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Sample records for bronsted acid site

  1. NH{sub 3} adsorption on the Lewis and Bronsted acid sites of MoO{sub 3} (0 1 0) surface: A cluster DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Zhifeng [College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); College of Material Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Fan, Junyan [Foundation Department, Shanxi Police Academy, No. 27 Second Section of Old Jinci Road, Taiyuan 030021, Shanxi (China); Zuo, Zhijun [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Li, Zhe, E-mail: lizhe@tyut.edu.cn [College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Zhang, Jinshan [College of Material Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China)

    2014-01-01

    The adsorption of NH{sub 3} on the Lewis and Bronsted acid sites of MoO{sub 3} (0 1 0) surface has been investigated based on the density functional theory (DFT) method using the clusters models. The calculated results indicate that NH{sub 3} could strongly adsorb on both the Lewis and Bronsted acid sites in the form of NH{sub 3} species and NH{sub 4}{sup +} respectively, whereas the adsorption on the Lewis acid site is found to be more favorable energetically than that on the Bronsted acid site. For the Lewis acid site Mulliken population analysis shows a donation of lone pairs from NH{sub 3} to the surface and activation of N–H bond. The overlaps of N-s, N-p and Mo-d orbitals suggest the strong interaction between N and Mo atoms. For the Bronsted acid site N–H bond is also activated by the formation of NH{sub 4}{sup +} species. The hybridizations between H and O atoms as well as N and H atoms are the major reasons for strong chemical adsorption of NH{sub 3} and the existence of NH{sub 4}{sup +} species, which partly attributed to the presence of N–H… O hydrogen bonds. Furthermore, the formation of a second Lewis acid site at adjacent or diagonal site results in slight changes of adsorption stability, structural changes and charge redistributions, suggesting its small influence on NH{sub 3} adsorption.

  2. Bronsted acid site number evaluation using isopropylamine decomposition on Y-zeolite contaminated with vanadium in a simultaneous DSC-TGA analyzer

    International Nuclear Information System (INIS)

    Osorio Perez, Yonnathan; Forero, Liliam Alexandra Palomeque; Torres, Diana Vanessa Cristiano; Trujillo, Carlos Alexander

    2008-01-01

    Acid-site catalyzed decomposition of isopropylamine was followed in a simultaneous DSC-TGA analyzer. USY zeolite samples with and without vanadium were studied. Results show that acid sites number decreases linearly with vanadium concentration in zeolite indicating that vanadium neutralizes acid sites on catalyst and the metal is able to move on the surface of the solid. The neutralizing species probably contain only one vanadium atom. The reaction enthalpy plus desorption heat of the products show that vanadium preferentially neutralizes the strongest acid sites on the zeolite. The application of the simultaneous DSC-TGA technique to quantify Bronsted acid sites on solids by this reaction is novel

  3. A computational study of the stretching frequencies of Bronsted acid sites in SAPO STA-7: preliminary comparison with infrared

    Czech Academy of Sciences Publication Activity Database

    Déroche, I.; Maurin, G.; Llewellyn, P.; Castro, M.; Wright, P. A.; Voláková, Martina; Čejka, Jiří

    2007-01-01

    Roč. 170, - (2007), s. 1660-1667 ISSN 0167-2991 Grant - others:Marie Curie Scholarship(XE) MRTN-CT-2004-005503 Institutional research plan: CEZ:AV0Z40400503 Source of funding: R - rámcový projekt EK Keywords : Bronsted acid * SAPO STA-7 material * zeolites Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.307, year: 2005

  4. Formation of Gd coordination polymer with 1D chains mediated by Bronsted acidic ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Qianqian; Han, Ying [Key Laboratory of Polar Materials and Devices, Ministry of Education, East China Normal University, Shanghai (China); Lin, Hechun, E-mail: hclin@ee.ecnu.edu.cn [Key Laboratory of Polar Materials and Devices, Ministry of Education, East China Normal University, Shanghai (China); Zhang, Yuanyuan; Duan, Chungang [Key Laboratory of Polar Materials and Devices, Ministry of Education, East China Normal University, Shanghai (China); Peng, Hui, E-mail: hpeng@ee.ecnu.edu.cn [Key Laboratory of Polar Materials and Devices, Ministry of Education, East China Normal University, Shanghai (China); Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006 (China)

    2017-03-15

    One dimensional coordination polymer Gd[(SO{sub 4})(NO{sub 3})(C{sub 2}H{sub 6}SO){sub 2}] (1) is prepared through the mediation of Bronsted acid ionic liquid, which crystallized in the monoclinic space of C2/c. In this polymer, adjacent Gd atoms are linked by two SO{sub 4}{sup 2-} ions to generate a 1-D chain, and all oxygen atoms in SO{sub 4}{sup 2-} groups are connected to three nearest Gd atoms in µ{sup 3}:η{sup 1}:η{sup 1}:η{sup 2} fashion. Gd, S and N from SO{sub 4}{sup 2-} and NO{sub 3}{sup -} are precisely coplanar. The planar is coordinated by a pair of DMSO molecules, which is parallel and linked by hydrogen bonding to form a three-dimensional supramolecular network. Magnetic susceptibility measurement of 1 reveals weak antiferromagnetic interactions between the Gd (III) ions. It exhibits relatively large magneto-caloric effect with –ΔS{sub m}=28.8 J Kg{sup −1} K{sup −1} for ΔH=7 T. - Graphical abstract: Coordination polymer Gd[(SO{sub 4})(NO{sub 3})(C{sub 2}H{sub 6}SO){sub 2}] was obtained mediated by Bronsted acid Ionic Liquid, which presents a 1-D chains collected by SO{sub 4}{sup 2-} groups. Magnetic susceptibility of the polymer reveals weak antiferromagnetic interactions between the Gd(III) ions with the relatively large magneto-caloric effect of –ΔS{sub m}=28.8 J Kg{sup −1} K{sup −1} for ΔH= 7T.

  5. Bronsted acid-functionalized choline chloride-butane sultone for the ...

    Indian Academy of Sciences (India)

    M P PADMA PRIYA

    2018-03-21

    Mar 21, 2018 ... Choline chloride and 1,4-butane sultone were combined to obtain a sulphonic acid-functionalized ..... Knifton J F and Sanderson J R 1990 Method for produc- ... alkenes via the Knoevenagel condensation Tetrahedron. Lett.

  6. Selectivity Enhancement in methylamine synthesis via postsynthesis modification of bronsted acidic mordenite

    NARCIS (Netherlands)

    Grundling, C.; Gründling, Christian; Mirth, G.C.; Eder-Mirth, Gabriele C.; Lercher, J.A.

    1996-01-01

    Methylamine synthesis from methanol and ammonia over parent and modified Brønsted acidic mordenites is studied byin situinfrared spectroscopy and kinetic analysis to elucidate the role of elementary steps for activity and selectivity.In situinfrared spectroscopy reveals that all methylammonium ions

  7. Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions

    OpenAIRE

    Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

    2015-01-01

    In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = TiIV, CuII, AlIII, SnIV, FeIII, CrIII, ZrIV and ZnII; for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with TixH3−4...

  8. Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions.

    Science.gov (United States)

    Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

    2015-09-16

    In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = Ti(IV), Cu(II), Al(III), Sn(IV), Fe(III), Cr(III), Zr(IV) and Zn(II); for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with Ti(x)H(3-4x)PW12O40 (Ti partial exchanged protons in saturated H3PW12O40), which demonstrated that the Lewis metal as an addenda atom (H5PW11TiO40) was less efficient than those as counter cations (Ti(x)H(3-4x)PW12O40). On the other hand, the highest conversion reached 92.2% in transesterification and 97.4% in esterification. Meanwhile, a good result was achieved by H5PW11TiO40 in which the total selectivity of DAG and TGA was 96.7%. In addition, calcination treatment to H5PW11TiO40 make it insoluble in water which resulted in a heterogeneous catalyst feasible for reuse.

  9. Sulfur tolerance of Pt/mordenites for benzene hydrogenation. Do Bronsted acid sites participate in hydrogenation?

    NARCIS (Netherlands)

    Simon, L.; van Ommen, J.G.; Jentys, A.; Lercher, J.A.

    2002-01-01

    The comparison of Pt electronic properties studied by in situ XANES and the kinetic study of benzene hydrogenation strongly suggests that the hydrogenation of benzene on Pt/mordenites occurs along two parallel reaction pathways. The routes proposed include (i) the monofunctional hydrogenation of

  10. SUPPLEMENTARY INFORMATION Bronsted acid functionalised ...

    Indian Academy of Sciences (India)

    raji

    In the above spectrum, the broad peak at 3307 cm-1 was due to stretching vibrations of. –CH2–OH group. The broadness of the peak could be due to hydrogen bonding of hydroxyl group with chloride in the zwitter ion. The –CH2 stretching vibrations were observed at 1473 cm-1. The –CH3 stretching vibrations were ...

  11. Effects of Bronsted acidity in the mechanism of selective oxidation of propane to acetone on CaY zeolite at room temperature.

    NARCIS (Netherlands)

    Xu, J.; Mojet, Barbara; van Ommen, J.G.; Lefferts, Leonardus

    2005-01-01

    The importance of Brønsted acid sites for partial oxidation of propane to acetone in CaY was investigated by in situ FTIR spectroscopy. With an increasing number of protons in Ca-Y, Volcano plots were observed for (1) amount of adsorbed propane; (2) initial acetone formation rate; (3) total amount

  12. Acid properties of catalysts as studied by CO adsorption

    International Nuclear Information System (INIS)

    Knozinger, H.

    1992-01-01

    CO is a soft base and can therefore, be used as a highly specific probe for acid sites on oxide surfaces. Relative acidity sequences of Bronsted sites can be established based on the IR-hydroxyl frequency shifts when CO is adsorbed by H-bonding at 77 K. Coordination of CO onto coordinately unsaturated cation sites (Lewis acid sites) leads to cation-sensitive carbonyl stretching frequency shifts. The CO stretching band postions can be correlated with the electric field strength exerted by the cation. A universal correlation seems to exist. Applications of these principles for the study of binary oxides; zeolites, supported oxides and sulfides will be discussed in this paper

  13. Synthesis of Trisubstituted Imidazoles Using Lewis and Bronsted Acid Catalysts

    OpenAIRE

    Hekmatshoar, Rahim; HEKMATSHOAR, Rahim; JAHANBAKHSHI, Hajar; MOUSAVIZADEH, Farnoosh; RAHNAMAFAR, Reyhane

    2010-01-01

    An efficient and one-pot method for the preparation of trisubstituted imidazoles by condensation of benzil, different aldehydes and ammonium acetate in the presence of  a catalytic amount of NiSO4.7H2O or H3BO3 under different conditions is reported.                    Key Words: Trisubstituted imidazoles, Multi-component &a...

  14. Assessing the acid properties of desilicated ZSM-5 by FTIR using CO and 2,4,6-trimethylpyridine (collidine) as molecular probes

    DEFF Research Database (Denmark)

    Holm, Martin Spangsberg; Svelle, S.; Joensen, F.

    2009-01-01

    Lewis acid sites were generated, presumably from dislodged framework aluminium. Collidine, which is too bulky to enter the micropore system of ZSM-5, could access Lewis acidity, suggesting that these sites were predominantly generated on the external surface or in the newly created mesopores....... Additionally, by first saturating the zeolite surface with collidine and subsequently adsorbing CO, we show that barely any Lewis acidity was uncoordinated post-collidine saturation while the Bronsted acidity continuously was protected behind the micropore system. It is hypothesized from the present study...

  15. Atomic polar tensors and acid-base properties of metal-oxide building blocks

    International Nuclear Information System (INIS)

    Ferris, K.F.

    1993-02-01

    The sensitivity of the atomic polar tensor to compositional substituents is reported for the alkali silicate series. Rotational invariants, effective atomic charge (GAPT) and charge normalized anisotropy and dipole (α n and γ n ) are used to characterize the charge distribution and chemical environment of the atomic sites. Comparison of α n and γ n with a series of known Bronsted and Lewis acids and bases suggests that these rotational invariants may act as indicators for metal-oxide site acidities. Basis set and electron correlation particularly affect the determined effective charge, but show minimal effect on α and γ quantities

  16. Effect of Bronsted Acids and Bases, and Lewis Acid (Sn(2+)) on the Regiochemistry of the Reaction of Amines with Trifluoromethyl-β-diketones: Reaction of 3-Aminopyrrole to Selectively Produce Regioisomeric 1H-Pyrrolo[3,2-b]pyridines.

    Science.gov (United States)

    De Rosa, Michael; Arnold, David; Hartline, Douglas; Truong, Linda; Verner, Roman; Wang, Tianwei; Westin, Christian

    2015-12-18

    Reaction of 3-aminopyrrole (as its salt) with trifluoromethyl-β-diketones gave γ-1H-pyrrolo[3,2-b]pyridines via reaction at the less reactive carbonyl group. The trifluoromethyl group increased the electrophilicity of the adjacent carbonyl group and decreased the basicity of the hydroxyl group of the CF3 amino alcohol formed. This amino alcohol was formed faster, but its subsequent dehydration to the β-enaminone was slow resulting in the preferential formation of the γ-regioisomer. Reaction of 4,4,4-trifluoro-1-phenyl-1,3-butadione with 3-aminopyrrole was carried out using a series of 6 amine buffers. Yields of the α-1H-pyrrolo[3,2-b]pyridine increased as the pKa of the amine buffer decreased. Surprisingly the yield went down at higher pKas. There was a change in mechanism as the reaction mixture became more basic. With strong amines trifluoromethyl-β-diketones were present mainly or completely as the enolate. Under reductive conditions (3-nitropyrrole/Sn/AcOH/trifluoromethyl-β-diketone) the α-1H-pyrrolo[3,2-b]pyridine was the major product as a result of Lewis acid catalysis by Sn(2+). Similar α-regiochemistry was observed when the reaction of the 3-aminopyrrole salt with trifluoromethyl-β-diketones was carried out in the presence of base and tin(II) acetate.

  17. Synthesis of 1,1-Diborylalkenes through a Bronsted Base Catalyzed Reaction between Terminal Alkynes and Bis(pinacolato)diboron

    OpenAIRE

    Morinaga, Akira; Nagao, Kazunori; Ohmiya, Hirohisa; Sawamura, Masaya

    2015-01-01

    A method for the synthesis of 1,1-diborylalkenes through a Bronsted base catalyzed reaction between terminal alkynes and bis(pinacolato)diboron has been developed. The procedure allows direct synthesis of functionalized 1,1-diborylalkenes from various terminal alkynes including propiolates, propiolamides, and 2-ethynylazoles.

  18. Bronsted imidazolium ionic liquids: Synthesis and comparison of their catalytic activities as pre-catalyst for biodiesel production through two stage process

    International Nuclear Information System (INIS)

    Elsheikh, Y.A.; Man, Zakaria; Bustam, M.A.; Yusup, Suzana; Wilfred, C.D.

    2011-01-01

    In the present work, study was undertaken to prepare biodiesel via a two-step transesterification process. The high free fatty acids (FFA) value contained in the crude palm oil (CPO), which cause several problems with the straight alkaline-catalyzed, were converted to fatty acid methyl esters (FAME) before introducing KOH-catalyzed transesterification step. In order to evaluate their catalytic activities, three Bronsted acidic imidazoliums were investigated. These ionic liquids (ILs) appeared to be promising candidates to replace conventional acidic catalyst for biodiesel production due to their unique properties. Among them, a longer side chains 1-butyl-3-methyl-imidazolium hydrogensulfate (BMIMHSO 4 ) was found to be more superior to the other two catalysts. Based on the experimental results, a catalyst (BIMHSO 4 ) concentration of 4.5 wt.%, methanol/CPO molar ratio of 12:1, a temperature of 160 o C, and agitation speed of 600 rpm provided a final CPO acid value lower than 1.0 mg KOH/CPO within 120 min. The second alkali-catalyze step was performed at agitation speed of 600 rpm, 60 o C, 1.0% KOH for 50 min. The final biodiesel product in 98.4% yield was analyzed by gas chromatography (GC). The determined physicochemical important properties of POME were confirmed with American Standards for Testing Material (ASTM).

  19. Detecting coevolving amino acid sites using Bayesian mutational mapping

    DEFF Research Database (Denmark)

    Dimmic, Matthew W.; Hubisz, Melissa J.; Bustamente, Carlos D.

    2005-01-01

    Motivation: The evolution of protein sequences is constrained by complex interactions between amino acid residues. Because harmful substitutions may be compensated for by other substitutions at neighboring sites, residues can coevolve. We describe a Bayesian phylogenetic approach to the detection...

  20. Enhancing Cooperativity in Bifunctional Acid–Pd Catalysts with Carboxylic Acid-Functionalized Organic Monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Coan, Patrick D. [Department of Chemical and Biological Engineering, University of Colorado—Boulder, Boulder, Colorado 80309, United States; Ellis, Lucas D. [Department of Chemical and Biological Engineering, University of Colorado—Boulder, Boulder, Colorado 80309, United States; Griffin, Michael B. [National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Schwartz, Daniel K. [Department of Chemical and Biological Engineering, University of Colorado—Boulder, Boulder, Colorado 80309, United States; Medlin, J. Will [Department of Chemical and Biological Engineering, University of Colorado—Boulder, Boulder, Colorado 80309, United States

    2018-03-01

    Cooperative catalysts containing a combination of noble metal hydrogenation sites and Bronsted acid sites are critical for many reactions, including the deoxygenation (DO) of biomass-derived oxygenates in the upgrading of pyrolysis oil. One route toward the design of cooperative catalysts is to tether two different catalytically active functions so that they are in close proximity while avoiding undesirable interactions that can block active sites. Here, we deposited carboxylic acid (CA)-functionalized organophosphonate monolayers onto Al2O3-supported Pd nanoparticle catalysts to prepare bifunctional catalysts containing both Bronsted acid and metal sites. Modification with phosphonic acids (PAs) improved activity and selectivity for gas-phase DO reactions, but the degree of improvement was highly sensitive to both the presence and positioning of the CA group, suggesting a significant contribution from both the PA and CA sites. Short spacer lengths of 1-2 methylene groups between the phosphonate head and CA tail were found to yield the best DO rates and selectivities, whereas longer chains performed similarly to self-assembled monolayers having alkyl tails. Results from a combination of density functional theory and Fourier transform infrared spectroscopy suggested that the enhanced catalyst performance on the optimally positioned CAs was due to the generation of strong acid sites on the Al2O3 support adjacent to the metal. Furthermore, the high activity of these sites was found to result from a hydrogen-bonded cyclic structure involving cooperativity between the phosphonate head group and CA tail function. More broadly, these results indicate that functional groups tethered to supports via organic ligands can influence catalytic chemistry on metal nanoparticles.

  1. Characterization of reference and site specific humic acids

    International Nuclear Information System (INIS)

    Kim, J.I.; Buckau, G.

    1988-11-01

    As a contribution to the interlaboratory exercise for the complexation of humic acid and colloid generation (COCO-Club activities) in the CEC project MIRAGE-II, the characterization of selected humic acids have been carried out at TU Muenchen, regarding their elemental compositions, inorganic impurities, spectroscopic properties, size distributions and proton exchange capacities. The commercial humic acid (Na salt) from Aldrich Co. is purified to a protonated form and used as reference material. Furthermore two humic acids extracted from groundwaters from Gorleben (FRG) and Boom Clay (B) are purified to protonated forms and taken as site specific materials. These three humic acids, together with the original Na salt from Aldrich Co., are included in the present characterization exercise. The results of characterization provide basic knowledge supporting the forthcoming study of complexation of actinides and fission products with humic acid and their migration processes in the geosphere. (orig.)

  2. Characterization of reference and site specific human acids

    International Nuclear Information System (INIS)

    Kim, J.I.; Buckau, G.

    1988-01-01

    As a part of the interlaboratory exercise for the complexation of humic acid and colloid generation (COCO-Club activities) in the CEC project MIRAGE-II, the characterization of humic acids have been carried out, as for their elemental compositions, inorganic impurities, spectroscopic properties, size distributions and proton exchange capacities. The commercial humic acid (Na salt) from Aldrich Co. is purified to a protonated form and used as a reference material, and the humic acid extracted from one of Gorleben groundwaters is also purified to a protonated form and taken as a site specific material. These two humic acids, together with the original Na salt from Aldrich Co., are included for the characterization exercise. The results of characterization provide a basic knowledge that supports the forthcoming study of complexation of humic acids with actinides and fission products in their migration processes in the geosphere. (orig.)

  3. Modeling Ethanol Decomposition on Transition Metals: A Combined Application of Scaling and Bronsted-Evans-Polanyi Relations

    DEFF Research Database (Denmark)

    Ferrin, P.; Simonetti, D.; Kandoi, S.

    2009-01-01

    calculations necessary to describe trends in activity and selectivity across metal and alloy surfaces, thus extending the reach of DFT to more complex systems. In-this work, the well-known family of Bronsted-Evans-Polanyi (BEP) correlations, connecting minima with maxima in the potential energy surface...... on a subset of these surfaces are calculated. Experiments on supported catalysts verify that this simple model is reasonably accurate in describing reactivity trends across metals, suggesting that the combination of BEP and scaling relations may substantially reduce the cost of DFT calculations required...

  4. Assessing College Students' Understanding of Acid Base Chemistry Concepts

    Science.gov (United States)

    Wan, Yanjun Jean

    2014-01-01

    Typically most college curricula include three acid base models: Arrhenius', Bronsted-Lowry's, and Lewis'. Although Lewis' acid base model is generally thought to be the most sophisticated among these three models, and can be further applied in reaction mechanisms, most general chemistry curricula either do not include Lewis' acid base model, or…

  5. Predicting protein amidation sites by orchestrating amino acid sequence features

    Science.gov (United States)

    Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

    2017-08-01

    Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

  6. The nature of the active site in heterogeneous metal catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk

    2008-01-01

    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced...

  7. Acidity of edge surface sites of montmorillonite and kaolinite

    Science.gov (United States)

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

    2013-09-01

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

  8. Nucleic acid constructs containing orthogonal site selective recombinases (OSSRs)

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, Joshua M.; Anderson, J. Christopher; Dueber, John E.

    2017-08-29

    The present invention provides for a recombinant nucleic acid comprising a nucleotide sequence comprising a plurality of constructs, wherein each construct independently comprises a nucleotide sequence of interest flanked by a pair of recombinase recognition sequences. Each pair of recombinase recognition sequences is recognized by a distinct recombinase. Optionally, each construct can, independently, further comprise one or more genes encoding a recombinase capable of recognizing the pair of recombinase recognition sequences of the construct. The recombinase can be an orthogonal (non-cross reacting), site-selective recombinase (OSSR).

  9. Remediation of acid tar sludge at a Superfund site

    International Nuclear Information System (INIS)

    Grajczak, P.; McManus, R.W.

    1995-01-01

    An old refinery site in Texas was safely remediated a year before schedule and for 25% less than original engineering estimates through aggressive project management and the application of an innovative design. The authors planned to solidify the petroleum acid sludge and place it in an on-site, constructed landfill. Careful evaluation of available solidification technologies lead to selection of the DCR process, a patented stabilization process far waste treatment. The technology offered low expansion factor, low reagent to waste ratio, and low cost. The process also proved to be efficient and safe, implemented using a custom-designed, transportable treatment unit. High treatment rates and continuous uninterrupted operation resulted in early completion of the waste treatment task

  10. Students' Understanding of Acids/Bases in Organic Chemistry Contexts

    Science.gov (United States)

    Cartrette, David P.; Mayo, Provi M.

    2011-01-01

    Understanding key foundational principles is vital to learning chemistry across different contexts. One such foundational principle is the acid/base behavior of molecules. In the general chemistry sequence, the Bronsted-Lowry theory is stressed, because it lends itself well to studying equilibrium and kinetics. However, the Lewis theory of…

  11. Sites that Can Produce Left-handed Amino Acids in the Supernova Neutrino Amino Acid Processing Model

    Science.gov (United States)

    Boyd, Richard N.; Famiano, Michael A.; Onaka, Takashi; Kajino, Toshitaka

    2018-03-01

    The Supernova Neutrino Amino Acid Processing model, which uses electron anti-neutrinos and the magnetic field from a source object such as a supernova to selectively destroy one amino acid chirality, is studied for possible sites that would produce meteoroids with partially left-handed amino acids. Several sites appear to provide the requisite magnetic field intensities and electron anti-neutrino fluxes. These results have obvious implications for the origin of life on Earth.

  12. Mesoporous Nb and Ta Oxides: Synthesis, Characterization and Applications in Heterogeneous Acid Catalysis

    Science.gov (United States)

    Rao, Yuxiang Tony

    In this work, a series of mesoporous Niobium and Tantalum oxides with different pore sizes (C6, C12, C18 , ranging from 12A to 30 A) were synthesized using the ligand-assisted templating approach and investigated for their activities in a wide range of catalytic applications including benzylation, alkylation and isomerization. The as-synthesized mesoporous materials were characterized by nitrogen adsorption, powder X-ray diffraction, transmission electron microscopy (TEM), scanning electron microscopy (SEM), thermo gravimetric analysis (TGA), differential scanning calorimetry (DSC), and solid-state Nuclear magnetic resonance (NMR) techniques. In order to probe into the structural and coordination geometry of mesoporous Nb oxide and in efforts to make meaningful comparisons of mesoporous niobia prepared by the amine-templating method with the corresponding bulk sol-gel prepared Nb2O5 phase, 17O magic-angle-spinning solid-state NMR studies were conducted. The results showed a very high local order in the mesoporous sample. The oxygen atoms are coordinated only as ONb 2 in contrast with bulk phases in which the oxygen atoms are always present in a mixture of ONb2 and ONb3 coordination environments. To enhance their surface acidities and thus improve their performance as solid acid catalysts in the acid-catalyzed reactions mentioned above, pure mesoporous Nb and Ta oxides were further treated with 1M sulfuric acid or phosphoric acid. Their surface acidities before and after acid treatment were measured by Fourier transform infraRed (FT IR), amine titration and temperature programmed desorption of ammonia (NH3-TPD). Results obtained in this study showed that sulfated mesoporous Nb and Ta oxides materials possess relative high surface areas (up to 612 m 2/g) and amorphous wormhole structure. These mesoporous structures are thus quite stable to acid treatment. It was also found that Bronsted (1540 cm-1) and Lewis (1450 cm-1) acid sites coexist in a roughly 50:50 mixture

  13. Teachers' Perceptions of the Teaching of Acids and Bases in Swedish Upper Secondary Schools

    Science.gov (United States)

    Drechsler, Michal; Van Driel, Jan

    2009-01-01

    We report in this paper on a study of chemistry teachers' perceptions of their teaching in upper secondary schools in Sweden, regarding models of acids and bases, especially the Bronsted and the Arrhenius model. A questionnaire consisting of a Likert-type scale was developed, which focused on teachers' knowledge of different models, knowledge of…

  14. Mutable Lewis and Bronsted Acidity of Aluminated SBA-15 as Revealed by NMR of Adsorbed Pyridine-(15)N

    Czech Academy of Sciences Publication Activity Database

    Gurinov, A. A.; Rozhkova, Yu. A.; Zukal, Arnošt; Čejka, Jiří; Shenderovich, I, G.

    2011-01-01

    Roč. 27, č. 19 (2011), s. 12115-12123 ISSN 0743-7463 R&D Projects: GA AV ČR KAN100400701; GA ČR GA203/08/0604 Institutional research plan: CEZ:AV0Z40400503 Keywords : 15N NMR * post-synthesis alumination * phase Beckmann rearrangement Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.186, year: 2011

  15. On the behavior of Bronsted-Evans-Polanyi Relations for Transition Metal Oxides

    Energy Technology Data Exchange (ETDEWEB)

    Vojvodic, Aleksandra

    2011-08-22

    Versatile Broensted-Evans-Polanyi (BEP) relations are found from density functional theory for a wide range of transition metal oxides including rutiles and perovskites. For oxides, the relation depends on the type of oxide, the active site and the dissociating molecule. The slope of the BEP relation is strongly coupled to the adsorbate geometry in the transition state. If it is final state-like the dissociative chemisorption energy can be considered as a descriptor for the dissociation. If it is initial state-like, on the other hand, the dissociative chemisorption energy is not suitable as descriptor for the dissociation. Dissociation of molecules with strong intramolecular bonds belong to the former and molecules with weak intramolecular bonds to the latter group. We show, for the prototype system La-perovskites, that there is a 'cyclic' behavior in the transition state characteristics upon change of the active transition metal of the oxide.

  16. Site specific incorporation of keto amino acids into proteins

    Science.gov (United States)

    Schultz, Peter G [La Jolla, CA; Wang, Lei [San Diego, CA

    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.

  17. Acidic and catalytic properties of hierarchical zeolites and hybrid ordered mesoporous materials assembled from MFI protozeolitic units

    Czech Academy of Sciences Publication Activity Database

    Serrano, D. P.; García, R. A.; Vicente, G.; Linares, M.; Vitvarová, Dana; Čejka, Jiří

    2011-01-01

    Roč. 279, č. 2 (2011), s. 366-380 ISSN 0021-9517 Institutional research plan: CEZ:AV0Z40400503 Keywords : hierarchical zeolites * hybrid zeolitic-mesostructured materials * Bronsted and Lewis acid centres Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.002, year: 2011

  18. Determining the location and nearest neighbours of aluminium in zeolites with atom probe tomography

    NARCIS (Netherlands)

    Perea, Daniel E.; Arslan, Ilke; Liu, Jia; Ristanovic, Zoran; Kovarik, Libor; Arey, Bruce W.; Lercher, Johannes A.; Bare, Simon R.; Weckhuysen, Bert M.

    Zeolite catalysis is determined by a combination of pore architecture and Bronsted acidity. As Bronsted acid sites are formed by the substitution of AlO4 for SiO4 tetrahedra, it is of utmost importance to have information on the number as well as the location and neighbouring sites of framework

  19. Site-specific labeling of proteins with NMR-active unnatural amino acids

    International Nuclear Information System (INIS)

    Jones, David H.; Cellitti, Susan E.; Hao Xueshi; Zhang Qiong; Jahnz, Michael; Summerer, Daniel; Schultz, Peter G.; Uno, Tetsuo; Geierstanger, Bernhard H.

    2010-01-01

    A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

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

    Science.gov (United States)

    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.

  1. Prediction of citrullination sites by incorporating k-spaced amino acid pairs into Chou's general pseudo amino acid composition.

    Science.gov (United States)

    Ju, Zhe; Wang, Shi-Yun

    2018-04-22

    As one of the most important and common protein post-translational modifications, citrullination plays a key role in regulating various biological processes and is associated with several human diseases. The accurate identification of citrullination sites is crucial for elucidating the underlying molecular mechanisms of citrullination and designing drugs for related human diseases. In this study, a novel bioinformatics tool named CKSAAP_CitrSite is developed for the prediction of citrullination sites. With the assistance of support vector machine algorithm, the highlight of CKSAAP_CitrSite is to adopt the composition of k-spaced amino acid pairs surrounding a query site as input. As illustrated by 10-fold cross-validation, CKSAAP_CitrSite achieves a satisfactory performance with a Sensitivity of 77.59%, a Specificity of 95.26%, an Accuracy of 89.37% and a Matthew's correlation coefficient of 0.7566, which is much better than those of the existing prediction method. Feature analysis shows that the N-terminal space containing pairs may play an important role in the prediction of citrullination sites, and the arginines close to N-terminus tend to be citrullinated. The conclusions derived from this study could offer useful information for elucidating the molecular mechanisms of citrullination and related experimental validations. A user-friendly web-server for CKSAAP_CitrSite is available at 123.206.31.171/CKSAAP_CitrSite/. Copyright © 2017. Published by Elsevier B.V.

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

    Science.gov (United States)

    Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

    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.

  3. Human acid β-glucosidase: isolation and amino acid sequence of a peptide containing the catalytic site

    International Nuclear Information System (INIS)

    Dinur, T.; Osiecki, K.M.; Legler, G.; Gatt, S.; Desnick, R.J.; Grabowski, G.A.

    1986-01-01

    Human acid β-glucosidase (D-glucosyl-N-acylsphingosine glucohydrolase, EC 3.2.1.45) cleaves the glucosidic bonds of glucosylceramide and synthetic β-glucosides. The deficient activity of this hydrolase is the enzymatic defect in the subtypes and variants of Gaucher disease, the most prevalent lysosomal storage disease. To isolate and characterize the catalytic site of the normal enzyme, brominated 3 H-labeled conduritol B epoxide ( 3 H-Br-CBE), which inhibits the enzyme by binding covalently to this site, was used as an affinity label. Under optimal conditions 1 mol of 3 H-Br-CBE bound to 1 mol of pure enzyme protein, indicating the presence of a single catalytic site per enzyme subunit. After V 8 protease digestion of the 3 H-Br-CBE-labeled homogeneous enzyme, three radiolabeled peptides, designated peptide A, B, or C, were resolved by reverse-phase HPLC. The partial amino acid sequence (37 residues) of peptide A (M/sub r/, 5000) was determined. The sequence of this peptide, which contained the catalytic site, had exact homology to the sequence near the carboxyl terminus of the protein, as predicted from the nucleotide sequence of the full-length cDNA encoding acid β-glucosidase

  4. Location and nature of calcium-binding sites in salivary acidic proline-rich phosphoproteins

    International Nuclear Information System (INIS)

    Bennick, A.; McLaughlin, A.C.; Grey, A.A.; Madapallimattam, G.

    1981-01-01

    The location of the calcium-binding sites in the human acidic proline-rich proteins, salivary proteins A and C, was determined by equilibrium dialysis of the tryptic peptides with buffers containing 45 Ca. All the calcium-binding sites are located in the NH 2 -terminal tryptic peptide (TX peptide). The nature of the calcium binding sites in the TX peptide and native salivary proteins A and C, as well as dephosphorylated proteins was compared. Two types of sites can be distinguished in peptide TX. Type I sites have an apparent dissociation constant (K) of 38 μM and are responsible for the binding of 2.6 mol of Ca/mol of peptide. The corresponding figures for Type II sites are 780 μM and 5.3 mol of Ca/mol of peptide. In the native proteins, the amount of calcium bound at the type II sites decreases to 3.9 mol of Ca/mol of proteins A and C and K increases to 1100 μM. The amount of calcium bound at type I sites decreases to 1.5 mol/mol of protein A and 0.6 mol/mol of protein C, but there is no change in K. Dephosphorylation affects the calcium binding at both types of sites. The experiments indicate that the COOH-terminal parts of the native proteins affect the number and the nature of the protein calcium-binding sites. Proton and phosphorous NMR data demonstrate that β-COOH in aspartic acid, as well as phosphoserine, are part of the calcium-binding sites. The difference in calcium binding to salivary proteins A and C may be due at least partially to differences in the environment of one or more aspartic acids

  5. Interaction of Palmitic Acid with Metoprolol Succinate at the Binding Sites of Bovine Serum Albumin

    Directory of Open Access Journals (Sweden)

    Mashiur Rahman

    2014-12-01

    Full Text Available Purpose: The aim of this study was to characterize the binding profile as well as to notify the interaction of palmitic acid with metoprolol succinate at its binding site on albumin. Methods: The binding of metoprolol succinate to bovine serum albumin (BSA was studied by equilibrium dialysis method (ED at 27°C and pH 7.4, in order to have an insight in the binding chemistry of the drug to BSA in presence and absence of palmitic acid. The study was carried out using ranitidine as site-1 and diazepam as site-2 specific probe. Results: Different analysis of binding of metoprolol succinate to bovine serum albumin suggested two sets of association constants: high affinity association constant (k1 = 11.0 x 105 M-1 with low capacity (n1 = 2 and low affinity association (k2 = 4.0×105 M-1 constant with high capacity (n2 = 8 at pH 7.4 and 27°C. During concurrent administration of palmitic acid and metoprolol succinate in presence or absence of ranitidine or diazepam, it was found that palmitic acid displaced metoprolol succinate from its binding site on BSA resulting reduced binding of metoprolol succinate to BSA. The increment in free fraction of metoprolol succinate was from 26.27% to 55.08% upon the addition of increased concentration of palmitic acid at a concentration of 0×10-5 M to 16×10-5 M. In presence of ranitidine and diazepam, palmitic acid further increases the free fraction of metoprolol succinate from 33.05% to 66.95% and 40.68% to 72.88%, respectively. Conclusion: This data provided the evidence of interaction at higher concentration of palmitic acid at the binding sites on BSA, which might change the pharmacokinetic properties of metoprolol succinate.

  6. Site directed mutagenesis of amino acid residues at the active site of mouse aldehyde oxidase AOX1.

    Directory of Open Access Journals (Sweden)

    Silvia Schumann

    Full Text Available Mouse aldehyde oxidase (mAOX1 forms a homodimer and belongs to the xanthine oxidase family of molybdoenzymes which are characterized by an essential equatorial sulfur ligand coordinated to the molybdenum atom. In general, mammalian AOs are characterized by broad substrate specificity and an yet obscure physiological function. To define the physiological substrates and the enzymatic characteristics of mAOX1, we established a system for the heterologous expression of the enzyme in Escherichia coli. The recombinant protein showed spectral features and a range of substrate specificity similar to the native protein purified from mouse liver. The EPR data of recombinant mAOX1 were similar to those of AO from rabbit liver, but differed from the homologous xanthine oxidoreductase enzymes. Site-directed mutagenesis of amino acids Val806, Met884 and Glu1265 at the active site resulted in a drastic decrease in the oxidation of aldehydes with no increase in the oxidation of purine substrates. The double mutant V806E/M884R and the single mutant E1265Q were catalytically inactive enzymes regardless of the aldehyde or purine substrates tested. Our results show that only Glu1265 is essential for the catalytic activity by initiating the base-catalyzed mechanism of substrate oxidation. In addition, it is concluded that the substrate specificity of molybdo-flavoenzymes is more complex and not only defined by the three characterized amino acids in the active site.

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

    Science.gov (United States)

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

    2009-01-28

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

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

    International Nuclear Information System (INIS)

    STALLINGS, MARY

    2004-01-01

    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

  9. Molecular Design of a Chiral Brønsted Acid with Two Different Acidic Sites: Regio-, Diastereo-, and Enantioselective Hetero-Diels-Alder Reaction of Azopyridinecarboxylate with Amidodienes Catalyzed by Chiral Carboxylic Acid-Monophosphoric Acid.

    Science.gov (United States)

    Momiyama, Norie; Tabuse, Hideaki; Noda, Hirofumi; Yamanaka, Masahiro; Fujinami, Takeshi; Yamanishi, Katsunori; Izumiseki, Atsuto; Funayama, Kosuke; Egawa, Fuyuki; Okada, Shino; Adachi, Hiroaki; Terada, Masahiro

    2016-09-07

    A chiral Brønsted acid containing two different acidic sites, chiral carboxylic acid-monophosphoric acid 1a, was designed to be a new and effective concept in catalytic asymmetric hetero-Diels-Alder reactions of azopyridinecarboxylate with amidodienes. The multipoint hydrogen-bonding interactions among the carboxylic acid, monophosphoric acid, azopyridinecarboxylate, and amidodiene achieved high catalytic and chiral efficiency, producing substituted 1,2,3,6-tetrahydropyridazines with excellent stereocontrol in a single step. This constitutes the first example of regio-, diastereo-, and enantioselective azo-hetero-Diels-Alder reactions by chiral Brønsted acid catalysis.

  10. Ammonia IRMS-TPD study on the distribution of acid sites in mordenite.

    Science.gov (United States)

    Niwa, Miki; Suzuki, Katsuki; Katada, Naonobu; Kanougi, Tomonori; Atoguchi, Takashi

    2005-10-13

    Using an IRMS-TPD (temperature programmed desorption) of ammonia, we studied the nature, strength, crystallographic location, and distribution of acid sites of mordenite. In this method, infrared spectroscopy (IR) and mass spectroscopy (MS) work together to follow the thermal behavior of adsorbed and desorbed ammonia, respectively; therefore, adsorbed species were identified, and their thermal behavior was directly connected with the desorption of ammonia during an elevation of temperature. IR-measured TPD of the NH4(+) cation was similar to MS-measured TPD, thus showing the nature of Brønsted acidity. From the behavior of OH bands, it was found that the Brønsted acid sites consisted of two kinds of OH bands at high and low wavenumbers, ascribable to OH bands situated on 12- and 8-member rings (MR) of mordenite structure, respectively. The amount and strength of these Brønsted hydroxyls were measured quantitatively based on a theoretical equation using a curve fitting method. Up to ca. 30% of the exchange degree, NH4(+) was exchanged with Na+ on the 12-MR to arrive at saturation; therefore, in this region, the Brønsted acid site was situated on the large pore of 12-MR. The NH4(+) cation was then exchanged with Na+ on 8-MR, and finally exceeded the amount on 12-MR. In the 99% NH4-mordenite, Brønsted acid sites were located predominantly on the 8-MR more than on the 12-MR. Irrespective of the NH4(+) exchange degree, the strengths deltaH of Brønsted OH were 145 and 153 kJ mol(-1) on the 12- and 8-MR, respectively; that is, the strength of Brønsted acid site on the 8-MR was larger than that on the 12-MR. A density functional theory (DFT) calculation supported the difference in the strengths of the acid sites. Catalytic cracking activity of the Brønsted acid sites on the 8-MR declined rapidly, while that on the 12-MR was remarkably kept. The difference in strength and/or steric capacity may cause such a difference in the life of a catalyst.

