived from PIASγ, a protein that interacts with Nurr1 in cellular extracts, and DHA also affects cellular Nurr1 transactivation. This work is the first structural report of a natural ligand binding to a canonical NR4A ligand-binding pocket and indicates a natural ligand can bind and affect Nurr1 function. PMID:27128111

  9. Investigation of metal binding sites on soil fulvic acid using Eu(III) luminescence spectroscopy

    SciTech Connect

    Yoon, T.H.; Moon, H. ); Park, Y.J.; Park, K.K. )

    1994-11-01

    The [sup 7]F[sub 0] [yields] [sup 5]D[sub 0] excitation spectra of Eu(III) complexed with soil fulvic acid (FA) were acquired over a range of solution pH (2.9-7.8) and FA concentrations (800-3200 mg L[sup [minus]1]) using a pulsed tunable dye laser system. The broad asymmetric excitation spectra were well-fitted to a sum of two conventional Lorentzian-shaped curves, revealing the existence of two types of carboxylate moieties for the binding of metal ions on FA which formed 1:1 (EuL[sup 2+]; L = carboxylate) and 1:2 complexes (EuL[sub 2][sup +]). The weaker binding species, EuL[sup 2+], seemed to be quite abundant and showed a rapid increase as the pH was raised from 2.9 to 6.3, but it was susceptible to hydrolysis at pH higher than 7 while the stronger binding species, EuL[sub 2][sup +], showed only a modest growth with an increase in pH. By contrast, on a more flexible synthetic linear polymer, poly(acrylic acid) (PAA) and poly(vinylbenzoic acid) (PVBA) as model polymers, EuL[sub 2][sup +] was seen as the dominant species except in acidic media. 28 refs., 10 figs., 3 tabs.

  10. [Studies of the fundamental nature of catalytic acidity, sites and intermediates]: Final performance (technical progress) report

    SciTech Connect

    Not Available

    1993-12-31

    This project was concerned with the fundamental nature of catalyst acidity in the H-zeolites and silica/alumina cracking catalysts. This report summarizes the progress on this project over the past five years. The titles of the twelve papers generated by this research are provided in the attached bibliography in chronological order.

  11. 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

  12. Chicoric acid binds to two sites and decreases the activity of the YopH bacterial virulence factor.

    PubMed

    Kuban-Jankowska, Alicja; Sahu, Kamlesh K; Gorska, Magdalena; Tuszynski, Jack A; Wozniak, Michal

    2016-01-19

    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

  13. 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. PMID:24861954

  14. Comparison of the density of gamma-aminobutyric acid in the ventromedial prefrontal cortex of patients with first-episode psychosis and healthy controls

    PubMed Central

    YANG, Zhilei; ZHU, Yajing; SONG, Zhenhua; MEI, Li; ZHANG, Jianye; CHEN, Tianyi; WANG, Yingchan; XU, Yifeng; JIANG, Kaida; LI, Yao; LIU, Dengtang

    2015-01-01

    Background Abnormality in the concentration and functioning of gamma-aminobutyric acid (γ-aminobutyric acid, GABA) in the brain is not only an important hypothetical link to the cause of schizophrenia but it may also be correlated with the cognitive decline and negative symptoms of schizophrenia. Studies utilizing high field magnetic resonance spectroscopy (MRS) report abnormal density of GABA in the ventromedial prefrontal cortex (vmPFC) of patients with chronic schizophrenia, but these results may be confounded by study participants’ prior use of antipsychotic medications. Aim Compare the density of GABA in the vmPFC of patients with first-episode psychosis to that in healthy controls and assess the relationship of GABA density in the vmPFC to the severity of psychotic symptoms. Methods Single-voxel 1H-MRS was used to assess the concentration of GABA and other metabolites in the vmPFC of 22 patients with first-episode psychosis (10 with schizophrenia and 12 with schizophreniform disorder) and 23 healthy controls. Thirteen of the 22 patients were drug-naïve and 9 had used antipsychotic medication for less than 3 days. The Positive and Negative Syndrome Scale (PANSS) was used to evaluate the severity of psychotic symptoms in the patient group. Results The mean (sd) GABA density in the vmPFC was significantly higher in patients than in controls (2.28 [0.54] v. 1.93 [0.32] mM, t=2.62, p=0.012). The densities of other metabolites – including N-acetylaspartic acid (NAA), glutamic acid (GLU), and glutamine (GLN) – were not significantly different between patients and controls. Among the patients, GABA density in the vmPFC was not significantly correlated with PANSS total score or with any of the three PANSS subscale scores for positive symptoms, negative symptoms, and general psychopathology. GABA concentration was not associated with the duration of illness, but it was significantly correlated with patient age (r=0.47, p=0.026). Conclusion Elevation of GABA

  15. 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).

  16. Optimal site-centered electronic structure basis set from a displaced-center expansion: Improved results via a priori estimates of saddle points in the density

    NASA Astrophysics Data System (ADS)

    Alam, Aftab; Johnson, D. D.

    2009-09-01

    Site-centered, electronic-structure methods use an expansion inside nonoverlapping “muffin-tin” (MT) spheres plus an interstitial basis set. As the boundary separating the more spherical from nonspherical density between atoms, the “saddle-point” radii (SPR) in the density provide an optimal spherical region for expanding in spherical harmonics, as used in augmented plane wave, muffin-tin orbital, and multiple-scattering [Korringa, Kohn, and Rostoker (KKR)] methods. These MT-SPR guarantee unique, convex Voronoi polyhedra at each site, in distinction to Bader topological cells. We present a numerically fast, two-center expansion to find SPR a priori from overlapping atomic charge densities, valid also for disordered alloys. We adopt this MT-SPR basis for KKR in the atomic sphere approximation and study (dis)ordered alloys with large differences in atomic size (fcc CoPt and bcc CrW). For this simple and unique improvement, we find formation energies and structural parameters in strikingly better agreement with more exact methods or experiment, and resolve issues with former results.

  17. 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

    NASA Astrophysics Data System (ADS)

    Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

    2015-08-01

    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.

  18. 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.

  19. Subnucleosomes and their relationships to the arrangement of histone binding sites along nucleosome deoxyribonucleic acid

    SciTech Connect

    Nelson, D.A.; Mencke, A.J.; Chambers, S.A.; Oosterhof, D.K.; Rill, R.L.