  11. Acid-base properties of 1-methyl-1,4-dilhydroborabenzene, CH3BC5H6

    International Nuclear Information System (INIS)

    Sullivan, S.A.; Sandford, H.; Beauchamp, J.L.; Ashe, A.J. III

    1978-01-01

    Ion cyclotron resonance techniques are employed to determine the gas-phase Bronsted and Lewis acidities as well as the Bronsted basicity of 1-methyl-1,4-dihydroborabenzene, CH 3 BC 5 H 6 . The ring proton is found to be highly acidic with PA(CH 3 BC 5 H 5 - ) = 337 +- 3 kcal/mol. This acidity results from the formation of 6π electron aromatic anion CH 3 BC 5 H 5 - , which is isoelectronic with toluene. Both the Lewis acidity toward F - as a reference base and the proton basicity of the parent molecule suggest that there is little interaction between the diene π system and the electron-deficient boron. This is further confirmed by the similarity of both negative and positive ion chemistry of the borabenzene to that of aliphatic boranes

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

    Science.gov (United States)

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

    2012-10-01

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

  13. Spontaneous dispersion of PdO onto acid sites of zeolites studied by in situ DXAFS

    CERN Document Server

    Okumura, K; Niwa, M; Yokota, S; Kato, K; Tanida, H; Uruga, T

    2003-01-01

    The generation of highly dispersed PdO over zeolite supports was studied using in situ energy-dispersive XAFS (DXAFS) technique. From the comparison with the Na-ZSM-5, it was found that the oxidation as well as the spontaneous dispersion of Pd was promoted through the interaction between PdO and acid sites of H-form zeolites. (author)

  14. The hydroxyl species and acid sites on diatomite surface: a combined IR and Raman study

    Science.gov (United States)

    Yuan, P.; Wu, D. Q.; He, H. P.; Lin, Z. Y.

    2004-04-01

    Diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), Raman spectroscopy of adsorbed pyridine molecules (Py-Raman) and in situ Py-IR have been used to investigate the hydroxyl species and acid sites on diatomite surfaces. The Lewis (L) and Brønsted (B) acid sites, and various hydroxyl species, including isolated hydroxyl groups, H-bonded hydroxyl groups and physically adsorbed water, are identified. The L acid sites in diatomite samples are resulted from the clay impurities, and the B acid sites are resulted from some moderate strength H-bonded hydroxyl groups. At room temperature, both of the isolated and H-bonded silanols associate with the physically adsorbed water by hydrogen bond. After calcination treatment, physically adsorbed water will be desorbed from the silanols, and the silanols will condense with the increase of temperature. Generally, the H-bonded silanols condense more easily than the isolated ones. The properties of surface hydroxyl species of diatomaceous silica are more similar to precipitated silica rather than fumed silica.

  15. Surface acidity of calcium phosphate and calcium hydroxyapatite: FTIR spectroscopic study of low-temperature CO adsorption

    International Nuclear Information System (INIS)

    Pekounov, Yassen; Chakarova, Kristina; Hadjiivanov, Konstantin

    2009-01-01

    The surface properties of calcium phosphate precursor (CP) and crystalline calcium hydroxyapatite (HA) prepared biomimetically have been studied by IR spectroscopy of adsorbed CO. Both samples are characterized by the absence of Bronsted acidity. Low-temperature CO adsorption on CP evacuated at 523 K leads to formation of only one family of Ca 2+ -CO species (2168 cm -1 ). The analysis indicates that the respective calcium ions on the surface are not isolated. Similar spectra were obtained with HA evacuated at 573 K. In this case, however, the Ca 2+ -CO band was detected at 2165 cm -1 due to enhanced lateral interaction between the adsorbed CO molecules. Another family of Ca 2+ sites (Ca 2+ -CO band at 2178 cm -1 ) was created after evacuation of the HA sample at 673 K. These sites were assumed to be a result of sample dehydroxylation. The results demonstrate the absence of any protonic acidity of the samples (i.e. P-OH surface groups) and weak electrostatic Lewis acidity caused by coordinatively unsaturated Ca 2+ cations.

  16. Brønsted acid sites based on penta-coordinated aluminum species

    Science.gov (United States)

    Wang, Zichun; Jiang, Yijiao; Lafon, Olivier; Trébosc, Julien; Duk Kim, Kyung; Stampfl, Catherine; Baiker, Alfons; Amoureux, Jean-Paul; Huang, Jun

    2016-12-01

    Zeolites and amorphous silica-alumina (ASA), which both provide Brønsted acid sites (BASs), are the most extensively used solid acid catalysts in the chemical industry. It is widely believed that BASs consist only of tetra-coordinated aluminum sites (AlIV) with bridging OH groups in zeolites or nearby silanols on ASA surfaces. Here we report the direct observation in ASA of a new type of BAS based on penta-coordinated aluminum species (AlV) by 27Al-{1H} dipolar-mediated correlation two-dimensional NMR experiments at high magnetic field under magic-angle spinning. Both BAS-AlIV and -AlV show a similar acidity to protonate probe molecular ammonia. The quantitative evaluation of 1H and 27Al sites demonstrates that BAS-AlV co-exists with BAS-AlIV rather than replaces it, which opens new avenues for strongly enhancing the acidity of these popular solid acids.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    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.

  18. Identification of nucleic acid binding sites on translin-associated factor X (TRAX protein.

    Directory of Open Access Journals (Sweden)

    Gagan Deep Gupta

    Full Text Available Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity.

  19. Identification of Nucleic Acid Binding Sites on Translin-Associated Factor X (TRAX) Protein

    Science.gov (United States)

    Gupta, Gagan Deep; Kumar, Vinay

    2012-01-01

    Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity. PMID:22427937

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  1. A review of acid drainage from waste rock dumps and mine sites (Australian and Scandinavia)

    International Nuclear Information System (INIS)

    Harries, J.R.

    1990-05-01

    This report reviews the literature from Australia and Scandinavia on acid drainage from pyritic waste rock dumps with an emphasis on measurements and theory of processes that control the rage of oxidation and the release of pollutants. Conditions within waste rock dumps have been measured at several mine sites and a range of rehabilitation treatments have been tried to reduce the release of pollutants. A number of models have been proposed to calculate air flow, water transport and geochemistry. The data and experience at the mine sites are compared with predictions of the models. Details of Australian and Swedish mine sites where waste rock is a source of acid drainage are described in the Appendices. 92 refs., 2 tabs., 10 figs

  2. Formation of Broensted acids sites in the reaction of cyclohexanol on NaCeY zeolites

    International Nuclear Information System (INIS)

    Vogt, O.; Nattich, M.; Datka, J.; Gil, B.

    2002-01-01

    This study was undertaken to elucidate why the catalytic activity of NaCeY in cyclohexanol reactions carried out in a pulse reactor increases with the pulse number. We studied therefore the effect of cyclohexanol and also of ethanol and water on catalytic activity NaCeY (of exchange degrees 36 and 72%) in cyclohexanol reactions: isomerization and disproportionation. We also studied the reaction of cyclohexanol and water with NaCeY zeolite by IR spectroscopy. Our results evidenced that new Broensted acid sites were formed by the reaction of cyclohexanol and water. This was shown by IR spectroscopy: the increase of Si-O 1 H-Al band 3638 cm -1 and in increase of ammonium ions band (upon ammonia adsorption). The new sites were formed by hydrolysis of Ce 3+ ions with water introduced in a pulse, or produced by dehydration of cyclohexanol catalyzed by acid sites. Formation of new Broensted acid sites resulted in an increase of catalytic activity of NaCeY in cyclohexane reaction as observed in this study and also in cyclohexanol reactions. (author)

  3. GABAA [gamma-aminobutyric acid] type binding sites on membranes of spermatozoa

    International Nuclear Information System (INIS)

    Erdoe, S.L.; Wekerle, L.

    1990-01-01

    The binding of [ 3 H] gamma-aminobutyric acid (GABA) to seminal membranes of swines and rams was examined. Specific, GABA binding was demonstrated in both species, which showed the features of GABA A type receptors. The affinity of binding was similar in both species, whereas the density of seminal GABA binding sites was 5 times higher in swine. Our findings suggest that GABA may have a direct effect on spermatozoa

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

    International Nuclear Information System (INIS)

    Dittmer, L.M.

    2006-01-01

    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

  5. Remedial action at the Acid/Pueblo Canyon site, Los Alamos, New Mexico. Final report

    International Nuclear Information System (INIS)

    1984-10-01

    The Acid/Pueblo Canyon site (TA-45) was designated in 1976 for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP). During the period 1943 to 1964 untreated and treated liquid wastes generated by nuclear weapons research activities at the Los Alamos Scientific Laboratory (LASL) were discharged into the two canyons. A survey of the site conducted by LASL in 1976 to 1977 identified two areas where radiological contamination exceeded criteria levels. The selected remedial action was based on extensive radiological characterization and comprehensive engineering assessments and comprised the excavation and disposal of 390 yd 3 of contaminated soil and rock. This document describes the background to the remedial action, the parties involved in administering and executing it, the chronology of the work, verification of the adequacy of the remedial action, and the cost incurred. 14 references, 5 figures, 5 tables

  6. Soil degradation by sulfuric acid disposition on uranium producing sites in south Bulgaria

    International Nuclear Information System (INIS)

    Atanasov, I.; Gribachev, P.

    1997-01-01

    This study assesses the damage of soils caused by spills of sulfuric acid solutions used for in situ leaching of uranium at eight uranium producing (by open-cast method) sites (total area of approximately 220 ha) in the region of Momino-Rakovski (South Bulgaria). The upper soil layer is cinnamonic pseudopodzolic ( or Eutric Planosols by FAO Legend, 1974). The results of the investigation show that the sulfuric acid spills caused strong acidification of upper (0-20 cm) and subsurface (20-60 cm) soil horizons which is expressed as decreasing of pH (H 2 O) to 2.9-3.5 and increasing of exchangeable H + and Al 3+ to 18 and 32% from CEC. Acid degradation of soils is combined with reducing of organic matter content. The average concentration of the total heavy metal content in the upper soil horizon (in ppm) is: Cd=1.5; Cu=30; Pb=25; Zn=40 and U=8. No significant differences were detected between the upper and subsurface soil layers . The heavy metal concentration did not exceed the Bulgarian standards for heavy metals and uranium content of soils. But the coarse texture of the top soil layers, the lack of carbonates, The low CEC and strong acidity determine a low buffering capacity of the investigated soils and this can be considered as hazardous for plants. This indicates that a future soil monitoring should be carried out in the region together with measures for neutralizing of soil acidity

  7. Site-specific estimates of water yield applied in regional acid sensitivity surveys across western Canada

    Directory of Open Access Journals (Sweden)

    Patrick D. SHAW

    2010-08-01

    Full Text Available Runoff or water yield is an important input to the Steady-State Water Chemistry (SSWC model for estimating critical loads of acidity. Herein, we present site-specific water yield estimates for a large number of lakes (779 across three provinces of western Canada (Manitoba, Saskatchewan, and British Columbia using an isotope mass balance (IMB approach. We explore the impact of applying site-specific hydrology as compared to use of regional runoff estimates derived from gridded datasets in assessing critical loads of acidity to these lakes. In general, the average water yield derived from IMB is similar to the long-term average runoff; however, IMB results suggest a much larger range in hydrological settings of the lakes, attributed to spatial heterogeneity in watershed characteristics and landcover. The comparison of critical loads estimates from the two methods suggests that use of average regional runoff data in the SSWC model may overestimate critical loads for the majority of lakes due to systematic skewness in the actual runoff distributions. Implications for use of site-specific hydrology in regional critical loads assessments across western Canada are discussed.

  8. Possible site-specific reagent for the general amino acid transport system of Saccharomyces cerevisiae.

    Science.gov (United States)

    Larimore, F S; Roon, R J

    1978-02-07

    The general amino acid transport system of Saccharomyces cerevisiae functions in the uptake of neutral, basic, and acidic amino acids. The amino acid analogue N-delta-chloroacetyl-L-ornithine (NCAO) has been tested as potential site specific reagent for this system. L-Tryptophan, which is transported exclusively by the general transport system, was used as a substrate. In the presence of glucose as an energy source, NCAO inhibited tryptophan transport competitively (Ki = 80 micrometer) during short time intervals (1-2 min), but adding 100 micrometer NCAO to a yeast cell suspension resulted in a time-dependent activation of tryptophan transport during the first 15 min of treatment. Following the activation a time-dependent decay of tryptophan transport activity occurred. Approximately 80% inactivation of the system was observed after 90 min. When a yeast cell suspension was treated with NCAO in the absence of an energy source, an 80% inactivation of tryptophan transport occurred in 90 min. The inactivation was noncompetitive (Ki congruent to 60 micrometer) and could not be reversed by the removal of the NCAO. Addition of a five-fold excess of L-lysine during NCAO treatment or prevented inactivation of tryptophan transport. Under parallel conditions of incubation, other closely related transport systems were not inhibited by NCAO.

  9. Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

    Science.gov (United States)

    Jelínek, Jan; Škoda, Petr; Hoksza, David

    2017-12-06

    Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.

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

    Science.gov (United States)

    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.

  11. Savannah River Site Tank Cleaning: Corrosion Rate For One Versus Eight Percent Oxalic Acid Solution

    International Nuclear Information System (INIS)

    Ketusky, E.; Subramanian, K.

    2011-01-01

    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

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

    International Nuclear Information System (INIS)

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

    1991-01-01

    Binding of 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

  13. Catalytic Ozonation of Toluene Using Chilean Natural Zeolite: The Key Role of Brønsted and Lewis Acid Sites

    Directory of Open Access Journals (Sweden)

    Serguei Alejandro-Martín

    2018-05-01

    Full Text Available The influence of surface physical-chemical characteristics of Chilean natural zeolite on the catalytic ozonation of toluene is presented in this article. Surface characteristics of natural zeolite were modified by acid treatment with hydrochloric acid and ion-exchange with ammonium sulphate. Prior to catalytic ozonation assays, natural and chemically modified zeolite samples were thermally treated at 623 and 823 K in order to enhance Brønsted and Lewis acid sites formation, respectively. Natural and modified zeolite samples were characterised by N2 adsorption at 77 K, elemental analysis, X-ray fluorescence, and Fourier transform infrared (FTIR spectroscopy, using pyridine as a probe molecule. The highest values of the reaction rate of toluene oxidation were observed when NH4Z1 and 2NH4Z1 zeolite samples were used. Those samples registered the highest density values of Lewis acid sites compared to other samples used here. Results indicate that the presence of strong Lewis acid sites at the 2NH4Z1 zeolite surface causes an increase in the reaction rate of toluene oxidation, confirming the role of Lewis acid sites during the catalytic ozonation of toluene at room temperature. Lewis acid sites decompose gaseous ozone into atomic oxygen, which reacts with the adsorbed toluene at Brønsted acid sites. On the other hand, no significant contribution of Brønsted acid sites on the reaction rate was registered when NH4Z1 and 2NH4Z1 zeolite samples were used.

  14. Creating diversity by site-selective peptide modification: a customizable unit affords amino acids with high optical purity.

    Science.gov (United States)

    Romero-Estudillo, Ivan; Boto, Alicia

    2013-11-15

    The development of peptide libraries by site-selective modification of a few parent peptides would save valuable time and materials in discovery processes, but still is a difficult synthetic challenge. Herein natural hydroxyproline is introduced as a "convertible" unit for the production of a variety of optically pure amino acids, including expensive N-alkyl amino acids, and to achieve the mild, efficient, and site-selective modification of peptides.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Izumikawa, Tomomi; Kitagawa, Hiroshi

    2015-05-01

    Thrombomodulin (TM) is a cell-surface glycoprotein and a critical mediator of endothelial anticoagulant function. TM exists as both a chondroitin sulfate (CS) proteoglycan (PG) form and a non-PG form lacking a CS chain (α-TM); therefore, TM can be described as a part-time PG. Previously, we reported that α-TM bears an immature, truncated linkage tetrasaccharide structure (GlcAβ1-3Galβ1-3Galβ1-4Xyl). However, the biosynthetic mechanism to generate part-time PGs remains unclear. In this study, we used several mutants to demonstrate that the amino acid sequence surrounding the CS attachment site influences the efficiency of chondroitin polymerization. In particular, the presence of acidic residues surrounding the CS attachment site was indispensable for the elongation of CS. In addition, mutants defective in CS elongation did not exhibit anti-coagulant activity, as in the case with α-TM. Together, these data support a model for CS chain assembly in which specific core protein determinants are recognized by a key biosynthetic enzyme involved in chondroitin polymerization. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Modification and characterization of sites giving acid cracking on aluminium oxide supports; Modification et caracterisation des sites responsables du craquage acide sur des supports a base d`alumine

    Energy Technology Data Exchange (ETDEWEB)

    Guillaume, D

    1997-10-23

    The aim of this work is to characterize the surface acid properties of {gamma} alumina, especially the nature, the amount, the strength and the environment of acid sites. The techniques that have been used are: the thermo-desorption of trimethyl-phosphine followed by {sup 31}P MAS NMR, the infrared spectroscopy, the n-heptane cracking, the modification of {gamma} alumina by the addition of chlorine, silicon and alkali (K{sup +}, Na{sup +}), alkaline-earths (Mg{sup 2+}, Ca{sup 2+}), lanthanum (La{sup 3+}) cations. The combination of these techniques has allowed to identify the surface acid properties of {gamma} alumina through the n-heptane transformation reactions under reforming conditions. We have shown that Lewis acidity is responsible for cracking reactions leading to C{sub 1}-C{sub 6} and C{sub 2}-C{sub 5} whereas the cracking of n-heptane producing C{sub 3}-C{sub 4} is due to Broensted acid sites. The isomerization and cyclization reactions both require weaker Broensted acid sites than cracking leading to C{sub 3}-C{sub 4}. The mechanisms involved in the formation of products of these reactions have been identified. Despite the complexity of surface acid properties of {gamma} alumina, this study has determined the environment of catalytically active sites, considering the presence of cation vacancies. (author) 206 refs.

  18. Structure–acidity correlation of supported tungsten(VI)-oxo-species: FT-IR and TPD studies of adsorbed pyridine and catalytic decomposition of 2-propanol

    Energy Technology Data Exchange (ETDEWEB)

    Zaki, M.I., E-mail: mizaki@mu.edu.eg; Mekhemer, G.A.H.; Fouad, N.E.; Rabee, A.I.M.

    2014-07-01

    The amount of 10 wt%-WO{sub 3} was supported on alumina, titania or silica by impregnation with aqueous solution of ammonium paratungstate and subsequent calcination at 500 °C for 10 h. Tungstate-related chemical and physical changes in the calcination products were resolved by ex-situ infrared (IR) spectroscopy. Nature of exposed surface acid sites were probed by in-situ IR spectroscopy of adsorbed pyridine (Py) molecules at room temperature (RT). The relative strength of the acid sites thus probed was gauged by combining results of temperature-programmed desorption (TPD) measurements of the RT-adsorbed Py with those communicated by in-situ IR spectra of residual Py on the surface after a brief thermoevacuation at high temperatures (100–300 °C). Reactivity of the surface acid sites was tested toward 2-propanal catalytic decomposition, and observed by in-situ IR gas phase spectra. Results obtained were correlated with predominant structures assumed by the supported tungstate species. Accordingly, polymerization of the supported tungstate into 2-/3-dimensional structures, was found to be relatively most advanced on favorable locations of titania surfaces as compared to the case on alumina or silica surfaces. Consequently, the Lewis acidity was strengthened, and strong Bronsted acidity was evolved, leading to a 2-propanol dehydration catalyst (tungstate/titania) of optimal activity and selectivity. Strong tungstate/support interfacial interactions were found to hamper the formation of the strongly acidic and catalytically active polymeric structures of the supported tungstate (i.e., the case on alumina or silica).

  19. Structure–acidity correlation of supported tungsten(VI)-oxo-species: FT-IR and TPD studies of adsorbed pyridine and catalytic decomposition of 2-propanol

    International Nuclear Information System (INIS)

    Zaki, M.I.; Mekhemer, G.A.H.; Fouad, N.E.; Rabee, A.I.M.

    2014-01-01

    The amount of 10 wt%-WO 3 was supported on alumina, titania or silica by impregnation with aqueous solution of ammonium paratungstate and subsequent calcination at 500 °C for 10 h. Tungstate-related chemical and physical changes in the calcination products were resolved by ex-situ infrared (IR) spectroscopy. Nature of exposed surface acid sites were probed by in-situ IR spectroscopy of adsorbed pyridine (Py) molecules at room temperature (RT). The relative strength of the acid sites thus probed was gauged by combining results of temperature-programmed desorption (TPD) measurements of the RT-adsorbed Py with those communicated by in-situ IR spectra of residual Py on the surface after a brief thermoevacuation at high temperatures (100–300 °C). Reactivity of the surface acid sites was tested toward 2-propanal catalytic decomposition, and observed by in-situ IR gas phase spectra. Results obtained were correlated with predominant structures assumed by the supported tungstate species. Accordingly, polymerization of the supported tungstate into 2-/3-dimensional structures, was found to be relatively most advanced on favorable locations of titania surfaces as compared to the case on alumina or silica surfaces. Consequently, the Lewis acidity was strengthened, and strong Bronsted acidity was evolved, leading to a 2-propanol dehydration catalyst (tungstate/titania) of optimal activity and selectivity. Strong tungstate/support interfacial interactions were found to hamper the formation of the strongly acidic and catalytically active polymeric structures of the supported tungstate (i.e., the case on alumina or silica).

  20. Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction.

    Science.gov (United States)

    López, Yosvany; Sharma, Alok; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Sattar, Abdul; Tsunoda, Tatsuhiko

    2018-01-19

    Post-translational modification is considered an important biological mechanism with critical impact on the diversification of the proteome. Although a long list of such modifications has been studied, succinylation of lysine residues has recently attracted the interest of the scientific community. The experimental detection of succinylation sites is an expensive process, which consumes a lot of time and resources. Therefore, computational predictors of this covalent modification have emerged as a last resort to tackling lysine succinylation. In this paper, we propose a novel computational predictor called 'Success', which efficiently uses the structural and evolutionary information of amino acids for predicting succinylation sites. To do this, each lysine was described as a vector that combined the above information of surrounding amino acids. We then designed a support vector machine with a radial basis function kernel for discriminating between succinylated and non-succinylated residues. We finally compared the Success predictor with three state-of-the-art predictors in the literature. As a result, our proposed predictor showed a significant improvement over the compared predictors in statistical metrics, such as sensitivity (0.866), accuracy (0.838) and Matthews correlation coefficient (0.677) on a benchmark dataset. The proposed predictor effectively uses the structural and evolutionary information of the amino acids surrounding a lysine. The bigram feature extraction approach, while retaining the same number of features, facilitates a better description of lysines. A support vector machine with a radial basis function kernel was used to discriminate between modified and unmodified lysines. The aforementioned aspects make the Success predictor outperform three state-of-the-art predictors in succinylation detection.

  1. Identification of metal ion binding sites based on amino acid sequences.

    Science.gov (United States)

    Cao, Xiaoyong; Hu, Xiuzhen; Zhang, Xiaojin; Gao, Sujuan; Ding, Changjiang; Feng, Yonge; Bao, Weihua

    2017-01-01

    The identification of metal ion binding sites is important for protein function annotation and the design of new drug molecules. This study presents an effective method of analyzing and identifying the binding residues of metal ions based solely on sequence information. Ten metal ions were extracted from the BioLip database: Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+ and Co2+. The analysis showed that Zn2+, Cu2+, Fe2+, Fe3+, and Co2+ were sensitive to the conservation of amino acids at binding sites, and promising results can be achieved using the Position Weight Scoring Matrix algorithm, with an accuracy of over 79.9% and a Matthews correlation coefficient of over 0.6. The binding sites of other metals can also be accurately identified using the Support Vector Machine algorithm with multifeature parameters as input. In addition, we found that Ca2+ was insensitive to hydrophobicity and hydrophilicity information and Mn2+ was insensitive to polarization charge information. An online server was constructed based on the framework of the proposed method and is freely available at http://60.31.198.140:8081/metal/HomePage/HomePage.html.

  2. Imaging Preferential Flow Pathways of Contaminants from Passive Acid Mine Drainage Mitigation Sites Using Electrical Resistivity

    Science.gov (United States)

    Kelley, N.; Mount, G.; Terry, N.; Herndon, E.; Singer, D. M.

    2017-12-01

    The Critical Zone represents the surficial and shallow layer of rock, air, water, and soil where most interactions between living organisms and the Earth occur. Acid mine drainage (AMD) resulting from coal extraction can influence both biological and geochemical processes across this zone. Conservative estimates suggest that more than 300 million gallons of AMD are released daily, making this acidic solution of water and contaminants a common issue in areas with legacy or current coal extraction. Electrical resistivity imaging (ERI) provides a rapid and minimally invasive method to identify and monitor contaminant pathways from AMD remediation systems in the subsurface of the Critical Zone. The technique yields spatially continuous data of subsurface resistivity that can be inverted to determine electrical conductivity as a function of depth. Since elevated concentrations of heavy metals can directly influence soil conductivity, ERI data can be used to trace the flow pathways or perhaps unknown mine conduits and transport of heavy metals through the subsurface near acid mine drainage sources. This study aims to examine preferential contaminant migration from those sources through substrate pores, fractures, and shallow mine workings in the near subsurface surrounding AMD sites in eastern Ohio and western Pennsylvania. We utilize time lapse ERI measures during different hydrologic conditions to better understand the variability of preferential flow pathways in relation to changes in stage and discharge within the remediation systems. To confirm ERI findings, and provide constraint to geochemical reactions occurring in the shallow subsurface, we conducted Inductively Coupled Plasma (ICP) spectrometry analysis of groundwater samples from boreholes along the survey transects. Through these combined methods, we can provide insight into the ability of engineered systems to contain and isolate metals in passive acid mine drainage treatment systems.

  3. Vapor-Phase Hydrodeoxygenation of Guaiacol to Aromatics over Pt/HBeta: Identification of the Role of Acid Sites and Metal Sites on the Reaction Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Nie, Lei [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Peng, Bo [Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Zhu, Xinli [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China

    2018-02-05

    Hydrodeoxygenation of guaiacol, a phenolic compound derived from lignin fraction of biomass, over a Pt/HBeta catalyst at 350 °C and atmospheric pressure produces benzene, toluene, xylenes, and C9+ aromatics with yield of 42%, 29%, 12%, and 5%, respectively. Reaction pathways for conversion of two functional groups (hydroxyl and methoxyl) over the bifunctional catalyst were studied. Both guaiacol and intermediate products (catechol and cyclopentanone) were fed onto zeolite HBeta and Pt/SiO2 to identify the individual role of acid site and metal site. Acid sites (mainly Brønsted acid site, BAS) catalyze transalkylation and dehydroxylation reactions in sequence, producing phenol, cresols and xylenols as the major products at high conversion. Pt sites catalyze demethylation reaction resulting in catechol as the primary product, which can either be deoxygenated to phenol followed by phenol to benzene, or decarbonylated to cyclopentanone and further to butane. The close proximity of Pt and BAS in bifunctional Pt/HBeta enables both transalkylation and deoxygenation reactions with inhibited demethylation and decarbonylation reactions, producing aromatics as major final products with a total yield > 85%. Both activity and stability of bifunctional Pt/HBeta during hydrodeoxygenation of guaiacol is improved compared to HBeta and Pt/SiO2. The addition of water to the feed further improves the activity and stability via hydrolysis of O-CH3 bond of guaiacol on BAS and removing coke around Pt.

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

    Science.gov (United States)

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

    2011-09-08

    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.

  5. Synthesis and Characterization of Tin (IV Tungstate Nanoparticles – A Solid Acid Catalyst

    Directory of Open Access Journals (Sweden)

    Manoj Sadanandan

    2012-12-01

    Full Text Available Tin (IV tungstate, a tetravalent metal acid salt was synthesized in the nanoform by chemical coprecipitation method using EDTA as capping agent. The material was found to be stable in mineral acids, bases and organic solvents except  in HF and aquaregia. The material was characterized using EDS, TG/DTA, FTIR, XRD, SEM, HRTEM and BET surface area measurement. The molecular formula of the compound is 2SnO2 3WO3.5H2O determined from elemental analysis using TG/DTA. Surface morphology and particle size were obtained using SEM and HRTEM. The surface area was found to be 205-225m2/g. The Na+ exchange capacity found to be 3.8 meq/g, indicates the presence of surface hydroxyl group and hence the presence of Bronsted acid sites. The catalytic activity of the material was tested by using esterification and oxidation as model reactions. For the esterification of different alcohols, the percentage yield was found to be high for n-alcohol compared to isomeric alcohols. Oxidation of benzyl alcohol gives benzaldehyde and benzoic acid as the only products. Copyright © 2012 by BCREC UNDIP. All rights reservedReceived: 12nd June 2012, Revised: 23rd July 2012, Accepted: 29th July 2012[How to Cite: S. Manoj, R. Beena, (2012. Synthesis and Characterization of tin(IV Tungstate Nanoparticles – A Solid Acid Catalyst. Bulletin of Chemical Reaction Engineering & Catalysis, 7 (2: 105-111. doi:10.9767/bcrec.7.2.3622.105-111] [How to Link / DOI: http://dx.doi.org/10.9767/bcrec.7.2.3622.105-111 ] | View in 

  6. Bronsted acidity of H-MCM-22 as probed by variable-temperature infrared spectroscopy of adsorbed CO and N-2

    Czech Academy of Sciences Publication Activity Database

    Delgado, M. R.; Bulánek, R.; Eliášová, Pavla; Arean, C. O.

    2014-01-01

    Roč. 227, MAY 2014 (2014), s. 45-49 ISSN 0920-5861 R&D Projects: GA ČR GBP106/12/G015 Institutional support: RVO:61388955 Keywords : adsorption * hydrogen bonding * IR probe molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.893, year: 2014

  7. Measuring the Bronsted acid strength of zeolites - does it correlate with the O-H frequency shift probed by a weak base?

    Czech Academy of Sciences Publication Activity Database

    Arean, C. O.; Delgado, M. R.; Nachtigall, P.; Thang, H. V.; Rubeš, M.; Bulánek, R.; Eliášová, Pavla

    2014-01-01

    Roč. 16, č. 21 (2014), s. 10129-10141 ISSN 1463-9076 R&D Projects: GA ČR GBP106/12/G015 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388955 Keywords : zeolites * catalysis * H-MSM+22 zeolites Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.493, year: 2014

  8. Signaling-sensitive amino acids surround the allosteric ligand binding site of the thyrotropin receptor.

    Science.gov (United States)

    Kleinau, Gunnar; Haas, Ann-Karin; Neumann, Susanne; Worth, Catherine L; Hoyer, Inna; Furkert, Jens; Rutz, Claudia; Gershengorn, Marvin C; Schülein, Ralf; Krause, Gerd

    2010-07-01

    The thyrotropin receptor [thyroid-stimulating hormone receptor (TSHR)], a G-protein-coupled receptor (GPCR), is endogenously activated by thyrotropin, which binds to the extracellular region of the receptor. We previously identified a low-molecular-weight (LMW) agonist of the TSHR and predicted its allosteric binding pocket within the receptor's transmembrane domain. Because binding of the LMW agonist probably disrupts interactions or leads to formation of new interactions among amino acid residues surrounding the pocket, we tested whether mutation of residues at these positions would lead to constitutive signaling activity. Guided by molecular modeling, we performed site-directed mutagenesis of 24 amino acids in this spatial region, followed by functional characterization of the mutant receptors in terms of expression and signaling, measured as cAMP accumulation. We found that mutations V421I, Y466A, T501A, L587V, M637C, M637W, S641A, Y643F, L645V, and Y667A located in several helices exhibit constitutive activity. Of note is mutation M637W at position 6.48 in transmembrane helix 6, which has a significant effect on the interaction of the receptor with the LMW agonist. In summary, we found that a high proportion of residues in several helices surrounding the allosteric binding site of LMW ligands in the TSHR when mutated lead to constitutively active receptors. Our findings of signaling-sensitive residues in this region of the transmembrane bundle may be of general importance as this domain appears to be evolutionarily retained among GPCRs.

  9. Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis.

    Directory of Open Access Journals (Sweden)

    Lu-Lu Zheng

    Full Text Available Pyrrolidone carboxylic acid (PCA is formed during a common post-translational modification (PTM of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR and incremental feature selection (IFS. We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations.

  10. A decade of monitoring at Swiss Long-Term Forest Ecosystem Research (LWF) sites: can we observe trends in atmospheric acid deposition and in soil solution acidity?

    Science.gov (United States)

    Pannatier, Elisabeth Graf; Thimonier, Anne; Schmitt, Maria; Walthert, Lorenz; Waldner, Peter

    2011-03-01

    Trends in atmospheric acid deposition and in soil solution acidity from 1995 or later until 2007 were investigated at several forest sites throughout Switzerland to assess the effects of air pollution abatements on deposition and the response of the soil solution chemistry. Deposition of the major elements was estimated from throughfall and bulk deposition measurements at nine sites of the Swiss Long-Term Forest Ecosystem Research network (LWF) since 1995 or later. Soil solution was measured at seven plots at four soil depths since 1998 or later. Trends in the molar ratio of base cations to aluminum (BC/Al) in soil solutions and in concentrations and fluxes of inorganic N (NO(3)-N + NH(4)-N), sulfate (SO(4)-S), and base cations (BC) were used to detect changes in soil solution chemistry. Acid deposition significantly decreased at three out of the nine study sites due to a decrease in total N deposition. Total SO(4)-S deposition decreased at the nine sites, but due to the relatively low amount of SO(4)-S load compared to N deposition, it did not contribute to decrease acid deposition significantly. No trend in total BC deposition was detected. In the soil solution, no trend in concentrations and fluxes of BC, SO(4)-S, and inorganic N were found at most soil depths at five out of the seven sites. This suggests that the soil solution reacted very little to the changes in atmospheric deposition. A stronger reduction in base cations compared to aluminum was detected at two sites, which might indicate that acidification of the soil solution was proceeding faster at these sites.

  11. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

    Directory of Open Access Journals (Sweden)

    Li Karen

    2008-12-01

    Full Text Available Abstract Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT or Whelan and Goldman (WAG models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination (e.g JTT + F. Variation in the evolutionary process between sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ distribution. However, sites in proteins also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. Results We analyzed 21 large protein alignments with two statistical tests designed to detect deviation of site-specific amino acid distributions from data simulated under the standard empirical substitution model: JTT+ F + Γ. We found that the number of states at a given site is, on average, smaller and the frequencies of these states are less uniform than expected based on a JTT + F + Γ substitution model. With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment. Principal components analyses indicate the existence of at least four major site-specific frequency classes in these 21 protein alignments. Using a mixture model with these four separate classes of site-specific state frequencies plus a fifth class of global frequencies (the JTT + cF + Γ model, significant improvements in model fit for real data sets can be achieved. This simple mixture model also reduces the long

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

    Science.gov (United States)

    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.

  13. Site and extent of amino acid digestion in dairy cattle fed with corn and its byproducts

    Directory of Open Access Journals (Sweden)

    Reginaldo Nassar Ferreira

    2015-02-01

    Full Text Available The study was conducted to evaluated the site and extent of dry matter (DM, crude protein (CP, methionine (Met, lysine (Lys, and threonine (Thr digestion of corn and byproducts obtained from corn germ mixed with different amounts of extruded or non-extruded ether extract (EE in dairy cattle. Treatments consisted in eight types of feed and two processing in a 4 × 2 factorial design. There were four feeds: corn grain cracked (Corn, corn germ meal with 1% EE (CG1, corn germ meal with 7% EE (CG7, and corn germ meal with 10% EE (CG10. The feeds were processed in one of two ways: extruded (Ex and not extruded. In situ techniques were used to determine DM, CP, Met, Lys, and Thr partial and total tract digestion. A basic diet was compounded of corn germ meal, soybean meal and coastcross hay in a 70:30 roughage to concentrate ratio. There was no interaction (P>0.05 between feeds and processing method. Extrusion improved (P0.05 for corn and corn germ meal mixed with 7 and 10% EE, regardless of EE processing method. The CP total tract digestibility of corn germ meal with 1% nonextruded EE was 16.62% higher (P<0.05 than that of the extruded form. The best total CP digestibility was obtained for corn germ meal with 7% EE, independently of the processing method. The effects of EE processing method on partial and total digestibility differed between amino acid. Corn and corn byproduct extrusion may improve dry matter digestibility, but do not necessarily influence crude protein digestion. Ruminal and intestinal digestibility of Met, Lys, and Thr depends on both feed type and processing method. Therefore, amino acid availability should be considered individually.

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

    Science.gov (United States)

    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.

  15. Modulation of salivation and heartburn in response to the site of acid infusion in the human oesophagus.

    Science.gov (United States)

    Dutta, S K; Agrawal, K; Mahmoud, M A

    2010-09-01

    The pathogenesis of gastro-oesophageal reflux disease includes increased acid reflux, reduced salivation and impaired peristalsis. This may depend upon the height of acid wave and magnitude of oesophageal mucosal exposure. Interestingly, the effect of site of acid infusion upon salivary secretion and heartburn has not been examined in any detail. To examine whether acid infusion in the upper oesophagus may cause increased salivation and heartburn as compared with acid infusion in the lower oesophagus. Twelve healthy male subjects (mean age 30) received infusions of HCl, citric acid and acetic acid at 10 and 20 cm above the lower oesophageal sphincter (LES) for fixed time periods. Parotid saliva collected periodically and heartburn severity scored using standardized scale. Standard statistical methods (paired t-tests, analysis of variance) were used to determine the significance of results. Acid infusion in the upper oesophagus increased parotid flow rate as compared with that in the lower oesophagus (P heartburn score at 20 cm as well as 10 cm above LES (P heartburn in response to acid infusion in the upper vs. lower part of the oesophagus. 2010 Blackwell Publishing Ltd.

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

    International Nuclear Information System (INIS)

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

    1985-01-01

    125 I-Lysergic acid diethylamide ( 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. 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 125 I-LSD binding site appears to represent a new type of serotonergic site which is located on non-neuronal cells in this tissue

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-12-31

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

  18. Food deprivation modulates gamma-aminobutyric acid receptors and peripheral benzodiazepine binding sites in rats.

    Science.gov (United States)

    Weizman, A; Bidder, M; Fares, F; Gavish, M

    1990-12-03

    The effect of 5 days of food deprivation followed by 5 days of refeeding on gamma-aminobutyric acid (GABA) receptors, central benzodiazepine receptors (CBR), and peripheral benzodiazepine binding sites (PBzS) was studied in female Sprague-Dawley rats. Starvation induced a decrease in the density of PBzS in peripheral organs: adrenal (35%; P less than 0.001), kidney (33%; P less than 0.01), and heart (34%; P less than 0.001). Restoration of [3H]PK 11195 binding to normal values was observed in all three organs after 5 days of refeeding. The density of PBzS in the ovary, pituitary, and hypothalamus was not affected by starvation. Food deprivation resulted in a 35% decrease in cerebellar GABA receptors (P less than 0.01), while CBR in the hypothalamus and cerebral cortex remained unaltered. The changes in PBzS observed in the heart and kidney may be related to the long-term metabolic stress associated with starvation and to the functional changes occurring in these organs. The down-regulation of the adrenal PBzS is attributable to the suppressive effect of hypercortisolemia on pituitary ACTH release. The reduction in cerebellar GABA receptors may be an adaptive response to food deprivation stress and may be relevant to the proaggressive effect of hunger.

  19. Enzyme active site mimics based on TriAzaCyclophane (TAC)-scaffolded peptides and amino acid residues

    NARCIS (Netherlands)

    Albada, H.B.

    2009-01-01

    This thesis describes the scope and limitations of the application of TriAzaCyclophane (TAC)-scaffolded peptides or amino acid residues as enzyme active site mimics, as ligands in asymmetric catalysis and as hydrolysis catalysts attached to vancomycin. For the mimicry of functional group enzymes, of

  20. Dehydroisomerization of n-butane over Pt-ZSMMMm5(I): effect of the metal loading and acid site concentration

    NARCIS (Netherlands)

    Pirngruber, G.D.; Seshan, Kulathuiyer; Lercher, J.A.

    1999-01-01

    The dehydroisomerization of n-butane to isobutene over Pt–ZSM5 catalysts with a high Si/Al ratio was studied. The catalytic activity increases with increasing metal loading. Butenes formed via dehydrogenation over the metallic particles are converted to isobutene over the Brønsted acid sites. The

  1. Triazacyclophane (TAC)-scaffolded histidine and aspartic acid residues as mimics of non-heme metalloenzyme active sites

    NARCIS (Netherlands)

    Albada, H.B.; Soulimani, F.; Jacobs, H.J.F.; Versluis, C.; Weckhuysen, B.M.; Liskamp, R.M.J.

    2012-01-01

    We describe the synthesis and coordination behaviour to copper(II) of two close structural triazacyclophane-based mimics of two often encountered aspartic acid and histidine containing metalloenzyme active sites. Coordination of these mimics to copper(I) and their reaction with molecular oxygen

  2. Dynamic HypA zinc site is essential for acid viability and proper urease maturation in Helicobacter pylori.

    Science.gov (United States)

    Johnson, Ryan C; Hu, Heidi Q; Merrell, D Scott; Maroney, Michael J

    2015-04-01

    Helicobacter pylori requires urease activity in order to survive in the acid environment of the human stomach. Urease is regulated in part by nickelation, a process that requires the HypA protein, which is a putative nickel metallochaperone that is generally associated with hydrogenase maturation. However, in H. pylori, HypA plays a dual role. In addition to an N-terminal nickel binding site, HypA proteins also contain a structural zinc site that is coordinated by two rigorously conserved CXXC sequences, which in H. pylori are flanked by His residues. These structural Zn sites are known to be dynamic, converting from Zn(Cys)4 centers at pH 7.2 to Zn(Cys)2(His)2 centers at pH 6.3 in the presence of Ni(ii) ions. In this study, mutant strains of H. pylori that express zinc site variants of the HypA protein are used to show that the structural changes in the zinc site are important for the acid viability of the bacterium, and that a reduction in acid viability in these variants can be traced in large measure to deficient urease activity. This in turn leads to a model that connects the Zn(Cys)4 coordination to urease maturation.

  3. Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites

    Directory of Open Access Journals (Sweden)

    Sato Yukuto

    2007-10-01

    Full Text Available Abstract Background The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization. Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (Pgi genes. Results Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate Pgi genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule. Conclusion This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.

  4. Gamma-aminobutyric acid-modulated benzodiazepine binding sites in bacteria

    International Nuclear Information System (INIS)

    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 [ 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 [ 3 H]diazepam binding are those that are active in displacing [ 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

  5. Screening and assessment of solidification/stabilization amendments suitable for soils of lead-acid battery contaminated site.

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Site-Directed Spin-Labeling of Nucleic Acids by Click Chemistry. Detection of Abasic Sites in Duplex DNA by EPR Spectroscopy

    DEFF Research Database (Denmark)

    Sigurdsson, Snorri; Vogel, Stefan; Shelke, Sandip

    2010-01-01

    and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair...... label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids...

  7. iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.

    Directory of Open Access Journals (Sweden)

    Yan Xu

    Full Text Available Posttranslational modifications (PTMs of proteins are responsible for sensing and transducing signals to regulate various cellular functions and signaling events. S-nitrosylation (SNO is one of the most important and universal PTMs. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for timely identifying the exact SNO sites in proteins because this kind of information is very useful for both basic research and drug development. Here, a new predictor, called iSNO-PseAAC, was developed for identifying the SNO sites in proteins by incorporating the position-specific amino acid propensity (PSAAP into the general form of pseudo amino acid composition (PseAAC. The predictor was implemented using the conditional random field (CRF algorithm. As a demonstration, a benchmark dataset was constructed that contains 731 SNO sites and 810 non-SNO sites. To reduce the homology bias, none of these sites were derived from the proteins that had [Formula: see text] pairwise sequence identity to any other. It was observed that the overall cross-validation success rate achieved by iSNO-PseAAC in identifying nitrosylated proteins on an independent dataset was over 90%, indicating that the new predictor is quite promising. Furthermore, a user-friendly web-server for iSNO-PseAAC was established at http://app.aporc.org/iSNO-PseAAC/, by which users can easily obtain the desired results without the need to follow the mathematical equations involved during the process of developing the prediction method. It is anticipated that iSNO-PseAAC may become a useful high throughput tool for identifying the SNO sites, or at the very least play a complementary role to the existing methods in this area.

  8. Defining proximity relationships in the tertiary structure of the dopamine transporter. Identification of a conserved glutamic acid as a third coordinate in the endogenous Zn(2+)-binding site

    DEFF Research Database (Denmark)

    Løland, Claus Juul; Norregaard, L; Gether, U

    1999-01-01

    , high affinity Zn(2+)-binding site. To achieve further insight into the tertiary organization of hDAT, we set out to identify additional residues involved in Zn(2+) binding and subsequently to engineer artificial Zn(2+)-binding sites. Ten aspartic acids and glutamic acids, predicted...

  9. New insights into Cu/SSZ-13 SCR catalyst acidity. Part I: Nature of acidic sites probed by NH 3 titration

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Jinyong; Gao, Feng; Kamasamudram, Krishna; Currier, Neal; Peden, Charles H. F.; Yezerets, Aleksey

    2017-04-01

    In this work we investigated an unusual acidity feature of a Cu/SSZ-13 catalyst used in selective catalytic reduction of NOx with NH3 (NH3-SCR). In particular, this catalyst showed two distinct NH3 desorption peaks in NH3-TPD measurements, in contrast to single, unresolved desorption peaks observed for other Cu-exchanged zeolites conventionally used in the SCR studies, including its isostructural but chemically different analogue Cu/SAPO-34. We further observed that the intensities of the two TPD peaks, which represented the amount of stored NH3, changed in opposite directions in response to progressive mild hydrothermal aging, while the total storage capacity was preserved. We proposed an explanation for this remarkable behavior, by using model reference samples and additional characterization techniques. At least three NH3 storage sites were identified: two distinct populations of Cu sites responsible for low-temperature NH3 storage, and Brønsted acid sites responsible for high-temperature NH3 storage. Contrary to the commonly accepted mechanism that Brønsted acid site loss during hydrothermal aging is driven by dealumination, we concluded that the decline in the number of Brønsted acid sites upon mild hydrothermal aging for Cu/SSZ-13 was not due to dealumination, but rather transformation of Cu sites, i.e., gradual conversion of ZCuOH (Cu2+ singly coordinated with Zeolite) to Z2Cu (Cu2+ doubly coordinated with Zeolite). This transformation was responsible for the increased low-temperature desorption peak in NH3-TPD since each ZCuOH adsorbed ~1 NH3 molecule while each Z2Cu adsorbed ~2 NH3 molecules under the conditions used here. These findings were used in Part II of this series of studies to develop a method for quantifying hydrothermal ageing of industrial Cu/SSZ-13 SCR catalysts. Authors would like to thank Randall Jines for his help with collecting the reactor data, Nancy W. Washton for measuring the NMR data and Tamas Varga for in-situ XRD measurements

  10. Assessment of acid mine drainage remediation schemes on ground water flow regimes at a reclaimed mine site

    International Nuclear Information System (INIS)

    Gabr, M.A.; Bowders, J.J.

    1994-01-01

    Ground water modeling and a field monitoring program were conducted for a 35-acre reclaimed surface mine site that continues to produce acid mine drainage (AMD). The modeling effort was focused on predicting the effectiveness of various remedial measures implemented at the site for the abatement of AMD on predicting the effectiveness of various remedial measures implemented at the site for the abatement of AMD production. The field work included surface surveys and monitoring of ground water levels with time, seepage areas, and sedimentation ponds located on the site. The surveys provided the physical and topographic characteristics of the site. Pump tests conducted at the site provided general hydraulic conductivities (k) for two major areas of the site; undisturbed area (k ≅ 2.9 x 10 -5 ft/s) and disturbed area (k ≅ 3.3 x 10 -4 ft/s to 2.0 x 10 -3 ft/s). The monitored ground water data indicated rapid change in ground water levels during recharge events. Such behavior is indicative of flow regime that is dominated by fracture flow. Modeling of an approximately 700 ft by 1,500 ft area of the site was achieved using the US GS code MODFLOW, and ground water field measurements were used to calibrate the model. A hydraulic conductivity of about 1.15 x 10 -3 ft/s was estimated for the undisturbed area and 1.15 x 10 -2 ft/s for the reclaimed area. Remedial measures for diverting the ground water away from the areas of spoil included the use of a subsurface seepage cutoff wall and discrete sealing techniques. Modeling results indicated that the most effective remedial technique for this site is the use of a subsurface seepage cutoff wall installed at the interface (highwall) between the disturbed and undisturbed zones. Using this scheme caused a dewatering effect in the reclaimed area and therefore reduction in the volume of the AMD generated at the site

  11. Allosteric ligands and their binding sites define γ-aminobutyric acid (GABA) type A receptor subtypes.

    Science.gov (United States)

    Olsen, Richard W

    2015-01-01

    GABAA receptors (GABA(A)Rs) mediate rapid inhibitory transmission in the brain. GABA(A)Rs are ligand-gated chloride ion channel proteins and exist in about a dozen or more heteropentameric subtypes exhibiting variable age and brain regional localization and thus participation in differing brain functions and diseases. GABA(A)Rs are also subject to modulation by several chemotypes of allosteric ligands that help define structure and function, including subtype definition. The channel blocker picrotoxin identified a noncompetitive channel blocker site in GABA(A)Rs. This ligand site is located in the transmembrane channel pore, whereas the GABA agonist site is in the extracellular domain at subunit interfaces, a site useful for low energy coupled conformational changes of the functional channel domain. Two classes of pharmacologically important allosteric modulatory ligand binding sites reside in the extracellular domain at modified agonist sites at other subunit interfaces: the benzodiazepine site and the high-affinity, relevant to intoxication, ethanol site. The benzodiazepine site is specific for certain GABA(A)R subtypes, mainly synaptic, while the ethanol site is found at a modified benzodiazepine site on different, extrasynaptic, subtypes. In the transmembrane domain are allosteric modulatory ligand sites for diverse chemotypes of general anesthetics: the volatile and intravenous agents, barbiturates, etomidate, propofol, long-chain alcohols, and neurosteroids. The last are endogenous positive allosteric modulators. X-ray crystal structures of prokaryotic and invertebrate pentameric ligand-gated ion channels, and the mammalian GABA(A)R protein, allow homology modeling of GABA(A)R subtypes with the various ligand sites located to suggest the structure and function of these proteins and their pharmacological modulation. © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Alfonta, Lital [San Diego, CA; Schultz, Peter G [La Jolla, CA; Zhang, Zhiwen [San Diego, CA

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2017-10-10

    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.

  14. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

    Science.gov (United States)

    Tkavc, Rok; Matrosova, Vera Y; Grichenko, Olga E; Gostinčar, Cene; Volpe, Robert P; Klimenkova, Polina; Gaidamakova, Elena K; Zhou, Carol E; Stewart, Benjamin J; Lyman, Mathew G; Malfatti, Stephanie A; Rubinfeld, Bonnee; Courtot, Melanie; Singh, Jatinder; Dalgard, Clifton L; Hamilton, Theron; Frey, Kenneth G; Gunde-Cimerman, Nina; Dugan, Lawrence; Daly, Michael J

    2017-01-01

    Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans . However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

  15. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149

    Directory of Open Access Journals (Sweden)

    Rok Tkavc

    2018-01-01

    Full Text Available Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute, heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

  16. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

    Science.gov (United States)

    Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

    2018-02-06

    A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

  17. Conceptual Model of Uranium in the Vadose Zone for Acidic and Alkaline Wastes Discharged at the Hanford Site Central Plateau

    Energy Technology Data Exchange (ETDEWEB)

    Truex, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Szecsody, James E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Qafoku, Nikolla [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Serne, R. Jeffrey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    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.

  18. Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

    DEFF Research Database (Denmark)

    Yang, Ziheng; Wong, Wendy Shuk Wan; Nielsen, Rasmus

    2005-01-01

    , with > 1 indicating positive selection. Statistical distributions are used to model the variation in among sites, allowing a subset of sites to have > 1 while the rest of the sequence may be under purifying selection with ... probabilities that a site comes from the site class with > 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and ratios for the site classes. In small data sets lacking...... information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated...

  19. Radiosynthesis and Evaluation of [(11)C]3-Hydroxycyclopent-1-enecarboxylic Acid as Potential PET Ligand for the High-Affinity γ-Hydroxybutyric Acid Binding Sites

    DEFF Research Database (Denmark)

    Jensen, Claus H; Hansen, Hanne D; Bay, Tina

    2017-01-01

    understanding of this population of binding sites. With its high specific affinity and monocarboxylate transporter (MCT1) mediated transport across the blood-brain barrier in pharmacological doses, 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA) seems like a suitable PET radiotracer candidate. Here, we report...... autoradiography on sections of pig brain was performed using [(3)H]HOCPCA. In vivo evaluation of [(11)C]HOCPCA showed no brain uptake, possibly due to a limited uptake of HOCPCA by the MCT1 transporter at tracer doses of [(11)C]HOCPCA....

  20. Phenylacetic acids and the structurally related non-steroidal anti-inflammatory drug diclofenac bind to specific gamma-hydroxybutyric acid sites in rat brain

    DEFF Research Database (Denmark)

    Wellendorph, Petrine; Høg, Signe; Skonberg, Christian

    2009-01-01

    with a twofold higher affinity than GHB. Measuring the affinities of structurally related NSAIDs for the [(3)H]NCS-382 site identified diclofenac, a clinically relevant NSAID (Voltaren, Diclon) of the phenylacetic acid (PAA) type, as a GHB ligand (K(i) value of 5.1 microM). Other non-NSAID PAAs also exhibited...... affinities similar to GHB. Our data raise the interesting possibility that the widely used over-the-counter drug compound, diclofenac, might affect GHB binding at relevant clinical dosages. Furthermore, the identification of PAAs as GHB ligands supplies new information about the structural preferences...

  1. Salicylic Acid and Jasmonic Acid Pathways are Activated in Spatially Different Domains Around the Infection Site During Effector-Triggered Immunity in Arabidopsis thaliana.

    Science.gov (United States)

    Betsuyaku, Shigeyuki; Katou, Shinpei; Takebayashi, Yumiko; Sakakibara, Hitoshi; Nomura, Nobuhiko; Fukuda, Hiroo

    2018-01-01

    The innate immune response is, in the first place, elicited at the site of infection. Thus, the host response can be different among the infected cells and the cells surrounding them. Effector-triggered immunity (ETI), a form of innate immunity in plants, is triggered by specific recognition between pathogen effectors and their corresponding plant cytosolic immune receptors, resulting in rapid localized cell death known as hypersensitive response (HR). HR cell death is usually limited to a few cells at the infection site, and is surrounded by a few layers of cells massively expressing defense genes such as Pathogenesis-Related Gene 1 (PR1). This virtually concentric pattern of the cellular responses in ETI is proposed to be regulated by a concentration gradient of salicylic acid (SA), a phytohormone accumulated around the infection site. Recent studies demonstrated that jasmonic acid (JA), another phytohormone known to be mutually antagonistic to SA in many cases, is also accumulated in and required for ETI, suggesting that ETI is a unique case. However, the molecular basis for this uniqueness remained largely to be solved. Here, we found that, using intravital time-lapse imaging, the JA signaling pathway is activated in the cells surrounding the central SA-active cells around the infection sites in Arabidopsis thaliana. This distinct spatial organization explains how these two phythormone pathways in a mutually antagonistic relationship can be activated simultaneously during ETI. Our results re-emphasize that the spatial consideration is a key strategy to gain mechanistic insights into the apparently complex signaling cross-talk in immunity. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

  2. CD44 Binding to Hyaluronic Acid Is Redox Regulated by a Labile Disulfide Bond in the Hyaluronic Acid Binding Site.

    Directory of Open Access Journals (Sweden)

    Helena Kellett-Clarke

    Full Text Available 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.

  3. Treatment of acidic mine waters from the Solbec-Cupra site using the Mediaflex{trademark} process; Traitement des eaux minieres acides du site Solbec-Cupra par le procede Mediaflex{sub TM}

    Energy Technology Data Exchange (ETDEWEB)

    Belanger, M -C; Ross, A; Shoiry, J [Valoraction Inc., Sherbrooke, PQ (Canada)

    1995-01-01

    Applications and development of Mediaflex{trademark} filter treatment technology are described. The method combines physical, chemical, and biological processes into a technology suitable for purification of sanitary landfill leachates, septic tank sludge, and acidic mine waters. More than a dozen of the patented filters are in use. The treatment can reach 99.9% removal of heavy metals and phenolic compounds present in waste water. Since installation of the Mediaflex{sub TM} filter at the Cambior Solbec-Cupra mining site more than 50,000 cubic metres of acidic mine waste waters (pH 5.5) have been treated. After Mediaflex{sub TM} filtration, the pH is approximately 8.0, with the heavy metal content reduced substantially. 3 refs., 4 figs., 3 tabs.

  4. An active site mutant of Escherichia coli cyclopropane fatty acid synthase forms new non-natural fatty acids providing insights on the mechanism of the enzymatic reaction.

    Science.gov (United States)

    E, Guangqi; Drujon, Thierry; Correia, Isabelle; Ploux, Olivier; Guianvarc'h, Dominique

    2013-12-01

    We have produced and purified an active site mutant of the Escherichia coli cyclopropane fatty acid synthase (CFAS) by replacing the strictly conserved G236 within cyclopropane synthases, by a glutamate residue, which corresponds to E146 of the homologous mycolic acid methyltransferase, Hma, producing hydroxymethyl mycolic acids. The G236E CFAS mutant had less than 1% of the in vitro activity of the wild type enzyme. We expressed the G236E CFAS mutant in an E. coli (DE3) strain in which the chromosomal cfa gene had been deleted. After extraction of phospholipids and conversion into the corresponding fatty acid methyl esters (FAMEs), we observed the formation of cyclopropanated FAMEs suggesting that the mutant retained some of the normal activity in vivo. However, we also observed the formation of new C17 methyl-branched unsaturated FAMEs whose structures were determined using GC/MS and NMR analyses. The double bond was located at different positions 8, 9 or 10, and the methyl group at position 10 or 9. Thus, this new FAMEs are likely arising from a 16:1 acyl chain of a phospholipid that had been transformed by the G236E CFAS mutant in vivo. The reaction catalyzed by this G236E CFAS mutant thus starts by the methylation of the unsaturated acyl chain at position 10 or 9 yielding a carbocation at position 9 or 10 respectively. It follows then two competing steps, a normal cyclopropanation or hydride shift/elimination events giving different combinations of alkenes. This study not only provides further evidence that cyclopropane synthases (CSs) form a carbocationic intermediate but also opens the way to CSs engineering for the synthesis of non-natural fatty acids. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Md Mehedi Hasan

    Full Text Available 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/.

  6. Catalytic Pyrolysis of Chilean Oak: Influence of Brønsted Acid Sites of Chilean Natural Zeolite

    Directory of Open Access Journals (Sweden)

    Serguei Alejandro Martín

    2017-11-01

    Full Text Available This paper proposes the Chilean natural zeolite as catalyst on bio-oil upgrade processes. The aim of this study was to analyze chemical composition of bio-oil samples obtained from catalytic pyrolysis of Chilean native oak in order to increase bio-oil stability during storage. In order to identify chemical compounds before and after storage, biomass pyrolysis was carried out in a fixed bed reactor at 623 K and bio-oil samples were characterized by gas chromatography/mass spectrophotometry (GC/MS. A bio-oil fractionation method was successfully applied here. Results indicate that bio-oil viscosity decreases due to active sites on the zeolite framework. Active acids sites were associated with an increment of alcohols, aldehydes, and hydrocarbon content during storage. Higher composition on aldehydes and alcohols after storage could be attributed to the occurrence of carbonyl reduction reactions that promotes them. These reactions are influenced by zeolite surface characteristics and could be achieved via the direct contribution of Brønsted acid sites to Chilean natural zeolite.

  7. Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization.

    Science.gov (United States)

    Lemloh, Marie-Louise; Altintoprak, Klara; Wege, Christina; Weiss, Ingrid M; Rothenstein, Dirk

    2017-01-28

    Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO₂ mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.

  8. Metal-Free, Site-Selective Peptide Modification by Conversion of "Customizable" Units into β-Substituted Dehydroamino Acids.

    Science.gov (United States)

    Saavedra, Carlos J; Hernández, Dácil; Boto, Alicia

    2018-01-12

    Our site-selective modification of serine or threonine units in peptides allows the generation of β-substituted dehydroamino acids, which increase peptide resistance to hydrolysis and may improve their biological properties. Both the terminal and internal positions can be modified, and different customizable units can be activated separately. Remarkably, high Z selectivity is achieved, even at internal positions. The conversion involves a one-pot oxidative radical scission/phosphorylation process by using the low-toxicity (diacetoxyiodo)benzene/iodine system as the scission reagent. The resulting α-amino phosphonates undergo a Horner-Wadsworth-Emmons reaction to produce the dehydroamino acid derivatives (in a Z/E ratio of usually >98:2) under mild and metal-free conditions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    International Nuclear Information System (INIS)

    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) 2 (H4) 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 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

  10. Remediation of acid mine drainage at the friendship hill national historic site with a pulsed limestone bed process

    Science.gov (United States)

    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 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 process in treatment of acid impaired waters that were

  11. Remediation of acid mine drainage at the friendship hill national historic site with a pulsed limestone bed process

    Science.gov (United States)

    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 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 process in treatment of acid impaired waters that were previously not amenable to low cost limestone treatment.

  12. Impact of acid mine drainages on surficial waters of an abandoned mining site.

    Science.gov (United States)

    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.

  13. Implications for the formation of abasic sites following modification of polydeoxycytidylic acid by acrolein in vitro

    International Nuclear Information System (INIS)

    Smith, R.A.; Sysel, I.A.; Tibbels, T.S.; Cohen, S.M.

    1988-01-01

    Polydeoxycytidylic acid (poly dC) was incubated with excess acrolein. A Nensorb 20 nucleic acid purification cartridge was used to bind the polymeric material in the poly dC/acrolein reaction mixture. The non-polymeric material eluted from this column had a UV absorbance four times higher than that of the control. The flourescence spectrum of the eluted material did not correspond to that of unmodified cytosine. Separate aliquots of the reaction mixture were digested to deoxynucleotide 3 ' -monophosphates by incubation with micrococcal nuclease and spleen phosphodiesterase. The products were converted to 3 2P-labelled deoxynucleotide 3 ' ,5-biphosphates by incubation with T4 polynucleotide kinase and excess [γ- 3 2P]ATP. The ' -monophosphate was selectively removed by incubation with nuclease P1. Two dimensional thin-layer chromatography (TLC) on polyethyleneimine cellulose (PEI)-cellulose and detection of 3 2P-labeled deoxynucleotide 5 ' -monophosphates by autoradiography failed to provide evidence for the formation of an acrolein adduct of deoxycytidine 5'-monophosphate. When acrolein-modified deoxycytidine 5 ' -monophosphate, was detected. These data show that acrolein-modified deoxycytidine 3 ' -monophosphates are substrates for 3 2P labeling by T4 polynucleotide kinase and are stable under the assay conditions employed

  14. Dephosphorylation of microtubule-binding sites at the neurofilament-H tail domain by alkaline, acid, and protein phosphatases.

    Science.gov (United States)

    Hisanaga, S; Yasugawa, S; Yamakawa, T; Miyamoto, E; Ikebe, M; Uchiyama, M; Kishimoto, T

    1993-06-01

    The dephosphorylation-induced interaction of neurofilaments (NFs) with microtubules (MTs) was investigated by using several phosphatases. Escherichia coli alkaline and wheat germ acid phosphatases increased the electrophoretic mobility of NF-H and NF-M by dephosphorylation, and induced the binding of NF-H to MTs. The binding of NFs to MTs was observed only after the electrophoretic mobility of NF-H approached the exhaustively dephosphorylated level when alkaline phosphatase was used. The number of phosphate remaining when NF-H began to bind to MTs was estimated by measuring phosphate bound to NF-H. NF-H did not bind to MTs even when about 40 phosphates from the total of 51 had been removed by alkaline phosphatase. The removal of 6 further phosphates finally resulted in the association of NF-H with MTs. A similar finding, that the restricted phosphorylation sites in the NF-H tail domain, but not the total amount of phosphates, were important for binding to MTs, was also obtained with acid phosphatases. In contrast to alkaline and acid phosphatases, four classes of protein phosphatases (protein phosphatases 1, 2A, 2B, and 2C) were ineffective for shifting the electrophoretic mobility of NF proteins and for inducing the association of NFs to MTs.

  15. Concentrations of nitrous acid, nitric acid, nitrite and nitrate in the gas and aerosol phase at a site in the emission zone during ESCOMPTE 2001 experiment

    Science.gov (United States)

    Acker, K.; Möller, D.; Auel, R.; Wieprecht, W.; Kalaß, D.

    2005-03-01

    Ground-based measurements were performed at the "Expérience sur Site pour COntraindre les Modèles de Pollution atmosphérique et de Transport d`Emissions" (ESCOMPTE) field site E3 (Realtor) about 30 km north of the urban environment of Marseille and east of the industrial centre Berre pond to investigate the formation of nitrous and nitric acid and to detect the distribution of reactive N-species between the gas and particle phase during photochemical pollution events. A wet denuder sampling for gases followed by a steam jet collection for aerosols was both coupled to anion chromatographic analysis. The analytical system provided data continuously with 30-min time resolution between June 13 and July 13, 2001. Indications for heterogeneous formation of nitrous acid during nighttime and daytime on ground and aerosol surfaces were found, the average HNO 2/NO 2 ratio was 6%. Highest concentrations were observed during two episodes of strong pollution accumulation when sea breeze transported industrial, traffic and urban pollution land-inwards. After nocturnal heterogeneous formation (about 0.1 ppb v h -1 were estimated corresponding to increasing HNO 2/NO 2 ratios) and accumulation processes up to 1.2 ppb v HNO 2 were observed. Their photolysis produces up to 5-9×10 6 OH cm -3 s -1 and will contribute significantly to initiation of the daily photochemistry in the lowest part of the troposphere. For the key tropospheric species, HNO 3 daily peaks up to 4 ppb v were detected.

  16. Eight amino acids form the ATP recognition site of Na(+)/K(+)-ATPase

    Czech Academy of Sciences Publication Activity Database

    Kubala, Martin; Teisinger, Jan; Ettrich, Rüdiger; Hofbauerová, Kateřina; Kopecký ml., Vladimír; Baumruk, V.; Krumscheid, R.; Plášek, J.; Schoner, W.; Amler, Evžen

    2003-01-01

    Roč. 42, č. 21 (2003), s. 6446-6452 ISSN 0006-2960 R&D Projects: GA ČR GA204/01/0254; GA ČR GA204/01/1001; GA ČR GA309/02/1479 Grant - others:GA-(CZ) CZE00/033 Institutional research plan: CEZ:AV0Z5011922; CEZ:MSM 123100001; CEZ:MSM 113100001; CEZ:MSM 113200001 Keywords : sodium pump * ATP-binding site * TNP-ATP Subject RIV: BO - Biophysics Impact factor: 3.922, year: 2003

  17. Isolation and properties of the acid site-specific endonuclease from mature eggs of the sea urchin Strongylocentrotus intermedius

    International Nuclear Information System (INIS)

    Sibirtsev, Yu.T.; Konechnyi, A.A.; Rasskazov, V.A.

    1986-01-01

    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 ∼ 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

  18. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections.

    Directory of Open Access Journals (Sweden)

    Janire Mingo

    Full Text Available 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.

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

    Directory of Open Access Journals (Sweden)

    Yusuke Kato

    2015-04-01

    Full Text Available 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.

  20. Policy for metal leaching and acid rock drainage at mine sites in British Columbia

    International Nuclear Information System (INIS)

    1998-07-01

    One of the major environmental issues facing the provincial government of British Columbia is the prevention of environmental impacts from metal leaching and acid rock drainage (ML/ARD). The government's major challenge in regulating ML/ARD is to ensure that all mines are planned and operated in a manner that allows for effective problem detection and mitigation, and that the mines emphasize problem prevention at the outset. This paper reviews the legislated requirements regarding ML/ARD prevention and lists guiding principles for the regulation of ML/ARD in the province. Some of the measures to predict and to mitigate ML/ARD include underwater storage of problematic materials, engineered covers, blending of wastes and drainage collection and treatment. Requirements applicable to construction materials, backfill, geotechnical and hydrological considerations, and security of funds for ML/ARD measures are also discussed

  1. Hierarchical SAPO‐34 Architectures with Tailored Acid Sites using Sustainable Sugar Templates

    Science.gov (United States)

    Miletto, Ivana; Ivaldi, Chiara; Paul, Geo; Chapman, Stephanie; Marchese, Leonardo; Raja, Robert

    2018-01-01

    Abstract In a distinct, bottom‐up synthetic methodology, monosaccharides (fructose and glucose) and disaccharides (sucrose) have been used as mesoporogens to template hierarchical SAPO‐34 catalysts. Detailed materials characterization, which includes solid‐state magic angle spinning NMR and probe‐based FTIR, reveals that, although the mesopore dimensions are modified by the identity of the sugar template, the desirable acid characteristics of the microporous framework are retained. When the activity of the hierarchical SAPO‐34 catalysts was evaluated in the industrially relevant Beckmann rearrangement, under liquid‐phase conditions, the enhanced mass‐transport properties of sucrose‐templated hierarchical SAPO‐34 were found to deliver a superior yield of ϵ‐caprolactam. PMID:29686961

  2. Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1982-01-01

    The binding sites of ribosomal proteins L18 and L25 on 5S RNA from Escherichia coli were probed with ribonucleases A, T1, and T2 and a double helix specific cobra venom endonuclease. The results for the protein-RNA complexes, which were compared with those for the free RNA [Douthwaite, S...... stearothermophilus 5S RNA. Several protein-induced changes in the RNA structures were identified; some are possibly allosteric in nature. The two prokaryotic 5S RNAs were also incubated with total 50S subunit proteins from E. coli and B. stearothermophilus ribosomes. Homologous and heterologous reconstitution....... stearothermophilus 5S RNA, which may have been due to a third ribosomal protein L5....

  3. Direct conversion of bio-ethanol to isobutene on nanosized Zn(x)Zr(y)O(z) mixed oxides with balanced acid-base sites.

    Science.gov (United States)

    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.

  4. Fatty Acid-Mediated Inhibition of Metal Binding to the Multi-Metal Site on Serum Albumin: Implications for Cardiovascular Disease.

    Science.gov (United States)

    Blindauer, Claudia A; Khazaipoul, Siavash; Yu, Ruitao; Stewart, Alan J

    2016-01-01

    Human serum albumin (HSA) is the major protein in blood plasma and is responsible for circulatory transport of a range of small molecules including fatty acids, metal ions and drugs. We previously identified the major plasma Zn2+ transport site on HSA and revealed that fatty-acid binding (at a distinct site called the FA2 site) and Zn2+ binding are interdependent via an allosteric mechanism. Since binding affinities of long-chain fatty acids exceed those of plasma Zn2+, this means that under certain circumstances the binding of fatty acid molecules to HSA is likely to diminish HSA Zn2+-binding, and hence affects the control of circulatory and cellular Zn2+ dynamics. This relationship between circulatory fatty acid and Zn2+ dynamics is likely to have important physiological and pathological implications, especially since it has been recognised that Zn2+ acts as a signalling agent in many cell types. Fatty acid levels in the blood are dynamic, but most importantly, chronic elevation of plasma fatty acid levels is associated with some metabolic disorders and disease states - including myocardial infarction and other cardiovascular diseases. In this article, we briefly review the metal-binding properties of albumin and highlight the importance of their interplay with fatty acid binding. We also consider the impact of this dynamic link upon levels and speciation of plasma Zn2+, its effect upon cellular Zn2+ homeostasis and its relevance to cardiovascular and circulatory processes in health and disease.

  5. Mapping Substance P Binding Sites on the Neurokinin-1 Receptor Using Genetic Incorporation of a Photoreactive Amino Acid

    DEFF Research Database (Denmark)

    Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas

    2014-01-01

    that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce...... the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact...

  6. Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids.

    Science.gov (United States)

    Pokhrel, Nilisha; Origanti, Sofia; Davenport, Eric Parker; Gandhi, Disha; Kaniecki, Kyle; Mehl, Ryan A; Greene, Eric C; Dockendorff, Chris; Antony, Edwin

    2017-09-19

    An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Influence of porous texture and surface chemistry on the CO₂ adsorption capacity of porous carbons: acidic and basic site interactions.

    Science.gov (United States)

    Sánchez-Sánchez, Angela; Suárez-García, Fabián; Martínez-Alonso, Amelia; Tascón, Juan M D

    2014-12-10

    Doped porous carbons exhibiting highly developed porosity and rich surface chemistry have been prepared and subsequently applied to clarify the influence of both factors on carbon dioxide capture. Nanocasting was selected as synthetic route, in which a polyaramide precursor (3-aminobenzoic acid) was thermally polymerized inside the porosity of an SBA-15 template in the presence of different H3PO4 concentrations. The surface chemistry and the porous texture of the carbons could be easily modulated by varying the H3PO4 concentration and carbonization temperature. Porous texture was found to be the determinant factor on carbon dioxide adsorption at 0 °C, while surface chemistry played an important role at higher adsorption temperatures. We proved that nitrogen functionalities acted as basic sites and oxygen and phosphorus groups as acidic ones toward adsorption of CO2 molecules. Among the nitrogen functional groups, pyrrolic groups exhibited the highest influence, while the positive effect of pyridinic and quaternary functionalities was smaller. Finally, some of these N-doped carbons exhibit CO2 heats of adsorption higher than 42 kJ/mol, which make them excellent candidates for CO2 capture.

  8. A flexible metal-organic framework with a high density of sulfonic acid sites for proton conduction

    Science.gov (United States)

    Yang, Fan; Xu, Gang; Dou, Yibo; Wang, Bin; Zhang, Heng; Wu, Hui; Zhou, Wei; Li, Jian-Rong; Chen, Banglin

    2017-11-01

    The design of stable electrolyte materials with high proton conductivity for use in proton exchange membrane fuel cells remains a challenge. Most of the materials explored have good conductivity at high relative humidity (RH), but significantly decreased conductivity at reduced RH. Here we report a chemically stable and structurally flexible metal-organic framework (MOF), BUT-8(Cr)A, possessing a three-dimensional framework structure with one-dimensional channels, in which high-density sulfonic acid (-SO3H) sites arrange on channel surfaces for proton conduction. We propose that its flexible nature, together with its -SO3H sites, could allow BUT-8(Cr)A to self-adapt its framework under different humid environments to ensure smooth proton conduction pathways mediated by water molecules. Relative to other MOFs, BUT-8(Cr)A not only has a high proton conductivity of 1.27 × 10-1 S cm-1 at 100% RH and 80 °C but also maintains moderately high proton conductivity at a wide range of RH and temperature.

  9. Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site.

    Science.gov (United States)

    Fetherolf, Morgan M; Boyd, Stefanie D; Taylor, Alexander B; Kim, Hee Jong; Wohlschlegel, James A; Blackburn, Ninian J; Hart, P John; Winge, Dennis R; Winkler, Duane D

    2017-07-21

    Metallochaperones are a diverse family of trafficking molecules that provide metal ions to protein targets for use as cofactors. The copper chaperone for superoxide dismutase (Ccs1) activates immature copper-zinc superoxide dismutase (Sod1) by delivering copper and facilitating the oxidation of the Sod1 intramolecular disulfide bond. Here, we present structural, spectroscopic, and cell-based data supporting a novel copper-induced mechanism for Sod1 activation. Ccs1 binding exposes an electropositive cavity and proposed "entry site" for copper ion delivery on immature Sod1. Copper-mediated sulfenylation leads to a sulfenic acid intermediate that eventually resolves to form the Sod1 disulfide bond with concomitant release of copper into the Sod1 active site. Sod1 is the predominant disulfide bond-requiring enzyme in the cytoplasm, and this copper-induced mechanism of disulfide bond formation obviates the need for a thiol/disulfide oxidoreductase in that compartment. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Pharmacology of morphine and morphine-3-glucuronide at opioid, excitatory amino acid, GABA and glycine binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Bartlett, S.E.; Smith, M.T. (Department of Pharmacy, The University of Queensland (Australia)); Dood, P.R. (Clinical Research Centre, Royal Brisbane Hospital Foundation, Brisbane (Australia))

    1994-07-01

    Morphine in high doses and its major metabolite, morphine-3-glucuronide, cause CNS excitation following intrathecal and intracerebroventricular administration by an unknown mechanism. This study investigated whether morphine and morphine-3-glucuronide interact at major excitatory (glutamate), major inhibitory (GABA or glycine), or opioid binding sites. Homogenate binding assays were performed using specific radioligands. At opioid receptors, morphine-3-glucuronide and morphine caused an equipotent sodium shift, consistent with morphine-3-glucuronide behaving as an agonist. This suggests that morphine-3-glucuronide-mediated excitation is not caused by an interaction at opioid receptors. Morphine-3-glucuronide and morphine caused a weak inhibition of the binding of [sup 3]H-MK801 (non-competitive antagonist) and [sup 125]I-ifenprodil (polyamine site antagonist), but at unphysiologically high concentrations. This suggests that CNS excitation would not result from an interaction of morphine-3-glucuronide and high-dose morphine with these sites on the NMDA receptor. Morphine-3-glucuronide and morphine inhibited the binding of [sup 3]H-muscimol (GABA receptor agonist), [sup 3]H-diazepam and [sup 3]H-flunitraxepam (benzodiazepine agonists) binding very weakly, suggesting the excitatory effects of morphine-3-glucuronide and high-dose morphine are not elicited through GABA[sub A] receptors. Morphine-3-glucuronide and high-dose morphine did not prevent re-uptake of glutamate into presynaptic nerve terminals. In addition, morphine-3-glucuronide and morphine did not inhibit the binding of [sup 3]H-strychnine (glycine receptor antagonist) to synaptic membranes prepared from bovine spinal cord. It is concluded that excitation caused by high-dose morphine and morphine-3-glucuronide is not mediated by an interaction with postsynaptic amino acid receptors. (au) (30 refs.).

  11. Impact of ursodeoxycholic acid on a CCK1R cholesterol-binding site may contribute to its positive effects in digestive function.

    Science.gov (United States)

    Desai, Aditya J; Dong, Maoqing; Harikumar, Kaleeckal G; Miller, Laurence J

    2015-09-01

    Dysfunction of the type 1 cholecystokinin (CCK) receptor (CCK1R) as a result of increased gallbladder muscularis membrane cholesterol has been implicated in the pathogenesis of cholesterol gallstones. Administration of ursodeoxycholic acid, which is structurally related to cholesterol, has been shown to have beneficial effects on gallstone formation. Our aims were to explore the possible direct effects and mechanism of action of bile acids on CCK receptor function. We studied the effects of structurally related hydrophobic chenodeoxycholic acid and hydrophilic ursodeoxycholic acid in vitro on CCK receptor function in the setting of normal and elevated membrane cholesterol. We also examined their effects on a cholesterol-insensitive CCK1R mutant (Y140A) disrupting a key site of cholesterol action. The results show that, similar to the impact of cholesterol on CCK receptors, bile acid effects were limited to CCK1R, with no effects on CCK2R. Chenodeoxycholic acid had a negative impact on CCK1R function, while ursodeoxycholic acid had no effect on CCK1R function in normal membranes but was protective against the negative impact of elevated cholesterol on this receptor. The cholesterol-insensitive CCK1R mutant Y140A was resistant to effects of both bile acids. These data suggest that bile acids compete with the action of cholesterol on CCK1R, probably by interacting at the same site, although the conformational impact of each bile acid appears to be different, with ursodeoxycholic acid capable of correcting the abnormal conformation of CCK1R in a high-cholesterol environment. This mechanism may contribute to the beneficial effect of ursodeoxycholic acid in reducing cholesterol gallstone formation. Copyright © 2015 the American Physiological Society.

  12. Determination of the positions of aluminum atoms introduced into SSZ-35 and the catalytic properties of the generated Brønsted acid sites.

    Science.gov (United States)

    Miyaji, Akimitsu; Kimura, Nobuhiro; Shiga, Akinobu; Hayashi, Yoshihiro; Nishitoba, Toshiki; Motokura, Ken; Baba, Toshihide

    2017-03-01

    The positions of aluminum (Al) atoms in SSZ-35 together with the characteristics of the generated protons were investigated by 27 Al multiple quantum magic-angle spinning (MQ-MAS), 29 Si MAS, and 1 H MAS NMR data analyses accompanied by a variable temperature 1 H MAS NMR analysis. The origin of the acidic -OH groups (Brønsted acid sites) generated by introducing Al atoms into the T sites was investigated and the T sites introduced into the Al atoms were revealed. To further determine the catalytic properties of the acidic protons generated in SSZ-35, the influence of the concentration of the Al atoms on the catalytic activity and selectivity during the transformation of toluene was examined.

  13. TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues.

    Science.gov (United States)

    Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

    2014-01-01

    microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents all received data in table formats that are easy to analyse further. The predicted data finds utility in molecular and evolutionary biology studies. They find use in studying miRNA binding sites in animals and plants. TmiRUSite and TmiROSite scripts are available for free from authors upon request and at https: //sites.google.com/site/malaheenee/downloads for download.

  14. Tannic acid and chromic chloride-induced binding of protein to red cells: a preliminary study of possible binding sites and reaction mechanisms.

    Science.gov (United States)

    Hunt, A F; Reed, M I

    1990-07-01

    The binding mechanisms and binding sites involved in the tannic acid and chromic chloride-induced binding of protein to red cells were investigated using the binding of IgA paraprotein to red cells as model systems. Inhibition studies of these model systems using amino acid homopolymers and compounds (common as red cell membrane constituents) suggest that the mechanisms involved are similar to those proposed for the conversion of hide or skin collagen to leather, as in commercial tanning. These studies also suggest that tannic acid-induced binding of IgA paraprotein to red cells involves the amino acid residues of L-arginine, L-lysine, L-histidine, and L-proline analogous to tanning with phenolic plant extracts. The amino acid residues of L-aspartate, L-glutamate and L-asparagine are involved in a similar manner in chronic chloride-induced binding of protein to red cells.

  15. TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues

    OpenAIRE

    Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

    2014-01-01

    microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents ...

  16. Scanning mutagenesis of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex

    Directory of Open Access Journals (Sweden)

    Nagib eAhsan

    2012-07-01

    Full Text Available The mitochondrial pyruvate dehydrogenase complex is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform scanning mutagenesis of the residues flanking the site of phosphorylation. Consistent with the results from phylogenetic analysis of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.