    1982-01-01

    Micrococcal nuclease cleaves within nucleosomes at sites spaced about 10.4 base pairs (bp) apart. Cleavages at sites equivalent to 30-35 bp from the ends of 146-bp cores cause spontaneous loss of an H2a-H2b pair associated with 30-40 bp length DNA. Cleavages at certain other sites do not affect the nucleosome integrity unless a solvent perturbant such as urea is added. Chromatin moderately digested with micrococcal nuclease, when fractionated by sedimentation or electrophoresis in the presence of 3 M urea, yielded four previously unobserved subnucleosomes with the following histone/DNA compositions: (H3)/sub 2/(H4)/sub 2/(H2a)(H2b)/95-115 bp; (H3)(H4)/70-80 bp DNA; (H2a)(H2b)/50-60 bp DNA; and (H1)/60-70 bp DNA. All but the latter subnucleosome were also obtained upon DNase I digestion of purified nucleosome cores labeled on the 5' ends with /sup 32/P. Only subnucleosomes that retained H2a and H2b also retained labeled ends. These results show that H2a and H2b are paired on the terminal 30-40 bp of core DNA, as suggested from analyses of histone-DNA cross-link products by Mirzabekov and coworkers. Considerations of the orgins and compositions of subnucleosomes and of cross-linking data suggest an expanded model for the locations of histone binding sites along nucleosome core DNA. The principal features of this model are (i) strong electrostatic binding sites of H2a and H2b occur at positions approximately 20-30 bp from the core ends, (ii) strong electrostatic binding sites of H3 and H4 occur primarily on the central 40 bp of core DNA, (iii) strong nonelectrostatic, urea-sensitive binding sites of H3 and H4 occur at positions approximately 30-50 bp from the core ends, and (iv) urea-sensitive binding sites of H2a or H2b may occur on the terminal 10-20 bp of core DNA.

  20. 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

  1. 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

  2. Prediction of posttranslational modification sites from amino acid sequences with kernel methods.

    PubMed

    Xu, Yan; Wang, Xiaobo; Wang, Yongcui; Tian, Yingjie; Shao, Xiaojian; Wu, Ling-Yun; Deng, Naiyang

    2014-03-01

    Post-translational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role which modifies the end product of gene expression and contributes to biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are both costly and time-consuming. Hence computational methods are highly desired. In this work, a novel encoding method PSPM (position-specific propensity matrices) is developed. Then a support vector machine (SVM) with the kernel matrix computed by PSPM is applied to predict the PTM sites. The experimental results indicate that the performance of new method is better or comparable with the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. A unified standalone software PTMPred is developed. It can be used to predict all types of PTM sites if the user provides the training datasets. The software can be freely downloaded from http://www.aporc.org/doc/wiki/PTMPred. PMID:24291233

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. The impact of the density and type of reactive sites on the characteristics of the atomic layer deposited WNxCy films

    NASA Astrophysics Data System (ADS)

    Martin Hoyas, A.; Travaly, Y.; Schuhmacher, J.; Sajavaara, T.; Whelan, C. M.; Eyckens, B.; Richard, O.; Giangrandi, S.; Brijs, B.; Vandervorst, W.; Maex, K.; Celis, J. P.; Jonas, A. M.; Vantomme, A.

    2006-03-01

    The growth of tungsten nitride carbide (WNxCy) films obtained by atomic layer deposition using triethylboron, tungsten hexafluoride, and ammonia precursors is determined by the density and type of reactive sites. The film properties change as a function of thickness. On silicon dioxide and silicon carbide, growth is initially nonlinear such that the transient regimes are characterized by island formation, as evidenced by a parabolic tungsten growth curve extending to film thicknesses of up to 5 nm. Such films have low densities of ~4-6 g cm-3 corresponding to only ~30%-45% of the bulk density of ~13.1 g cm-3 determined for a WN0.45C0.55 composition. X-ray reflectivity, thermal desorption, and elastic recoil detection spectroscopies reveal surface roughening and compositional and density differences close to the substrate surface. The offset from linear growth in the case of WNxCy films deposited on silicon dioxide is induced by the initial reaction of silanol and siloxane groups with triethylborane resulting in passivating ethylsilyl groups on the surface. A transient regime is not observed for WNxCy growth on hydrogen-terminated silicon with the initial growth being dominated by the reduction of tungsten hexafluoride to tungsten. On silicon nitride a short transient regime is observed relative to the carbide and oxide surfaces attributed to the enhanced binding of the triethylboron precursor.

  13. 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...

  14. 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.

  15. 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.

  16. Toward Fast and Accurate Evaluation of Charge On-Site Energies and Transfer Integrals in Supramolecular Architectures Using Linear Constrained Density Functional Theory (CDFT)-Based Methods.

    PubMed

    Ratcliff, Laura E; Grisanti, Luca; Genovese, Luigi; Deutsch, Thierry; Neumann, Tobias; Danilov, Denis; Wenzel, Wolfgang; Beljonne, David; Cornil, Jérôme

    2015-05-12

    A fast and accurate scheme has been developed to evaluate two key molecular parameters (on-site energies and transfer integrals) that govern charge transport in organic supramolecular architecture devices. The scheme is based on a constrained density functional theory (CDFT) approach implemented in the linear-scaling BigDFT code that exploits a wavelet basis set. The method has been applied to model disordered structures generated by force-field simulations. The role of the environment on the transport parameters has been taken into account by building large clusters around the active molecules involved in the charge transfer. PMID:26574411

  17. 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

  18. (3H) 5,7-dichlorokynurenic acid, a high affinity ligand for the NMDA receptor glycine regulatory site

    SciTech Connect

    Hurt, S.D.; Baron, B.M. )

    1991-01-01

    The NMDA subtype of glutamate receptors is allosterically linked to a strychnine-insensitive glycine regulatory site. Kynurenic acid and its halogenated derivatives are non-competitive NMDA antagonists acting at the glycine site. The authors have prepared (3H) 5,7-dichlorokyrurenic acid (DCKA) as an antagonist radioligand and have characterized its binding. 3-Bromo-5,7-DCKA was catalytically dehalogenated in the presence of tritium gas and HPLC purified to yield (3H) 5,7-DCKA with a specific activity of 17.6 Ci/mmol. (3H) 5,7-DCKA bound to rat brain synaptosomes with a Kd of 69 {plus minus} 23 nM and Bmax = 14.5 {plus minus} 3.2 pmoles/mg protein. Binding was 65-70% specific at 10 nM (3H) 5,7-DCKA. This ligand is thus more selective and has higher affinity than (3H) glycine, in addition to being an antagonist.

  19. 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. PMID:27445084

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. A surface site as polydentate ligand of a metal complex: Density functional studies of rhenium subcarbonyls supported on magnesium oxide

    SciTech Connect

    Hu, A.; Neyman, K.M.; Staufer, M.; Belling, T.; Gates, B.C.; Roesch, N.