  17. A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity.

    Directory of Open Access Journals (Sweden)

    Kate M Peters

    Full Text Available Structures of the multidrug-binding repressor protein QacR with monovalent and bivalent cationic drugs revealed that the carboxylate side-chains of E90 and E120 were proximal to the positively charged nitrogens of the ligands ethidium, malachite green and rhodamine 6G, and therefore may contribute to drug neutralization and binding affinity. Here, we report structural, biochemical and in vivo effects of substituting these glutamate residues. Unexpectedly, substitutions had little impact on ligand affinity or in vivo induction capabilities. Structures of QacR(E90Q and QacR(E120Q with ethidium or malachite green took similar global conformations that differed significantly from all previously described QacR-drug complexes but still prohibited binding to cognate DNA. Strikingly, the QacR(E90Q-rhodamine 6G complex revealed two mutually exclusive rhodamine 6G binding sites. Despite multiple structural changes, all drug binding was essentially isoenergetic. Thus, these data strongly suggest that rather than contributing significantly to ligand binding affinity, the role of acidic residues lining the QacR multidrug-binding pocket is primarily to attract and guide cationic drugs to the "best available" positions within the pocket that elicit QacR induction.

  18. Accelerated wound healing in mice by on-site production and delivery of CXCL12 by transformed lactic acid bacteria.

    Science.gov (United States)

    Vågesjö, Evelina; Öhnstedt, Emelie; Mortier, Anneleen; Lofton, Hava; Huss, Fredrik; Proost, Paul; Roos, Stefan; Phillipson, Mia

    2018-02-20

    Impaired wound closure is a growing medical problem associated with metabolic diseases and aging. Immune cells play important roles in wound healing by following instructions from the microenvironment. Here, we developed a technology to bioengineer the wound microenvironment and enhance healing abilities of the immune cells. This resulted in strongly accelerated wound healing and was achieved by transforming Lactobacilli with a plasmid encoding CXCL12. CXCL12-delivering bacteria administrated topically to wounds in mice efficiently enhanced wound closure by increasing proliferation of dermal cells and macrophages, and led to increased TGF-β expression in macrophages. Bacteria-produced lactic acid reduced the local pH, which inhibited the peptidase CD26 and consequently enhanced the availability of bioactive CXCL12. Importantly, treatment with CXCL12-delivering Lactobacilli also improved wound closure in mice with hyperglycemia or peripheral ischemia, conditions associated with chronic wounds, and in a human skin wound model. Further, initial safety studies demonstrated that the topically applied transformed bacteria exerted effects restricted to the wound, as neither bacteria nor the chemokine produced could be detected in systemic circulation. Development of drugs accelerating wound healing is limited by the proteolytic nature of wounds. Our technology overcomes this by on-site chemokine production and reduced degradation, which together ensure prolonged chemokine bioavailability that instructed local immune cells and enhanced wound healing. Copyright © 2018 the Author(s). Published by PNAS.

  19. Oxidative dehydration of glycerol to acrylic acid over vanadium-impregnated zeolite beta

    Energy Technology Data Exchange (ETDEWEB)

    Pestana, Carolina F.M.; Guerra, Antonio C.O.; Turci, Cassia C. [Universidade Federal do Rio de Janeiro, RJ (Brazil). Inst. de Quimica; Ferreira, Glaucio B. [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Inst. de Quimica; Mota, Claudio J.A., E-mail: cmota@iq.ufrj.br [INCT Energia e Ambiente, Universidade Federal do Rio de Janeiro, RJ (Brazil)

    2013-01-15

    The oxidative dehydration of glycerol to acrylic acid was studied over vanadium-impregnated zeolite Beta. Catalysts were prepared by wet impregnation of ammonium metavanadate over ammonium-exchanged zeolite Beta, followed by air calcination at 823 K. Impregnation reduced the specific surface area, but did not significantly affected the acidity (Bronsted and Lewis) of the zeolites. The catalytic evaluation was carried out in a fixed bed flow reactor using air as the carrier and injecting glycerol by means of a syringe pump. Acrolein was the main product, with acetaldehyde and hydroxy-acetone (acetol) being also formed. Acrylic acid was formed with approximately 25% selectivity at 548 K over the impregnated zeolites. The result can be explained by XPS (X-ray photoelectron spectroscopy) measurements, which indicated a good dispersion of the vanadium inside the pores. (author)

  20. Oxidative dehydration of glycerol to acrylic acid over vanadium-impregnated zeolite beta

    International Nuclear Information System (INIS)

    Pestana, Carolina F.M.; Guerra, Antonio C.O.; Turci, Cassia C.

    2013-01-01

    The oxidative dehydration of glycerol to acrylic acid was studied over vanadium-impregnated zeolite Beta. Catalysts were prepared by wet impregnation of ammonium metavanadate over ammonium-exchanged zeolite Beta, followed by air calcination at 823 K. Impregnation reduced the specific surface area, but did not significantly affected the acidity (Bronsted and Lewis) of the zeolites. The catalytic evaluation was carried out in a fixed bed flow reactor using air as the carrier and injecting glycerol by means of a syringe pump. Acrolein was the main product, with acetaldehyde and hydroxy-acetone (acetol) being also formed. Acrylic acid was formed with approximately 25% selectivity at 548 K over the impregnated zeolites. The result can be explained by XPS (X-ray photoelectron spectroscopy) measurements, which indicated a good dispersion of the vanadium inside the pores. (author)

  1. Ion binding by humic and fulvic acids: A computational procedure based on functional site heterogeneity and the physical chemistry of polyelectrolyte solutions

    International Nuclear Information System (INIS)

    Marinsky, J.A.; Reddy, M.M.; Ephraim, J.; Mathuthu, A.

    1988-04-01

    Ion binding equilibria for humic and fulvic acids are examined from the point of view of functional site heterogeneity and the physical chemistry of polyelectrolyte solutions. A detailed explanation of the potentiometric properties of synthetic polyelectrolytes and ion-exchange gels is presented first to provide the basis for a parallel consideration of the potentiometric properties exhibited by humic and fulvic acids. The treatment is then extended to account for functional site heterogeneity. Sample results are presented for analysis of the ion-binding reactions of a standard soil fulvic acid (Armadale Horizons Bh) with this approach to test its capability for anticipation of metal ion removal from solution. The ultimate refined model is shown to be adaptable, after appropriate consideration of the heterogeneity and polyelectrolyte factors, to programming already available for the consideration of ion binding by inorganics in natural waters. (orig.)

  2. Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis.

    Science.gov (United States)

    Lee, Hyunji; Park, Jiyoung; Jung, Chaewon; Han, Dongfei; Seo, Jiyoung; Ahn, Joong-Hoon; Chong, Youhoon; Hur, Hor-Gil

    2015-11-01

    The enzyme ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4 catalyzes the decarboxylation reaction of lignin monomers and phenolic compounds such as p-coumaric acid, caffeic acid, and ferulic acid into their corresponding 4-vinyl derivatives, that is, 4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol, respectively. Among various ferulic acid decarboxylase enzymes, we chose the FADase from Enterobacter sp. Px6-4, whose crystal structure is known, and produced mutants to enhance its catalytic activity by random and site-directed mutagenesis. After three rounds of sequential mutations, FADase(F95L/D112N/V151I) showed approximately 34-fold higher catalytic activity than wild-type for the production of 4-vinylguaiacol from ferulic acid. Docking analyses suggested that the increased activity of FADase(F95L/D112N/V151I) could be due to formation of compact active site compared with that of the wild-type FADase. Considering the amount of phenolic compounds such as lignin monomers in the biomass components, successfully bioengineered FADase(F95L/D112N/V151I) from Enterobacter sp. Px6-4 could provide an ecofriendly biocatalytic tool for producing diverse styrene derivatives from biomass.

  3. Design, Synthesis, and in Vitro Pharmacology of New Radiolabeled γ-Hydroxybutyric Acid Analogues Including Photolabile Analogues with Irreversible Binding to the High-Affinity γ-Hydroxybutyric Acid Binding Sites

    DEFF Research Database (Denmark)

    Sabbatini, Paola; Wellendorph, Petrine; Høg, Signe

    2010-01-01

    γ-Hydroxybutyric acid (GHB) is a psychotropic compound endogenous to the brain. Despite its potential physiological significance, the complete molecular mechanisms of action remain unexplained. To facilitate the isolation and identification of the high-affinity GHB binding site, we herein report ...

  4. Applications of site-specific labeling to study HAMLET, a tumoricidal complex of α-lactalbumin and oleic acid.

    Science.gov (United States)

    Mercer, Natalia; Ramakrishnan, Boopathy; Boeggeman, Elizabeth; Qasba, Pradman K

    2011-01-01

    Alpha-lactalbumin (α-LA) is a calcium-bound mammary gland-specific protein that is found in milk. This protein is a modulator of β1,4-galactosyltransferase enzyme, changing its acceptor specificity from N-acetyl-glucosamine to glucose, to produce lactose, milk's main carbohydrate. When calcium is removed from α-LA, it adopts a molten globule form, and this form, interestingly, when complexed with oleic acid (OA) acquires tumoricidal activity. Such a complex made from human α-LA (hLA) is known as HAMLET (Human A-lactalbumin Made Lethal to Tumor cells), and its tumoricidal activity has been well established. In the present work, we have used site-specific labeling, a technique previously developed in our laboratory, to label HAMLET with biotin, or a fluoroprobe for confocal microscopy studies. In addition to full length hLA, the α-domain of hLA (αD-hLA) alone is also included in the present study. We have engineered these proteins with a 17-amino acid C-terminal extension (hLA-ext and αD-hLA-ext). A single Thr residue in this extension is glycosylated with 2-acetonyl-galactose (C2-keto-galactose) using polypeptide-α-N-acetylgalactosaminyltransferase II (ppGalNAc-T2) and further conjugated with aminooxy-derivatives of fluoroprobe or biotin molecules. We found that the molten globule form of hLA and αD-hLA proteins, with or without C-terminal extension, and with and without the conjugated fluoroprobe or biotin molecule, readily form a complex with OA and exhibits tumoricidal activity similar to HAMLET made with full-length hLA protein. The confocal microscopy studies with fluoroprobe-labeled samples show that these proteins are internalized into the cells and found even in the nucleus only when they are complexed with OA. The HAMLET conjugated with a single biotin molecule will be a useful tool to identify the cellular components that are involved with it in the tumoricidal activity.

  5. Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability

    NARCIS (Netherlands)

    Fernandez, J.; Yaman, I.; Mishra, R.; Merrick, W. C.; Snider, M. D.; Lamers, W. H.; Hatzoglou, M.

    2001-01-01

    The cationic amino acid transporter, Cat-1, facilitates the uptake of the essential amino acids arginine and lysine. Amino acid starvation causes accumulation and increased translation of cat-1 mRNA, resulting in a 58-fold increase in protein levels and increased arginine uptake. A bicistronic mRNA

  6. Evaluation of Fe(II) oxidation at an acid mine drainage site using laboratory-scale reactors

    Science.gov (United States)

    Brown, Juliana; Burgos, William

    2010-05-01

    Acid mine drainage (AMD) is a severe environmental threat to the Appalachian region of the Eastern United States. The Susquehanna and Potomac River basins of Pennsylvania drain to the Chesapeake Bay, which is heavily polluted by acidity and metals from AMD. This study attempted to unravel the complex relationships between AMD geochemistry, microbial communities, hydrodynamic conditions, and the mineral precipitates for low-pH Fe mounds formed downstream of deep mine discharges, such as Lower Red Eyes in Somerset County, PA, USA. This site is contaminated with high concentrations of Fe (550 mg/L), Mn (115 mg/L), and other trace metals. At the site 95% of dissolved Fe(II) and 56% of total dissolved Fe is removed without treatment, across the mound, but there is no change in the concentration of trace metals. Fe(III) oxides were collected across the Red Eyes Fe mound and precipitates were analyzed by X-ray diffraction, electron microscopy and elemental analysis. Schwertmannite was the dominant mineral phase with traces of goethite. The precipitates also contained minor amounts of Al2O3, MgO,and P2O5. Laboratory flow-through reactors were constructed to quantify Fe(II) oxidation and Fe removal over time at terrace and pool depositional facies. Conditions such as residence time, number of reactors in sequence and water column height were varied to determine optimal conditions for Fe removal. Reactors with sediments collected from an upstream terrace oxidized more than 50% of dissolved Fe(II) at a ten hour residence time, while upstream pool sediments only oxidized 40% of dissolved Fe(II). Downstream terrace and pool sediments were only capable of oxidizing 25% and 20% of Fe(II), respectively. Fe(II) oxidation rates measured in the reactors were determined to be between 3.99 x 10-8and 1.94 x 10-7mol L-1s-1. The sediments were not as efficient for total dissolved Fe removal and only 25% was removed under optimal conditions. The removal efficiency for all sediments

  7. Long chain fatty acids alter the interactive binding of ligands to the two principal drug binding sites of human serum albumin.

    Directory of Open Access Journals (Sweden)

    Keishi Yamasaki

    Full Text Available A wide variety of drugs bind to human serum albumin (HSA at its two principal sites, namely site I and site II. A number of reports indicate that drug binding to these two binding sites are not completely independent, and that interactions between ligands of these two discrete sites can play a role. In this study, the effect of the binding of long-chain fatty acids on the interactive binding between dansyl-L-asparagine (DNSA; site I ligand and ibuprofen (site II ligand at pH6.5 was examined. Binding experiments showed that the binding of sodium oleate (Ole to HSA induces conformational changes in the molecule, which, in turn, changes the individual binding of DNSA and ibuprofen, as well as the mode of interaction between these two ligands from a 'competitive-like' allosteric interaction in the case of the defatted HSA conformer to a 'nearly independent' binding in the case of non-defatted HSA conformer. Circular dichroism measurements indicated that ibuprofen and Ole are likely to modify the spatial orientation of DNSA at its binding site. Docking simulations suggest that the long-distance electric repulsion between DNSA and ibuprofen on defatted HSA contributes to a 'competitive-like' allosteric interaction, whereas extending the distance between ligands and/or increasing the flexibility or size of the DNSA binding site in fatted HSA evokes a change in the interaction mode to 'nearly independent' binding. The present findings provide further insights into the structural dynamics of HSA upon the binding of fatty acids, and its effects on drug binding and drug-drug interactions that occur on HSA.

  8. Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, Jason W.; Coussens, Nathan P.; Allen, Simon; Houtman, Jon C.D.; Turner, Keith H.; Zaleski, Anthony; Ramaswamy, S.; Gibson, Bradford W.; Apicella, Michael A. (Iowa); (Buck Inst.)

    2012-11-14

    Nontypeable Haemophilus influenzae is an opportunistic human pathogen causing otitis media in children and chronic bronchitis and pneumonia in patients with chronic obstructive pulmonary disease. The outer membrane of nontypeable H. influenzae is dominated by lipooligosaccharides (LOS), many of which incorporate sialic acid as a terminal nonreducing sugar. Sialic acid has been demonstrated to be an important factor in the survival of the bacteria within the host environment. H. influenzae is incapable of synthesizing sialic acid and is dependent on scavenging free sialic acid from the host environment. To achieve this, H. influenzae utilizes a tripartite ATP-independent periplasmic transporter. In this study, we characterize the binding site of the extracytoplasmic solute receptor (SiaP) from nontypeable H. influenzae strain 2019. A crystal structure of N-acetyl-5-neuraminic acid (Neu5Ac)-bound SiaP was determined to 1.4 {angstrom} resolution. Thermodynamic characterization of Neu5Ac binding shows this interaction is enthalpically driven with a substantial unfavorable contribution from entropy. This is expected because the binding of SiaP to Neu5Ac is mediated by numerous hydrogen bonds and has several buried water molecules. Point mutations targeting specific amino acids were introduced in the putative binding site. Complementation with the mutated siaP constructs resulted either in full, partial, or no complementation, depending on the role of specific residues. Mass spectrometry analysis of the O-deacylated LOS of the R127K point mutation confirmed the observation of reduced incorporation of Neu5Ac into the LOS. The decreased ability of H. influenzae to import sialic acid had negative effects on resistance to complement-mediated killing and viability of biofilms in vitro, confirming the importance of sialic acid transport to the bacterium.

  9. The dependence of natural regeneration of forest trees on upper soil conditions and acidity at damaged sites in the Black Forest, Germany

    International Nuclear Information System (INIS)

    Littek, T.

    1993-06-01

    It was the goal of this study to investigate the influence of different upper soil conditions on the germination and establishment, as well as the growth, of young plants of various tree species. For this purpose, four test plots in the region of the Black Forest were laid out, in which, by various means of site preparation and fertilization, the upper soils were changed. Natural seeding of common spruce, European silver-fir, beech, sycamore maple, European mountainash, and grey alder was simulated by means of controlled sowing. For comparison, a greenhouse experiment was carried out, examining the germination and development of the same tree species in various soil substrata, using different fertilizers, and under the influence of artificial acid rain. The most important results - with a high level of variation depending on the tree species examined - can be summarized as follows: Based on the results of field and greenhouse experiments, as well as on the investigations of other authors, it can be concluded that natural regeneration of forest stands is considerably impeded under conditions of increasing soil acidity and by high acid depositions. This is seen directly as the result of unfavorable chemical conditions in the upper soil, as well as indirectly due to deteriorating competitiveness against other vegetation. Site preparation and lime or dolomite fertilization can be important measures in the practice of forestry, to encourage natural regeneration in highly acidic sites with an unfavourable humus layer and a high presence of competing vegetation. (orig./UWA). 2 figs., 85 tabs., 269 refs [de

  10. Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

    Directory of Open Access Journals (Sweden)

    Sheng Zhi-Ya

    2008-02-01

    Full Text Available Abstract Background As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequences becomes increasingly important in the post-genomic era. A new encoding scheme was employed to improve the prediction of mucin-type O-glycosylation sites in mammalian proteins. Results A new protein bioinformatics tool, CKSAAP_OGlySite, was developed to predict mucin-type O-glycosylation serine/threonine (S/T sites in mammalian proteins. Using the composition of k-spaced amino acid pairs (CKSAAP based encoding scheme, the proposed method was trained and tested in a new and stringent O-glycosylation dataset with the assistance of Support Vector Machine (SVM. When the ratio of O-glycosylation to non-glycosylation sites in training datasets was set as 1:1, 10-fold cross-validation tests showed that the proposed method yielded a high accuracy of 83.1% and 81.4% in predicting O-glycosylated S and T sites, respectively. Based on the same datasets, CKSAAP_OGlySite resulted in a higher accuracy than the conventional binary encoding based method (about +5.0%. When trained and tested in 1:5 datasets, the CKSAAP encoding showed a more significant improvement than the binary encoding. We also merged the training datasets of S and T sites and integrated the prediction of S and T sites into one single predictor (i.e. S+T predictor. Either in 1:1 or 1:5 datasets, the performance of this S+T predictor was always slightly better than those predictors where S and T sites were independently predicted, suggesting that the molecular recognition of O-glycosylated S/T sites seems to be similar and the increase of the S+T predictor's accuracy may be a result of expanded training datasets. Moreover, CKSAAP_OGlySite was also shown to have better performance when benchmarked against two existing predictors. Conclusion Because of CKSAAP

  11. Long-range atmospheric transport of volatile monocarboxylic acids with Asian dust over a high mountain snow site, central Japan

    Directory of Open Access Journals (Sweden)

    T. Mochizuki

    2016-11-01

    Full Text Available To understand the long-range transport of monocarboxylic acids from the Asian continent to the Japanese islands, we collected snowpack samples from a pit sequence (depth ca. 6 m at the Murodo-Daira snowfield near the summit of Mt. Tateyama, central Japan, in 2009 and 2011. Snow samples (n = 16 were analyzed for normal (C1–C10, branched chain (iC4–iC6, aromatic (benzoic and toluic acid isomers, and hydroxyl (glycolic and lactic monocarboxylic acids, together with inorganic ions and dissolved organic carbon (DOC. Acetic acid (C2 was found to be a dominant species (average 125 ng g−1, followed by formic acid (C1 (85.7 ng g−1 and isopentanoic acid (iC5 (20.0 ng g−1. We found a strong correlation (r =  0.88 between formic plus acetic acids and non-sea-salt Ca2+ that is a proxy of Asian dust. Contributions of total monocarboxylic acids to DOC in 2009 (21.2 ± 11.6 % were higher than that in 2011 (3.75 ± 2.62 %, being consistent with higher intensity of Asian dust in 2009 than in 2011. Formic plus acetic acids also showed a positive correlation (r =  0.90 with benzoic acid that is a tracer of automobile exhaust, indicating that monocarboxylic acids and their precursors are largely emitted from anthropogenic sources in China and/or secondarily produced in the atmosphere by photochemical processing. In addition, the ratio of formic plus acetic acids to nss–Ca2+ (0.27 was significantly higher than those (0.00036–0.0018 obtained for reference dust materials of Chinese loess deposits from the Tengger and Gobi deserts. This result suggests that volatile and semi-volatile organic acids are adsorbed on the alkaline dust particles during long-range atmospheric transport. Entrainment of organic acids by dusts is supported by a good correlation (r = 0.87 between formic plus acetic acids and pH of melt snow samples. Our study suggests that Asian alkaline dusts may be a carrier of volatile monocarboxylic

  12. Aluminium and titanium modified mesoporous TUD-1: A bimetal acid catalyst for Biginelli reaction

    Science.gov (United States)

    Pasupathi, M.; Santhi, N.; Pachamuthu, M. P.; Alamelu Mangai, G.; Ragupathi, C.

    2018-05-01

    Using a simple, non-surfactant template triethanolamine (TEA), bimetal (Al3+ and Ti4+ ions) incorporated mesoporous catalyst AlTiTUD-1 (Si/Al+Ti = 50) was synthesized. The catalyst was characterized by XRD (Low and High angle), N2 Sorption, FTIR, SEM, TEM, DR UV Visible, and pyridine adsorbed FT-IR techniques. The XRD and N2 sorption studies confirmed its amorphous, mesoporous nature, which possessed a BET surface area of 590 m2 g-1 and pore diameter of 4.4 nm. The Al3+ and Ti4+ co-ordination within the TUD-1 was evaluated by DR UV-Vis. Pyridine adsorbed FTIR revealed both Bronsted (B) and Lewis (L) acidity, which is responsible for the catalytic activity. The acid catalyst showed a good catalytic performance in Biginelli type multicomponent coupling reaction for the substituted aldehydes, ethyl acetoacetate and thiourea to yield about 70% in reflux condition.

  13. Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids

    DEFF Research Database (Denmark)

    Chin, Joanna Y; Kuan, Jean Y; Lonkar, Pallavi S

    2008-01-01

    Splice-site mutations in the beta-globin gene can lead to aberrant transcripts and decreased functional beta-globin, causing beta-thalassemia. Triplex-forming DNA oligonucleotides (TFOs) and peptide nucleic acids (PNAs) have been shown to stimulate recombination in reporter gene loci in mammalian...... DNA fragments, can promote single base-pair modification at the start of the second intron of the beta-globin gene, the site of a common thalassemia-associated mutation. This single base pair change was detected by the restoration of proper splicing of transcripts produced from a green fluorescent...

  14. CHARACTERIZATION OF SORBENT PRODUCED THROUGH IMMOBILIZATION OF HUMIC ACID ON CHITOSAN USING GLUTARALDEHYDE AS CROSS-LINKING AGENT AND Pb(II ION AS ACTIVE SITE PROTECTOR

    Directory of Open Access Journals (Sweden)

    Uripto Trisno Santoso

    2010-12-01

    Full Text Available Sorbent produced through immobilization of humic acid (HA on chitosan using glutaraldehyde as cross-linking agent and Pb(II ions as active site protector has been characterized. Active sorption site of HA was protected by reacting HA with Pb(II ion, and the protected-HA was then activated by glutaraldehyde, crosslinked onto chitosan, and deprotected by 0.1 M disodium ethylenediamine tetra-acetic acid (Na2EDTA. The protected-crosslinking method enhanced the content of immobilized-HA and its chemical stability. Based on the FTIR spectra, crosslinking of HA on chitosan probably occurred through a chemical reaction. The sorption capacity of sorbent still remains unchanged after the second regeneration, but some of HA start to be soluble. The latter shows that cross-linking reaction between HA and chitosan is through formation an unstable product. The effectiveness of sorbent regeneration can also be identified by the XRD pattern.

  15. N-Glycosylation Improves the Pepsin Resistance of Histidine Acid Phosphatase Phytases by Enhancing Their Stability at Acidic pHs and Reducing Pepsin's Accessibility to Its Cleavage Sites

    Science.gov (United States)

    Niu, Canfang; Luo, Huiying; Shi, Pengjun; Huang, Huoqing; Wang, Yaru; Yang, Peilong

    2015-01-01

    N-Glycosylation can modulate enzyme structure and function. In this study, we identified two pepsin-resistant histidine acid phosphatase (HAP) phytases from Yersinia kristensenii (YkAPPA) and Yersinia rohdei (YrAPPA), each having an N-glycosylation motif, and one pepsin-sensitive HAP phytase from Yersinia enterocolitica (YeAPPA) that lacked an N-glycosylation site. Site-directed mutagenesis was employed to construct mutants by altering the N-glycosylation status of each enzyme, and the mutant and wild-type enzymes were expressed in Pichia pastoris for biochemical characterization. Compared with those of the N-glycosylation site deletion mutants and N-deglycosylated enzymes, all N-glycosylated counterparts exhibited enhanced pepsin resistance. Introduction of the N-glycosylation site into YeAPPA as YkAPPA and YrAPPA conferred pepsin resistance, shifted the pH optimum (0.5 and 1.5 pH units downward, respectively) and improved stability at acidic pH (83.2 and 98.8% residual activities at pH 2.0 for 1 h). Replacing the pepsin cleavage sites L197 and L396 in the immediate vicinity of the N-glycosylation motifs of YkAPPA and YrAPPA with V promoted their resistance to pepsin digestion when produced in Escherichia coli but had no effect on the pepsin resistance of N-glycosylated enzymes produced in P. pastoris. Thus, N-glycosylation may improve pepsin resistance by enhancing the stability at acidic pH and reducing pepsin's accessibility to peptic cleavage sites. This study provides a strategy, namely, the manipulation of N-glycosylation, for improvement of phytase properties for use in animal feed. PMID:26637601

  16. Single-Atom Mn Active Site in a Triol-Stabilized β-Anderson Manganohexamolybdate for Enhanced Catalytic Activity towards Adipic Acid Production

    Directory of Open Access Journals (Sweden)

    Jianhui Luo

    2018-03-01

    Full Text Available Adipic acid is an important raw chemical for the commercial production of polyamides and polyesters. The traditional industrial adipic acid production utilizes nitric acid to oxidize KA oil (mixtures of cyclohexanone and cyclohexanol, leading to the emission of N2O and thus causing ozone depletion, global warming, and acid rain. Herein, we reported an organically functionalized β-isomer of Anderson polyoxometalates (POMs nanocluster with single-atom Mn, β-{[H3NC(CH2O3]2MnMo6O18}− (1, as a highly active catalyst to selectively catalyze the oxidation of cyclohexanone, cyclohexanol, or KA oil with atom economy use of 30% H2O2 for the eco-friendly synthesis of adipic acid. The catalyst has been characterized by single crystal and powder XRD, XPS, ESI-MS, FT-IR, and NMR. A cyclohexanone (cyclohexanol conversion of >99.9% with an adipic acid selectivity of ~97.1% (~85.3% could be achieved over catalyst 1 with high turnover frequency of 2427.5 h−1 (2132.5 h−1. It has been demonstrated that the existence of Mn3+ atom active site in catalyst 1 and the special butterfly-shaped topology of POMs both play vital roles in the enhancement of catalytic activity.

  17. Newly identified essential amino acid residues affecting ^8-sphingolipid desaturase activity revealed by site-directed mutagenesis

    Science.gov (United States)

    In order to identify amino acid residues crucial for the enzymatic activity of ^8-sphingolipid desaturases, a sequence comparison was performed among ^8-sphingolipid desaturases and ^6-fatty acid desaturase from various plants. In addition to the known conserved cytb5 (cytochrome b5) HPGG motif and...

  18. Biosynthesis of N-glycolyneuraminic acid. The primary site of hydroxylation of N-acetylneuraminic acid is the cytosolic sugar nucleotide pool.

    Science.gov (United States)

    Muchmore, E A; Milewski, M; Varki, A; Diaz, S

    1989-12-05

    N-Glycolylneuraminic acid (Neu5Gc) is an oncofetal antigen in humans and is developmentally regulated in rodents. We have explored the biology of N-acetylneuraminic acid hydroxylase, the enzyme responsible for conversion of the parent sialic acid, N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. We show that the major sialic acid in all compartments of murine myeloma cell lines is Neu5Gc. Pulse-chase analysis in these cells with the sialic acid precursor [6-3H]N-acetylmannosamine demonstrates that most of the newly synthesized Neu5Gc appears initially in the cytosolic low-molecular weight pool bound to CMP. The percentage of Neu5Gc on membrane-bound sialic acids closely parallels that in the CMP-bound pool at various times of chase, whereas that in the free sialic acid pool is very low initially, and rises only later during the chase. This implies that conversion from Neu5Ac to Neu5Gc occurs primarily while Neu5Ac is in its sugar nucleotide form. In support of this, the hydroxylase enzyme from a variety of tissues and cells converted CMP-Neu5Ac to CMP-Neu5Gc, but showed no activity towards free or alpha-glycosidically bound Neu5Ac. Furthermore, the majority of the enzyme activity is found in the cytosol. Studies with isolated intact Golgi vesicles indicate that CMP-Neu5Gc can be transported and utilized for transfer of Neu5Gc to glycoconjugates. The general properties of the enzyme have also been investigated. The Km for CMP-Neu5Ac is in the range of 0.6-2.5 microM. No activity can be detected against the beta-methylglycoside of Neu5Ac. On the other hand, inhibition studies suggest that the enzyme recognizes both the 5'-phosphate group and the pyrimidine base of the substrate. Taken together, the data allow us to propose pathways for the biosynthesis and reutilization of Neu5Gc, with initial conversion from Neu5Ac occurring primarily at the level of the sugar nucleotide. Subsequent release and reutilization of Neu5Gc could then account for the higher steady-state level

  19. Dual Mode Fluorophore-Doped Nickel Nitrilotriacetic Acid-Modified Silica Nanoparticles Combine Histidine-Tagged Protein Purification with Site-Specific Fluorophore Labeling

    OpenAIRE

    Kim, Sung Hoon; Jeyakumar, M.; Katzenellenbogen, John A.

    2007-01-01

    We present the first example of a fluorophore-doped nickel chelate surface- modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700–900 TMRs per ca. 23-nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni+2. Silica-embedded TMR retains very high quantum yield, is resistant to quenc...

  20. Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA) and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction.

    Science.gov (United States)

    Baalmann, Mathis; Best, Marcel; Wombacher, Richard

    2018-01-01

    Here, we describe a two-step protocol for selective protein labeling based on enzyme-mediated peptide labeling utilizing lipoic acid ligase (LplA) and bioorthogonal chemistry. The method can be applied to purified proteins, protein in cell lysates, as well as living cells. In a first step a W37V mutant of the lipoic acid ligase (LplA W37V ) from Escherichia coli is utilized to ligate a synthetic chemical handle site-specifically to a lysine residue in a 13 amino acid peptide motif-a short sequence that can be genetically expressed as a fusion with any protein of interest. In a second step, a molecular probe can be attached to the chemical handle in a bioorthogonal Diels-Alder reaction with inverse electron demand (DA inv ). This method is a complementary approach to protein labeling using genetic code expansion and circumvents larger protein tags while maintaining label specificity, providing experimental flexibility and straightforwardness.

  1. Molecular distribution, seasonal variation, chemical transformation and sources of dicarboxylic acids and related compounds in atmospheric aerosols at remote marine Gosan site, Jeju Island

    Science.gov (United States)

    Kundu, S.; Kawamura, K.; Lee, M.

    2009-12-01

    : A homologous series of C2-C12 α, ω-dicarboxylic acids, ω-oxocarboxylic acids (C2-C9), pyruvic acid and α-dicarbonyls (C2-C3) were detected in atmospheric aerosols collected between April 2003 and April 2004 from remote marine Gosan site (33°29‧ N, 126°16‧ E) located in Jeju Island, South Korea. They were determined using a GC-FID and GC/MS. Total diacid concentration ranged from 130 to 1911 ng m-3 (av. 642 ng m-3), whereas total oxoacid concentration ranged from 7 to 155 ng m-3 (av. 43 ng m-3), and pyruvic acid and α-dicarbonyls ranged from 0.5 to 15 ng m-3 (av. 5 ng m-3) and 2-108 ng m-3 (av. 17.3 ng m-3), respectively. Oxalic (C2) acid was the most abundant in all seasons followed by malonic (C3) or succinic (C4) acid, and phthalic (Ph) acid. The concentration of diacids decreased with an increase in carbon number except for azelaic (C9) acid, which was more abundant than suberic (C8) acid. Glyoxylic acid was predominant ω-oxoacid contributing to 92% of total ω-oxoacid. Total diacids, oxoacids and dicarbonyls showed maximum concentrations in spring and occasionally in winter, while minimum concentrations were observed in summer. Air mass trajectory analysis suggests that either spring or winter maxima can be explained by strong continental outflow associated with cold front passages, while summer minima are associated with warm southerly flows, which transport clean marine air from low latitudes to Jeju Island. The comparison between total diacid concentration level of this study and other study results of urban and remote sites of East Asia reveals that Gosan site is more heavily influenced by the continental outflow from China. The seasonal variation of malonic/succinic (C3/C4), malic/succinic (hC4/C4), fumaric/maleic (F/M), oxalic/pyruvic (C2/Py) and oxalic/Glyoxal (C2/Gly) ratios showed maxima in summer due to an enhanced photo-production and degradation of diacids and related compounds. Throughout all seasons C3/C4 ratio at Gosan site, located

  2. Effect of Number of Various-Type Acid Sites Located on 20 % Co/ZrO2 • SiO2 Sample Surface on Parameters of Catalytic Process in Synthesis of High-Octane Motor Fuel Components

    Directory of Open Access Journals (Sweden)

    A. P. Nesenchouk

    2011-01-01

    Full Text Available The paper considers an effect of ZrO2 content in 20%Co/xZrO2∙(100 – xSiO2 (x = 0, 10, 15, 25, 30, 40 and 100 mass percent catalyst carriers on their catalytic properties. Temperature programmed desorption of NH3 has made it possible to determine relations between their acid and catalytic properties. The paper reveals the TPD spectrum is the result of 4 overlapping peaks originating during NH3 desorption from the respective groups of acid sites. Total acidity of samples and contribution of separate acid site groups into the given acidity have been have been determined in the paper. The paper contains graphical dependences of a various-type acid site number on  content of zirconium oxide in the carrier. Correlations between change in various-type acid site number and catalytic process parameters (CO conversion, C5+ hydrocarbon output and  C5+ isoparaffin output have been found in the paper. The paper shows that the highest values of CO conversion and C5+ hydrocarbon output correspond to maximum number of acid sites, and that number accounts for a peak of desorbed ammonia at Tmax = 122 °C, while the lowest isoparaffin output corresponds to minimum number of acid sites, which characterizes a peak of desorbed ammonia at Tmax = 224–257 °C. 

  3. Conserved amino acid motifs from the novel Piv/MooV family of transposases and site-specific recombinases are required for catalysis of DNA inversion by Piv.

    Science.gov (United States)

    Tobiason, D M; Buchner, J M; Thiel, W H; Gernert, K M; Karls, A C

    2001-02-01

    Piv, a site-specific invertase from Moraxella lacunata, exhibits amino acid homology with the transposases of the IS110/IS492 family of insertion elements. The functions of conserved amino acid motifs that define this novel family of both transposases and site-specific recombinases (Piv/MooV family) were examined by mutagenesis of fully conserved amino acids within each motif in Piv. All Piv mutants altered in conserved residues were defective for in vivo inversion of the M. lacunata invertible DNA segment, but competent for in vivo binding to Piv DNA recognition sequences. Although the primary amino acid sequences of the Piv/MooV recombinases do not contain a conserved DDE motif, which defines the retroviral integrase/transposase (IN/Tnps) family, the predicted secondary structural elements of Piv align well with those of the IN/Tnps for which crystal structures have been determined. Molecular modelling of Piv based on these alignments predicts that E59, conserved as either E or D in the Piv/MooV family, forms a catalytic pocket with the conserved D9 and D101 residues. Analysis of Piv E59G confirms a role for E59 in catalysis of inversion. These results suggest that Piv and the related IS110/IS492 transposases mediate DNA recombination by a common mechanism involving a catalytic DED or DDD motif.

  4. Biosynthesis of N-glycolyneuraminic acid. The primary site of hydroxylation of N-acetylneuraminic acid is the cytosolic sugar nucleotide pool

    Energy Technology Data Exchange (ETDEWEB)

    Muchmore, E.A.; Milewski, M.; Varki, A.; Diaz, S. (San Diego Veterans Administration Medical Center, CA (USA))

    1989-12-05

    N-Glycolylneuraminic acid (Neu5Gc) is an oncofetal antigen in humans and is developmentally regulated in rodents. We have explored the biology of N-acetylneuraminic acid hydroxylase, the enzyme responsible for conversion of the parent sialic acid, N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. We show that the major sialic acid in all compartments of murine myeloma cell lines is Neu5Gc. Pulse-chase analysis in these cells with the sialic acid precursor (6-3H)N-acetylmannosamine demonstrates that most of the newly synthesized Neu5Gc appears initially in the cytosolic low-molecular weight pool bound to CMP. The percentage of Neu5Gc on membrane-bound sialic acids closely parallels that in the CMP-bound pool at various times of chase, whereas that in the free sialic acid pool is very low initially, and rises only later during the chase. This implies that conversion from Neu5Ac to Neu5Gc occurs primarily while Neu5Ac is in its sugar nucleotide form. In support of this, the hydroxylase enzyme from a variety of tissues and cells converted CMP-Neu5Ac to CMP-Neu5Gc, but showed no activity towards free or alpha-glycosidically bound Neu5Ac. Furthermore, the majority of the enzyme activity is found in the cytosol. Studies with isolated intact Golgi vesicles indicate that CMP-Neu5Gc can be transported and utilized for transfer of Neu5Gc to glycoconjugates. The general properties of the enzyme have also been investigated. The Km for CMP-Neu5Ac is in the range of 0.6-2.5 microM. No activity can be detected against the beta-methylglycoside of Neu5Ac. On the other hand, inhibition studies suggest that the enzyme recognizes both the 5'-phosphate group and the pyrimidine base of the substrate. Taken together, the data allow us to propose pathways for the biosynthesis and reutilization of Neu5Gc.

  5. Aspartic acid 397 in subunit B of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae forms part of a sodium-binding site, is involved in cation selectivity, and affects cation-binding site cooperativity.

    Science.gov (United States)

    Shea, Michael E; Juárez, Oscar; Cho, Jonathan; Barquera, Blanca

    2013-10-25

    The Na(+)-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMNC).

  6. Catalytically important amino-acid residues of abalone alginate lyase HdAly assessed by site-directed mutagenesis

    OpenAIRE

    Yamamoto, Sayo; Sahara, Takehiko; Sato, Daisuke; Kawasaki, Kosei; Ohgiya, Satoru; Inoue, Akira; Ojima, Takao

    2008-01-01

    Alginate lyase is an enzyme that degrades alginate chains via β-elimination and has been used for the production of alginate oligosaccharides and protoplasts from brown algae. Previously, we deduced the amino-acid sequence of an abalone alginate lyase, HdAly, from its cDNA sequence and, through multiple amino-acid sequence alignment, found that several basic amino-acid residues were highly conserved among the polysaccharide-lyase family 14 (PL-14) enzymes including HdAly. In the present study...

  7. Enhancement in catalytic activity of Aspergillus niger XynB by selective site-directed mutagenesis of active site amino acids.

    Science.gov (United States)

    Wu, Xiuyun; Tian, Zhennan; Jiang, Xukai; Zhang, Qun; Wang, Lushan

    2018-01-01

    XynB from Aspergillus niger ATCC1015 (AnXynB) is a mesophilic glycoside hydrolase (GH) family 11 xylanase which holds great potentials in a wide variety of industrial applications. In the present study, the catalytic activity and stability of AnXynB were improved by a combination of computational and experimental approaches. Virtual mutation and molecular dynamics simulations indicated that the introduction of Glu and Asn altered the interaction network at the - 3 subsite. Interestingly, the double mutant S41N/T43E displayed 72% increase in catalytic activity when compared to the wild type (WT). In addition, it also showed a better thermostability than the WT enzyme. Kinetic determination of the T43E and S41N/T43E mutants suggested that the higher xylanase activity is probably due to the increasing binding affinity of enzyme and substrate. Consequently, the enzyme activity and thermostability of AnXynB was both increased by selective site-directed mutagenesis at the - 3 subsite of its active site architecture which provides a good example for a successfully engineered enzyme for potential industrial application. Moreover, the molecular evolution approach adopted in this study led to the design of a library of sequences that captures a meaningful functional diversity in a limited number of protein variants.

  8. A human fatty acid synthase inhibitor binds β-ketoacyl reductase in the keto-substrate site.

    Science.gov (United States)

    Hardwicke, Mary Ann; Rendina, Alan R; Williams, Shawn P; Moore, Michael L; Wang, Liping; Krueger, Julie A; Plant, Ramona N; Totoritis, Rachel D; Zhang, Guofeng; Briand, Jacques; Burkhart, William A; Brown, Kristin K; Parrish, Cynthia A

    2014-09-01

    Human fatty acid synthase (hFAS) is a complex, multifunctional enzyme that is solely responsible for the de novo synthesis of long chain fatty acids. hFAS is highly expressed in a number of cancers, with low expression observed in most normal tissues. Although normal tissues tend to obtain fatty acids from the diet, tumor tissues rely on de novo fatty acid synthesis, making hFAS an attractive metabolic target for the treatment of cancer. We describe here the identification of GSK2194069, a potent and specific inhibitor of the β-ketoacyl reductase (KR) activity of hFAS; the characterization of its enzymatic and cellular mechanism of action; and its inhibition of human tumor cell growth. We also present the design of a new protein construct suitable for crystallography, which resulted in what is to our knowledge the first co-crystal structure of the human KR domain and includes a bound inhibitor.

  9. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues.

    Science.gov (United States)

    Gillner, Danuta M; Bienvenue, David L; Nocek, Boguslaw P; Joachimiak, Andrzej; Zachary, Vincentos; Bennett, Brian; Holz, Richard C

    2009-01-01

    The catalytic and structural properties of the H67A and H349A dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae were investigated. On the basis of sequence alignment with the carboxypeptidase from Pseudomonas sp. strain RS-16, both H67 and H349 were predicted to be Zn(II) ligands. The H67A DapE enzyme exhibited a decreased catalytic efficiency (180-fold) compared with wild-type (WT) DapE towards N-succinyldiaminopimelic acid. No catalytic activity was observed for H349A under the experimental conditions used. The electronic paramagnetic resonance (EPR) and electronic absorption data indicate that the Co(II) ion bound to H349A-DapE is analogous to that of WT DapE after the addition of a single Co(II) ion. The addition of 1 equiv of Co(II) to H67A DapE provides spectra that are very different from those of the first Co(II) binding site of the WT enzyme, but that are similar to those of the second binding site. The EPR and electronic absorption data, in conjunction with the kinetic data, are consistent with the assignment of H67 and H349 as active-site metal ligands for the DapE from H. influenzae. Furthermore, the data suggest that H67 is a ligand in the first metal binding site, while H349 resides in the second metal binding site. A three-dimensional homology structure of the DapE from H. influenzae was generated using the X-ray crystal structure of the DapE from Neisseria meningitidis as a template and superimposed on the structure of the aminopeptidase from Aeromonas proteolytica (AAP). This homology structure confirms the assignment of H67 and H349 as active-site ligands. The superimposition of the homology model of DapE with the dizinc(II) structure of AAP indicates that within 4.0 A of the Zn(II) binding sites of AAP all of the amino acid residues of DapE are nearly identical.

  10. The Cu2+-nitrilotriacetic acid complex improves loading of α-helical double histidine site for precise distance measurements by pulsed ESR

    Science.gov (United States)

    Ghosh, Shreya; Lawless, Matthew J.; Rule, Gordon S.; Saxena, Sunil

    2018-01-01

    Site-directed spin labeling using two strategically placed natural histidine residues allows for the rigid attachment of paramagnetic Cu2+. This double histidine (dHis) motif enables extremely precise, narrow distance distributions resolved by Cu2+-based pulsed ESR. Furthermore, the distance measurements are easily relatable to the protein backbone-structure. The Cu2+ ion has, till now, been introduced as a complex with the chelating agent iminodiacetic acid (IDA) to prevent unspecific binding. Recently, this method was found to have two limiting concerns that include poor selectivity towards α-helices and incomplete Cu2+-IDA complexation. Herein, we introduce an alternative method of dHis-Cu2+ loading using the nitrilotriacetic acid (NTA)-Cu2+ complex. We find that the Cu2+-NTA complex shows a four-fold increase in selectivity toward α-helical dHis sites. Furthermore, we show that 100% Cu2+-NTA complexation is achievable, enabling precise dHis loading and resulting in no free Cu2+ in solution. We analyze the optimum dHis loading conditions using both continuous wave and pulsed ESR. We implement these findings to show increased sensitivity of the Double Electron-Electron Resonance (DEER) experiment in two different protein systems. The DEER signal is increased within the immunoglobulin binding domain of protein G (called GB1). We measure distances between a dHis site on an α-helix and dHis site either on a mid-strand or a non-hydrogen bonded edge-strand β-sheet. Finally, the DEER signal is increased twofold within two α-helix dHis sites in the enzymatic dimer glutathione S-transferase exemplifying the enhanced α-helical selectivity of Cu2+-NTA.

  11. Mechanistic Effects of Water on the Fe-Catalyzed Hydrodeoxygenation of Phenol. The Role of Brønsted Acid Sites

    Energy Technology Data Exchange (ETDEWEB)

    Hensley, Alyssa J. R. [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; Wang, Yong [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; Mei, Donghai [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; McEwen, Jean-Sabin [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and

    2018-01-30

    A mechanistic understanding of the roles of water is essential for developing highly active and selective catalysts for hydrodeoxygenation (HDO) reactions since water is ubiquitous in such reaction systems. Here, we present a study for phenol HDO on Fe catalysts using density functional theory which examines the effect of water on three elementary pathways for phenol HDO using an explicit solvation model. The presence of water is found to significantly decrease activation barriers required by hydrogenation reactions via two pathways. First, the proton transfer in the hydrogen bonding network of the liquid water phase is nearly barrierless, which significantly promotes the direct through space tautomerization of phenol. Second, due to the high degree of oxophilicity on Fe, liquid water molecules are found to be easily dissociated into surface hydroxyl groups that can act as Brønsted acid sites. These sites dramatically promote hydrogenation reactions on the Fe surface. As a result, the hydrogen assisted dehydroxylation becomes the dominant phenol HDO pathway. This work provides new fundamental insights into aqueous phase HDO of biomass-derived oxygenates over Fe-based catalysts; e.g., the activity of Fe-based catalysts can be optimized by tuning the surface coverage of Brønsted acid sites via surface doping.

  12. Reduction of NO adlayers on Pt(110) and Pt(111) in acidic media: evidence for adsorption site-specific reduction

    NARCIS (Netherlands)

    Rosca, V.; Beltramo, G.L.; Koper, M.T.M.

    2005-01-01

    We present a combined in situ Fourier transform infrared reflection-absorption spectroscopy and voltammetric study of the reduction of saturated and subsaturated NO adlayers on Pt(111) and Pt(110) single-crystal surfaces in acidic media. The stripping voltammetry experiments and the associated

  13. Effects of neonatal. gamma. -ray irradiation on rat hippocampus: Pt. 2; Development of excitatory amino acid binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Dessi, F; Represa, A; Ben-Ari, Y [Institut National de la Sante et de la Recherche Medicale (INSERM), 75 - Paris (France)

    1991-01-01

    In the rat, neonatal irradiation produces a destruction of denate granule cells and prevents the development of the mossy fibre-CA3 pyramidal cell synapse. The developmental increase of high affinity kainate binding sites in the stratum lucidum was reduced on the irradiated side as compared with the control side. This suggests that a proportion of high affinity kainate binding sites is associated with mossy fibres. In contrast, the development profile of N-methyl-D-aspartate binding sites, which are associated with associational and commissural synapses in CA3, was not affected by irradiation. The role that afferent fibres may play in the development of pyramidal cells is discussed in connection with the modulatory effects of glutamate receptors on the development of neurons. (author).

  14. Acid rock drainage in the uranium mining and milling site of Pocos de Caldas, Brazil -- duration assessment, pollutant generation modelling and remediation strategies

    International Nuclear Information System (INIS)

    Fernandes, H.M.; Franklin, M.R.

    2002-01-01

    This geochemical modeling work was carried out to simulate the acid drainage generation from one of the waste-rock piles at the Pocos de Caldas uranium mining site. The mathematical code STEADQYL was used. The estimated results were in good agreement for sulphate and uranium concentrations and the duration of the acid water generation was estimated to be about 500 years. The effect of covering the dump with a material that minimized oxygen diffusion was assessed. Projections indicated that covering the dump with a 1.0 m thickness of a material (like clay), which had an oxygen diffusion coefficient of 10 9 m 2 ·s 1 , would reduce the pollutant concentrations to acceptable values. The estimated cost, when using this strategy, would be about US $10 million. (author)

  15. Quantitative 3D Fluorescence Imaging of Single Catalytic Turnovers Reveals Spatiotemporal Gradients in Reactivity of Zeolite H-ZSM-5 Crystals upon Steaming

    NARCIS (Netherlands)

    Ristanovic, Zoran|info:eu-repo/dai/nl/328233005; Hofmann, Jan P.|info:eu-repo/dai/nl/355351110; De Cremer, Gert; Kubarev, Alexey V.; Rohnke, Marcus; Meirer, Florian; Hofkens, Johan; Roeffaers, Maarten B. J.; Weckhuysen, Bert M.|info:eu-repo/dai/nl/285484397

    2015-01-01

    Optimizing the number, distribution, and accessibility of Bronsted acid sites in zeolite-based catalysts is of a paramount importance to further improve their catalytic performance. However, it remains challenging to measure real-time changes in reactivity of single zeolite catalyst particles by

  16. The dapE-encoded N-succinyl-L,L-Diaminopimelic Acid Desuccinylase from Haemophilus influenzae Contains two Active Site Histidine Residues

    Science.gov (United States)

    Gillner, Danuta M.; Bienvenue, David L.; Nocek, Boguslaw P.; Joachimiak, Andrzej; Zachary, Vincentos; Bennett, Brian; Holz, Richard C.

    2009-01-01

    The catalytic and structural properties of the H67A and H349A altered dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from H. influenzae were investigated. Based on sequence alignment with CPG2 both H67 and H349 were predicted to be Zn(II) ligands. Catalytic activity was observed for the H67A altered DapE enzyme which exhibited kcat = 1.5 ± 0.5 sec−1 and Km = 1.4 ± 0.3 mM. No catalytic activity was observed for H349A under the experimental conditions used. The EPR and electronic absorption data indicate that the Co(II) ion bound to H349A-DapE is analogous to WT DapE after the addition of a single Co(II) ion. The addition of one equivalent of Co(II) to H67A altered DapE provides spectra that are very different from the first Co(II) binding site of the WT enzyme, but similar to the second binding site. The EPR and electronic absorption data, in conjunction with the kinetic data, are consistent with the assignment of H67 and H349 as active site metal ligands for the DapE from H. influenzae. Furthermore, the data suggest that H67 is a ligand in the first metal binding site while H349 resides in the second metal binding site. A three-dimensional homology structure of the DapE from H. influenzae was generated using the X-ray crystal structure of the DapE from N. meningitidis as a template and superimposed on the structure of AAP. This homology structure confirms the assignment of H67 and H349 as active site ligands. The superimposition of the homology model of DapE with the dizinc(II) structure of AAP indicates that within 4.0 Å of the Zn(II) binding sites of AAP, all of the amino acid residues of DapE are nearly identical. PMID:18712420

  17. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections

    NARCIS (Netherlands)

    Mingo, J.; Erramuzpe, A.; Luna, S.; Aurtenetxe, O.; Amo, L.; Diez, I.; Schepens, J.T.G.; Hendriks, W.J.A.J.; Cortes, J.M.; Pulido, R.

    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

  18. Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs{sup +}-selective binding site

    Energy Technology Data Exchange (ETDEWEB)

    Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu; Adachi, Motoyasu; Tamada, Taro [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Kawamoto, Masahide [Kyushu Synchrotron Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841-0005 (Japan); Tokunaga, Hiroko; Ishibashi, Matsujiro [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Blaber, Michael [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300 (United States); Tokunaga, Masao [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Kuroki, Ryota, E-mail: kuroki.ryota@jaea.go.jp [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan)

    2015-03-01

    The tertiary structure of a β-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr{sup 2+}-binding sites and one Cs{sup +}-binding site were discovered in the HaBLA molecule. Environmentally friendly absorbents are needed for Sr{sup 2+} and Cs{sup +}, as the removal of the radioactive Sr{sup 2+} and Cs{sup +} that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs{sup +} or Sr{sup 2+}. The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P3{sub 1} using X-ray crystallography. Moreover, the locations of bound Sr{sup 2+} and Cs{sup +} ions were identified by anomalous X-ray diffraction. The location of one Cs{sup +}-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na{sup +} (90 mM Na{sup +}/10 mM Cs{sup +}). From an activity assay using isothermal titration calorimetry, the bound Sr{sup 2+} and Cs{sup +} ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs{sup +}-binding site provides important information that is useful for the design of artificial Cs{sup +}-binding sites that may be useful in the bioremediation of radioactive isotopes.

  19. Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs+-selective binding site

    International Nuclear Information System (INIS)

    Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide; Tokunaga, Hiroko; Ishibashi, Matsujiro; Blaber, Michael; Tokunaga, Masao; Kuroki, Ryota

    2015-01-01

    The tertiary structure of a β-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr 2+ -binding sites and one Cs + -binding site were discovered in the HaBLA molecule. Environmentally friendly absorbents are needed for Sr 2+ and Cs + , as the removal of the radioactive Sr 2+ and Cs + that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs + or Sr 2+ . The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P3 1 using X-ray crystallography. Moreover, the locations of bound Sr 2+ and Cs + ions were identified by anomalous X-ray diffraction. The location of one Cs + -specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na + (90 mM Na + /10 mM Cs + ). From an activity assay using isothermal titration calorimetry, the bound Sr 2+ and Cs + ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs + -binding site provides important information that is useful for the design of artificial Cs + -binding sites that may be useful in the bioremediation of radioactive isotopes

  20. Observation of new particle formation and measurement of sulfuric acid, ammonia, amines and highly oxidized organic molecules at a rural site in central Germany

    Directory of Open Access Journals (Sweden)

    A. Kürten

    2016-10-01

    Full Text Available The exact mechanisms for new particle formation (NPF under different boundary layer conditions are not known yet. One important question is whether amines and sulfuric acid lead to efficient NPF in the atmosphere. Furthermore, it is not clear to what extent highly oxidized organic molecules (HOMs are involved in NPF. We conducted field measurements at a rural site in central Germany in the proximity of three larger dairy farms to investigate whether there is a connection between NPF and the presence of amines and/or ammonia due to the local emissions from the farms. Comprehensive measurements using a nitrate chemical ionization–atmospheric pressure interface time-of-flight (CI-APi-TOF mass spectrometer, a proton-transfer-reaction mass spectrometer (PTR-MS, particle counters and differential mobility analyzers (DMAs, as well as measurements of trace gases and meteorological parameters, were performed. We demonstrate here that the nitrate CI-APi-TOF is suitable for sensitive measurements of sulfuric acid, amines, a nitrosamine, ammonia, iodic acid and HOMs. NPF was found to correlate with sulfuric acid, while an anti-correlation with RH, amines and ammonia is observed. The anti-correlation between NPF and amines could be due to the efficient uptake of these compounds by nucleating clusters and small particles. Much higher HOM dimer (C19/C20 compounds concentrations during the night than during the day indicate that these HOMs do not efficiently self-nucleate as no nighttime NPF is observed. Observed iodic acid probably originates from an iodine-containing reservoir substance, but the iodine signals are very likely too low to have a significant effect on NPF.

  1. A cluster DFT study of NH{sub 3} and NO adsorption on the (MoO{sub 2}){sup 2+}/HZSM-5 surface: Lewis versus Brønsted acid sites

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Zhifeng [College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); College of Material Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Zuo, Zhijun [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Li, Zhe, E-mail: lizhe@tyut.edu.cn [College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Zhang, Jinshan [College of Material Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China)

    2014-12-01

    Graphical abstract: - Highlights: • NH{sub 3} adsorption is found to be more favorable energetically than NO adsorption on both Lewis and Brønsted acid sites. • Lewis and Brønsted acid sites are competitive energetically for NH{sub 3} adsorption. • Reduced-state Mo{sup 5+} is suggested to play a key role in adsorption and activation of NO{sub x} together with the adsorbed NH{sub 4}{sup +}. - Abstract: A systematic DFT study was carried out to investigate NH{sub 3} and NO adsorption on both Lewis and Brønsted acid sites of (MoO{sub 2}){sup 2+}/HZSM-5 catalyst by using cluster models. The adsorption energy results indicate that NH{sub 3} could strongly adsorb on both Lewis and Brønsted acid sites in the form of coordinated NH{sub 3} and NH{sub 4}{sup +}, respectively, whereas NO represents poorer adsorption ability. It is also found that Lewis and Brønsted acid sites are competitive energetically for NH{sub 3} adsorption. According to the difference in the proposed mechanisms for NH{sub 3} adsorption on different acid sites, particular attention has been focused on the first dissociation of coordinated NH{sub 3} for Lewis acid site and the effect of Mo site on the introduction of NO for Brønsted acid site. For the coordinated NH{sub 3} on Lewis acid site, the more electron donation from NH{sub 3} is, the greater its adsorption stability is and the higher active its H atoms are. In addition, DOS results show that stability of the H atoms is enhanced by interacting with framework oxygen and especially the H atoms chemical-bonded with framework oxygen. For the NH{sub 4}{sup +} on Brønsted acid site, reduced-state Mo{sup 5+} holds stronger reducibility and oxidizability than terminal oxygen, which is suggested to play a key role in adsorption and activation of NO{sub x} together with the adsorbed NH{sub 4}{sup +}.

  2. Tracking the Chemical Transformations at the Brønsted Acid Site upon Water-Induced Deprotonation in a Zeolite Pore

    Energy Technology Data Exchange (ETDEWEB)

    Vjunov, Aleksei; Wang, Meng; Govind, Niranjan; Huthwelker, Thomas; Shi, Hui; Mei, Donghai; Fulton, John L.; Lercher, Johannes A.

    2017-10-23

    We report the structural changes induced by Brønsted acidic site deprotonation in a zeolite with MFI structure as a function of temperature up to 430°C using in situ Al K-edge X-ray absorption fine structure spectroscopy (XAFS). At ambient conditions, the protons are present as hydrated hydronium ions (H3O+(H2O)n) that are ion-paired to the anionic, Al tetrahedral (T) site. At elevated temperatures, loss of water molecules hydrating the hydronium ions leads to an unstable free hydronium ion that disso-ciates to form the hydroxylated T-site. The formation of this (-O3)-Al-(OH-) species leads to the elongation of one of the four Al-O bonds and causes significant distortion of the tetrahedral symmetry about the Al atom. This distortion leads to the appearance of new pre-edge features in the Al K-edge X-ray absorption near edge structure (XANES) spectra. The pre-edge peak assignment is confirmed by time-dependent density functional theory calculation of the XANES spectrum. The XANES spectra are also sensitive to solutes or solvent that are in proximity to the T-site. A second structural transition occurs at about the same temperature, namely the conversion of a minor fraction of extra-framework octahedral Al present in the sample at ambient conditions to a tetrahedral species through the de-coordination of H2O-ligands. Both IR spectroscopy and thermogravimetric analysis (TGA) are further used to confirm the overall chemical transformation of the T-site.

  3. Identifying key controls on the behavior of an acidic-U(VI) plume in the Savannah River Site using reactive transport modeling.

    Science.gov (United States)

    Bea, Sergio A; Wainwright, Haruko; Spycher, Nicolas; Faybishenko, Boris; Hubbard, Susan S; Denham, Miles E

    2013-08-01

    Acidic low-level waste radioactive waste solutions were discharged to three unlined seepage basins at the F-Area of the Department of Energy (DOE) Savannah River Site (SRS), South Carolina, USA, from 1955 through 1989. Despite many years of active remediation, the groundwater remains acidic and contaminated with significant levels of U(VI) and other radionuclides. Monitored Natural Attenuation (MNA) is a desired closure strategy for the site, based on the premise that regional flow of clean background groundwater will eventually neutralize the groundwater acidity, immobilizing U(VI) through adsorption. An in situ treatment system is currently in place to accelerate this in the downgradient portion of the plume and similar measures could be taken upgradient if necessary. Understanding the long-term pH and U(VI) adsorption behavior at the site is critical to assess feasibility of MNA along with the in-situ remediation treatments. This paper presents a reactive transport (RT) model and uncertainty quantification (UQ) analyses to explore key controls on the U(VI)-plume evolution and long-term mobility at this site. Two-dimensional numerical RT simulations are run including the saturated and unsaturated (vadose) zones, U(VI) and H(+) adsorption (surface complexation) onto sediments, dissolution and precipitation of Al and Fe minerals, and key hydrodynamic processes are considered. UQ techniques are applied using a new open-source tool that is part of the developing ASCEM reactive transport modeling and analysis framework to: (1) identify the complex physical and geochemical processes that control the U(VI) plume migration in the pH range where the plume is highly mobile, (2) evaluate those physical and geochemical parameters that are most controlling, and (3) predict the future plume evolution constrained by historical, chemical and hydrological data. The RT simulation results show a good agreement with the observed historical pH and concentrations of U(VI), nitrates

  4. ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs.

    Science.gov (United States)

    Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

    2013-01-01

    Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. In these oxidation-reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.

  5. Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

    Science.gov (United States)

    Baltrusaitis, Jonas; Hatch, Courtney; Orlando, Roberto

    2012-08-02

    The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

  6. Dual-mode fluorophore-doped nickel nitrilotriacetic acid-modified silica nanoparticles combine histidine-tagged protein purification with site-specific fluorophore labeling.

    Science.gov (United States)

    Kim, Sung Hoon; Jeyakumar, M; Katzenellenbogen, John A

    2007-10-31

    We present the first example of a fluorophore-doped nickel chelate surface-modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700-900 TMRs per ca. 23 nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni2+. Silica-embedded TMR retains very high quantum yield, is resistant to quenching by buffer components, and is modestly quenched and only to a certain depth (ca. 2 nm) by surface-attached Ni2+. When exposed to a bacterial lysate containing estrogen receptor alpha ligand binding domain (ERalpha) as a minor component, these beads showed very high specificity binding, enabling protein purification in one step. The capacity and specificity of these beads for binding a his-tagged protein were characterized by electrophoresis, radiometric counting, and MALDI-TOF MS. ERalpha, bound to TMR-SiO2-NTA-Ni++ beads in a site-specific manner, exhibited good activity for ligand binding and for ligand-induced binding to coactivators in solution FRET experiments and protein microarray fluorometric and FRET assays. This dual-mode type TMR-SiO2-NTA-Ni2+ system represents a powerful combination of one-step histidine-tagged protein purification and site-specific labeling with multiple fluorophore species.

  7. Sulfur-Hz(CHx)y(z = 0,1) functionalized metal oxide nanostructure decorated interfaces: Evidence of Lewis base and Brönsted acid sites – Influence on chemical sensing

    International Nuclear Information System (INIS)

    Laminack, William; Baker, Caitlin; Gole, James

    2015-01-01

    Nanostructure metal oxide decorated n-type extrinsic porous silicon (PS) semiconductor interfaces are modified through in-situ interaction with acidic ethane and butane thiols (EtSH, BuSH) and basic diethyl sulfide (Et 2 S). Highly sensitive conductometric sensor evaluations and X-ray Photoelectron Spectroscopy demonstrate the effect of sulfur group functionalization modifying the acidity of the metal oxides and their interaction with NH 3 . SEM micrographs demonstrate that the sulfur treated particles are less than 30 nm in size. EDAX studies confirm the chemical composition of the modified nanoparticles and suggest the surface interaction of the sulfides and thiols. The acidic thiols can form Brönsted acidic sites enhancing the acidity of the metal oxides, thus broadening the initial metal oxide acidity range. The sulfides interact to lower the Lewis acidity of nanostructured metal oxide sites. Conductometric response matrices with NH 3 at room temperature, corresponding to the thiol and sulfide treated nanostructures of the metal oxides TiO 2 , SnO x , Ni x O, Cu x O, and Au x O (x >> 1) are evaluated for a dominant electron transduction process forming the basis for reversible chemical sensing in the absence of chemical bond formation. Treatment with the acidic thiols enhances the metal center acidity. It is suggested that the thiols can interact to increase the Brönsted acidity of the doped metal oxide surface if they maintain SH bonds. This process may account for the shift in Lewis acidity as the Brönsted acid sites counter the decrease in Lewis acidity resulting from the interaction of S-(CH x ) y groups. In contrast, treatment with basic Et 2 S decreases the Lewis acidity of the metal oxide sites, enhancing the basicity of the decorated interface. XPS measurements indicate a change in binding energy (BE) of the metal and oxygen centers. The observed changes in conductometric response do not represent a simple increase in surface acidity or basicity but

  8. Acid neutralizing capacity and leachate results for igneous rocks, with associated carbon contents of derived soils, Animas River AML site, Silverton, Colorado

    Science.gov (United States)

    Yager, Douglas B.; Stanton, Mark R.; Choate, LaDonna M.; Burchell,

    2009-01-01

    Mine planning efforts have historically overlooked the possible acid neutralizing capacity (ANC) that local igneous rocks can provide to help neutralize acidmine drainage. As a result, limestone has been traditionally hauled to mine sites for use in neutralizing acid drainage. Local igneous rocks, when used as part of mine life-cycle planning and acid mitigation strategy, may reduce the need to transport limestone to mine sites because these rocks can contain acid neutralizing minerals. Igneous hydrothermal events often introduce moderately altered mineral assemblages peripheral to more intensely altered rocks that host metal-bearing veins and ore bodies. These less altered rocks can contain ANC minerals (calcite-chlorite-epidote) and are referred to as a propylitic assemblage. In addition, the carbon contents of soils in areas of new mining or those areas undergoing restoration have been historically unknown. Soil organic carbon is an important constituent to characterize as a soil recovery benchmark that can be referred to during mine cycle planning and restoration. This study addresses the mineralogy, ANC, and leachate chemistry of propylitic volcanic rocks that host polymetallic mineralization in the Animas River watershed near the historical Silverton, Colorado, mining area. Acid titration tests on volcanic rocks containing calcite (2 – 20 wt %) and chlorite (6 – 25 wt %), have ANC ranging from 4 – 146 kg/ton CaCO3 equivalence. Results from a 6-month duration, kinetic reaction vessel test containing layered pyritic mine waste and underlying ANC volcanic rock (saturated with deionized water) indicate that acid generating mine waste (pH 2.4) has not overwhelmed the ANC of propylitic volcanic rocks (pH 5.8). Sequential leachate laboratory experiments evaluated the concentration of metals liberated during leaching. Leachate concentrations of Cu-Zn-As-Pb for ANC volcanic rock are one-to-three orders of magnitude lower when compared to leached solution from

  9. Bioaccumulation of metals in reeds collected from an acid mine drainage contaminated site in winter and spring.

    Science.gov (United States)

    Guo, Lin; Cutright, Teresa J

    2016-01-01

    Wetland plants such as Phragmites australis has been used to treat acid mine drainage (AMD) contaminated soil which is a serious environmental issue worldwide. This project investigated metal plaque content(s) and metal uptake in reeds grown in an AMD field in winter and spring. The results indicated that the level of Fe plaque was much higher than Mn and Al plaque as the soil contained more Fe than Al and Mn. The amounts of Mn and Al plaque formed on reeds in spring were not significantly different from that in winter (p > .05). However, more Fe plaque was formed on reeds collected in spring. The concentrations of metals in underground organs were positively related to the metal levels in soils. More Mn and Al transferred to the aboveground tissues of reeds during the spring while the Fe levels in reeds did not significantly vary with seasons. Roots and rhizomes were the main organs for Fe sequestration (16.3 ± 4.15 mg/g in roots in spring) while most Al was sequestered in the shoots of reeds (2.05 ± 0.09 mg/g in shoots in spring). Further research may be needed to enhance the translocation of metals in reeds and increase the phytoremediation efficiency.

  10. Tracing the Evolutionary History of the CAP Superfamily of Proteins Using Amino Acid Sequence Homology and Conservation of Splice Sites.

    Science.gov (United States)

    Abraham, Anup; Chandler, Douglas E

    2017-10-01

    Proteins of the CAP superfamily play numerous roles in reproduction, innate immune responses, cancer biology, and venom toxicology. Here we document the breadth of the CAP (Cysteine-RIch Secretory Protein (CRISP), Antigen 5, and Pathogenesis-Related) protein superfamily and trace the major events in its evolution using amino acid sequence homology and the positions of exon/intron borders within their genes. Seldom acknowledged in the literature, we find that many of the CAP subfamilies present in mammals, where they were originally characterized, have distinct homologues in the invertebrate phyla. Early eukaryotic CAP genes contained only one exon inherited from prokaryotic predecessors and as evolution progressed an increasing number of introns were inserted, reaching 2-5 in the invertebrate world and 5-15 in the vertebrate world. Focusing on the CRISP subfamily, we propose that these proteins evolved in three major steps: (1) origination of the CAP/PR/SCP domain in bacteria, (2) addition of a small Hinge domain to produce the two-domain SCP-like proteins found in roundworms and anthropoids, and (3) addition of an Ion Channel Regulatory domain, borrowed from invertebrate peptide toxins, to produce full length, three-domain CRISP proteins, first seen in insects and later to diversify into multiple subtypes in the vertebrate world.

  11. iSulf-Cys: Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids.

    Science.gov (United States)

    Xu, Yan; Ding, Jun; Wu, Ling-Yun

    2016-01-01

    Cysteine S-sulfenylation is an important post-translational modification (PTM) in proteins, and provides redox regulation of protein functions. Bioinformatics and structural analyses indicated that S-sulfenylation could impact many biological and functional categories and had distinct structural features. However, major limitations for identifying cysteine S-sulfenylation were expensive and low-throughout. In view of this situation, the establishment of a useful computational method and the development of an efficient predictor are highly desired. In this study, a predictor iSulf-Cys which incorporated 14 kinds of physicochemical properties of amino acids was proposed. With the 10-fold cross-validation, the value of area under the curve (AUC) was 0.7155 ± 0.0085, MCC 0.3122 ± 0.0144 on the training dataset for 20 times. iSulf-Cys also showed satisfying performance in the independent testing dataset with AUC 0.7343 and MCC 0.3315. Features which were constructed from physicochemical properties and position were carefully analyzed. Meanwhile, a user-friendly web-server for iSulf-Cys is accessible at http://app.aporc.org/iSulf-Cys/.

  12. Electrochemically active microorganisms from an acid mine drainage-affected site promote cathode oxidation in microbial fuel cells

    KAUST Repository

    Rojas, Claudia; Vargas, Ignacio T.; Bruns, Mary Ann; Regan, John M.

    2017-01-01

    The limited database of acidophilic or acidotolerant electrochemically active microorganisms prevents advancements on microbial fuel cells (MFCs) operated under low pH. In this study, three MFCs were used to enrich cathodic biofilms using acid mine drainage (AMD) sediments as inoculum. Linear sweep voltammetry showed cathodic current plateaus of 5.5 (± 0.7) mA at about − 170 mV vs Ag/AgCl and 8.5 (± 0.9) mA between − 500 mV to − 450 mV vs Ag/AgCl for biofilms developed on small graphite fiber brushes. After gamma irradiation, biocathodes exhibited a decrease in current density approaching that of abiotic controls. Electrochemical impedance spectroscopy showed six-fold lower charge transfer resistance with viable biofilm. Pyrosequencing data showed that Proteobacteria and Firmicutes dominated the biofilms. Acidithiobacillus representatives were enriched in some biocathodes, supporting the potential importance of these known iron and sulfur oxidizers as cathodic biocatalysts. Other acidophilic chemolithoautotrophs identified included Sulfobacillus and Leptospirillum species. The presence of chemoautotrophs was consistent with functional capabilities predicted by PICRUSt related to carbon fixation pathways in prokaryotic microorganisms. Acidophilic or acidotolerant heterotrophs were also abundant; however, their contribution to cathodic performance is unknown. This study directs subsequent research efforts to particular groups of AMD-associated bacteria that are electrochemically active on cathodes.

  13. Electrochemically active microorganisms from an acid mine drainage-affected site promote cathode oxidation in microbial fuel cells

    KAUST Repository

    Rojas, Claudia

    2017-08-03

    The limited database of acidophilic or acidotolerant electrochemically active microorganisms prevents advancements on microbial fuel cells (MFCs) operated under low pH. In this study, three MFCs were used to enrich cathodic biofilms using acid mine drainage (AMD) sediments as inoculum. Linear sweep voltammetry showed cathodic current plateaus of 5.5 (± 0.7) mA at about − 170 mV vs Ag/AgCl and 8.5 (± 0.9) mA between − 500 mV to − 450 mV vs Ag/AgCl for biofilms developed on small graphite fiber brushes. After gamma irradiation, biocathodes exhibited a decrease in current density approaching that of abiotic controls. Electrochemical impedance spectroscopy showed six-fold lower charge transfer resistance with viable biofilm. Pyrosequencing data showed that Proteobacteria and Firmicutes dominated the biofilms. Acidithiobacillus representatives were enriched in some biocathodes, supporting the potential importance of these known iron and sulfur oxidizers as cathodic biocatalysts. Other acidophilic chemolithoautotrophs identified included Sulfobacillus and Leptospirillum species. The presence of chemoautotrophs was consistent with functional capabilities predicted by PICRUSt related to carbon fixation pathways in prokaryotic microorganisms. Acidophilic or acidotolerant heterotrophs were also abundant; however, their contribution to cathodic performance is unknown. This study directs subsequent research efforts to particular groups of AMD-associated bacteria that are electrochemically active on cathodes.

  14. Nucleophilic addition to olefins. 7. Kinetic deuterium isotope effects as criterion for an enforced preassociation mechanism in the hydrolysis of substituted benzylidene Meldrum's acids

    International Nuclear Information System (INIS)

    Bernasconi, C.F.; Leonarduzzi, G.D.

    1982-01-01

    The hydrolysis of the title compounds occurs in four steps: (1) nucleophilic attack by water or hydroxide ion to form the addition complex T/sub OH/ - ; (2) carbon protonation of T/sub OH/ - to form T/sub OH/ 0 ; (3) oxygen deprotonation of T/sub OH/ 0 to form T/sub OH/ 0 - ; (4) collapse of the tetrahedral intermediate T/sub OH/ - into the respective benzaldehyde and Meldrum's acid anion. There is also a water-catalyzed collapse of T/sub OH/ 0 which becomes dominant in strongly acidic solution. In basic solution carbon protonation of T/sub OH/ - (step 2) is rate limiting; in strongly acidic media the water-catalyzed collapse of T/sub OH/ 0 is rate limiting for all substrates. In moderatly acidic solution two types of behavior were observed. With the p-nitro derivative step 4 is rate limiting at high, step 3 at low buffer concentrations. The latter situation is equivalent to a diffusion-controlled trapping mechanism in the reverse direction. With the parent and the p-methoxy derivative, collapse of T/sub OH/ 0 - occurs before the protonated base catalyst generated in step 3 can diffuse away; this is equivalent to an enforced preassociation mechanism in the reverse direction and is analogous to the reaction of thiol anions with acetaldehyde studied by Gilbert and Jencks. Our interpretation is strongly supported by (1) α secondary kinetic deuterium isotope effects which are large for the preassociation mechanism but essentially nil for the trapping mechanism and (2) by Bronsted #betta# values around 0.8 in the case of the preassociation mechanism and 1.0 for the trapping mechanism. The mechanism for the water-catalyzed collapse of T/sub OH/ 0 - is probably concerted, a conclusion which is supported by a large positive deviation from the Bronsted plot for base catalysis and by a large α secondary kinetic deuterium isotope effect

  15. Engineering D-Amino Acid Containing Collagen Like Peptide at the Cleavage Site of Clostridium histolyticum Collagenase for Its Inhibition.

    Directory of Open Access Journals (Sweden)

    Punitha Velmurugan

    Full Text Available Collagenase is an important enzyme which plays an important role in degradation of collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism of this degradation has not yet been completely understood. In the field of biomedical and protein engineering, the design and development of new peptide based materials is of main concern. In the present work an attempt has been made to study the effect of DAla in collagen like peptide (imino-poor region of type I collagen on the structure and stability of peptide against enzyme hydrolysis. Effect of replacement of DAla in the collagen like peptide has been studied using circular dichroic spectroscopy (CD. Our findings suggest that, DAla substitution leads to conformational changes in the secondary structure and favours the formation of polyproline II conformation than its L-counterpart in the imino-poor region of collagen like peptides. Change in the chirality of alanine at the cleavage site of collagenase in the imino-poor region inhibits collagenolytic activity. This may find application in design of peptides and peptidomimics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins.

  16. The cholesterol, fatty acid and triglyceride synthesis pathways regulated by site 1 protease (S1P) are required for efficient replication of severe fever with thrombocytopenia syndrome virus.

    Science.gov (United States)

    Urata, Shuzo; Uno, Yukiko; Kurosaki, Yohei; Yasuda, Jiro

    2018-06-12

    Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by the SFTS virus (SFTSV), which has a high mortality rate. Currently, no licensed vaccines or therapeutic agents have been approved for use against SFTSV infection. Here, we report that the cholesterol, fatty acid, and triglyceride synthesis pathways regulated by S1P is involved in SFTSV replication, using CHO-K1 cell line (SRD-12B) that is deficient in site 1 protease (S1P) enzymatic activity, PF-429242, a small compound targeting S1P enzymatic activity, and Fenofibrate and Lovastatin, which inhibit triglyceride and cholesterol synthesis, respectively. These results enhance our understanding of the SFTSV replication mechanism and may contribute to the development of novel therapies for SFTSV infection. Copyright © 2018. Published by Elsevier Inc.

  17. 11beta-hydroxysteroid dehydrogenase complementary deoxyribonucleic acid in rainbow trout: cloning, sites of expression, and seasonal changes in gonads.

    Science.gov (United States)

    Kusakabe, Makoto; Nakamura, Ikumi; Young, Graham

    2003-06-01

    11beta-Hydroxysteroid dehydrogenases (11beta-HSDs) are important steroidogenic enzymes for catalyzing the interconversion of active glucocorticoid (cortisol and corticosterone) and inert 11-keto forms (cortisone and 11-dehydrocorticosterone) in mammals. In teleosts, 11beta-HSD also plays a role in the production of the predominant androgen, 11-ketotestosterone, in male fish. In this study we cloned cDNAs encoding rainbow trout 11beta-HSD (rt11beta-HSD) from testes and head kidney. The predicted amino acid sequence, hydrophobicity analysis, and transient transfection assays with rt11beta-HSD in HEK293 cells showed that rt11beta-HSD is a homolog of mammalian 11beta-HSD type 2. rt11beta-HSD transcripts are present in steroidogenic tissues and in a number of other tissues. Strong in situ hybridization signals for rt11beta-HSD transcripts were found in Leydig cells of testes, in thecal cells of the early vitellogenic ovarian follicles, and in thecal and granulosa cells of the midvitellogenic and postovulatory follicles. Weaker signals were also found in head kidney interrenal cells from juvenile rainbow trout. Seasonal changes in rt11beta-HSD transcripts in testes showed a pattern similar to that of stress-induced serum cortisol levels, but not to serum androgen levels. High levels of rt11beta-HSD transcripts were found in ovarian follicles from late vitellogenesis through ovulation. These results raise the possibility of a role for rt11beta-HSD in the protection of developing gonads from the inhibitory effects of stress-induced cortisol.

  18. Uncoupled hydrogen and volatile fatty acids generation in a two-step biotechnological anaerobic process fed with actual site wastewater.

    Science.gov (United States)

    Monti, Matilde; Scoma, Alberto; Martinez, Gonzalo; Bertin, Lorenzo; Fava, Fabio

    2015-05-25

    Among agro-wastes, olive mill wastewater (OMW) truly qualifies as a high impact organic residue due to its biochemical-rich composition and high annual production. In the present investigation, dephenolized OMW (OMWdeph) was employed as the feedstock for a biotechnological two-stage anaerobic process dedicated to the production of biohydrogen and volatile fatty acids (VFAs), respectively. To this end, two identically configured packed-bed biofilm reactors were operated sequentially. In the first, the hydraulic retention time was set to 1 day, whereas in the second it was equal to 5 days. The rationale was to decouple the hydrolysis of the organic macronutrients held by the OMWdeph, so as to quantitatively generate a biogas enriched in H2 (first stage aim), for the acidogenesis of the residual components left after hydrolysis, to then produce a highly concentrated mixture of VFAs (second stage aim). Results showed that the generation of H2 and VFAs was effectively split, with carbohydrates and lipids, respectively, being the main substrates of the two processes. About 250 ml H2 L(-1) day(-1) was produced, corresponding to a yield of 0.36 mol mol(-1) of consumed carbohydrates (expressed as glucose equivalents). The overall concentration of VFAs in the acidogenic process was 13.80 g COD L(-1), so that 2.76 g COD L(-1) day(-1) was obtained. Second generation biorefineries use a selected fraction of an organic waste to conduct a microbiologically-driven pathway towards the generation of one target molecule. With the proposed approach, a greater value of the waste was attained, since the multi-purpose two-stage process did not entail competition for substrates between the first and the second steps. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Probing the active site of MIO-dependent 2,3-aminomutases, key catalysts in the biosynthesis of beta-amino acids incorporated in secondary metabolites

    Science.gov (United States)

    Bruner, Steven D.; Cooke, Heather

    2012-01-01

    The tyrosine aminomutase SgTAM produces (S)-β-tyrosine from l-tyrosine in the biosynthesis of the enediyne antitumor antibiotic C-1027. This conversion is promoted by the methylideneimidazole-5-one (MIO) prosthetic group. MIO was first identified in the homologous family of ammonia lyases, which deaminate aromatic amino acids to form α,β-unsaturated carboxylates. Studies of substrate specificity have been described for lyases but there have been no reports in altering the substrate specificity of aminomutases. Furthermore, it remains unclear as to what structural properties are responsible for catalyzing the presumed readdition of the amino group into the α,β-unsaturated intermediates to form β-amino acids. Attempts to elucidate specificity and mechanistic determinants of SgTAM have also proved to be difficult as it is recalcitrant to perturbations to the active site via mutagenesis. An X-ray co-crystal structure of the SgTAM mutant of the catalytic base with l-tyrosine verified important substrate binding residues as well as the enzymatic base. Further mutagenesis revealed that removal of these crucial interactions renders the enzyme inactive. Proposed structural determinants for mutase activity probed via mutagenesis, time-point assays and X-ray crystallography revealed a complicated role for these residues in maintaining key quaternary structure properties that aid in catalysis. PMID:20577998

  20. Sonolytic and Silent Polymerization of Methacrlyic Acid Butyl Ester Catalyzed by a New Onium Salt with bis-Active Sites in a Biphasic System — A Comparative Investigation

    Directory of Open Access Journals (Sweden)

    Perumberkandgai A. Vivekanand

    2013-02-01

    Full Text Available Currently, ingenious new analytical and process experimental techniques which are environmentally benign techniques, viz., ultrasound irradiation, have become immensely popular in promoting various reactions. In this work, a novel soluble multi-site phase transfer catalyst (PTC viz., 1,4-bis-(propylmethyleneammounium chloridebenzene (BPMACB was synthesized and its catalytic efficiency was assessed by observing the kinetics of sonolytic polymerization of methacrylic acid butyl ester (MABE using potassium persulphate (PPS as an initiator. The ultrasound–multi-site phase transfer catalysis (US-MPTC-assisted polymerization reaction was compared with the silent (non-ultrasonic polymerization reaction. The effects of the catalyst and various reaction parameters on the catalytic performance were in detail investigated by following the kinetics of polymerization of MABE in an ethyl acetate-water biphasic system. From the detailed kinetic investigation we propose a plausible mechanism. Further the kinetic results demonstrate clearly that ultrasound-assisted phase-transfer catalysis significantly increased the reaction rate when compared to silent reactions. Notably, this environmentally benign and cost-effective process has great potential to be applied in various polymer industries.