    1999-05-12

    Notwithstanding the importance of supported organometallic species as industrial catalysts, most are nonuniform mixtures, with only a few being well-characterized at the atomic level. Rhenium subcarbonyls on MgO, in contrast, consist of nearly uniform surface species and are among the best-studied organometallic complexes on oxides. EXAFS and infrared spectra showed that decomposition of the precursors [HRe(CO){sub 5}], [H{sub 3}Re{sub 3}(CO){sub 12}], and [Re{sub 2}(CO){sub 10}] on MgO powder results in fragments, assigned as Re(CO){sub 3}{sup n+}, coordinated to surface ligands. The concept of a surface site as a polydentate ligand evokes the remarkable circumstance in which the adsorbate-substrate bonds are as strong as metal-ligand bonds in common transition metal complexes, as shown by the present investigation.

  6. 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

  7. Acid-induced change in ozone-reactive site in indole ring of tryptophan

    SciTech Connect

    Matsumura, Sueo Yoshimura, Ayuko; Okazaki, Kazuyuki; Fijitani, Noboru; Hattori, Hideki

    2009-03-13

    It is well established that ozone as well as oxygen activated by tryptophan 2,3-dioxygenase or indoleamine 2,3-dioxygenase cleave the 2,3-C=C bond of the indole ring of tryptophan to produce N-formylkynurenine. In the present study, however, we found that exposure of tryptophan to aqueous ozone at and below pH 4.5 generated a different compound. The compound was identified as kynurenine by high performance liquid chromatography and mass spectrometry. Exposure of N-formylkynurenine to acidic ozone did not generate a significant amount of kynurenine, indicating that the kynurenine was not produced via N-formylkynurenine. Acidic ozone thus appears to cleave the 1, 2-N-C bond in place of the 2,3-C=C bond of the indole ring, followed by liberation of the 2-C atom. The 1,2-N-C bond and 2,3-C=C bond are likely to undergo changes in their nature of bonding on acidification, enabling ozone to react with the former bond but not with the latter bond.

  8. Fatty Acids and Breast Cancer: Make Them on Site or Have Them Delivered.

    PubMed

    Kinlaw, William B; Baures, Paul W; Lupien, Leslie E; Davis, Wilson L; Kuemmerle, Nancy B

    2016-10-01

    Brisk fatty acid (FA) production by cancer cells is accommodated by the Warburg effect. Most breast and other cancer cell types are addicted to fatty acids (FA), which they require for membrane phospholipid synthesis, signaling purposes, and energy production. Expression of the enzymes required for FA synthesis is closely linked to each of the major classes of signaling molecules that stimulate BC cell proliferation. This review focuses on the regulation of FA synthesis in BC cells, and the impact of FA, or the lack thereof, on the tumor cell phenotype. Given growing awareness of the impact of dietary fat and obesity on BC biology, we will also examine the less-frequently considered notion that, in addition to de novo FA synthesis, the lipolytic uptake of preformed FA may also be an important mechanism of lipid acquisition. Indeed, it appears that cancer cells may exist at different points along a "lipogenic-lipolytic axis," and FA uptake could thwart attempts to exploit the strict requirement for FA focused solely on inhibition of de novo FA synthesis. Strategies for clinically targeting FA metabolism will be discussed, and the current status of the medicinal chemistry in this area will be assessed. J. Cell. Physiol. 231: 2128-2141, 2016. © 2016 Wiley Periodicals, Inc. PMID:26844415

  9. 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.

  10. 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

  11. 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

  12. Increase in the Bmax of gamma-aminobutyric acid-A recognition sites in brain regions of mice receiving diazepam.

    PubMed Central

    Ferrero, P; Guidotti, A; Costa, E

    1984-01-01

    gamma-Aminobutyric acid (GABA) receptors were characterized in vivo by studying ex vivo the binding of [3H]muscimol to cerebellum, cortex, hippocampus, and corpus striatum of mice receiving intravenous injections of tracer doses of high-specific-activity (approximately equal to 30 Ci/mmol) [3H]muscimol. This ligand binds with high affinity (apparent Kd, 2-3 X 10(-9) M) to a single population of binding sites (apparent Bmax, 250-180 fmol per 10 mg of protein). Pharmacological studies using drugs that selectively bind to GABAA or GABAB receptors suggest that [3H]muscimol specifically labels a GABAA recognition site. Moreover, diazepam (1.5 mumol/kg, i.p.) increases the Bmax but fails to change the affinity of [3H]muscimol binding to different brain areas. This diazepam-elicited increase in Bmax is blocked in mice receiving the diazepam antagonist Ro 15-1788 (ethyl-8-fluoro-5,6-dihydro-5-methyl-6-oxo-4H-imidazo[1,5a]-[1,4] benzodiazepine-3-carboxylate). Since the diazepam-induced increase of [3H]muscimol binding is paralleled by a significant potentiation of the inhibitory effect of muscimol on locomotor activity, it is proposed that the facilitatory action on GABAergic transmission elicited in vivo by diazepam is mediated by an increase in the Bmax of the binding sites of GABAA receptors. Images PMID:6326115

  13. 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

  14. 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.

  15. 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

  16. 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

  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. 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. PMID:22907828

  19. 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.

  20. 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

  1. 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. PMID:26650435

  2. Tunable translational control using site-specific unnatural amino acid incorporation in Escherichia coli

    PubMed Central

    2015-01-01

    Translation of target gene transcripts in Escherichia coli harboring UAG amber stop codons can be switched on by the amber-codon-specific incorporation of an exogenously supplied unnatural amino acid, 3-iodo-L-tyrosine. Here, we report that this translational switch can control the translational efficiency at any intermediate magnitude by adjustment of the 3-iodo-L-tyrosine concentration in the medium, as a tunable translational controller. The translational efficiency of a target gene reached maximum levels with 10−5 M 3-iodo-L-tyrosine, and intermediate levels were observed with suboptimal concentrations (approximately spanning a 2-log10 concentration range, 10−7–10−5 M). Such intermediate-level expression was also confirmed in individual bacteria. PMID:25945307

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. Drug-nucleic acid interactions: conformational flexibility at the intercalation site.

    PubMed Central

    Berman, H M; Neidle, S; Stodola, R K

    1978-01-01

    The conformational features of the intercalation site in polynucleotides were examined. We found that, for all the crystal structures of drug-dinucleoside complexes studied thus far, two torsion angles differ from those found in A RNA (phi and chi) and that alternate sugar puckering is not a prerequisite for intercalation. This intercalation geometry, which is the basis of helix axis displacement in a polymer, would necessitate conformational changes in the adjacent nucleotides. The base-turn angle is less sensitive to the conformation of the backbone than it is to small alterations in the base-pairing geometry. We postulate that this angle is dependent on the nature of the intercalating drug. PMID:273246

  9. 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.