  1. Acid-generating salts and their relationship to the chemistry of groundwater and storm runoff at an abandoned mine site in southwestern Indiana, USA

    International Nuclear Information System (INIS)

    Bayless, E.R.; Olyphant, G.A.

    1993-01-01

    Cation distributions in twenty samples of acid-generating salts were compared to those in groundwater and storm runoff from a coal-refuse deposit in an effort to identify source-product relationships. Two mineral suites, one primarily composed of melanterite, rozenite and szomolnokite, and the other composed almost entirely of copiapite, were found to be most abundant at the study site. Comparisons of cation distributions in salts with those in water samples led to an hypothesis that a copiapite-rich suite precipitated from vadose-zone groundwater that was brought to the surface by evaporative forcing. The copiapite-rich suite, which contained larger concentrations of aluminum, calcium and zinc than the melanterite-rozenite-szomolnokite mineral suite, was the primary source of solutes in captured storm runoff. An analysis of samples collected during a summer thunderstorm indicated that the chemistry of surface runoff varied little with time or with distance downstream. The cation distributions in samples of groundwater indicated that iron-rich pore waters observed near the surface in late autumn may have influenced water chemistry in the deeper portions of the unsaturated zone during the 1989 recharge season. The results of this study show that the solutes produced by the two observed salt suites can be distinguished by their mole percent iron and that the source-product relationships can explain observed variability in mine drainage chemistry at the study site

  2. Mechanism of hydrodenitrogenation. Final report, September 1, 1989--August 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, R.

    1992-11-30

    In this project it was proposed that the selectivity of the HDN reaction can be affected by an alteration of the catalyst acidity since it is possible that an acidic Hofmann-like deamination C--N--C bonds. Such a possibility was verified in this work by studying the denitrogenation of piperidine over acidic catalysts, and it was demonstrated that Bronsted acid sites are active for the denitrogenation of N-heterocycles, whereas Lewis sites are not. To better understand the role of acidic sites in the presence of hydrogenation and hydrogenolysis sites, molybdena was supposed on a series of acidic aluminas, and the resulting new acidity and molybdic phases were characterized. The oxidized catalysts supported on silica-aluninas showed increases from 3 to 150% of weak, medium and strong acid sites, which were produced by the molybdena phases. The new acidity was both of Lewis and Bronsted type, the predominance of one over the other depending upon support composition, as well as on loading and state of oxidation of Mo. High-alumina supports and low Mo loading favor dispersed Mo species, in particular bidentate and monodentate di-oxo Mo species. The latter is responsible for the new Bronsted acidity. Coordinative unsaturation of polymolybdates is responsible for the new Lewis acidity, which is increased upon reduction of Mo. High-silica supports favor monodentate species (high Bronsted acidity) up to 4 wt % MoO{sub 3}. Beyond that, polymolybdate species and Lewis acidity predominate. The nature of the reduced molybdena phases is obviously affected by support composition. The HDN reaction of pyridine was utilized to assess the variation in activity and selectivity produced by the nature of the support.

  3. Mechanism of hydrodenitrogenation

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, R.

    1992-11-30

    In this project it was proposed that the selectivity of the HDN reaction can be affected by an alteration of the catalyst acidity since it is possible that an acidic Hofmann-like deamination C--N--C bonds. Such a possibility was verified in this work by studying the denitrogenation of piperidine over acidic catalysts, and it was demonstrated that Bronsted acid sites are active for the denitrogenation of N-heterocycles, whereas Lewis sites are not. To better understand the role of acidic sites in the presence of hydrogenation and hydrogenolysis sites, molybdena was supposed on a series of acidic aluminas, and the resulting new acidity and molybdic phases were characterized. The oxidized catalysts supported on silica-aluninas showed increases from 3 to 150% of weak, medium and strong acid sites, which were produced by the molybdena phases. The new acidity was both of Lewis and Bronsted type, the predominance of one over the other depending upon support composition, as well as on loading and state of oxidation of Mo. High-alumina supports and low Mo loading favor dispersed Mo species, in particular bidentate and monodentate di-oxo Mo species. The latter is responsible for the new Bronsted acidity. Coordinative unsaturation of polymolybdates is responsible for the new Lewis acidity, which is increased upon reduction of Mo. High-silica supports favor monodentate species (high Bronsted acidity) up to 4 wt % MoO[sub 3]. Beyond that, polymolybdate species and Lewis acidity predominate. The nature of the reduced molybdena phases is obviously affected by support composition. The HDN reaction of pyridine was utilized to assess the variation in activity and selectivity produced by the nature of the support.

  4. Biogeochemical Regeneration of a Nodule Mining Disturbance Site: Trace Metals, DOC and Amino Acids in Deep-Sea Sediments and Pore Waters

    Directory of Open Access Journals (Sweden)

    Sophie A. L. Paul

    2018-04-01

    Full Text Available Increasing interest in deep-sea mineral resources, such as polymetallic nodules, calls for environmental research about possible impacts of mineral exploitation on the deep-sea ecosystem. So far, little geochemical comparisons of deep-sea sediments before and after mining induced disturbances have been made, and thus long-term environmental effects of deep-sea mining are unknown. Here we present geochemical data from sediment cores from an experimental disturbance area at 4,100 m water depth in the Peru Basin. The site was revisited in 2015, 26 years after a disturbance experiment mimicking nodule mining was carried out and compared to sites outside the experimental zone which served as a pre-disturbance reference. We investigated if signs of the disturbance are still visible in the solid phase and the pore water after 26 years or if pre-disturbance conditions have been re-established. Additionally, a new disturbance was created during the cruise and sampled 5 weeks later to compare short- and longer-term impacts. The particulate fraction and pore water were analyzed for major and trace elements to study element distribution and processes in the surface sediment. Pore water and bottom water samples were also analyzed for oxygen, nitrate, dissolved organic carbon, and dissolved amino acids, to examine organic matter degradation processes. The study area of about 11 km2 was found to be naturally more heterogeneous than expected, requiring an analysis of spatial variability before the disturbed and undisturbed sites can be compared. The disturbed sites exhibit various disturbance features: some surface sediments were mixed through, others had the top layer removed and some had additional material deposited on top. Pore water constituents have largely regained pre-disturbance gradients after 26 years. The solid phase, however, shows clear differences between disturbed and undisturbed sites in the top 20 cm so that the impact is still visible in the

  5. Chemical characteristics of dicarboxylic acids and related organic compounds in PM2.5 during biomass-burning and non-biomass-burning seasons at a rural site of Northeast China.

    Science.gov (United States)

    Cao, Fang; Zhang, Shi-Chun; Kawamura, Kimitaka; Liu, Xiaoyan; Yang, Chi; Xu, Zufei; Fan, Meiyi; Zhang, Wenqi; Bao, Mengying; Chang, Yunhua; Song, Wenhuai; Liu, Shoudong; Lee, Xuhui; Li, Jun; Zhang, Gan; Zhang, Yan-Lin

    2017-12-01

    Fine particulate matter (PM2.5) samples were collected using a high-volume air sampler and pre-combusted quartz filters during May 2013 to January 2014 at a background rural site (47 ∘ 35 N, 133 ∘ 31 E) in Sanjiang Plain, Northeast China. A homologous series of dicarboxylic acids (C 2 -C 11 ) and related compounds (oxoacids, α-dicarbonyls and fatty acids) were analyzed by using a gas chromatography (GC) and GC-MS method employing a dibutyl ester derivatization technique. Intensively open biomass-burning (BB) episodes during the harvest season in fall were characterized by high mass concentrations of PM2.5, dicarboxylic acids and levoglucosan. During the BB period, mass concentrations of dicarboxylic acids and related compounds were increased by up to >20 times with different factors for different organic compounds (i.e., succinic (C 4 ) acid > oxalic (C 2 ) acid > malonic (C 3 ) acid). High concentrations were also found for their possible precursors such as glyoxylic acid (ωC 2 ), 4-oxobutanoic acid, pyruvic acid, glyoxal, and methylglyoxal as well as fatty acids. Levoglucosan showed strong correlations with carbonaceous aerosols (OC, EC, WSOC) and dicarboxylic acids although such good correlations were not observed during non-biomass-burning seasons. Our results clearly demonstrate biomass burning emissions are very important contributors to dicarboxylic acids and related compounds. The selected ratios (e.g., C 3 /C 4 , maleic acid/fumaric acid, C 2 /ωC 2 , and C 2 /levoglucosan) were used as tracers for secondary formation of organic aerosols and their aging process. Our results indicate that organic aerosols from biomass burning in this study are fresh without substantial aging or secondary production. The present chemical characteristics of organic compounds in biomass-burning emissions are very important for better understanding the impacts of biomass burning on the atmosphere aerosols. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Binding of 3,4,5,6-Tetrahydroxyazepanes to the Acid-[beta]-glucosidase Active Site: Implications for Pharmacological Chaperone Design for Gaucher Disease

    Energy Technology Data Exchange (ETDEWEB)

    Orwig, Susan D.; Tan, Yun Lei; Grimster, Neil P.; Yu, Zhanqian; Powers, Evan T.; Kelly, Jeffery W.; Lieberman, Raquel L. (Scripps); (GIT)

    2013-03-07

    Pharmacologic chaperoning is a therapeutic strategy being developed to improve the cellular folding and trafficking defects associated with Gaucher disease, a lysosomal storage disorder caused by point mutations in the gene encoding acid-{beta}-glucosidase (GCase). In this approach, small molecules bind to and stabilize mutant folded or nearly folded GCase in the endoplasmic reticulum (ER), increasing the concentration of folded, functional GCase trafficked to the lysosome where the mutant enzyme can hydrolyze the accumulated substrate. To date, the pharmacologic chaperone (PC) candidates that have been investigated largely have been active site-directed inhibitors of GCase, usually containing five- or six-membered rings, such as modified azasugars. Here we show that a seven-membered, nitrogen-containing heterocycle (3,4,5,6-tetrahydroxyazepane) scaffold is also promising for generating PCs for GCase. Crystal structures reveal that the core azepane stabilizes GCase in a variation of its proposed active conformation, whereas binding of an analogue with an N-linked hydroxyethyl tail stabilizes GCase in a conformation in which the active site is covered, also utilizing a loop conformation not seen previously. Although both compounds preferentially stabilize GCase to thermal denaturation at pH 7.4, reflective of the pH in the ER, only the core azepane, which is a mid-micromolar competitive inhibitor, elicits a modest increase in enzyme activity for the neuronopathic G202R and the non-neuronopathic N370S mutant GCase in an intact cell assay. Our results emphasize the importance of the conformational variability of the GCase active site in the design of competitive inhibitors as PCs for Gaucher disease.

  7. Fluorescence quenching of graphene oxide combined with the site-specific cleavage of restriction endonuclease for deoxyribonucleic acid demethylase activity assay

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Lijuan; Qian, Yingdan; Wu, Ping; Zhang, Hui; Cai, Chenxin, E-mail: cxcai@njnu.edu.cn

    2015-04-15

    Highlights: • An approach for sensitive and selective DNA demethylase activity assay is reported. • This assay is based on the fluorescence quenching of GO and site-specific cleavage of endonuclease. • It can determine as low as 0.05 ng mL{sup −1} of MBD2 with a linear range of 0.2–300 ng mL{sup −1}. • It has an ability to recognize MBD2 from other possibly coexisting proteins and cancer cell extracts. • It can avoid false signals, requiring no bisulfite conversion, PCR amplification, radioisotope-labeling. - Abstract: We report on the development of a sensitive and selective deoxyribonucleic acid (DNA) demethylase (using MBD2 as an example) activity assay by coupling the fluorescence quenching of graphene oxide (GO) with the site-specific cleavage of HpaII endonuclease to improve the selectivity. This approach was developed by designing a single-stranded probe (P1) that carries a binding region to facilitate the interaction with GO, which induces fluorescence quenching of the labeled fluorophore (FAM, 6-carboxyfluorescein), and a sensing region, which contains a hemi-methylated site of 5′-CmCGG-3′, to specifically recognize the target (T1, a 32-mer DNA from the promoter region of p53 gene) and hybridize with it to form a P1/T1 duplex. After demethylation with MBD2, the duplex can be specifically cleaved using HpaII, which releases the labeled FAM from the GO surface and results in the recovery of fluorescence. However, this cleavage is blocked by the hemi-methylation of this site. Thus, the magnitude of the recovered fluorescence signal is related to the MBD2 activity, which establishes the basis of the DNA demethylase activity assay. This assay can determine as low as ∼(0.05 ± 0.01) ng mL{sup −1} (at a signal/noise of 3) of MBD2 with a linear range of 0.2–300 ng mL{sup −1} and recognize MBD2 from other possibly coexisting proteins and cancer cell extracts. The advantage of this assay is its ability to avoid false signals and no

  8. The Fatty Acid Profile Analysis of Cyperus laxus Used for Phytoremediation of Soils from Aged Oil Spill-Impacted Sites Revealed That This Is a C18:3 Plant Species.

    Directory of Open Access Journals (Sweden)

    Noemí Araceli Rivera Casado

    Full Text Available The effect of recalcitrant hydrocarbons on the fatty acid profile from leaf, basal corm, and roots of Cyperus laxus plants cultivated in greenhouse phytoremediation systems of soils from aged oil spill-impacted sites containing from 16 to 340 g/Kg total hydrocarbons (THC was assessed to investigate if this is a C18:3 species and if the hydrocarbon removal during the phytoremediation process has a relationship with the fatty acid profile of this plant. The fatty acid profile was specific to each vegetative organ and was strongly affected by the hydrocarbons level in the impacted sites. Leaf extracts of plants from uncontaminated soil produced palmitic acid (C16, octadecanoic acid (C18:0, unsaturated oleic acids (C18:1-C18:3, and unsaturated eichosanoic (C20:2-C20:3 acids with a noticeable absence of the unsaturated hexadecatrienoic acid (C16:3; this finding demonstrates, for the first time, that C. laxus is a C18:3 plant. In plants from the phytoremediation systems, the total fatty acid contents in the leaf and the corm were negatively affected by the hydrocarbons presence; however, the effect was positive in root. Interestingly, under contaminated conditions, unusual fatty acids such as odd numbered carbons (C15, C17, C21, and C23 and uncommon unsaturated chains (C20:3n6 and C20:4 were produced together with a remarkable quantity of C22:2 and C24:0 chains in the corm and the leaf. These results demonstrate that weathered hydrocarbons may drastically affect the lipidic composition of C. laxus at the fatty acid level, suggesting that this species adjusts the cover lipid composition in its vegetative organs, mainly in roots, in response to the weathered hydrocarbon presence and uptake during the phytoremediation process.

  9. The Fatty Acid Profile Analysis of Cyperus laxus Used for Phytoremediation of Soils from Aged Oil Spill-Impacted Sites Revealed That This Is a C18:3 Plant Species

    Science.gov (United States)

    Montes Horcasitas, María del Carmen; Rodríguez Vázquez, Refugio; Esparza García, Fernando José; Pérez Vargas, Josefina; Ariza Castolo, Armando; Ferrera-Cerrato, Ronald; Gómez Guzmán, Octavio

    2015-01-01

    The effect of recalcitrant hydrocarbons on the fatty acid profile from leaf, basal corm, and roots of Cyperus laxus plants cultivated in greenhouse phytoremediation systems of soils from aged oil spill-impacted sites containing from 16 to 340 g/Kg total hydrocarbons (THC) was assessed to investigate if this is a C18:3 species and if the hydrocarbon removal during the phytoremediation process has a relationship with the fatty acid profile of this plant. The fatty acid profile was specific to each vegetative organ and was strongly affected by the hydrocarbons level in the impacted sites. Leaf extracts of plants from uncontaminated soil produced palmitic acid (C16), octadecanoic acid (C18:0), unsaturated oleic acids (C18:1-C18:3), and unsaturated eichosanoic (C20:2-C20:3) acids with a noticeable absence of the unsaturated hexadecatrienoic acid (C16:3); this finding demonstrates, for the first time, that C. laxus is a C18:3 plant. In plants from the phytoremediation systems, the total fatty acid contents in the leaf and the corm were negatively affected by the hydrocarbons presence; however, the effect was positive in root. Interestingly, under contaminated conditions, unusual fatty acids such as odd numbered carbons (C15, C17, C21, and C23) and uncommon unsaturated chains (C20:3n6 and C20:4) were produced together with a remarkable quantity of C22:2 and C24:0 chains in the corm and the leaf. These results demonstrate that weathered hydrocarbons may drastically affect the lipidic composition of C. laxus at the fatty acid level, suggesting that this species adjusts the cover lipid composition in its vegetative organs, mainly in roots, in response to the weathered hydrocarbon presence and uptake during the phytoremediation process. PMID:26473488

  10. The Fatty Acid Profile Analysis of Cyperus laxus Used for Phytoremediation of Soils from Aged Oil Spill-Impacted Sites Revealed That This Is a C18:3 Plant Species.

    Science.gov (United States)

    Rivera Casado, Noemí Araceli; Montes Horcasitas, María del Carmen; Rodríguez Vázquez, Refugio; Esparza García, Fernando José; Pérez Vargas, Josefina; Ariza Castolo, Armando; Ferrera-Cerrato, Ronald; Gómez Guzmán, Octavio; Calva Calva, Graciano

    2015-01-01

    The effect of recalcitrant hydrocarbons on the fatty acid profile from leaf, basal corm, and roots of Cyperus laxus plants cultivated in greenhouse phytoremediation systems of soils from aged oil spill-impacted sites containing from 16 to 340 g/Kg total hydrocarbons (THC) was assessed to investigate if this is a C18:3 species and if the hydrocarbon removal during the phytoremediation process has a relationship with the fatty acid profile of this plant. The fatty acid profile was specific to each vegetative organ and was strongly affected by the hydrocarbons level in the impacted sites. Leaf extracts of plants from uncontaminated soil produced palmitic acid (C16), octadecanoic acid (C18:0), unsaturated oleic acids (C18:1-C18:3), and unsaturated eichosanoic (C20:2-C20:3) acids with a noticeable absence of the unsaturated hexadecatrienoic acid (C16:3); this finding demonstrates, for the first time, that C. laxus is a C18:3 plant. In plants from the phytoremediation systems, the total fatty acid contents in the leaf and the corm were negatively affected by the hydrocarbons presence; however, the effect was positive in root. Interestingly, under contaminated conditions, unusual fatty acids such as odd numbered carbons (C15, C17, C21, and C23) and uncommon unsaturated chains (C20:3n6 and C20:4) were produced together with a remarkable quantity of C22:2 and C24:0 chains in the corm and the leaf. These results demonstrate that weathered hydrocarbons may drastically affect the lipidic composition of C. laxus at the fatty acid level, suggesting that this species adjusts the cover lipid composition in its vegetative organs, mainly in roots, in response to the weathered hydrocarbon presence and uptake during the phytoremediation process.

  11. Three-dimensional hydrogeological modeling to assess the elevated-water-table technique for controlling acid generation from an abandoned tailings site in Quebec, Canada

    Science.gov (United States)

    Ethier, Marie-Pier; Bussière, Bruno; Broda, Stefan; Aubertin, Michel

    2018-01-01

    The Manitou Mine sulphidic-tailings storage facility No. 2, near Val D'Or, Canada, was reclaimed in 2009 by elevating the water table and applying a monolayer cover made of tailings from nearby Goldex Mine. Previous studies showed that production of acid mine drainage can be controlled by lowering the oxygen flux through Manitou tailings with a water table maintained at the interface between the cover and reactive tailings. Simulations of different scenarios were performed using numerical hydrogeological modeling to evaluate the capacity of the reclamation works to maintain the phreatic surface at this interface. A large-scale numerical model was constructed and calibrated using 3 years of field measurements. This model reproduced the field measurements, including the existence of a western zone on the site where the phreatic level targeted is not always met during the summer. A sensitivity analysis was performed to assess the response of the model to varying saturated hydraulic conductivities, porosities, and grain-size distributions. Higher variations of the hydraulic heads, with respect to the calibrated scenario results, were observed when simulating a looser or coarser cover material. Long-term responses were simulated using: the normal climatic data, data for a normal climate with a 2-month dry spell, and a simplified climate-change case. Environmental quality targets were reached less frequently during summer for the dry spell simulation as well as for the simplified climate-change scenario. This study illustrates how numerical simulations can be used as a key tool to assess the eventual performance of various mine-site reclamation scenarios.

  12. Second site escape of a T20-dependent HIV-1 variant by a single amino acid change in the CD4 binding region of the envelope glycoprotein

    Directory of Open Access Journals (Sweden)

    Berkhout Ben

    2006-11-01

    Full Text Available Abstract Background We previously described the selection of a T20-dependent human immunodeficiency virus type-1 (HIV-1 variant in a patient on T20 therapy. The fusion inhibitor T20 targets the viral envelope (Env protein by blocking a conformational switch that is critical for viral entry into the host cell. T20-dependent viral entry is the result of 2 mutations in Env (GIA-SKY, creating a protein that undergoes a premature conformational switch, and the presence of T20 prevents this premature switch and rescues viral entry. In the present study, we performed 6 independent evolution experiments with the T20-dependent HIV-1 variant in the absence of T20, with the aim to identify second site compensatory changes, which may provide new mechanistic insights into Env function and the T20-dependence mechanism. Results Escape variants with improved replication capacity appeared within 42 days in 5 evolution cultures. Strikingly, 3 cultures revealed the same single amino acid change in the CD4 binding region of Env (glycine at position 431 substituted for arginine: G431R. This mutation was sufficient to abolish the T20-dependence phenotype and restore viral replication in the absence of T20. The GIA-SKY-G431R escape variant produces an Env protein that exhibits reduced syncytia formation and reduced cell-cell fusion activity. The escape variant was more sensitive to an antibody acting on an early gp41 intermediate, suggesting that the G431R mutation helps preserve a pre-fusion Env conformation, similar to T20 action. The escape variant was also less sensitive to soluble CD4, suggesting a reduced CD4 receptor affinity. Conclusion The forced evolution experiments indicate that the premature conformational switch of the T20-dependent HIV-1 Env variant (GIA-SKY can be corrected by a second site mutation in Env (GIA-SKY-G431R that affects the interaction with the CD4 receptor.

  13. The DNA binding site specificity and antiproliferative property of ternary Pt(II) and Zn(II) complexes of phenanthroline and N,N'-ethylenediaminediacetic acid.

    Science.gov (United States)

    Nakamura, Yusuke; Taruno, Yoko; Sugimoto, Masashi; Kitamura, Yusuke; Seng, Hoi Ling; Kong, Siew Ming; Ng, Chew Hee; Chikira, Makoto

    2013-03-14

    The binding site specificity of the ternary complexes, [M(II)(phen)(edda)] (M(II) = Pt(2+) and Zn(2+); phen = 1,10-phenanthroline; edda = N,N'-ethylenediaminediacetic acid), for the self-complementary oligonucleotides (ODNs), ds(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12))(2) (ODN1) and ds(C(1)G(2)C(3)G(4)T(5)A(6)T(7)A(8)C(9)G(10)C(11)G(12))(2) (ODN2), was studied by NMR measurements. The results indicated that [Pt(ii)(phen)(edda)] was partially intercalated between C(3)/G(10) and G(4)/C(9) base pairs of ODN1 and ODN2 in the major grooves, whereas [Zn(II)(phen)(edda)] was bound specifically to the TATA region of ODN2 in the minor groove and to the terminal G(2)/C(11) base pair of ODN1 in the major groove. The preference for the TATA sequence over the AATT sequence in the binding of [Zn(phen)(edda)] was attributed to the wider minor groove width of the TATA sequence. The bindings of the complexes to ct-DNA were also studied by UV, CD, and fluorescence spectroscopy. Additionally, the antiproliferative property of [Pt(II)(phen)(edda)] towards MCF7 breast cancer cells and normal MCF10-A cells was compared with that of [Zn(II)(phen)(edda)].

  14. Acidic gases, ammonia and water-soluble ions in PM 2.5 at a coastal site in the Pearl River Delta, China

    Science.gov (United States)

    Hu, Min; Wu, Zhijun; Slanina, J.; Lin, Peng; Liu, Shang; Zeng, Limin

    Real-time measurements of acidic trace gases (HCl, HNO 3, HONO, and SO 2), ammonia, and water-soluble ions in PM 2.5 were conducted at Xinken, a coastal site downwind of Guangzhou, from 4 October to 4 November 2004, as part of the Pearl River Delta (PRD) intensive field campaign. The average concentrations of HCl, HONO, HNO 3, SO 2, and NH 3 are 2.8, 2.9, 6.3, 55.4, and 7.3 μg m -3, respectively, and 2.4, 7.2, 24.1, and 9.2 μg m -3 for Cl -, NO 3-, SO 42-, and NH 4+ in PM 2.5. The diurnal variations of both HCl and HNO 3 showed higher concentrations during daytime and lower concentrations at night, and aerosol Cl - and NO 3- showed an opposite diurnal patterns to HCl and HNO 3. The diurnal variation of NH 3 showed the similar pattern to that of aerosol NH 4+ with lower concentration during daytime and higher concentration at night. The average concentration of SO 2 during daytime was higher than that at night. The transportation of urban plumes to the sampling site could explain the higher concentration of SO 2 during daytime. HONO showed a clear diurnal variation with lower concentration during daytime and higher concentration at night. The HONO concentrations were positively correlated with the particle surface area concentrations, suggesting the formation of HONO through the heterogeneous conversion on particle surfaces could be significant. The ionic charge balance analysis included the cations derived from filter measurements indicates that the contribution of the cations in fine particle (PM 1.8) to the charge balance is not pronounced. The theoretical equilibrium constant ( Ke) of NH 4NO 3 is higher than the observed concentration product ( Km=[NH 3]×[HNO 3]) during daytime, and lower than Km at night. This indicates that the atmospheric conditions during the sampling period did not favor the formation of NH 4NO 3 during daytime.

  15. Positron spectroscopy studies of zeolites

    Science.gov (United States)

    Hung, Ku-Jung

    The lineshapes of two-dimensional angular correlation of electron-positron annihilation radiation (2D-ACAR) in alumina and several zeolites were measured as a function of internal surface areas. In all cases, the lineshape parameter S from 2D-ACAR spectra were found to vary proportionally with internal surface area. In order to investigate the Bronsted acidity in NaHY zeolite, the lineshape parameter evaluation from 2D-ACAR measurements for varied acidity in NaHY zeolites by ion-exchange and thermal desorption were presented. The result from this investigation has demonstrated that the Bronsted acidity in NaHY zeolite was found to vary linearly with the lineshape parameter of the angular correlation spectrum of the sample. The lineshapes of 2D-ACAR spectra were determined for different base adsorbed HY-zeolite samples under a temperature controlled heating system in order to investigate, in-situ, the acid strength and number of Bronsted acid sites in the sample. Results have shown that the lineshape parameter of the angular correlation spectrum of the sample increases with the strength of adsorbed base and decreases with the number of Bronsted acid sites in the sample. This indicated that the lineshape parameter is sensitive to all of the strengths and concentrations of Bronsted acid sites in the HY-zeolite samples. The result from this study has also demonstrated that the large size base, pyridine, would reduce the possibility of positronium formation in the sample by filling the cage to eliminate the internal surface areas where the positroniums are likely to form. However, the small size base, ammonia, did not show any effect on the internal surface areas. Owing to the fact that this technique monitors only the Bronsted acid sites that situate on the surface which relates to the catalytic activity, there is little ambiguity about the location of the source of information obtained. The findings presented in this dissertation point out the fact that such lineshape

  16. Increasing the Thermostable Sugar-1-Phosphate Nucleotidylyltransferase Activities of the Archaeal ST0452 Protein through Site Saturation Mutagenesis of the 97th Amino Acid Position.

    Science.gov (United States)

    Honda, Yuki; Zang, Qian; Shimizu, Yasuhiro; Dadashipour, Mohammad; Zhang, Zilian; Kawarabayasi, Yutaka

    2017-02-01

    The ST0452 protein is a bifunctional protein exhibiting sugar-1-phosphate nucleotidylyltransferase (sugar-1-P NTase) and amino-sugar-1-phosphate acetyltransferase activities and was isolated from the thermophilic archaeon Sulfolobus tokodaii Based on the previous observation that five single mutations increased ST0452 sugar-1-P NTase activity, nine double-mutant ST0452 proteins were generated with the intent of obtaining enzymes exhibiting a further increase in catalysis, but all showed less than 15% of the wild-type N-acetyl-d-glucosamine-1-phosphate uridyltransferase (GlcNAc-1-P UTase) activity. The Y97A mutant exhibited the highest activity of the single-mutant proteins, and thus site saturation mutagenesis of the 97th position (Tyr) was conducted. Six mutants showed both increased GlcNAc-1-P UTase and glucose-1-phosphate uridyltransferase activities, eight mutants showed only enhanced GlcNAc-1-P UTase activity, and six exhibited higher GlcNAc-1-P UTase activity than that of the Y97A mutant. Kinetic analyses of three typical mutants indicated that the increase in sugar-1-P NTase activity was mainly due to an increase in the apparent k cat value. We hypothesized that changing the 97th position (Tyr) to a smaller amino acid with similar electronic properties would increase activity, and thus the Tyr at the corresponding 103rd position of the Escherichia coli GlmU (EcGlmU) enzyme was replaced with the same residues. The Y103N mutant EcGlmU showed increased GlcNAc-1-P UTase activity, revealing that the Tyr at the 97th position of the ST0452 protein (103rd position in EcGlmU) plays an important role in catalysis. The present results provide useful information regarding how to improve the activity of natural enzymes and how to generate powerful enzymes for the industrial production of sugar nucleotides. It is typically difficult to increase enzymatic activity by introducing substitutions into a natural enzyme. However, it was previously found that the ST0452 protein

  17. Adsorption of ammonia on vanadium-antimony mixed oxides

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, Hernan; German, Estefania [Departamento e Instituto de Fisica del Sur, Universidad Nacional del Sur-CONICET, Avda. Alem 1253, (8000) Bahia Blanca (Argentina); Juan, Alfredo, E-mail: cajuan@uns.edu.ar [Departamento e Instituto de Fisica del Sur, Universidad Nacional del Sur-CONICET, Avda. Alem 1253, (8000) Bahia Blanca (Argentina); Irigoyen, Beatriz [Departamento de Ingenieria Quimica, Facultad de Ingenieria, Universidad de Buenos Aires, Pabellon de Industrias, Ciudad Universitaria, (1428) Ciudad Autonoma de Buenos Aires (Argentina)

    2012-02-01

    We analyzed the adsorption of ammonia (NH{sub 3}) on the VSbO{sub 4}(1 1 0) catalyst surface using density functional theory (DFT) calculations. We followed the evolution of the chemical bonds between different atoms of the resulting NH{sub 3}/VSbO{sub 4} system and the changes in the electronic structure of the catalyst. NH{sub 3} preferential adsorption geometries were analyzed through the crystal orbital overlap population (COOP) concept and the density of states (DOS) curves. The VSbO{sub 4}(1 1 0) surface exhibits Lewis and Bronsted acid sites on which the ammonia molecule can interact. On the Lewis acid site, NH{sub 3} adsorption resulted in the interaction between the N and a surface V-isolated cation. On Bronsted acid site, N interacted with a surface H coming from the chemical dissociation of water. The COOP analysis indicate that NH{sub 3} interaction on the VSbO{sub 4}(1 1 0) surface is weak. In addition, the DOS curves show more developed electronic interactions for NH{sub 3} adsorption on Lewis acid site than over Bronsted acid site.

  18. Ibotenic acid and thioibotenic acid

    DEFF Research Database (Denmark)

    Hermit, Mette B; Greenwood, Jeremy R; Nielsen, Birgitte

    2004-01-01

    In this study, we have determined and compared the pharmacological profiles of ibotenic acid and its isothiazole analogue thioibotenic acid at native rat ionotropic glutamate (iGlu) receptors and at recombinant rat metabotropic glutamate (mGlu) receptors expressed in mammalian cell lines....... Thioibotenic acid has a distinct pharmacological profile at group III mGlu receptors compared with the closely structurally related ibotenic acid; the former is a potent (low microm) agonist, whereas the latter is inactive. By comparing the conformational energy profiles of ibotenic and thioibotenic acid...... with the conformations preferred by the ligands upon docking to mGlu1 and models of the other mGlu subtypes, we propose that unlike other subtypes, group III mGlu receptor binding sites require a ligand conformation at an energy level which is prohibitively expensive for ibotenic acid, but not for thioibotenic acid...

  19. Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose-5-phosphate binding

    DEFF Research Database (Denmark)

    Willemoës, Martin; Nilsson, Dan; Hove-Jensen, Bjarne

    1996-01-01

    The three conserved aspartic acid residues of the 5-phospho-d-ribosyl a-1-diphosphate binding site (213-GRDCVLVDDMIDTGGT-228) of Escherichia coli phosphoribosyl diphosphate synthetase were studied by analysis of the mutant enzymes D220E, D220F, D221A, D224A, and D224S. The mutant enzymes showed...... enzymes were dependent on the metal ion present, suggesting a function of the investigated aspartic acid residues both in the binding of ribose 5-phosphate, possibly via a divalent metal ion, and in the interaction with a divalent metal ion during catalysis....

  20. Site-specific antibodies distinguish single amino acid substitutions in position 57 in HLA-DQ beta-chain alleles associated with insulin-dependent diabetes

    DEFF Research Database (Denmark)

    Atar, D; Dyrberg, T; Michelsen, Birgitte

    1989-01-01

    The HLA-DQ beta-chain gene shows a close association with susceptibility or resistance to autoimmune insulin-dependent diabetes mellitus (IDDM) and it has been suggested that the amino acid in position 57 may be of pathogenetic importance. To study the expression of the IDDM associated HLA-DQ beta......-chain alleles, we immunized rabbits with 12 to 13 amino acid long peptides representing HLA-DQw7 and -DQw8 allelic sequences, differing only by one amino acid in position 57 being aspartic acid (Asp) and alanine (Ala), respectively. Immunoblot analysis of lymphoblastoid cells showed that several antisera...

  1. Acquisition of a novel eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site confers intracellular cleavage of an H7N7 influenza virus hemagglutinin

    International Nuclear Information System (INIS)

    Hamilton, Brian S.; Sun, Xiangjie; Chung, Changik; Whittaker, Gary R.

    2012-01-01

    A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appear to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.

  2. Acquisition of a novel eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site confers intracellular cleavage of an H7N7 influenza virus hemagglutinin

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, Brian S.; Sun, Xiangjie; Chung, Changik [Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY 14853 (United States); New York Center of Excellence for Influenza Research and Surveillance, University of Rochester Medical Center, Rochester NY 14627 (United States); Whittaker, Gary R., E-mail: grw7@cornell.edu [Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY 14853 (United States); New York Center of Excellence for Influenza Research and Surveillance, University of Rochester Medical Center, Rochester NY 14627 (United States)

    2012-12-05

    A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appear to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.

  3. Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

    Science.gov (United States)

    Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

    2016-02-23

    In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

  4. Spatial and temporal characteristics of PM2.5 acidity during autumn in marine and coastal area of Bohai Sea, China, based on two-site contrast

    Science.gov (United States)

    Zhou, Ming; Zhang, Yufen; Han, Yan; Wu, Jianhui; Du, Xiang; Xu, Hong; Feng, Yinchang; Han, Suqin

    2018-04-01

    In-situ pH of atmospheric particulate, defined as the pH value of aqueous phase in ambient aerosol, has been reported to have significant influence on the formation progress of secondary aerosol, especially through the heterogeneous pathway. In this study, PM2.5 samples were collected in the marine and costal area of Bohai Sea from September 8th to October 8th in 2013, with daytime and nighttime separated. Eight water-soluble ions including SO42 -, NO3-, Cl-, NH4+, K+, Ca2 +, Na+ and Mg2 + were analyzed by ion chromatography. The in-situ pH of PM2.5 was estimated using Aerosol Inorganics Model II, with meteorological parameters (temperature and relative humidity) and basic chemical composition data (concentrations of water-soluble ions) serving as input. Five indicators were conjunctively applied to describe the spatial and temporal characteristics of PM2.5 acidity over Bohai Sea during autumn. As a result, strong acidity was found in both marine and coastal area. Marine area had a stronger acidity under a more NH4+-deficiency and humid condition. And the difference of PM2.5 acidity between daytime and nighttime was more obvious in coastal area than that in marine area, with stronger acidity observed during the daytime. Local SO2 emission was identified as an important factor influencing the diurnal variation of aerosol acidity. Meanwhile, sulfurous species were identified as a mixture of NH4HSO4 and H2SO4 in marine area while a mixture of NH4HSO4 and (NH4)2SO4 in the coastal area. Analysis in the impact of aerosol acidity on nitrate formation has indicated that heterogeneous pathways were important in nitrate formation in coastal area of Bohai Sea as well as the homogeneous pathways.

  5. Conversion of the low affinity ouabain-binding site of non-gastric H,K-ATPase into a high affinity binding site by substitution of only five amino acids.

    NARCIS (Netherlands)

    Qiu, L.Y.; Swarts, H.G.P.; Tonk, E.C.; Willems, P.H.G.M.; Koenderink, J.B.; Pont, J.J.H.H.M. de

    2006-01-01

    P-type ATPases of the IIC subfamily exhibit large differences in sensitivity toward ouabain. This allows a strategy in which ouabain-insensitive members of this subfamily are used as template for mutational elucidation of the ouabain-binding site. With this strategy, we recently identified seven

  6. Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

    Science.gov (United States)

    Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

    2016-06-07

    As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. The acidic functional groups of humic acid

    Energy Technology Data Exchange (ETDEWEB)

    Shanxiang, Li; Shuhe, Sun; Zhai Zongxi, Wu Qihu

    1983-09-01

    The acidic functional groups content, pK value, DELTAH and DELTAS of humic acid (HA) and nitro-humic acid (NHA) were determined by potentiometry, conductometry and calorimetric titration. The thermodynamic parameters of carboxylic groups and phenolic hydroxyl groups of humic acid are similar to that of simple hydroxy-benzoic acid. The configuration sites of acidic functional groups in humic acid from different coals are different. The carbonyl groups on aromatic rings are probably ortho to phenolic -OH for HA and NHA extracted from Huangxian's brown coal and Japanese lignite, while those from Lingshi's weathered coal are not. The weak -COOH groups of the latter possess higher chemical activity. The -COOH content in HA increases, phenolic -OH group decreases and the chemical acidity of acidic functional groups increases when HA is oxidized by nitric acid. (14 refs.)

  8. Piracetam Defines a New Binding Site for Allosteric Modulators of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors§

    Science.gov (United States)

    Ahmed, Ahmed H.; Oswald, Robert E.

    2010-01-01

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to both GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators. PMID:20163115

  9. Piracetam defines a new binding site for allosteric modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors.

    Science.gov (United States)

    Ahmed, Ahmed H; Oswald, Robert E

    2010-03-11

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators.

  10. Daytime formation of nitrous acid at a coastal remote site in Cyprus indicating a common ground source of atmospheric HONO and NO

    NARCIS (Netherlands)

    Meusel, Hannah; Kuhn, Uwe; Reiffs, Andreas; Mallik, Chinmay; Harder, Hartwig; Martinez, Monica; Schuladen, Jan; Bohn, Birger; Parchatka, Uwe; Crowley, John N.; Fischer, Horst; Tomsche, Laura; Novelli, Anna; Hoffmann, Thorsten; Janssen, Ruud H.H.; Hartogensis, Oscar; Pikridas, Michael; Vrekoussis, Mihalis; Bourtsoukidis, Efstratios; Weber, Bettina; Lelieveld, Jos; Williams, Jonathan; Pöschl, Ulrich; Cheng, Yafang; Su, Hang

    2016-01-01

    Characterization of daytime sources of nitrous acid (HONO) is crucial to understand atmospheric oxidation and radical cycling in the planetary boundary layer. HONO and numerous other atmospheric trace constituents were measured on the Mediterranean island of Cyprus during the CYPHEX (Cyprus

  11. Biosynthetic origin of acetic acid using SNIF-NMR; Determinacao da origem biossintetica de acido acetico atraves da tecnica 'Site Specific Natural Isotopic Fractionation Studied by Nuclear Magnetic Resonance (SNIF-NMR)'

    Energy Technology Data Exchange (ETDEWEB)

    Boffo, Elisangela Fabiana; Ferreira, Antonio Gilberto [Sao Carlos Univ., SP (Brazil). Dept. de Quimica

    2006-05-15

    The main purpose of this work is to describe the use of the technique Site-Specific Natural Isotopic Fractionation of hydrogen (SNIF-NMR), using {sup 2}H and {sup 1}H NMR spectroscopy, to investigate the biosynthetic origin of acetic acid in commercial samples of Brazilian vinegar. This method is based on the deuterium to hydrogen ratio at a specific position (methyl group) of acetic acitained by fermentation, through different biosynthetic mechanisms, which result in different isotopic ratios. We measured the isotopic ratio of vinegars obtained through C{sub 3}, C{sub 4}, and CAM biosynthetic mechanisms, blends of C{sub 3} and C{sub 4} (agrins) and synthetic acetic acid. (author)

  12. Specific labeling of the thyroxine binding site in thyroxine-binding globulin: determination of the amino acid composition of a labeled peptide fragment isolated from a proteolytic digest of the derivatized protein.