  10. Characterization of an intracellular hyaluronic acid binding site in isolated rat hepatocytes

    SciTech Connect

    Frost, S.J.; Raja, R.H.; Weigel, P.H. )

    1990-11-13

    125I-HA, prepared by chemical modification at the reducing sugar, specifically binds to rat hepatocytes in suspension or culture. Intact hepatocytes have relatively few surface 125I-HA binding sites and show low specific binding. However, permeabilization of hepatocytes with the nonionic detergent digitonin results in increased specific 125I-HA binding (45-65%) and a very large increase in the number of specific 125I-HA binding sites. Scatchard analysis of equilibrium 125I-HA binding to permeabilized hepatocytes in suspension at 4 degrees C indicates a Kd = 1.8 x 10(-7) M and 1.3 x 10(6) molecules of HA (Mr approximately 30,000) bound per cell at saturation. Hepatocytes in primary culture for 24 h show the same affinity but the total number of HA molecules bound per cell at saturation decreases to approximately 6.2 x 10(5). Increasing the ionic strength above physiologic concentrations decreases 125I-HA binding to permeable cells, whereas decreasing the ionic strength above causes an approximately 4-fold increase. The divalent cation chelator EGTA does not prevent binding nor does it release 125I-HA bound in the presence of 2 mM CaCl2, although higher divalent cation concentrations stimulate 125I-HA binding. Ten millimolar CaCl2 or MnCl2 increases HA binding 3-6-fold compared to EGTA-treated cells. Ten millimolar MgCl2, SrCl2, or BaCl2 increased HA binding by 2-fold. The specific binding of 125I-HA to digitonin-treated hepatocytes at 4{degrees}C increased greater than 10-fold at pH 5.0 as compared to pH 7.

  11. Serum uric acid and low-density lipoprotein cholesterol levels are independent predictors of coronary artery disease in Asian Indian patients with type 2 diabetes mellitus

    PubMed Central

    Jayashankar, C. A.; Andrews, Henley Punnen; Vijayasarathi; Pinnelli, Venkata BharatKumar; Shashidharan, Basappaji; Nithin Kumar, H. N.; Vemulapalli, Swaapnika

    2016-01-01

    Aim: We aimed to identify the predictors of coronary artery disease (CAD) in patients with type 2 diabetes mellitus (type 2 DM). Methods: About fifty Asian Indian patients with type 2 DM patients aged >40 years and fifty sex- and age-matched nondiabetic controls were enrolled for this study. Following complete medical history and baseline clinical data, laboratory investigations were performed to assess fasting and postprandial plasma glucose levels, lipid profile, blood urea, serum creatinine, and serum uric acid levels. Results: Body mass index (BMI), waist-to-hip ratio, serum uric acid, serum total cholesterol, low-density lipoprotein (LDL) cholesterol, triglycerides, very LDL cholesterol were significantly higher among diabetic patients compared to controls. On univariate analysis, serum LDL cholesterol (odds ratio [OR]: 29.67, P < 0.001), serum uric acid (OR: 25.65, P < 0.001), low high-density lipoprotein (HDL) cholesterol (OR: 21.12, P < 0.001), hypertension (OR: 17.06, P < 0.001), family history of cardiovascular disease (CVD) (OR: 9.43, P = 0.002), and duration of diabetes (OR: 4.65, P = 0.03) were identified as predictors of CVD among diabetic patients. On multivariate regression, only LDL cholesterol (OR: 1.51, P = 0.002) and serum uric acid (OR: 1.21, P = 0.01) were the independent predictors of CAD among diabetic patients. Significant positive correlation of serum uric acid with duration of diabetes (r = 0.38, P = 0.006), BMI (r = 0.35, P = 0.01), triglycerides (r = 0.356, P = 0.01), LDL cholesterol (r = 0.38, P = 0.007), HDL cholesterol (r = −0.514, P < 0.001), and hypertension (r = 0.524, P < 0.001) was observed. Conclusion: Serum LDL cholesterol and hyperuricemia may serve as independent predictors of CAD among Asian Indian subjects with type 2 DM. PMID:27433067

  12. 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

  13. 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 generation of reactive oxygen species (ROS). In addition, the anti-apoptotic effect of ellagic acid was partially inhibited by a PI3K inhibitor (wortmannin) and a specific eNOS inhibitor (cavtratin) but not by an ERK inhibitor (PD98059). In exploring the underlying mechanisms of ellagic acid action, we found that oxLDL decreased Akt and eNOS phosphorylation, which in turn activated NF-{kappa}B and downstream pro-apoptotic signaling events including calcium accumulation, destabilization of mitochondrial permeability, and disruption of the balance between pro- and anti-apoptotic Bcl-2 proteins. Those alterations induced by oxLDL, however, were attenuated by pretreatment with ellagic acid. The inhibition of oxLDL-induced endothelial apoptosis by ellagic acid is due at least in part to its anti-oxidant activity and its ability to modulate the PI3K/Akt/eNOS signaling pathway.

  14. 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

  15. Active-site dynamics of SpvC virulence factor from Salmonella Typhimurium and density functional theory study of phosphothreonine lyase catalysis

    PubMed Central

    Smith, Gregory K.; Ke, Zhihong; Hengge, Alvan C.; Xu, Dingguo; Xie, Daiqian; Guo, Hua

    2009-01-01

    The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a β-elimination mechanism. To understand this unique phosphothreonine lyase catalysis, the dynamics of the enzyme-substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31+G(d,p) level of theory. The DFT calculations indicate the reaction proceeds via a single transition state, featuring a concerted proton abstraction from the α carbon by Lys136 and β elimination of the phosphate leaving group. Key kinetic isotopic effects are predicted based on the truncated active-site model. PMID:19715325

  16. 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

  17. Studies on mass attenuation coefficient, effective atomic number and electron density of some amino acids in the energy range 0.122-1.330 MeV

    NASA Astrophysics Data System (ADS)

    Pawar, Pravina P.; Bichile, Govind K.

    2013-11-01

    The total mass attenuation coefficients of some amino acids, such as Glycine (C2H5NO2), DL-Alanine (C3H7NO2), Proline (C5H9NO2), L-Leucine (C6H13NO2 ), L-Arginine (C6H14N4O2) and L-Arginine Monohydrochloride (C6H15ClN4O2), 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 10.2% 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) tend to be almost constant as a function of gamma-ray energy. The results show that, the experimental values of mass attenuation coefficients, effective atomic numbers and effective electron densities are in good agreement with the theoretical values with less than 1% error.