    Science.gov (United States)

    Tabachnick, M; Perret, V

    1987-08-01

    [125I] Thyroxine has been covalently bound to the thyroxine binding site in thyroxine-binding globulin by reaction with the bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene. An average of 0.47 mol of [125I] thyroxine was incorporated per mol protein; nonspecific binding amounted to 8%. A labeled peptide fragment was isolated from a proteolytic digest of the derivatized protein by HPLC and its amino acid composition was determined. Comparison with the amino acid sequence of thyroxine-binding globulin indicated partial correspondence of the labeled peptide with two possible regions in the protein. These regions also coincide with part of the barrel structure present in the closely homologous protein, alpha 1-antitrypsin.

  13. USE OF AN EQUILIBRIUM MODEL TO FORECAST DISSOLUTION EFFECTIVENESS, SAFETY IMPACTS, AND DOWNSTREAM PROCESSABILITY FROM OXALIC ACID AIDED SLUDGE REMOVAL IN SAVANNAH RIVER SITE HIGH LEVEL WASTE TANKS 1-15

    International Nuclear Information System (INIS)

    KETUSKY, EDWARD

    2005-01-01

    This thesis details a graduate research effort written to fulfill the Magister of Technologiae in Chemical Engineering requirements at the University of South Africa. The research evaluates the ability of equilibrium based software to forecast dissolution, evaluate safety impacts, and determine downstream processability changes associated with using oxalic acid solutions to dissolve sludge heels in Savannah River Site High Level Waste (HLW) Tanks 1-15. First, a dissolution model is constructed and validated. Coupled with a model, a material balance determines the fate of hypothetical worst-case sludge in the treatment and neutralization tanks during each chemical adjustment. Although sludge is dissolved, after neutralization more is created within HLW. An energy balance determines overpressurization and overheating to be unlikely. Corrosion induced hydrogen may overwhelm the purge ventilation. Limiting the heel volume treated/acid added and processing the solids through vitrification is preferred and should not significantly increase the number of glass canisters

  14. Modelando a coordenação de fosfato com o sítio ativo das fosfatases ácidas púrpuras Modeling the coordination of phosphate to the active site of purple acid phosphatases

    OpenAIRE

    Marcos Aires de Brito; Ademir Neves; Luiz R. Zilli

    1997-01-01

    We present a new binuclear complex, Fe2III(BBPMP)(OH)(O2 P(OPh)2) ClO4.CH3OH, 3, where BBPMP is the anion of 2,6-bis(2-hydroxybenzyl)(2-pyridylmethyl) aminomethyl-4-methylphenol, as a suitable model for the chromophoric site of purple acid phosphatases coordinated to phosphate. The complex was obtained by the reaction of complex 2, Fe2III(BBPMP)(O2P(OPh) 2)2 ClO4.H2O, in CH3CN with one equivalent of triethylamine. Based on the chromophoric properties of the model complex, lmax = 560 nm/ e = 4...

  15. Characterization of N-type glycosylation sites and glycan structures of Purple Acid Phosphatase Phytases from Wheat (Triticum aestivum L.)

    DEFF Research Database (Denmark)

    Dionisio, Giuseppe; Brinch-Pedersen, Henrik; Welinder, Karen Gjesing

    2011-01-01

    Wheat (Triticum aestivum L.) possesses preformed phytase activity in the grain that is essential to make phosphate available to cell metabolism and in food and feed (Brejnholt S. et al., 2011). Cereals contain the purple acid phosphatase type of phytases, PAPhy (Dionisio G. et al., 2011a). Mature......., Skov L. Brinch-Pedersen H. (2011). The degradation of phytate by microbial and wheat phytases is dependent on the phytate matrix and the phytase origin. J. Sci. Food Agri. (in press). Dionisio G., Madsen C.K., Holm P.B., Welinder K.G., Jørgensen M., Stoger E., Arcalis E., Brinch-Pedersen H. (2011a......) Cloning and Characterization of Purple Acid Phosphatase Phytases from Wheat (Triticum aestivum L.), Barley (Hordeum vulgare L.), Maize (Zea maize L.) and Rice (Oryza sativa L.). Plant Physiol. [in press, Jan 10, Epub ahead of print] Dionisio G., Brinch-Pedersen H., Welinder K.G., Jørgensen M. (2011b...

  16. Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding

    International Nuclear Information System (INIS)

    Vaezeslami, Soheila; Jia, Xiaofei; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H.

    2008-01-01

    A water network stabilizes the structure of cellular retionic acid binding protein II. The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the α2 helix at its entrance. This chain of interactions acts as a ‘pillar’ that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the α2 helix adopting an altered conformation compared with wild-type CRABPII

  17. Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots.

    Science.gov (United States)

    Missihoun, Tagnon D; Kotchoni, Simeon O; Bartels, Dorothea

    2016-01-01

    Plant aldehyde dehydrogenases (ALDHs) play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.

  18. Active Sites of Reduced Epidermal Fluorescence1 (REF1 Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots.

    Directory of Open Access Journals (Sweden)

    Tagnon D Missihoun

    Full Text Available Plant aldehyde dehydrogenases (ALDHs play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.

  19. Characterization of limestone reacted with acid-mine drainage in a pulsed limestone bed treatment system at the Friendship Hill National Historical Site, Pennsylvania, USA

    Science.gov (United States)

    Hammarstrom, J.M.; Sibrell, P.L.; Belkin, H.E.

    2003-01-01

    Armoring of limestone is a common cause of failure in limestone-based acid-mine drainage (AMD) treatment systems. Limestone is the least expensive material available for acid neutralization, but is not typically recommended for highly acidic, Fe-rich waters due to armoring with Fe(III) oxyhydroxide coatings. A new AMD treatment technology that uses CO2 in a pulsed limestone bed reactor minimizes armor formation and enhances limestone reaction with AMD. Limestone was characterized before and after treatment with constant flow and with the new pulsed limestone bed process using AMD from an inactive coal mine in Pennsylvania (pH = 2.9, Fe = 150 mg/l, acidity = 1000 mg/l CaCO3). In constant flow experiments, limestone is completely armored with reddish-colored ochre within 48 h of contact in a fluidized bed reactor. Effluent pH initially increased from the inflow pH of 2.9 to over 7, but then decreased to 6 during operation. Limestone removed from a pulsed bed pilot plant is a mixture of unarmored, rounded and etched limestone grains and partially armored limestone and refractory mineral grains (dolomite, pyrite). The ???30% of the residual grains in the pulsed flow reactor that are armored have thicker (50- to 100-??m), more aluminous coatings and lack the gypsum rind that develops in the constant flow experiment. Aluminium-rich zones developed in the interior parts of armor rims in both the constant flow and pulsed limestone bed experiments in response to pH changes at the solid/solution interface. ?? 2003 Elsevier Ltd. All rights reserved.

  20. The site of net absorption of Ca from the intestinal tract of growing pigs and effect of phytic acid, Ca level and Ca source on Ca digestibility.

    Science.gov (United States)

    González-Vega, J Caroline; Walk, Carrie L; Liu, Yanhong; Stein, Hans H

    2014-01-01

    An experiment was conducted to test the hypothesis that the standardised digestibility of Ca in calcium carbonate and Lithothamnium calcareum Ca is not different regardless of the level of dietary Ca, and that phytic acid affects the digestibility of Ca in these two ingredients to the same degree. The objectives were to determine where in the intestinal tract Ca absorption takes place and if there are measurable quantities of basal endogenous Ca fluxes in the stomach, small intestine or large intestine. Diets contained calcium carbonate or L. calcareum Ca as the sole source of Ca, 0% or 1% phytic acid and 0.4% or 0.8% Ca. A Ca-free diet was also formulated and used to measure endogenous fluxes and losses of Ca. Nine growing pigs (initial body weight 23.8 ± 1.3 kg) were cannulated in the duodenum and in the distal ileum, and faecal, ileal and duodenal samples were collected. Duodenal endogenous fluxes of Ca were greater (p calcareum Ca diets, but that was not the case if calcium carbonate was the source of Ca (interaction, p calcareum Ca was greater (p calcareum Ca. In conclusion, under the conditions of this experiment, standardised digestibility of Ca is not affected by the level of phytic acid, but may be affected by dietary Ca level depending on the Ca source. Calcium from calcium carbonate is mostly absorbed before the duodenum, but Ca from L. calcareum Ca is mostly absorbed in the jejunum and ileum.

  1. Structural and catalytic characterization of mechanical mixtures of Pt/WOx-ZrO2 and Al2O3

    International Nuclear Information System (INIS)

    Contreras, J.L.; Fuentes, G.A.; Navarrete, J.; Vazquez, A.; Zeifert, B.; Salmones, J.; Nuno, L.

    2010-01-01

    The effect of the Bronsted/Lewis acid ratio on isomerization of n-heptane using Al 2 O 3 as a source of Lewis acidity and WOx/ZrO 2 as a source of Bronsted and Lewis acidity was studied and controlled using mechanical mixtures of these solids. These mixtures were characterized by surface area, infrared spectroscopy of pyridine, X-ray diffraction and Raman spectroscopy. It was found that the presence of W=O stretching mode which was consistent with the presence of oxotungstate species which were the precursors of the acid sites. It was found out that as the oxotungstate structures increased, the selectivity to n-heptane isomers increased while the hydrocracking and dehydrocyclization selectivity decreased. The presence of Bronsted acidity of the WOx/ZrO 2 domains, the increase of Knudsen diffusivity and the loss of Pt metallic area by strong interaction of the Pt with the WOx/ZrO 2 explain this catalytic behavior.

  2. Structural and catalytic characterization of mechanical mixtures of Pt/WOx-ZrO{sub 2} and Al{sub 2}O{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Contreras, J.L., E-mail: jlcl@correo.azc.uam.m [Universidad Autonoma Metropolitana-Azcapotzalco, CBI, Dpto. Energia, Av. Sn. Pablo 180, Col. Reynosa, C.P. 02200, Mexico, DF (Mexico); Fuentes, G.A. [Universidad Autonoma Metropolitana-Iztapalapa, CBI, Depto. de IPH C.P. 09340, Mexico, DF (Mexico); Navarrete, J.; Vazquez, A. [Instituto Mexicano del Petroleo, IBP, Ger. de Catalizadores, Eje Central Lazaro Cardenas No. 152, C.P. 07300, Mexico, DF (Mexico); Zeifert, B.; Salmones, J. [Instituto Politecnico Nacional Mexico, ESIQIE, Laboratorio de Catalisis y Materiales, C.P. 07738, Mexico, DF (Mexico); Nuno, L. [Universidad Autonoma Metropolitana-Azcapotzalco, CBI, Dpto. Energia, Av. Sn. Pablo 180, Col. Reynosa, C.P. 02200, Mexico, DF (Mexico)

    2010-04-16

    The effect of the Bronsted/Lewis acid ratio on isomerization of n-heptane using Al{sub 2}O{sub 3} as a source of Lewis acidity and WOx/ZrO{sub 2} as a source of Bronsted and Lewis acidity was studied and controlled using mechanical mixtures of these solids. These mixtures were characterized by surface area, infrared spectroscopy of pyridine, X-ray diffraction and Raman spectroscopy. It was found that the presence of W=O stretching mode which was consistent with the presence of oxotungstate species which were the precursors of the acid sites. It was found out that as the oxotungstate structures increased, the selectivity to n-heptane isomers increased while the hydrocracking and dehydrocyclization selectivity decreased. The presence of Bronsted acidity of the WOx/ZrO{sub 2} domains, the increase of Knudsen diffusivity and the loss of Pt metallic area by strong interaction of the Pt with the WOx/ZrO{sub 2} explain this catalytic behavior.

  3. PM{sub 2.5} acidity at a background site in the Pearl River Delta region in fall-winter of 2007–2012

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Xiaoxin [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (China); Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hong Kong (China); Shenzhen Research Institute, Hong Kong Polytechnic University (China); Guo, Hai, E-mail: ceguohai@polyu.edu.hk [Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hong Kong (China); Shenzhen Research Institute, Hong Kong Polytechnic University (China); Wang, Xinming, E-mail: wangxm@gig.ac.cn [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (China); Ding, Xiang; He, Quanfu; Liu, Tengyu; Zhang, Zhou [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (China)

    2015-04-09

    Highlights: • 24-h PM{sub 2.5} samples were collected in fall-winter of 2007–2012. • The annual reduction trends of [H{sup +}]{sub total} and [H{sup +}]{sub in-situ} of PM{sub 2.5} was −32 ± 1.5 and −9 ± 1.7 nmol m{sup −3}, respectively. • On hazy days, the concentration of OM showed significant enhancement when [H{sup +}]{sub in-situ} ranged from 85 to 240 nmol m{sup −3}. • [H{sup +}]{sub in-situ} presented a close relationship with NO{sub 3}{sup −} formation mechanisms in low and high acidity of PM{sub 2.5}. - Abstract: Based on field observations and thermodynamic model simulation, the annual trend of PM{sub 2.5} acidity and its characteristics on non-hazy and hazy days in fall-winter of 2007–2012 in the Pearl River Delta region were investigated. Total acidity ([H{sup +}]{sub total}) and in-situ acidity ([H{sup +}]{sub in-situ}) of PM{sub 2.5} significantly decreased (F-test, p < 0.05) at a rate of −32 ± 1.5 nmol m{sup −3} year{sup −1} and −9 ± 1.7 nmol m{sup −3} year{sup −1}, respectively. The variation of acidity was mainly caused by the change of the PM{sub 2.5} component, i.e., the decreasing rates of [H{sup +}]{sub total} and [H{sup +}]{sub in-situ} due to the decrease of sulfate (SO{sub 4}{sup 2−}) exceeded the increasing rate caused by the growth of nitrate (NO{sub 3}{sup −}). [H{sup +}]{sub total}, [H{sup +}]{sub in-situ} and liquid water content on hazy days were 0.9–2.2, 1.2–3.5 and 2.0–3.0 times those on non-hazy days, respectively. On hazy days, the concentration of organic matter (OM) showed significant enhancement when [H{sup +}]{sub in-situ} increased (t-test, p < 0.05), while this was not observed on non-hazy days. Moreover, when the acidity was low (i.e., R = [NH{sub 4}{sup +}]/(2 × [SO{sub 4}{sup 2−}] + [NO{sub 3}{sup −}]) > 0.6), NH{sub 4}NO{sub 3} was most likely formed via homogenous reaction. When the acidity was high (R ≤ 0.6), the gas-phase formation of NH{sub 4}NO{sub 3} was

  4. Site and extent of digestion, duodenal flow, and intestinal disappearance of total and esterified fatty acids in sheep fed a high-concentrate diet supplemented with high-linoleate safflower oil.

    Science.gov (United States)

    Atkinson, R L; Scholljegerdes, E J; Lake, S L; Nayigihugu, V; Hess, B W; Rule, D C

    2006-02-01

    Our objective was to determine duodenal and ileal flows of total and esterified fatty acids and to determine ruminal fermentation characteristics and site and extent of nutrient digestion in sheep fed an 80% concentrate diet supplemented with high-linoleate (77%) safflower oil at 0, 3, 6, and 9% of DM. Oil was infused intraruminally along with an isonitrogenous basal diet (fed at 2% of BW) that contained bromegrass hay, cracked corn, corn gluten meal, urea, and limestone. Four crossbred wethers (BW = 44.3 +/- 15.7 kg) fitted with ruminal, duodenal, and ileal cannulas were used in a 4 x 4 Latin square experiment, in which 14 d of dietary adaptation were followed by 4 d of duodenal, ileal, and ruminal sampling. Fatty acid intake increased (linear, P = 0.004 to 0.001) with increased dietary safflower oil. Digestibilities of OM, NDF, and N were not affected (P = 0.09 to 0.65) by increased dietary safflower oil. For total fatty acids (free plus esterified) and esterified fatty acids, duodenal flow of most fatty acids, including 18:2c-9,c-12, increased (P = 0.006 to 0.05) with increased dietary oil. Within each treatment, duodenal flow of total and esterified 18:2c-9,c-12 was similar (P = 0.32), indicating that duodenal flow of this fatty acid occurred because most of it remained esterified. Duodenal flow of esterified 18:1t-11 increased (P = 0.08) with increased dietary safflower oil, indicating that reesterification of ruminal fatty acids occurred. Apparent small intestinal disappearance of most fatty acids was not affected (P = 0.19 to 0.98) by increased dietary safflower oil, but increased (P = 0.05) for 18:2c-9,c-12, which ranged from 87.0 to 97.4%, and for 18:2c-9,t-11 (P = 0.03), which ranged from 37.9% with no added oil to 99.2% with supplemental oil. For esterified fatty acids, apparent small intestinal disappearance was from 80% for 18:3c-9,c-12,c-15 at the greatest level of dietary oil up to 100% for 18:1t-11 and 18:1c-12 with 0% oil. We concluded that

  5. Influence of amino acid residues near the active site of cytochrome P450 from Bacillus megaterium on the selectivity of n-octane oxidation to octanol regioisomers

    Science.gov (United States)

    Miyaji, Akimitsu; Baba, Toshihide

    2017-09-01

    A mutant of cytochrome P450 from Bacillus megaterium (CYP450BM-3) was prepared by replacing two alanine residues around active site of the enzyme, alanine 328 and alanine 82, with leucine and tryptophan, respectively. The CYP450BM-3 mutant produced 2-octanol selectively from n-octane under atmospheric temperature and pressure; its selectivity was 74%. Furthermore, the mutant produced 1-octanol, which is not produced by wild-type enzyme.

  6. Bromopyruvate, an active site-directed inactivator of E. coli 2-keto-4-hydroxyglutarate(KHG) aldolase, modifies glutamic acid residue-45

    International Nuclear Information System (INIS)

    Vlahos, C.J.; Dekker, E.E.

    1987-01-01

    E. coli KHG-aldolase (2-keto-4-hydroxyglutarate ↔ pyruvate + glyoxylate), a novel trimeric Class I aldolase, requires one active-site lysine residue (Lys 133)/subunit for Schiff-base formation as well as one arginine residue (Arg 49)/subunit for catalytic activity. The substrate analog, 3-bromopyruvate (BRPY), causes a time- and concentration-dependent loss of KHG-aldolase activity. This inactivation is regarded as active site-directed since: (a) BRPY modification results in complete loss of enzymatic activity; (b) saturation kinetics are exhibited, suggesting that a reversible complex is formed between the aldolase and BRPY prior to the rate-limiting inactivation step; (c) over 90% of the initial aldolase activity is protected by either substrate, pyruvate or KHG; (d) 1.1 mol of 14 C-BRPY is bound/enzyme subunit. Peptide isolation and sequencing show that the incorporated radioactivity is associated with residue Glu-45. Denaturation of the enzyme with guanidine x HCl following treatment with excess 14 C-BRPY allows for the incorporation of carbon-14 at Cys-159 and Cys-180 as well. The presence of pyruvate protects Glu-45 from being esterified but does not prevent the alkylation of the two cysteine residues. These results suggest that Glu-45 is essential for the catalytic activity of E. coli KHG-aldolase, most likely functioning as the active-site amphoteric proton donor/acceptor moiety that is involved in the overall mechanism of the reaction catalyzed by this enzyme

  7. Inhibitors of acid secretion can benefit gastric wound repair independent of luminal pH effects on the site of damage

    Science.gov (United States)

    Demitrack, Elise S; Aihara, Eitaro; Kenny, Susan; Varro, Andrea; Montrose, Marshall H

    2012-01-01

    Background and aims The authors’ goal was to measure pH at the gastric surface (pHo) to understand how acid secretion affects the repair of microscopic injury to the gastric epithelium. Methods Microscopic gastric damage was induced by laser light, during confocal/two-photon imaging of pH-sensitive dyes (Cl-NERF, BCECF) that were superfused over the mucosal surface of the exposed gastric corpus of anaesthetised mice. The progression of repair was measured in parallel with pHo. Experimental conditions included varying pH of luminal superfusates, and using omeprazole (60 mg/kg ip) or famotidine (30 mg/kg ip) to inhibit acid secretion. Results Similar rates of epithelial repair and resting pHo values (~pH 4) were reported in the presence of luminal pH 3 or pH 5. Epithelial repair was unreliable at luminal pH 2 and pHo was lower (2.5±0.2, P pH 3). Epithelial repair was slower at luminal pH 7 and pHo was higher (6.4±0.1, PpH 3 or pH 7, omeprazole reduced maximal damage size and accelerated epithelial repair, although only at pH 3 did omeprazole further increase surface pH above the level caused by imposed damage. At luminal pH 7, famotidine also reduced maximal damage size and accelerated epithelial repair. Neither famotidine nor omeprazole raised plasma gastrin levels during the time course of the experiments. Conclusions Epithelial repair in vivo is affected by luminal pH variation, but the beneficial effects of acutely blocking acid secretion extend beyond simply raising luminal and/or surface pH. PMID:21997560

  8. Implementation of an ex situ stabilization technique at the Sand Springs superfund site to solidify and stabilize acid tar sludges involving a quick-lime based stabilization process and innovative equipment design

    International Nuclear Information System (INIS)

    McManus, R.W.; Grajczak, P.; Wilcoxson, J.C.; Webster, S.D.

    1997-01-01

    An old refinery site was safely remediated a year before schedule and for 25% less than final engineering estimates for the stabilization remedy thanks to energetic project management and innovative design involving ex situ stabilization/solidification of acid tar sludges. A quicklime based process, Dispersion by Chemical Reaction (DCR trademark), was employed to solidify and stabilize (SS) over 103,000 cubic meters (135,000 cubic yards) of petroleum waste, mostly acidic tarry sludge. The SS process was selected over competing methods because it afforded minimal volume increase, could readily achieve Record of Decision (ROD) specified physical and chemical treatment goals, could be implemented with treatment equipment that minimized emissions, and could be performed with low reagent usage and at low cost. To ensure treatment goals were achieved and an accelerated schedule met, a custom designed and fabricated transportable treatment unit (TTU) was employed to implement the process. The treated material was visually soil-like in character, it was left in stockpiles for periods of time, and it was placed and compacted in the on site landfill using standard earth-moving equipment

  9. Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Ou, Yu-Yen

    2016-07-30

    Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase. The convert process is involved in producing ATP which provides energy in a lot of cellular processes. In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Therefore, predicting FAD binding sites in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. We used an independent data set to evaluate the performance of the proposed method, which had an accuracy of 69.84 %. We compared the performance of the proposed method in analyzing two newly discovered electron transport protein sequences with that of the general FAD binding predictor presented by Mishra and Raghava and determined that the accuracy of the proposed method improved by 9-45 % and its Matthew's correlation coefficient was 0.14-0.5. Furthermore, the proposed method enabled reducing the number of false positives significantly and can provide useful information for biologists. We developed a method that is based on PSSM profiles and SAAPs for identifying FAD binding sites in newly discovered electron transport protein sequences. This approach achieved a significant improvement after we added SAAPs to PSSM features to analyze FAD binding proteins in the electron transport chain. The proposed method can serve as an effective tool for predicting FAD binding sites in electron

  10. The dapE-encoded N-succinyl-L,L-Diaminopimelic Acid Desuccinylase from Haemophilus influenzae Contains two Active Site Histidine Residues

    OpenAIRE

    Gillner, Danuta M.; Bienvenue, David L.; Nocek, Boguslaw P.; Joachimiak, Andrzej; Zachary, Vincentos; Bennett, Brian; Holz, Richard C.

    2008-01-01

    The catalytic and structural properties of the H67A and H349A altered dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from H. influenzae were investigated. Based on sequence alignment with CPG2 both H67 and H349 were predicted to be Zn(II) ligands. Catalytic activity was observed for the H67A altered DapE enzyme which exhibited kcat = 1.5 ± 0.5 sec−1 and Km = 1.4 ± 0.3 mM. No catalytic activity was observed for H349A under the experimental conditions used. The EPR and ele...

  11. Application of polyacrylic acid-poly-N,N-dimethyldiallylammonium chloride polyelectrolyte complexes for structuring of polluted soil of Semipalatinsk nuclear test site

    International Nuclear Information System (INIS)

    Sabantseva, T.; Bashenova, A.; Orazzhanova, L.K.; Yashkarova, M.G.; Bimendina, L.A.

    2002-01-01

    The present communication is devoted to investigation of structuring efficiency of polyacrylic acid-poly-N,N-dimethyldiallylammonium chloride (PAA-PDMDAACI) polyelectrolyte complexes. The granulometric analysis of selected soil samples before and after the treatment of aqueous solution of PAA, PDMDAACI and PAA-PDMDAACI complexes at different molar ratio of polymer components and polymer concentrations was carried out. Analysis shows that nonstoichiometric polyelectrolyte complex [PAA]:[PDMDAACI]=3:1 possesses the best structuring effect. But this result is worse than in the case using of [PAA]:[polyethylene glycol]=1:1 inter-polymer complex

  12. Systemic administration of kainic acid induces selective time dependent decrease in [125I]insulin-like growth factor I, [125I]insulin-like growth factor II and [125I]insulin receptor binding sites in adult rat hippocampal formation

    International Nuclear Information System (INIS)

    Quirion, R.; Chabot, J.-G.; Dore, S.; Seto, D.; Kar, S.

    1997-01-01

    Administration of kainic acid evokes acute seizure in hippocampal pathways that results in a complex sequence of functional and structural alterations resembling human temporal lobe epilepsy. The structural alterations induced by kainic acid include selective loss of neurones in CA1-CA3 subfields and the hilar region of the dentate gyrus followed by sprouting and permanent reorganization of the synaptic connections of the mossy fibre pathways. Although the neuronal degeneration and process of reactive synaptogenesis have been extensively studied, at present little is known about means to prevent pathological conditions leading to kainate-induced cell death. In the present study, to address the role of insulin-like growth factors I and II, and insulin in neuronal survival as well as synaptic reorganization following kainate-induced seizure, the time course alterations of the corresponding receptors were evaluated. Additionally, using histological preparations, the temporal profile of neuronal degeneration and hypertrophy of resident astroglial cells were also studied. [ 125 I]Insulin-like growth factor I binding was found to be decreased transiently in almost all regions of the hippocampal formation at 12 h following treatment with kainic acid. The dentate hilar region however, exhibited protracted decreases in [ 125 I]insulin-like growth factor I receptor sites throughout (i.e. 30 days) the study. [ 125 I]Insulin-like growth factor II receptor binding sites in the hippocampal formation were found to be differentially altered following systemic administration of kainic acid. A significant decrease in [ 125 I]insulin-like growth factor II receptor sites was observed in CA1 subfield and the pyramidal cell layer of the Ammon's horn at all time points studied whereas the hilar region and the stratum radiatum did not exhibit alteration at any time. A kainate-induced decrease in [ 125 I]insulin receptor binding was noted at all time points in the molecular layer of the

  13. Site-dependent modulating effects of conjugated fatty acids from safflower oil in a rat two-stage carcinogenesis model in female Sprague-Dawley rats.

    Science.gov (United States)

    Kimoto, N; Hirose, M; Futakuchi, M; Iwata, T; Kasai, M; Shirai, T

    2001-07-10

    Modifying effects of dietary administration of conjugated fatty acids from safflower oil (CFA-S), rich in conjugated linoleic acid, on major organs were examined in the post-initiation stage of a two-stage carcinogenesis model in female rats. Groups of 21 or 22 F344 female rats were treated sequentially with 2,2'-dihydroxy-di-n-propylnitosamine (intragastrically, i.g.), 7,12-dimethylbenz[a]anthracene (i.g.), 1,2-dimethylhydrazine (subcutaneously) and N-butyl-N-(4-hydroxybutyl)nitrosamine (in drinking water) during the first 3 weeks for initiation, and then administered diet containing 1 or 0.1% CFA-S for 33 weeks. Further groups of animals were treated with carcinogens or 1% CFA-S alone, or maintained as non-treated controls. All surviving animals were killed at week 36, and major organs were examined histopathologically for development of pre-neoplastic and neoplastic lesions. The 1 and 0.1% CFA-S treatment significantly decreased the incidence and multiplicity of mammary carcinomas, though a clear dose response was not observed. In the urinary bladder, the incidence of papillary or nodular hyperplasia but not tumors was significantly increased in the 1% CFA-S-treated group. The results indicate that low dose CFA-S may find application as a potent chemopreventor of mammary carcinogenesis.

  14. The influence of sampling site and time upon umbilical cord blood acid-base status and PO2 in the newborn infant

    DEFF Research Database (Denmark)

    Paerregaard, A; Nickelsen, C N; Brandi, L

    1987-01-01

    Measurement of umbilical cord blood acid-base status is routinely carried out in many obstetric centers. Umbilical cord blood pH, PO2, PCO2 and SBE (standard base excess) may change between clamping of the cord and analysis due to diffusion and metabolism. It was the aim of this study to evaluate...... partum and pH, PO2 and PCO2 were measured and SBE calculated. As demonstrated in table I, the vein blood pH and PO2 values were higher and PCO2 values lower than in the artery blood. The changes over time are given in figure 1 with the 1 min values as points of reference. Changes within the first 15...... minutes were modest. A significant fall in vein pH, vein SBE and artery PO2 and a significant rise in artery PCO2 was found. Greater variation in the changes over time was found in artery than in vein blood, being most evident for the 30 min values. Although significant changes in the umbilical cord acid...

  15. Using environmental isotopes to characterize hydrologic processes of the Nelson Tunnel acid mine drainage site, West Willow Creek watershed, Creede, CO

    Science.gov (United States)

    Krupicka, A.; Williams, M. W.

    2010-12-01

    Acid mine drainage continues to be a pressing ecological issue across the Mountain West. Traditional remediation strategies usually involve the installation of an expensive and unsightly “end-of-pipe” water treatment plant without a full understanding of the overall hydrology of the system. In this study we show how applying water chemistry techniques to investigate water sources, ages, flow paths and residence times in a watershed affected by acid mine drainage can lead to alternative, less expensive methods of reclamation. We use both radiogenic (3H and 14C) and stable (18O and D) environmental isotopes to age waters and characterize the level of surface and groundwater interaction. Tritium content for waters collected in the tunnel was largely found to be 0-3 TU, indicating an age of greater than 50 years. This was supported by 14C values of DIC in tunnel samples that indicated ages and a hydraulic residence time on the order of hundreds to thousands of years. Stable isotopes 18O and D plotted closely to the Global Meteoric Water Line (GMWL). Combined with the heavy faulting and dominant welded volcanic tuffs of the region, this all indicates a system with very little surface-ground water interaction and a long, deep, likely channelized flow path. A future up-gradient pumping test would help confirm these findings and further elucidate the location and mechanism of the system’s primary recharge to the mine workings.

  16. Functional modulation of cerebral gamma-aminobutyric acidA receptor/benzodiazepine receptor/chloride ion channel complex with ethyl beta-carboline-3-carboxylate: Presence of independent binding site for ethyl beta-carboline-3-carboxylate

    Energy Technology Data Exchange (ETDEWEB)

    Taguchi, J.; Kuriyama, K. (Kyoto Prefectural Univ. of Medicine (Japan))

    1990-05-01

    Effect of ethyl beta-carboline-3-carboxylate (beta-CCE) on the function of gamma-aminobutyric acid (GABA)A receptor/benzodiazepine receptor/chloride ion channel complex was studied. Beta-CCE noncompetitively and competitively inhibited (3H)flunitrazepam binding to benzodiazepine receptor, but not (3H)muscimol binding to GABAA receptor as well as t-(3H)butylbicycloorthobenzoate (( 3H) TBOB) binding to chloride ion channel, in particulate fraction of the mouse brain. Ro15-1788 also inhibited competitively (3H) flunitrazepam binding. On the other hand, the binding of beta-(3H)CCE was inhibited noncompetitively and competitively by clonazepam and competitively by Ro15-1788. In agreement with these results, benzodiazepines-stimulated (3H)muscimol binding was antagonized by beta-CCE and Ro15-1788. Gel column chromatography for the solubilized fraction from cerebral particulate fraction by 0.2% sodium deoxycholate (DOC-Na) in the presence of 1 M KCl indicated that beta-(3H)CCE binding site was eluted in the same fraction (molecular weight, 250,000) as the binding sites for (3H)flunitrazepam, (3H)muscimol and (3H)TBOB. GABA-stimulated 36Cl- influx into membrane vesicles prepared from the bovine cerebral cortex was stimulated and attenuated by flunitrazepam and beta-CCE, respectively. These effects of flunitrazepam and beta-CCE on the GABA-stimulated 36Cl- influx were antagonized by Ro15-1788. The present results suggest that the binding site for beta-CCE, which resides on GABAA receptor/benzodiazepine receptor/chloride ion channel complex, may be different from that for benzodiazepine. Possible roles of beta-CCE binding site in the allosteric inhibitions on benzodiazepine binding site as well as on the functional coupling between chloride ion channel and GABAA receptor are also suggested.

  17. Specificity of the photoreaction of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen with ribonucleic acid. Identificaton of reactive sites in Escherichia coli phenylalanine-accepting transfer ribonucleic acid

    Energy Technology Data Exchange (ETDEWEB)

    Bachellerie, J.P.; Hearst, J.E.

    1982-03-16

    In order to test the potential of psoralen photo-addition for the probing of RNA conformation at sequence resolution, the specificity of the reaction of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) with Escherichia coli tRNA/sup Phe/ was analyzed. The sites of HMT covalent addition have been identified by a combination of analytical techniques involving chemical cleavage of the tRNA/sup Phe/ molecule at the m/sup 7/G site and gel electrophoresis of RNase T/sub 1/ digests together with paper electrophoretic characterization of HMT-modified nucleotides and oligonucleotides. HMT photoaddition shows a very high preference for uracil residues. However, important differences in HMT photoreactivity are observed for various U sites of the tRNA/sup Phe/ molecule. Reactivity of specific bases has been correlated with partial melting of the molecule. Data available so far indicate a strong preference of the photo-reactive probe for a ''loose'' helical conformation as compared with a tight helix, whereas a random coil appears poorly reactive. (JMT)

  18. Micro-ribonucleic acid-binding site variants of type 2 diabetes candidate loci predispose to gestational diabetes mellitus in Chinese Han women.

    Science.gov (United States)

    Wang, Xiaojing; Li, Wei; Ma, Liangkun; Ping, Fan; Liu, Juntao; Wu, Xueyan; Mao, Jiangfeng; Wang, Xi; Nie, Min

    2018-01-20

    Emerging evidence has suggested that the genetic background of gestational diabetes mellitus (GDM) was analogous to type 2 diabetes mellitus. In contrast to type 2 diabetes mellitus, the genetic studies for GDM were limited. Accordingly, the aim of the present study was to extensively explore the influence of micro-ribonucleic acid-binding single-nucleotide polymorphisms (SNPs) in type 2 diabetes mellitus candidate loci on GDM susceptibility in Chinese. A total of 839 GDM patients and 900 controls were enrolled. Six micro-ribonucleic acid-binding SNPs were selected from 30 type 2 diabetes mellitus susceptibility loci and genotyped using TaqMan allelic discrimination assays. The minor allele of three SNPs, PAX4 rs712699 (OR 1.366, 95% confidence interval 1.021-1.828, P = 0.036), KCNB1 rs1051295 (OR 1.579, 95% confidence interval 1.172-2.128, P = 0.003) and MFN2 rs1042842 (OR 1.398, 95% confidence interval 1.050-1.862, P = 0.022) were identified to significantly confer higher a risk of GDM in the additive model. The association between rs1051295 and increased fasting plasma glucose (b = 0.006, P = 0.008), 3-h oral glucose tolerance test plasma glucose (b = 0.058, P = 0.025) and homeostatic model assessment of insulin resistance (b = 0.065, P = 0.017) was also shown. Rs1042842 was correlated with higher 3-h oral glucose tolerance test plasma glucose (b = 0.056, P = 0.028). However, no significant correlation between the other included SNPs (LPIN1 rs1050800, VPS26A rs1802295 and NLRP3 rs10802502) and GDM susceptibility were observed. The present findings showed that micro-ribonucleic acid-binding SNPs in type 2 diabetes mellitus candidate loci were also associated with GDM susceptibility, which further highlighted the similar genetic basis underlying GDM and type 2 diabetes mellitus. © 2018 The Authors. Journal of Diabetes Investigation published by Asian Association for the Study of Diabetes (AASD) and John Wiley & Sons Australia, Ltd.

  19. Evolutionary conservativeness of electric field in the Cu,Zn superoxide dismutase active site. Evidence for co-ordinated mutation of charged amino acid residues.

    Science.gov (United States)

    Desideri, A; Falconi, M; Polticelli, F; Bolognesi, M; Djinovic, K; Rotilio, G

    1992-01-05

    Equipotential lines were calculated, using the Poisson-Boltzmann equation, for six Cu,Zn superoxide dismutases with different protein electric charge and various degrees of sequence homology, namely those from ox, pig, sheep, yeast, and the isoenzymes A and B from the amphibian Xenopus laevis. The three-dimensional structures of the porcine and ovine superoxide dismutases were obtained by molecular modelling reconstruction using the structure of the highly homologous bovine enzyme as a template. The three-dimensional structure of the evolutionary distant yeast Cu,Zn superoxide dismutase was recently resolved by us, while computer-modelled structures are available for X. laevis isoenzymes. The six proteins display large differences in the net protein charge and distribution of electrically charged surface residues but the trend of the equipotential lines in the proximity of the active sites was found to be constant in all cases. These results are in line with the very similar catlytic rate constants experimentally measured for the corresponding enzyme activities. This analysis shows that electrostatic guidance for the enzyme-substrate interaction in Cu,Zn superoxide dismutases is related to a spatial distribution of charges, arranged so as to maintain, in the area surrounding the active sites, an identical electrostatic potential distribution, which is conserved in the evolution of this protein family.

  20. Solid acid catalysis from fundamentals to applications

    CERN Document Server

    Hattori, Hideshi

    2014-01-01

    IntroductionTypes of solid acid catalystsAdvantages of solid acid catalysts Historical overviews of solid acid catalystsFuture outlookSolid Acids CatalysisDefinition of acid and base -Brnsted acid and Lewis acid-Acid sites on surfacesAcid strengthRole of acid sites in catalysisBifunctional catalysisPore size effect on catalysis -shape selectivity-Characterization of Solid Acid Catalysts Indicator methodTemperature programmed desorption (TPD) of ammoniaCalorimetry of adsorption of basic moleculesInfrare

  1. Synthesis of a specific monolithic column with artificial recognition sites for L-glutamic acid via cryo-crosslinking of imprinted nanoparticles.

    Science.gov (United States)

    Göktürk, Ilgım; Üzek, Recep; Uzun, Lokman; Denizli, Adil

    2016-06-01

    In this study, a new molecular imprinting (MIP)-based monolithic cryogel column was prepared using chemically crosslinked molecularly imprinted nanoparticles, to achieve a simplified chromatographic separation (SPE) for a model compound, L-glutamic acid (L-Glu). Cryogelation through crosslinking of imprinted nanoparticles forms stable monolithic cryogel columns. This technique reduces the leakage of nanoparticles and increases the surface area, while protecting the structural features of the cryogel for stable and efficient recognition of the template molecule. A non-imprinted monolithic cryogel column (NIP) was also prepared, using non-imprinted nanoparticles produced without the addition of L-Glu during polymerization. The molecularly imprinted monolithic cryogel column (MIP) indicates apparent recognition selectivity and a good adsorption capacity compared to the NIP. Also, we have achieved a significant increase in the adsorption capacity, using the advantage of high surface area of the nanoparticles.

  2. Acid-base relations in epithelium of turtle bladder: site of active step in acidification and role of metabolic CO2.

    Science.gov (United States)

    Steinmetz, P R

    1969-07-01

    The acid-base relations across the two surfaces of the epithelium of the turtle bladder were examined. By means of the 5,5-dimethyl-2,4-oxazolidinedione (DMO) technique the intracellular OH(-) concentration was measured in the presence and absence of a transepithelial pH gradient. When both sides of the bladder were bathed with solutions free of exogenous CO(2) and bicarbonate at pH 7.41 ([OH(-)] = 239 nmoles/liter), the epithelial cells were alkaline, the mean intracellular [OH(-)] being 347nmoles/liter. This alkalinity of the cells was preserved in bladders that secreted H(+) against a gradient of over 2 pH units. In bathing solutions stirred with 4.85% CO(2) and buffered with 25 mM HCO(3) (-) at pH 7.41 the intracellular [OH(-)] was lower than in CO(2)-free solutions and close to the extracellular [OH(-)]. In the CO(2)-free system anaerobiosis caused increased alkalinity of the cells and inhibition of H(+) secretion presumably by decreased metabolic CO(2) production. Carbonic acid inhibitors reduced H(+) secretion, but had no significant effect on the alkalinity of the cells. An inactive analogue of acetazolamide had no effect on H(+) secretion. The results indicate that the active step in acidification is located near the mucosal surface of the epithelium and that the alkali formed within the epithelial cells moves passively into the serosal solution along an electro-chemical gradient. The inhibitory effect of certain sulfonamides on H(+) secretion by the bladder is directly correlated with their known carbonic anhydrase inhibitory activity, but not associated with a measurable change in the mean intracellular [OH(-)].