  18. Acid mine drainage risks - A modeling approach to siting mine facilities in Northern Minnesota USA

    NASA Astrophysics Data System (ADS)

    Myers, Tom

    2016-02-01

    Most watershed-scale planning for mine-caused contamination concerns remediation of past problems while future planning relies heavily on engineering controls. As an alternative, a watershed scale groundwater fate and transport model for the Rainy Headwaters, a northeastern Minnesota watershed, has been developed to examine the risks of leaks or spills to a pristine downstream watershed. The model shows that the risk depends on the location and whether the source of the leak is on the surface or from deeper underground facilities. Underground sources cause loads that last longer but arrive at rivers after a longer travel time and have lower concentrations due to dilution and attenuation. Surface contaminant sources could cause much more short-term damage to the resource. Because groundwater dominates baseflow, mine contaminant seepage would cause the most damage during low flow periods. Groundwater flow and transport modeling is a useful tool for decreasing the risk to downgradient sources by aiding in the placement of mine facilities. Although mines are located based on the minerals, advance planning and analysis could avoid siting mine facilities where failure or leaks would cause too much natural resource damage. Watershed scale transport modeling could help locate the facilities or decide in advance that the mine should not be constructed due to the risk to downstream resources.

  19. Changes in polysialic acid expression on myeloid cells during differentiation and recruitment to sites of inflammation: Role in phagocytosis

    PubMed Central

    Stamatos, Nicholas M; Zhang, Lei; Jokilammi, Anne; Finne, Jukka; Chen, Wilbur H; El-Maarouf, Abderrahman; Cross, Alan S; Hankey, Kim G

    2014-01-01

    Polysialic acid (polySia) is a unique linear homopolymer of α2,8-linked sialic acid that has been studied extensively as a posttranslational modification of neural cell adhesion molecule in the central nervous system. Only two proteins are known to be polysialylated in cells of the immune system: CD56 on human natural killer cells and murine bone marrow (BM) leukocytes, and neuropilin-2 (NRP-2) on dendritic cells (DCs). We tested the hypothesis that polySia expression is regulated during maturation and migration of leukocytes and plays a role in functional activity. Using wild-type and NCAM−/− mice, we show that BM neutrophils express only polysialylated CD56, whereas a subset of BM monocytes expresses polysialylated CD56 and/or another polysialylated protein(s). We demonstrate that polysialylated CD56 expression is progressively down-regulated in wild-type monocytes and monocyte-derived cells during migration from BM through peripheral blood to pulmonary and peritoneal sites of inflammation. Freshly isolated monocyte-derived peritoneal macrophages are devoid of polySia yet re-express polySia on NRP-2 and an additional protein(s) after maintenance in culture. Removal of polySia from these cells enhances phagocytosis of Klebsiella pneumoniae, suggesting that down-regulation of polySia on macrophages facilitates bacterial clearance. Using wild-type and NRP-2−/− mice, we demonstrate that NRP-2 and an additional protein(s) are polysialylated by ST8 SiaIV in BM-derived DCs. We conclude that polySia expression in monocyte-derived cells is dynamically regulated by ST8 SiaIV activity and by expression of carrier proteins during recruitment to sites of inflammation and influences cellular interactions with microbes, contributing to innate and adaptive immune responses. PMID:24865221

  20. Site-directed mutagenesis of tobacco anionic peroxidase: Effect of additional aromatic amino acids on stability and activity.

    PubMed

    Poloznikov, A A; Zakharova, G S; Chubar, T A; Hushpulian, D M; Tishkov, V I; Gazaryan, I G

    2015-08-01

    Tobacco anionic peroxidase (TOP) is known to effectively catalyze luminol oxidation without enhancers, in contrast to horseradish peroxidase (HRP). To pursue structure-activity relationship studies for TOP, two amino acids have been chosen for mutation, namely Thr151, close to the heme plane, and Phe140 at the entrance to the active site pocket. Three mutant forms TOP F140Y, T151W and F140Y/T151W have been expressed in Escherichia coli, and reactivated to yield active enzymes. Single-point mutations introducing additional aromatic amino acid residues at the surface of TOP exhibit a significant effect on the enzyme catalytic activity and stability as judged by the results of steady-state and transient kinetics studies. TOP T151W is up to 4-fold more active towards a number of aromatic substrates including luminol, whereas TOP F140Y is 2-fold more stable against thermal inactivation and 8-fold more stable in the reaction course. These steady-state observations have been rationalized with the help of transient kinetic studies on the enzyme reaction with hydrogen peroxide in a single turnover regime. The stopped-flow data reveal (a) an increased stability of F140Y Compound I towards hydrogen peroxide, and thus, a higher operational stability as compared to the wild-type enzyme, and (b) a lesser leakage of oxidative equivalents from TOP T151W Compound I resulting in the increased catalytic activity. The results obtained show that TOP unique properties can be further improved for practical applications by site-directed mutagenesis. PMID:25957835

  1. Long chain polyunsaturated fatty acids alter oxytocin signaling and receptor density in cultured pregnant human myometrial smooth muscle cells.

    PubMed

    Kim, Paul Y; Zhong, Miao; Kim, Yoon-Sun; Sanborn, Barbara M; Allen, Kenneth G D

    2012-01-01

    Epidemiological studies and interventional clinical trials indicate that consumption of long chain n-3 polyunsaturated fatty acids (LC n-3 PUFA) such as docosahexaenoic acid (DHA) lengthen gestational duration. Although the mechanisms are not well understood, prostaglandins (PG) of the 2-series are known to play a role in the initiation and progress of labor. In animal studies, modest DHA provision has been shown to reduce placental and uterine PGE(2) and PGF(2α), matrix metalloproteinase (MMP)-2 and MMP-9 expression, and placental collagenase activity. However, modulation of PG biosynthesis may not account for all the effects of LC n-3 PUFAs in labor. We investigated one potential PG-independent mechanism of LC PUFA action using cultured pregnant human myometrial smooth muscle cells. Our goal was to characterize the effect of LC PUFA treatment on oxytocin signaling, a potent uterotonic hormone involved in labor. The addition of 10 µM-100 µM DHA or arachidonic acid (AA) to the culture media for 48 h resulted in dose dependent enrichment of these fatty acids in membrane lipid. DHA and AA significantly inhibited phosphatidylinositol turnover and [Ca(2+)](i) mobilization with oxytocin stimulation compared to bovine serum albumin control and equimolar oleic acid. DHA and AA significantly reduced oxytocin receptor membrane concentration without altering binding affinity or rate of receptor internalization. These findings demonstrate a role for LC n-3 PUFAs in regulation of oxytocin signaling and provide new insight into additional mechanisms pertaining to reports of dietary fish and fish oil consumption prolonging gestation. PMID:22848573

  2. An arylaminopyridazine derivative of gamma-aminobutyric acid (GABA) is a selective and competitive antagonist at the GABAA receptor site.

    PubMed Central

    Chambon, J P; Feltz, P; Heaulme, M; Restle, S; Schlichter, R; Biziere, K; Wermuth, C G

    1985-01-01

    In view of finding a new gamma-aminobutyric acid (GABA) receptor ligand we synthesized an arylaminopyridazine derivative of GABA, SR 95103 [2-(carboxy-3'-propyl)-3-amino-4-methyl-6-phenylpyridazinium chloride]. SR 95103 displaced [3H]GABA from rat brain membranes with an apparent Ki of 2.2 microM and a Hill number near 1.0. SR 95103 (1-100 microM) antagonized the GABA-mediated enhancement of [3H]diazepam binding in a concentration-dependent manner without affecting [3H]diazepam binding per se. SR 95103 competitively antagonized GABA-induced membrane depolarization in rat spinal ganglia. In all these experiments, the potency of SR 95103 was close to that of bicuculline. SR 95103 (100 microM) did not interact with a variety of central receptors--in particular the GABAB, the strychnine, and the glutamate receptors--did not inhibit Na+-dependent synaptosomal GABA uptake, and did not affect GABA-transaminase and glutamic acid decarboxylase activities. Intraperitoneally administered SR 95103 elicited clonicotonic seizures in mice (ED50 = 180 mg/kg). On the basis of these results it is postulated that St 95103 is a competitive antagonist of GABA at the GABAA receptor site. In addition to being an interesting lead structure for the search of GABA ligands, SR 95103 could also be a useful tool to investigate GABA receptor subtypes because it is freely soluble in water and chemically stable. Images PMID:2984669

  3. Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair (Rae1∙Nup98)

    SciTech Connect

    Quan, Beili; Seo, Hyuk-Soo; Blobel, Günter; Ren, Yi

    2014-07-01

    mRNA export factor 1 (Rae1) and nucleoporin 98 (Nup98) are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). How Rae1 functions in mRNA export and how M protein targets both Rae1 and Nup98 are not understood at the molecular level. To obtain structural insights, we assembled a 1:1:1 complex of M•Rae1•Nup98 and established a crystal structure at 3.15-Å resolution. We found that the M protein contacts the Rae1•Nup98 heterodimer principally by two protrusions projecting from the globular domain of M like a finger and thumb. Both projections clamp to the side of the β-propeller of Rae1, with the finger also contacting Nup98. The most prominent feature of the finger is highly conserved Methionine 51 (Met51) with upstream and downstream acidic residues. The complementary surface on Rae1 displays a deep hydrophobic pocket, into which Met51 fastens like a bolt, and a groove of basic residues on either side, which bond to the acidic residues of the finger. Notably, the M protein competed for in vitro binding of various oligonucleotides to Rae1•Nup98. We localized this competing activity of M to its finger using a synthetic peptide. Collectively, our data suggest that Rae1 serves as a binding protein for the phosphate backbone of any nucleic acid and that the finger of M mimics this ligand. In the context of mRNA export, we propose that a given mRNA segment, after having been deproteinated by helicase, is transiently reproteinated by Nup98-tethered Rae1. We suggest that such repetitive cycles provide cytoplasmic stopover sites required for ratcheting mRNA across the nuclear pore.

  4. Effects of lactic acid bacteria on low-density lipoprotein susceptibility to oxidation and aortic fatty lesion formation in hyperlipidemic hamsters.

    PubMed

    Ito, M; Oishi, K; Yoshida, Y; Okumura, T; Sato, T; Naito, E; Yokoi, W; Sawada, H

    2015-01-01

    We investigated the effects of Streptococcus thermophilus YIT 2001, a strain of lactic acid bacteria, on the susceptibility of low-density lipoprotein (LDL) to oxidation and the formation of aortic fatty lesions in hyperlipidemic hamsters. S. thermophilus YIT 2001 had the highest in vitro antioxidative activity against LDL oxidation among the 79 strains of lactic acid bacteria and bifidobacteria tested, which was about twice that of S. thermophilus YIT 2084. The lag time of LDL oxidation in the YIT 2001 feeding group was significantly longer than in controls, but was unchanged in the YIT 2084 group. After the feeding of YIT 2001, lag times were prolonged and areas of aortic fatty lesions were dose-dependently attenuated, although there were no effects on plasma lipid levels. These results suggest that YIT 2001 has the potential to prevent the formation of aortic fatty lesions by inhibiting LDL oxidation. PMID:25380799

  5. Evolution of nuclear retinoic acid receptor alpha (RARα) phosphorylation sites. Serine gain provides fine-tuned regulation.

    PubMed

    Samarut, Eric; Amal, Ismail; Markov, Gabriel V; Stote, Roland; Dejaegere, Annick; Laudet, Vincent; Rochette-Egly, Cécile

    2011-07-01

    The human nuclear retinoic acid (RA) receptor alpha (hRARα) is a ligand-dependent transcriptional regulator, which is controlled by a phosphorylation cascade. The cascade starts with the RA-induced phosphorylation of a serine residue located in the ligand-binding domain, S(LBD), allowing the recruitment of the cdk7/cyclin H/MAT1 subcomplex of TFIIH through the docking of cyclin H. It ends by the subsequent phosphorylation by cdk7 of an other serine located in the N-terminal domain, S(NTD). Here, we show that this cascade relies on an increase in the flexibility of the domain involved in cyclin H binding, subsequently to the phosphorylation of S(LBD). Owing to the functional importance of RARα in several vertebrate species, we investigated whether the phosphorylation cascade was conserved in zebrafish (Danio rerio), which expresses two RARα genes: RARα-A and RARα-B. We found that in zebrafish RARαs, S(LBD) is absent, whereas S(NTD) is conserved and phosphorylated. Therefore, we analyzed the pattern of conservation of the phosphorylation sites and traced back their evolution. We found that S(LBD) is most often absent outside mammalian RARα and appears late during vertebrate evolution. In contrast, S(NTD) is conserved, indicating that the phosphorylation of this functional site has been under ancient high selection constraint. This suggests that, during evolution, different regulatory circuits control RARα activity. PMID:21297158

  6. CS2 activation at uranium(III) siloxide ate complexes: the effect of a Lewis acidic site.

    PubMed

    Camp, Clément; Cooper, Oliver; Andrez, Julie; Pécaut, Jacques; Mazzanti, Marinella

    2015-02-14

    Multimetallic cooperative binding of heteroallenes provides an attractive route to their activation, but the reduction of CS(2) at heterobimetallic sites, associating an electron-rich metal with a main group Lewis acid has not been explored. Here we show that the presence of a heterometallic U, K site plays an important role in the CS(2) reduction by uranium(iii) complexes of the electron-rich and the sterically demanding tris(tert-butoxy)siloxide ligand. Specifically, the ion-pair complex [K(18c6)][U(OSi(O(t)Bu)(3))(4)], 1, leads preferentially to the reductive disproportionation of CS(2) to K(2)CS(3) and CS. The crystal structure of the thiocarbonate intermediate complex [U(OSi(O(t)Bu(3)(4) (μ(3)-κ(2):κ(2):κ(2-)CS(3))K(2)(18c6)(2)], 2, isolated from the toluene reaction mixture has been determined. In contrast, the heterobimetallic complex [U(OSi(O(t)Bu(3)(4)K], 3, promotes preferentially the reductive dimerization of CS(2) to K(2)C(2)S(4) and K(2)C(3)S(5). The [K(2)C(2)S(4)(DMSO)(3)](n), 5, and [U(OSi(O(t)Bu)(3))(4)K(2)(C(3)S(5))](n), 6, polymeric compounds were isolated from this reaction and structurally characterized. PMID:25436831

  7. Multiplex Detection of Functional G Protein-Coupled Receptors Harboring Site-Specifically Modified Unnatural Amino Acids

    PubMed Central

    2015-01-01

    We developed a strategy for identifying positions in G protein-coupled receptors that are amenable to bioorthogonal modification with a peptide epitope tag under cell culturing conditions. We introduced the unnatural amino acid p-azido-l-phenylalanine (azF) into human CC chemokine receptor 5 (CCR5) at site-specific amber codon mutations. We then used strain-promoted azide–alkyne [3+2] cycloaddition to label the azF-CCR5 variants with a FLAG peptide epitope-conjugated aza-dibenzocyclooctyne (DBCO) reagent. A microtiter plate-based sandwich fluorophore-linked immunosorbent assay was used to probe simultaneously the FLAG epitope and the receptor using infrared dye-conjugated antibodies so that the extent of DBCO incorporation, corresponding nominally to labeling efficiency, could be quantified ratiometrically. The extent of incorporation of DBCO at the various sites was evaluated in the context of a recent crystal structure of maraviroc-bound CCR5. We observed that labeling efficiency varied dramatically depending on the topological location of the azF in CCR5. Interestingly, position 109 in transmembrane helix 3, located in a hydrophobic cavity on the extracellular side of the receptor, was labeled most efficiently. Because the bioorthogonal labeling and detection strategy described might be used to introduce a variety of different peptide epitopes or fluorophores into engineered expressed receptors, it might prove to be useful for a wide range of applications, including single-molecule detection studies of receptor trafficking and signaling mechanism. PMID:25524496

  8. Sedimentation Rates at IODP Site U1424 since the Pliocene Deciphered from Spectral Analyses of RGB and GRA Bulk Density Profiles

    NASA Astrophysics Data System (ADS)

    Gorgas, T. J.; Tada, R.; Irino, T.; Clemens, S. C.; Ziegler, M.; Holbourn, A. E.; Murray, R. W.; Alvarez Zarikian, C. A.

    2014-12-01

    Sedimentation Rates (SRs) for IODP Site U1424 in the Japan Basin (40o11.40'N, 138o13.90'E) 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 SR's, which differed from those established through coarse-scaled biostratigraphic and paleomagnetic data. SR profiles from our analysis exhibit similar excursions and features in both depth and age domains, with GRA representing a smoothed version of the SR profile derived from RGB data while exhibiting slight offsets in high-to-low SRs downhole versus those observed in RBG data. Both GRA and RGB profiles show a distinct periodicity in the waveband of Milankovitch cycles. The pronounced Milankovitch cyclicity suggests that climate variability and trends in SRs at Site U1424 was responding to insolation patterns during the past 4.5 Myr. A dominance of the 100 ky cycle (eccentricity) throughout the entire normalized spectral amplitude profile might be observed; however, for the purpose of fine-tuning our high-resolution Age-Depth model to fit the low-resolution Age-Depth model from biostratigraphic and paleomagnetic data, choosing obliquity (41 ky) and precession (19-23 ky) cycles as tuning-frequency produced a closer fit between high-and-low-resolution models than using the prominent eccentricity cycles (100 and 400 ky). Relatively low SRs are found when evolutive amplitude spectra are dominated by obliquity and eccentricity periods. In contrast, significant SR peaks at Site U1424 often occur when strong precessional amplitudes coexist with obliquity and eccentricity cycles. Lower SR values at Site U1424 are interpreted to reflect a decrease in diatom flux and relative increase in detrital fraction. By contrast moderate to higher SRs were associated with lower

  9. Effective atomic number and electron density of amino acids within the energy range of 0.122-1.330 MeV

    NASA Astrophysics Data System (ADS)

    More, Chaitali V.; Lokhande, Rajkumar M.; Pawar, Pravina P.

    2016-08-01

    Photon attenuation coefficient calculation methods have been widely used to accurately study the properties of amino acids such as n-acetyl-L-tryptophan, n-acetyl-L-tyrosine, D-tryptophan, n-acetyl-L-glutamic acid, D-phenylalanine, and D-threonine. In this study, mass attenuation coefficients (μm) of these amino acids for 0.122-, 0.356-, 0.511-, 0.662-, 0.884-, 1.170, 1.275-, 1.330-MeV photons are determined using the radio-nuclides Co57, Ba133, Cs137, Na22, Mn54, and Co60. NaI (Tl) scintillation detection system was used to detect gamma rays with a resolution of 8.2% at 0.662 MeV. The calculated attenuation coefficient values were then used to determine total atomic cross sections (σt), molar extinction coefficients (ε), electronic cross sections (σe), effective atomic numbers (Zeff), and effective electron densities (Neff) of the amino acids. Theoretical values were calculated based on the XCOM data. Theoretical and experimental values are found to be in a good agreement (error<5%). The variations of μm, σt, ε, σe, Zeff, and Neff with energy are shown graphically. The values of μm, σt, ε, σe are higher at lower energies, and they decrease sharply as energy increases; by contrast, Zeff and Neff were found to be almost constant.

  10. Negative regulation of the rat stromelysin gene promoter by retinoic acid is mediated by an AP1 binding site.

    PubMed Central

    Nicholson, R C; Mader, S; Nagpal, S; Leid, M; Rochette-Egly, C; Chambon, P

    1990-01-01

    Stromelysin is a member of the metalloproteinase family which plays an important role in extracellular matrix remodelling during many normal and disease processes. We show here that in polyomavirus-transformed rat embryo fibroblast cells (PyT21), the transcription from the stromelysin gene is repressed by the vitamin A derivative retinoic acid (RA). Furthermore, expression vectors encoding the human RA receptors hRAR-alpha, hRAR-beta and hRAR-gamma repress chloramphenicol acetyltransferase (CAT) expression from stromelysin promoter-CAT gene expression vectors in RA-treated PyT21 and human HeLa cells, as determined by transient transfection assays. Through mutation and deletion analysis, we show that the RA dependent repression is mediated by a 25 bp region from nucleotide positions -72 to -48 of the rat stromelysin 5'-flanking DNA sequence. Further mutation analysis of this region indicates that the DNA sequence required for RA dependent repression colocalizes with an AP1 binding site which is essential for promoter activity. We show also that RA represses the transcriptional activity of a reporter gene containing a TPA responding AP1 binding site driving the HSV tk promoter. Thus the RAR-RA complex appears to repress transcription of the stromelysin gene by blocking activation by positive regulatory factors. However, we found no evidence supporting the possibility that the RA dependent repression could be due to RAR binding to the AP1 binding site or to the AP1 components c-fos and c-jun. Images Fig. 1. Fig. 2. Fig. 4. Fig. 6. Fig. 7. Fig. 8. PMID:2176152

  11. Hydrogeology and ground-water quality of the Chromic Acid Pit site, US Army Air Defense Artillery Center and Fort Bliss, El Paso, Texas

    USGS Publications Warehouse

    Abeyta, Cynthia G.; Thomas, C.L.

    1996-01-01

    The Chromic Acid Pit site is an inactive waste disposal site that is regulated by the Resource Conservation and Recovery Act of 1976. The 2.2-cubic-yard cement-lined pit was operated from 1980 to 1983 by a contractor to the U.S. Army Air Defense Artillery Center and Fort Bliss. The pit, located on the Fort Bliss military reservation, in El Paso, Texas, was used for disposal and evaporation of chromic acid waste generated from chrome plating operations. The site was certified closed in 1989 and the Texas Natural Resources Conservation Commission issued Permit Number HW-50296 (U.S. Environmental Protection Agency Permit Number TX4213720101), which approved and implemented post-closure care for the Chromic Acid Pit site. In accordance with an approved post-closure plan, the U.S. Geological Survey is cooperating with the U.S. Army in evaluating hydrogeologic conditions and ground- water quality at the site. One upgradient and two downgradient ground-water monitoring wells were installed adjacent to the chromic acid pit by a private contractor. Quarterly ground-water sampling of these wells by the U.S. Geological Survey began in December 1993. The Chromic Acid Pit site is situated in the Hueco Bolson intermontane valley. The Hueco Bolson is a primary source of ground water in the El Paso area. City of El Paso and U.S. Army water-supply wells are located on all sides of the study area and are completed 600 to more than 1,200 feet below land surface. The ground-water level in the area of the Chromic Acid Pit site has declined about 25 feet from 1982 to 1993. Depth to water at the Chromic Acid Pit site in September 1994 was about 284 feet below land surface; ground-water flow is to the southeast. Ground-water samples collected from monitoring wells at the Chromic Acid Pit site contained dissolved-solids concentrations of 442 to 564 milligrams per liter. Nitrate as nitrogen concentrations ranged from 2.1 to 2.7 milligrams per liter; nitrite plus nitrate as nitrogen

  12. Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures

    PubMed Central

    2013-01-01

    Background Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in cellular processes. Given the high-throughput mass spectrometry-based experiments, the desire to annotate the catalytic kinases for in vivo phosphorylation sites has motivated. Thus, a variety of computational methods have been developed for performing a large-scale prediction of kinase-specific phosphorylation sites. However, most of the proposed methods solely rely on the local amino acid sequences surrounding the phosphorylation sites. An increasing number of three-dimensional structures make it possible to physically investigate the structural environment of phosphorylation sites. Results In this work, all of the experimental phosphorylation sites are mapped to the protein entries of Protein Data Bank by sequence identity. It resulted in a total of 4508 phosphorylation sites containing the protein three-dimensional (3D) structures. To identify phosphorylation sites on protein 3D structures, this work incorporates support vector machines (SVMs) with the information of linear motifs and spatial amino acid composition, which is determined for each kinase group by calculating the relative frequencies of 20 amino acid types within a specific radial distance from central phosphorylated amino acid residue. After the cross-validation evaluation, most of the kinase-specific models trained with the consideration of structural information outperform the models considering only the sequence information. Furthermore, the independent testing set which is not included in training set has demonstrated that the proposed method could provide a comparable performance to other popular tools. Conclusion The proposed method is shown to be capable of predicting kinase-specific phosphorylation sites on 3D structures and has been implemented as a web server which is freely accessible at http://csb.cse.yzu.edu.tw/PhosK3D/. Due to the difficulty of identifying the kinase-specific phosphorylation

  13. Molecular Dynamics Simulations of Adsorption of Poly(acrylic acid) and Poly(methacrylic acid) on Dodecyltrimethylammonium Chloride Micelle in Water: Effect of Charge Density.

    PubMed

    Sulatha, Muralidharan S; Natarajan, Upendra

    2015-09-24

    We have investigated the interaction of dodecyltrimethylammonium chloride (DoTA) micelle with weak polyelectrolytes, poly(acrylic acid) and poly(methacrylic acid). Anionic as well as un-ionized forms of the polyelectrolytes were studied. Polyelectrolyte-surfactant complexes were formed within 5-11 ns of the simulation time and were found to be stable. Association is driven purely by electrostatic interactions for anionic chains whereas dispersion interactions also play a dominant role in the case of un-ionized chains. Surfactant headgroup nitrogen atoms are in close contact with the carboxylic oxygens of the polyelectrolyte chain at a distance of 0.35 nm. In the complexes, the polyelectrolyte chains are adsorbed on to the hydrophilic micellar surface and do not penetrate into the hydrophobic core of the micelle. Polyacrylate chain shows higher affinity for complex formation with DoTA as compared to polymethacrylate chain. Anionic polyelectrolyte chains show higher interaction strength as compared to corresponding un-ionized chains. Anionic chains act as polymeric counterion in the complexes, resulting in the displacement of counterions (Na(+) and Cl(-)) into the bulk solution. Anionic chains show distinct shrinkage upon adsorption onto the micelle. Detailed information about the microscopic structure and binding characteristics of these complexes is in agreement with available experimental literature. PMID:26355463