  3. α-Amino Acid Derived Benzimidazole-Linked Rhodamines: A Case of Substitution Effect at the Amino Acid Site toward Spiro Ring Opening for Selective Sensing of Al3+ Ions.

    Science.gov (United States)

    Majumdar, Anupam; Mondal, Subhendu; Daniliuc, Constantin G; Sahu, Debashis; Ganguly, Bishwajit; Ghosh, Sourav; Ghosh, Utpal; Ghosh, Kumaresh

    2017-08-07

    α-Amino acid derived benzimidazole-linked rhodamines have been synthesized, and their metal ion sensing properties have been evaluated. Experimentally, l-valine- and l-phenylglycine-derived benzimidazole-based rhodamines 1 and 2 selectively recognize Al 3+ ion in aqueous CH 3 CN (CH 3 CN/H 2 O 4/1 v/v, 10 mM tris HCl buffer, pH 7.0) over the other cations by exhibiting color and "turn-on" emission changes. In contrast, glycine-derived benzimidazole 3 remains silent in the recognition event and emphasizes the role of α-substitution of amino acid undertaken in the design. The fact has been addressed on the basis of the single-crystal X-ray structures and theoretical calculations. Moreover, pink 1·Al 3+ and 2·Al 3+ ensembles selectively sensed F - ions over other halides through a discharge of color. Importantly, compounds 1 and 2 are cell permeable and have been used as imaging reagents for the detection of Al 3+ uptake in human lung carcinoma cell line A549.

  4. 5-(Piperidin-4-yl)-3-Hydroxypyrazole: A Novel Scaffold for Probing the Orthosteric γ-Aminobutyric Acid Type A Receptor Binding Site

    DEFF Research Database (Denmark)

    Krall, Jacob; Kongstad, Kenneth Thermann; Nielsen, Birgitte

    2014-01-01

    A series of bioisosteric N1- and N2-substituted 5-(piperidin-4-yl)-3-hydroxypyrazole analogues of the partial GABAAR agonists 4-PIOL and 4-PHP have been designed, synthesized, and characterized pharmacologically. The unsubstituted 3-hydroxypyrazole analogue of 4-PIOL (2 a; IC50∼300 μM) is a weak...... indicate that the N1-substituted analogues of 4-PIOL and 4-PHP, 2 a–k, and previously reported 3-substituted 4-PHP analogues share a common binding mode to the orthosteric binding site in the receptor. Interestingly, the core scaffold of the N2-substituted analogues of 4-PIOL and 4-PHP, 3 b...

  5. MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

    Science.gov (United States)

    Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

    2013-11-25

    We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

  6. Observation and modeling of ambient nitrous acid (HONO) at a rural site (Wangdu) in the North China Plain in summer 2014

    Science.gov (United States)

    Liu, Y.; Lu, K.; Li, X.; Dong, H.; Tan, Z.; Wu, Y.; Zeng, L.; Bohn, B.; Broch, S.; Zou, Q.; Fuchs, H.; Hofzumahaus, A.; Holland, F.; Rohrer, F.; Min, K. E.; Brown, S. S.; Wahner, A.; Zhang, Y.

    2017-12-01

    The photolysis of HONO, was frequently determined to be the major OH primary production channels in the city clusters of China. However, the source of ambient HONO is still a mystery needs to be elucidated. In the framework of an integrated field experiment performed at a rural site in the North China Plain (NCP), HONO was measured by two LOPAP instruments and one CEAS instrument in order to obtain the best quality of the observations and comprehensive parameters that support the exploration of the HONO budget were completely available. In general, the observed HONO concentrations by these three different instruments showed reasonable good agreement as indicated by the high correlation efficiencies while the difference of the regression slopes showed the HONO measured uncertainty is about 15% which is twice about the known uncertainties from each instrument. The diurnal variation of the observed HONO concentrations showed high value (1 -5 ppb) at night and small values (100 - 500 ppt) around noon time which is similar to other reported campaigns. With the assumption of photo stationary state, the missing HONO source is determined experimentally constrained to the observed HONO, jHONO, OH, and NO. Possible HONO formation rates from the chemical reactions as proposed from literatures were calculated in the framework of an observational based box model. It is found that heteorogeneous uptake of NO2 on the ground and the photolysis of nitrate were the major HONO sources for this site when constrained with the recommended kinetc parameters. Uncertainty analysis showed that the uptake coefficient of NO2 and the photolysis frequency of nitrate are the important kinetc factors to be determined in the future studies. In addition, the direct emission of HONO from soil is found to be very important for a few days after fertilization.

  7. H9N2 influenza virus acquires intravenous pathogenicity on the introduction of a pair of di-basic amino acid residues at the cleavage site of the hemagglutinin and consecutive passages in chickens

    Directory of Open Access Journals (Sweden)

    Sakoda Yoshihiro

    2011-02-01

    Full Text Available Abstract Background Outbreaks of avian influenza (AI caused by infection with low pathogenic H9N2 viruses have occurred in poultry, resulting in serious economic losses in Asia and the Middle East. It has been difficult to eradicate the H9N2 virus because of its low pathogenicity, frequently causing in apparent infection. It is important for the control of AI to assess whether the H9N2 virus acquires pathogenicity as H5 and H7 viruses. In the present study, we investigated whether a non-pathogenic H9N2 virus, A/chicken/Yokohama/aq-55/2001 (Y55 (H9N2, acquires pathogenicity in chickens when a pair of di-basic amino acid residues is introduced at the cleavage site of its HA molecule. Results rgY55sub (H9N2, which had four basic amino acid residues at the HA cleavage site, replicated in MDCK cells in the absence of trypsin after six consecutive passages in the air sacs of chicks, and acquired intravenous pathogenicity to chicken after four additional passages. More than 75% of chickens inoculated intravenously with the passaged virus, rgY55sub-P10 (H9N2, died, indicating that it is pathogenic comparable to that of highly pathogenic avian influenza viruses (HPAIVs defined by World Organization for Animal Health (OIE. The chickens inoculated with the virus via the intranasal route, however, survived without showing any clinical signs. On the other hand, an avirulent H5N1 strain, A/duck/Hokkaido/Vac-1/2004 (Vac1 (H5N1, acquired intranasal pathogenicity after a pair of di-basic amino acid residues was introduced into the cleavage site of the HA, followed by two passages by air sac inoculation in chicks. Conclusion The present results demonstrate that an H9N2 virus has the potential to acquire intravenous pathogenicity in chickens although the morbidity via the nasal route of infection is lower than that of H5N1 HPAIV.

  8. Folic acid-targeted disulfide-based cross-linking micelle for enhanced drug encapsulation stability and site-specific drug delivery against tumors

    Directory of Open Access Journals (Sweden)

    Zhang Y

    2016-03-01

    Full Text Available Yumin Zhang,1,* Junhui Zhou,2,* Cuihong Yang,1 Weiwei Wang,3 Liping Chu,1 Fan Huang,1 Qiang Liu,1 Liandong Deng,2 Deling Kong,3 Jianfeng Liu,1 Jinjian Liu1 1Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, 2Department of Polymer Science and Technology, School of Chemical Engineering and Technology, Tianjin University, 3Tianjin Key Laboratory of Biomaterial Research, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, People’s Republic of China *These authors contributed equally in this work Abstract: Although the shortcomings of small molecular antitumor drugs were efficiently improved by being entrapped into nanosized vehicles, premature drug release and insufficient tumor targeting demand innovative approaches that boost the stability and tumor responsiveness of drug-loaded nanocarriers. Here, we show the use of the core cross-linking method to generate a micelle with enhanced drug encapsulation ability and sensitivity of drug release in tumor. This kind of micelle could increase curcumin (Cur delivery to HeLa cells in vitro and improve tumor accumulation in vivo. We designed and synthesized the core cross-linked micelle (CCM with polyethylene glycol and folic acid-polyethylene glycol as the hydrophilic units, pyridyldisulfide as the cross-linkable and hydrophobic unit, and disulfide bond as the cross-linker. CCM showed spherical shape with a diameter of 91.2 nm by the characterization of dynamic light scattering and transmission electron microscope. Attributed to the core cross-linking, drug-loaded CCM displayed higher Nile Red or Cur-encapsulated stability and better sensitivity to glutathione than noncross-linked micelle (NCM. Cellular uptake and in vitro antitumor studies proved the enhanced endocytosis and better cytotoxicity of CCM-Cur against

  9. Overview of the LADCO winter nitrate study: hourly ammonia, nitric acid and PM2.5 composition at an urban and rural site pair during PM2.5 episodes in the US Great Lakes region

    Directory of Open Access Journals (Sweden)

    S. Shaw

    2012-11-01

    Full Text Available An overview of the LADCO (Lake Michigan Air Directors Consortium Winter Nitrate Study (WNS is presented. Sampling was conducted at ground level at an urban-rural pair of sites during January–March 2009 in eastern Wisconsin, toward the western edge of the US Great Lakes region. Areas surrounding these sites experience multiday episodes of wintertime PM2.5 pollution characterized by high fractions of ammonium nitrate in PM, low wind speeds, and air mass stagnation. Hourly surface monitoring of inorganic gases and aerosols supplemented long-term 24-h aerosol chemistry monitoring at these locations. The urban site (Milwaukee, WI experienced 13 PM2.5 episodes, defined as periods where the seven-hour moving average PM2.5 concentration exceeded 27 μg m−3 for at least four consecutive hours. The rural site experienced seven episodes by the same metric, and all rural episodes coincided with urban episodes. Episodes were characterized by low pressure systems, shallow/stable boundary layer, light winds, and increased temperature and relative humidity relative to climatological mean conditions. They often occurred in the presence of regional snow cover at temperatures near freezing, when snow melt and sublimation could generate fog and strengthen the boundary layer inversion. Substantial contribution to nitrate production from nighttime chemistry of ozone and NO2 to N2O5 and nitric acid is likely and requires further investigation. Pollutant-specific urban excess during episode and non-episode conditions is presented. The largest remaining uncertainties in the conceptual model of the wintertime episodes are the variability from episode-to-episode in ammonia emissions, the balance of daytime and nighttime nitrate production, the relationship between ammonia controls, NOx controls and ammonium nitrate reductions, and the extent to which snow and fog are causal (either through meteorological or chemical processes rather than just correlated with episodes

  10. Hyaluronic acid and chondroitin sulfate content of osteoarthritic human knee cartilage: site-specific correlation with weight-bearing force based on femorotibial angle measurement.

    Science.gov (United States)

    Otsuki, Shuhei; Nakajima, Mikio; Lotz, Martin; Kinoshita, Mitsuo

    2008-09-01

    This study analyzed glycosaminoglycan (GAG) content in specific compartments of the knee joint to determine the impact of malalignment and helped refine indications for osteotomy. To assess malalignment, the radiological femorotibial angle (FTA) was measured and knee joints were also graded for OA severity with the Kellgren/Lawrence (K/L) classification. Cartilage samples were obtained from 36 knees of 32 OA patients undergoing total knee replacement surgery. Explants were harvested from the medial femoral condyle (MFC), lateral femoral condyle (LFC), patellar groove (PG), and lateral posterior femoral condyle (LPC). Concentrations of hyaluronic acid (HA) and chondroitin sulfate (CS) were measured by high-performance liquid chromatography (HPLC). With OA severity, the average FTA significantly increased. HA and CS content in MFC was negatively correlated with radiographic FTA. In LFC, HA ratio, which is HA content in lateral condyle divided by medial condyle and chondroitin 6 sulfate, increased until about 190 degrees FTA. Importantly, at >190 degrees these contents were significantly decreased. HA and CS content of the femoral condyle shows topographic differences that are related to OA grade and weight-bearing force based on FTA. The clinical relevance is that osteotomy may not be indicated for patients with severe varus (>190 degrees) abnormalities. (c) 2008 Orthopaedic Research Society

  11. A chemical approach for site-specific identification of NMR signals from protein side-chain NH{sub 3}{sup +} groups forming intermolecular ion pairs in protein–nucleic acid complexes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Kurtis M. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States); Gorenstein, David G. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Iwahara, Junji, E-mail: juiwahar@utmb.edu, E-mail: j.iwahara@utmb.edu [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)

    2015-05-15

    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH{sub 3}{sup +} groups forming the intermolecular ion pairs. A characteristic change in their {sup 1}H and {sup 15}N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain {sup 15}N and DNA phosphorodithiaote {sup 31}P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well.

  12. A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

    International Nuclear Information System (INIS)

    Anderson, Kurtis M.; Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani; Gorenstein, David G.; Iwahara, Junji

    2015-01-01

    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH 3 + groups forming the intermolecular ion pairs. A characteristic change in their 1 H and 15 N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain 15 N and DNA phosphorodithiaote 31 P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well

  13. Staphylococcal nuclease active-site amino acids: pH dependence of tyrosines and arginines by 13C NMR and correlation with kinetic studies

    International Nuclear Information System (INIS)

    Grissom, C.G.; Markley, J.L.

    1989-01-01

    The pH and temperature dependence of the kinetic parameters of staphylococcal nuclease have been examined with three p-nitrophenyl phosphate containing DNA analogues that vary as to 3'-substituent. With wild-type (Foggi variant) nuclease (nuclease wt) and the substrates thymidine 3'-phosphate 5'-(p-nitrophenyl phosphate) (PNPdTp), thymidine 3'-methylphosphonate 5'-(p-nitrophenyl phosphate) (PNPdTp Me), and thymidine 5'-(p-nitrophenyl phosphate) (PNPdT), k cat remains nearly constant at 13 min -1 . However, k cat /k m with nuclease wt varies considerably. The data suggests that the inflection k cat /K m with pK a at 9.67 arises from ionization of tyrosine-85, which hydrogen bonds to the divalent 3'-phosphomonester of substrates with this substituent. The enthalpy of ionization of both deprotonation steps in the k cat /K m versus pH profile is 5 kcal/mol. 13 C NMR has been used to determine the pK a values of the arginine and tyrosine residues. The results do not rule out arginine as a candidate for the acidic catalyst that protonates the 5'-ribose alkoxide prior to product release. The phenolic hydroxyl carbon of tyrosine-85 has been assigned by comparing the 13 C NMR spectrum of nuclease wt and nuclease Y85F. This correlation between pK a values along with the absence of other candidates indicates that the ionization of tyrosine-85 is the pK a seen in the k cat /K m vs pH profile for substrates with a divalent 3'-phosphomonester. This conclusion is consistent with the proposed role of tyrosine-85 as a hydrogen-bond donor to the 3'-phosphomonoester of substrates poised for exonucleolytic hydrolysis

  14. Conversion of Dimethyl Ether to Branched Hydrocarbons Over Cu/BEA: the Roles of Lewis Acidic and Metallic Sites in H2 Incorporation

    Energy Technology Data Exchange (ETDEWEB)

    Hensley, Jesse E.; Schaidle, Joshua A.; Ruddy, Daniel A.; Cheah, Singfoong; Habas, Susan E.; Pan, Ming; Zhang, Guanghui; Miller, Jeffrey T.

    2017-04-26

    Conversion of biomass to fuels remains as one of the most promising approach to support our energy needs. It has been previously shown that the gasification of non-edible cellulosic biomass can be used to derive fuels like methanol and dimethyl ether (DME). However, the use of methanol and DME is limited due to the fact that they have low energy densities, poor lubricity and lower viscosity when compared to long-chain hydrocarbons. Increasing the blending percentage can also lead to undesired amounts of oxygenated molecules in the transportation fuel infrastructure, which restrict their applicability as jet or diesel fuels. Consequently, the petroleum-derived hydrocarbons remain as the main constituent of the middle-distillate based fuels. One way to increase the share of biofuels in middle-distillates is to use methanol/DME as building blocks for producing renewable, energy-dense hydrocarbons. One way to achieve this is by catalytically converting the DME and methanol to light olefins, followed by oligomerization to higher molecular weight premium alkanes, which can directly be used as kerosene/diesel fuels. Here, we report the catalytic dimerization of biomass-derived deoxygenated olefins into transportation fuel-range hydrocarbons under liquid-phase stirred-batch conditions. Specifically, the effect of operating conditions, such as reaction temperature, solvent-type, reaction duration and olefin-structure, on the conversion, selectivity and kinetics of dimerization of triptene (2,3,3-trimethyl-1-butene) were investigated. Triptene, as previously reported, is one of the major products of DME-homologation reaction over a BEA zeolite4. We show that triptene can be converted to high quality middle-distillates using a commercially available ion-exchange acid resin, Amberlyst-35 (dry) by the process of catalytic dimerization.

  15. Electrical Resistance Tomography to Monitor Mitigation of Metal-Toxic Acid-Leachates Ruby Gulch Waste Rock Repository Gilt Edge Mine Superfund Site, South Dakota USA

    Science.gov (United States)

    Versteeg, R.; Heath, G.; Richardson, A.; Paul, D.; Wangerud, K.

    2003-12-01

    At a cyanide heap-leach open-pit mine, 15-million cubic yards of acid-generating sulfides were dumped at the head of a steep-walled mountain valley, with 30 inches/year precipitation generating 60- gallons/minute ARD leachate. Remediation has reshaped the dump to a 70-acre, 3.5:1-sloped geometry, installed drainage benches and runoff diversions, and capped the repository and lined diversions with a polyethylene geomembrane and cover system. Monitoring was needed to evaluate (a) long-term geomembrane integrity, (b) diversion liner integrity and long-term effectiveness, (c) ARD geochemistry, kinetics and pore-gas dynamics within the repository mass, and (d) groundwater interactions. Observation wells were paired with a 600-electrode resistivity survey system. Using near-surface and down-hole electrodes and automated data collection and post-processing, periodic two- and three-dimensional resistivity images are developed to reflect current and changed-conditions in moisture, temperature, geochemical components, and flow-direction analysis. Examination of total resistivity values and time variances between images allows direct observation of liner and cap integrity with precise identification and location of leaks; likewise, if runoff migrates from degraded diversion ditches into the repository zone, there is an accompanying and noticeable change in resistivity values. Used in combination with monitoring wells containing borehole resistivity electrodes (calibrated with direct sampling of dump water/moisture, temperature and pore-gas composition), the resistivity arrays allow at-depth imaging of geochemical conditions within the repository mass. The information provides early indications of progress or deficiencies in de-watering and ARD- mitigation that is the remedy intent. If emerging technologies present opportunities for secondary treatment, deep resistivity images may assist in developing application methods and evaluating the effectiveness of any reagents

  16. Site Features

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of various site features from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times...

  17. Extended hormone binding site of the human thyroid stimulating hormone receptor: distinctive acidic residues in the hinge region are involved in bovine thyroid stimulating hormone binding and receptor activation.

    Science.gov (United States)

    Mueller, Sandra; Kleinau, Gunnar; Jaeschke, Holger; Paschke, Ralf; Krause, Gerd

    2008-06-27

    The human thyroid stimulating hormone receptor (hTSHR) belongs to the glycoprotein hormone receptors that bind the hormones at their large extracellular domain. The extracellular hinge region of the TSHR connects the N-terminal leucine-rich repeat domain with the membrane-spanning serpentine domain. From previous studies we reasoned that apart from hormone binding at the leucine-rich repeat domain, additional multiple hormone contacts might exist at the hinge region of the TSHR by complementary charge-charge recognition. Here we investigated highly conserved charged residues in the hinge region of the TSHR by site-directed mutagenesis to identify amino acids interacting with bovine TSH (bTSH). Indeed, the residues Glu-297, Glu-303, and Asp-382 in the TSHR hinge region are essential for bTSH binding and partially for signal transduction. Side chain substitutions showed that the negative charge of Glu-297 and Asp-382 is necessary for recognition of bTSH by the hTSHR. Multiple combinations of alanine mutants of the identified positions revealed an increased negative effect on hormone binding. An assembled model suggests that the deciphered acidic residues form negatively charged patches at the hinge region resulting in an extended binding mode for bTSH on the hTSHR. Our data indicate that certain positively charged residues of bTSH might be involved in interaction with the identified negatively charged amino acids of the hTSHR hinge region. We demonstrate that the hinge region represents an extracellular intermediate connector for both hormone binding and signal transduction of the hTSHR.

  18. Evidence of site-specific fragmentation on thioacetic acid, CH3C(O)SH, irradiated with synchrotron radiation around the S 2p and O 1s regions.

    Science.gov (United States)

    Erben, Mauricio F; Geronés, Mariana; Romano, Rosana M; Della Védova, Carlos O

    2006-01-26

    Site-specific fragmentations following S 2p and O 1s photoexcitation of thioacetic acid, CH3C(O)SH, have been studied by means of synchrotron radiation. Total ion yield (TIY) spectra were measured and multicoincidence techniques, which include photoelectron-photoion coincidence (PEPICO) and photoelectron-photoion-photoion coincidence (PEPIPICO) time-of-flight mass spectrometry, were applied. The equivalent-core approximation was employed in order to estimate ionization transition values, and the observed peaks were tentatively assigned. A site-specific fragmentation is moderately observed by comparing the mass spectra collected at resonant energies around the inner and shallow inner shell S 2p and O 1s ionization edges. Beside H+ ion, the most abundant ions observed at the S 2p edge excitation were CH3CO+, SH+, S+, and CH3+. At the O 1s region the large CH3CO+ fragment was depressed, and small CHx+ (x = 0, 1, 2, 3), S+, and SH+ fragments were dominant. The dissociation dynamic for the main ion-pair production has been discussed. Two- and three-body dissociation channels have been observed in the PEPIPICO spectra, and the dissociation mechanisms were proposed.

  19. Site decontamination

    International Nuclear Information System (INIS)

    Bicker, A.E.

    1981-01-01

    Among the several DOE sites that have been radiologically decontaminated under the auspices of the Nevada Operations Office are three whose physical characteristics are unique. These are the Tatum Dome Test Site (TDTS) near Hattiesburg, Mississippi; a location of mountainous terrain (Pahute Mesa) on the Nevada Test Site; and the GNOME site near Carlsbad, New Mexico. In each case the contamination, the terrain, and the climate conditions were different. This presentation includes a brief description of each site, the methods used to perform radiological surveys, the logistics required to support the decontamination (including health physics and sample analysis), and the specific techniques used to reduce or remove the contamination

  20. Invariant amino acids in the Mur peptide synthetases of bacterial peptidoglycan synthesis and their modification by site-directed mutagenesis in the UDP-MurNAc:L-alanine ligase from Escherichia coli.

    Science.gov (United States)

    Bouhss, A; Mengin-Lecreulx, D; Blanot, D; van Heijenoort, J; Parquet, C

    1997-09-30

    The comparison of the amino acid sequences of 20 cytoplasmic peptidoglycan synthetases (MurC, MurD, MurE, MurF, and Mpl) from various bacterial organisms has allowed us to detect common invariants: seven amino acids and the ATP-binding consensus sequence GXXGKT/S all at the same position in the alignment. The Mur synthetases thus appeared as a well-defined class of closely functionally related proteins. The conservation of a constant backbone length between certain invariants suggested common structural motifs. Among the other enzymes catalyzing a peptide bond formation driven by ATP hydrolysis to ADP and Pi, only folylpoly-gamma-l-glutamate synthetases presented the same common conserved amino acid residues, except for the most N-terminal invariant D50. Site-directed mutageneses were carried out to replace the K130, E174, H199, N293, N296, R327, and D351 residues by alanine in the MurC protein from Escherichia coli taken as model. For this purpose, plasmid pAM1005 was used as template, MurC being highly overproduced in this genetic setting. Analysis of the Vmax values of the mutated proteins suggested that residues K130, E174, and D351 are essential for the catalytic process whereas residues H199, N293, N296, and R327 were not. Mutations K130A, H199A, N293A, N296A, and R327A led to important variations of the Km values for one or more substrates, thereby indicating that these residues are involved in the structure of the active site and suggesting that the binding order of the substrates could be ATP, UDP-MurNAc, and alanine. The various mutated murC plasmids were tested for their effects on the growth, cell morphology, and peptidoglycan cell content of a murC thermosensitive strain at 42 degrees C. The observed effects (complementation, altered morphology, and reduced peptidoglycan content) paralleled more or less the decreased values of the MurC activity of each mutant.

  1. Site organization and site arrangement

    International Nuclear Information System (INIS)

    Boissonnet, B.; Macqueron, J.F.

    1976-01-01

    The present paper deals with criteria for the choice of a production unit or power plant site, the organization and development of a site in terms of its particular characteristics and takes into account personnel considerations in site organizations as well as the problem of integrating the architecture into the environment. (RW) [de

  2. Coal mine site reclamation

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-02-15

    Coal mine sites can have significant effects on local environments. In addition to the physical disruption of land forms and ecosystems, mining can also leave behind a legacy of secondary detrimental effects due to leaching of acid and trace elements from discarded materials. This report looks at the remediation of both deep mine and opencast mine sites, covering reclamation methods, back-filling issues, drainage and restoration. Examples of national variations in the applicable legislation and in the definition of rehabilitation are compared. Ultimately, mine site rehabilitation should return sites to conditions where land forms, soils, hydrology, and flora and fauna are self-sustaining and compatible with surrounding land uses. Case studies are given to show what can be achieved and how some landscapes can actually be improved as a result of mining activity.

  3. Site operations

    International Nuclear Information System (INIS)

    House, W.B.; Ebenhack, D.G.

    1989-01-01

    This chapter is a discussion of the management and operations practices used at the Barnwell Waste Management Facility in Barnwell, SC. The following topics are discussed: (1) Waste receiving and inspection, including manifest and certificates of compliance, radiological surveys, disposition of nonconforming items, and decontamination and disposition of secondary waste streams; (2) Waste disposal, including Title 10 CFR 61 requirements, disposal area evaluations, shipment offloading, container emplacement, and radiation protection; (3) Trench closure, including trench backfilling, trench capping, and permanent markers; (4) Site maintenance and stabilization, including trench maintenance, surface water management, and site closure activities; (5) Site monitoring programs, including operational monitoring, and environmental monitoring program; (6) Personnel training and qualifications, including basic training program, safety training program, special skills training, and physical qualifications; (7) Records management, including waste records, personnel training records, personnel dosimetry records, site monitoring records, trench qualification and construction records, and site drawings and stabilization records; (8) Site security; (9) Emergency response plans; and (10) Quality assurance

  4. Various Bee Pheromones Binding Affinity, Exclusive Chemosensillar Localization, and Key Amino Acid Sites Reveal the Distinctive Characteristics of Odorant-Binding Protein 11 in the Eastern Honey Bee, Apis cerana.

    Science.gov (United States)

    Song, Xin-Mi; Zhang, Lin-Ya; Fu, Xiao-Bin; Wu, Fan; Tan, Jing; Li, Hong-Liang

    2018-01-01

    Odorant-binding proteins (OBPs) are the critical elements responsible for binding and transporting odors and pheromones in the sensitive olfactory system in insects. Honey bees are representative social insects that have complex odorants and pheromone communication systems relative to solitary insects. Here, we first cloned and characterized OBP11 ( AcerOBP11 ), from the worker bees antennae of Eastern honey bee, Apis cerana . Based on sequence and phylogenetic analysis, most sequences homologous to AcerOBP11 belong to the typical OBPs family. The transcriptional expression profiles showed that AcerOBP11 was expressed throughout the developmental stages and highly specifically expressed in adult antennae. Using immunofluorescence localization, AcerOBP11 in worker bee's antennae was only localized in the sensilla basiconica (SB) near the fringe of each segment. Fluorescence ligand-binding assay showed that AcerOBP11 protein had strong binding affinity with the tested various bee pheromones components, including the main queen mandibular pheromones (QMPs), methyl p-hydroxybenzoate (HOB), and ( E )-9-oxo-2-decanoic acid (9-ODA), alarm pheromone (n-hexanol), and worker pheromone components. AcerOBP11 also had strong binding affinity to plant volatiles, such as 4-Allylveratrole. Based on the docking and site-directed mutagenesis, two key amino acid residues (Ile97 and Ile140) were involved in the binding of AcerOBP11 to various bee pheromones. Taken together, we identified that AcerOBP11 was localized in a single type of antennal chemosensilla and had complex ligand-binding properties, which confer the dual-role with the primary characteristics of sensing various bee pheromones and secondary characteristics of sensing general odorants. This study not only prompts the theoretical basis of OBPs-mediated bee pheromones recognition of honey bee, but also extends the understanding of differences in pheromone communication between social and solitary insects.

  5. Various Bee Pheromones Binding Affinity, Exclusive Chemosensillar Localization, and Key Amino Acid Sites Reveal the Distinctive Characteristics of Odorant-Binding Protein 11 in the Eastern Honey Bee, Apis cerana

    Directory of Open Access Journals (Sweden)

    Xin-Mi Song

    2018-04-01

    Full Text Available Odorant-binding proteins (OBPs are the critical elements responsible for binding and transporting odors and pheromones in the sensitive olfactory system in insects. Honey bees are representative social insects that have complex odorants and pheromone communication systems relative to solitary insects. Here, we first cloned and characterized OBP11 (AcerOBP11, from the worker bees antennae of Eastern honey bee, Apis cerana. Based on sequence and phylogenetic analysis, most sequences homologous to AcerOBP11 belong to the typical OBPs family. The transcriptional expression profiles showed that AcerOBP11 was expressed throughout the developmental stages and highly specifically expressed in adult antennae. Using immunofluorescence localization, AcerOBP11 in worker bee's antennae was only localized in the sensilla basiconica (SB near the fringe of each segment. Fluorescence ligand-binding assay showed that AcerOBP11 protein had strong binding affinity with the tested various bee pheromones components, including the main queen mandibular pheromones (QMPs, methyl p-hydroxybenzoate (HOB, and (E-9-oxo-2-decanoic acid (9-ODA, alarm pheromone (n-hexanol, and worker pheromone components. AcerOBP11 also had strong binding affinity to plant volatiles, such as 4-Allylveratrole. Based on the docking and site-directed mutagenesis, two key amino acid residues (Ile97 and Ile140 were involved in the binding of AcerOBP11 to various bee pheromones. Taken together, we identified that AcerOBP11 was localized in a single type of antennal chemosensilla and had complex ligand-binding properties, which confer the dual-role with the primary characteristics of sensing various bee pheromones and secondary characteristics of sensing general odorants. This study not only prompts the theoretical basis of OBPs-mediated bee pheromones recognition of honey bee, but also extends the understanding of differences in pheromone communication between social and solitary insects.

  6. Site-saturation engineering of lysine 47 in cyclodextrin glycosyltransferase from Paenibacillus macerans to enhance substrate specificity towards maltodextrin for enzymatic synthesis of 2-O-D-glucopyranosyl-L-ascorbic acid (AA-2G).

    Science.gov (United States)

    Han, Ruizhi; Liu, Long; Shin, Hyun-dong; Chen, Rachel R; Du, Guocheng; Chen, Jian

    2013-07-01

    In this work, the site-saturation engineering of lysine 47 in cyclodextrin glycosyltransferase (CGTase) from Paenibacillus macerans was conducted to improve the specificity of CGTase towards maltodextrin, which can be used as a cheap and easily soluble glycosyl donor for the enzymatic synthesis of 2-O-D-glucopyranosyl-L-ascorbic acid (AA-2G) by CGTase. When using maltodextrin as glycosyl donor, four mutants K47F (lysine→ phenylalanine), K47L (lysine→ leucine), K47V (lysine→ valine) and K47W (lysine→ tryptophan) showed higher AA-2G yield as compared with that produced by the wild-type CGTase. The transformation conditions (temperature, pH and the mass ratio of L-ascorbic acid to maltodextrin) were optimized and the highest titer of AA-2G produced by the mutant K47L could reach 1.97 g/l, which was 64.2% higher than that (1.20 g/l) produced by the wild-type CGTase. The reaction kinetics analysis confirmed the enhanced maltodextrin specificity, and it was also found that compared with the wild-type CGTase, the four mutants had relatively lower cyclization activities and higher disproportionation activities, which was favorable for AA-2G synthesis. The mechanism responsible for the enhanced substrate specificity was further explored by structure modeling and it was indicated that the enhancement of maltodextrin specificity may be due to the short residue chain and the removal of hydrogen bonding interactions between the side chain of residue 47 and the sugar at -3 subsite. Here the obtained mutant CGTases, especially the K47L, has a great potential in the production of AA-2G with maltodextrin as a cheap and easily soluble substrate.

  7. USGS Tracks Acid Rain

    Science.gov (United States)

    Gordon, John D.; Nilles, Mark A.; Schroder, LeRoy J.

    1995-01-01

    The U.S. Geological Survey (USGS) has been actively studying acid rain for the past 15 years. When scientists learned that acid rain could harm fish, fear of damage to our natural environment from acid rain concerned the American public. Research by USGS scientists and other groups began to show that the processes resulting in acid rain are very complex. Scientists were puzzled by the fact that in some cases it was difficult to demonstrate that the pollution from automobiles and factories was causing streams or lakes to become more acidic. Further experiments showed how the natural ability of many soils to neutralize acids would reduce the effects of acid rain in some locations--at least as long as the neutralizing ability lasted (Young, 1991). The USGS has played a key role in establishing and maintaining the only nationwide network of acid rain monitoring stations. This program is called the National Atmospheric Deposition Program/National Trends Network (NADP/NTN). Each week, at approximately 220 NADP/NTN sites across the country, rain and snow samples are collected for analysis. NADP/NTN site in Montana. The USGS supports about 72 of these sites. The information gained from monitoring the chemistry of our nation's rain and snow is important for testing the results of pollution control laws on acid rain.

  8. In vivo evaluation of [{sup 11}C]-3-[2-[(3-methoxyphenylamino)carbonyl]ethenyl]-4,6-dichloroindole- 2-carboxylic acid ([{sup 11}C]3MPICA) as a PET radiotracer for the glycine site of the NMDA ion channel

    Energy Technology Data Exchange (ETDEWEB)

    Waterhouse, Rikki N. E-mail: rnw7@columbia.edu; Sultana, Abida; Laruelle, M

    2002-11-01

    Alterations in normal NMDA receptor composition, densities and function have been implicated in the pathophysiology of certain neurological and neuropsychiatric disorders such as Parkinson's Disease, Huntington's Chorea, schizophrenia, alcoholism and stroke. In our first effort to provide PET ligands for the NMDA/glycine site, we reported the synthesis of a novel high affinity glycine site ligand, 3-[2-[(3-methoxyphenylamino)carbonyl]ethenyl]-4,6-dichloroindole-2 -carboxylic acid ((3MPICA), Ki=4.8{+-}0.9 nM) and the corresponding carbon-11 labeled PET ligand, [{sup 11}C]3MPICA. We report here the in vivo evaluation of [{sup 11}C]3MPICA in rats. Biodistribution analysis revealed that [{sup 11}C]3MPICA exhibited low degree of brain penetration and high blood concentration. The average uptake at two minutes was highest in the cerebellum (0.19{+-}0.04 %ID/g) and thalamus (0.18{+-}0.05 %ID/g) and lower in the hippocampus (0.13{+-}0.03) and frontal cortex (0.11{+-}0.04 %ID/g). The radioactivity cleared quickly from all brain regions examined. Administration of unlabeled 3MPICA (1 mg/kg, i.v.) revealed at 60 minutes a small general reduction in regional brain radioactivity concentrations in treated animals versus controls, however, the blood radioactivity concentration was also lowered, confounding the assessment of the degree of saturable binding. Warfarin co-administration (100 mg/kg, i.v.) significantly lowered blood activity at 5 minutes post-injection (-27%, P<0.01) but failed to significantly increase the brain uptake of the radiotracer. In view of these results, and especially considering the low brain penetration of this tracer, [{sup 11}C]3MPICA does not appear to be a promising PET radiotracer for in vivo use.

  9. In vivo evaluation of [11C]-3-[2-[(3-methoxyphenylamino)carbonyl]ethenyl]-4,6-dichloroindole- 2-carboxylic acid ([11C]3MPICA) as a PET radiotracer for the glycine site of the NMDA ion channel

    International Nuclear Information System (INIS)

    Waterhouse, Rikki N.; Sultana, Abida; Laruelle, M.

    2002-01-01

    Alterations in normal NMDA receptor composition, densities and function have been implicated in the pathophysiology of certain neurological and neuropsychiatric disorders such as Parkinson's Disease, Huntington's Chorea, schizophrenia, alcoholism and stroke. In our first effort to provide PET ligands for the NMDA/glycine site, we reported the synthesis of a novel high affinity glycine site ligand, 3-[2-[(3-methoxyphenylamino)carbonyl]ethenyl]-4,6-dichloroindole-2 -carboxylic acid ((3MPICA), Ki=4.8±0.9 nM) and the corresponding carbon-11 labeled PET ligand, [ 11 C]3MPICA. We report here the in vivo evaluation of [ 11 C]3MPICA in rats. Biodistribution analysis revealed that [ 11 C]3MPICA exhibited low degree of brain penetration and high blood concentration. The average uptake at two minutes was highest in the cerebellum (0.19±0.04 %ID/g) and thalamus (0.18±0.05 %ID/g) and lower in the hippocampus (0.13±0.03) and frontal cortex (0.11±0.04 %ID/g). The radioactivity cleared quickly from all brain regions examined. Administration of unlabeled 3MPICA (1 mg/kg, i.v.) revealed at 60 minutes a small general reduction in regional brain radioactivity concentrations in treated animals versus controls, however, the blood radioactivity concentration was also lowered, confounding the assessment of the degree of saturable binding. Warfarin co-administration (100 mg/kg, i.v.) significantly lowered blood activity at 5 minutes post-injection (-27%, P 11 C]3MPICA does not appear to be a promising PET radiotracer for in vivo use

  10. Structure-function relationships in the Na,K-ATPase α subunit: site-directed mutagenesis of glutamine-111 to arginine and asparagine-122 to aspartic acid generates a ouabain-resistant enzyme

    International Nuclear Information System (INIS)

    Price, E.M.; Lingrel, J.B.

    1988-01-01

    Na,K-ATPases from various species differ greatly in their sensitivity to cardiac glycosides such as ouabain. The sheep and human enzymes are a thousand times more sensitive than the corresponding ones from rat and mouse. To define the region of the α1 subunit responsible for this differential sensitivity, chimeric cDNAs of sheep and rat were constructed and expressed in ouabain-sensitive HeLa cells. The construct containing the amino-terminal half of the rat α1 subunit coding region and carboxyl-terminal half of the sheep conferred the ouabain-resistant phenotype to HeLa cells while the reverse construct did not. This indicates that the determinants involved in ouabain sensitivity are located in the amino-terminal half of the Na,K-ATPase α subunit. By use of site-directed mutagenesis, the amino acid sequence of the first extracellular domain (H1-H2) of the sheep α1 subunit was changed to that of the rat. When expressed in HeLa cells, this mutated sheep α1 construct, like the rat/sheep chimera, was able to confer ouabain resistance to these cells. Furthermore, similar results were observed when HeLa cells were transfected with a sheep α1 cDNA containing only two amino acid substitutions. The resistant cells, whether transfected with the rat α1 cDNA, the rat/sheep chimera, or the mutant sheep α1 cDNAs, exhibited identical biochemical characteristics including ouabain-inhibitable cell growth, 86 Rb + uptake, and Na,K-ATPase activity. These results demonstrate that the presence of arginine and aspartic acid on the amino end and carboxyl end, respectively, of the H1-H2 extracellular domain of the Na,K-ATPase α subunit together is responsible for the ouabain-resistant character of the rat enzyme and the corresponding residues in the sheep α1 subunit (glutamine and asparagine) are somehow involved in ouabain binding

  11. Structure-function relationships in the Na,K-ATPase. cap alpha. subunit: site-directed mutagenesis of glutamine-111 to arginine and asparagine-122 to aspartic acid generates a ouabain-resistant enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Price, E.M.; Lingrel, J.B.

    1988-11-01

    Na,K-ATPases from various species differ greatly in their sensitivity to cardiac glycosides such as ouabain. The sheep and human enzymes are a thousand times more sensitive than the corresponding ones from rat and mouse. To define the region of the ..cap alpha..1 subunit responsible for this differential sensitivity, chimeric cDNAs of sheep and rat were constructed and expressed in ouabain-sensitive HeLa cells. The construct containing the amino-terminal half of the rat ..cap alpha..1 subunit coding region and carboxyl-terminal half of the sheep conferred the ouabain-resistant phenotype to HeLa cells while the reverse construct did not. This indicates that the determinants involved in ouabain sensitivity are located in the amino-terminal half of the Na,K-ATPase ..cap alpha.. subunit. By use of site-directed mutagenesis, the amino acid sequence of the first extracellular domain (H1-H2) of the sheep ..cap alpha..1 subunit was changed to that of the rat. When expressed in HeLa cells, this mutated sheep ..cap alpha..1 construct, like the rat/sheep chimera, was able to confer ouabain resistance to these cells. Furthermore, similar results were observed when HeLa cells were transfected with a sheep ..cap alpha..1 cDNA containing only two amino acid substitutions. The resistant cells, whether transfected with the rat ..cap alpha..1 cDNA, the rat/sheep chimera, or the mutant sheep ..cap alpha..1 cDNAs, exhibited identical biochemical characteristics including ouabain-inhibitable cell growth, /sup 86/Rb/sup +/ uptake, and Na,K-ATPase activity. These results demonstrate that the presence of arginine and aspartic acid on the amino end and carboxyl end, respectively, of the H1-H2 extracellular domain of the Na,K-ATPase ..cap alpha.. subunit together is responsible for the ouabain-resistant character of the rat enzyme and the corresponding residues in the sheep ..cap alpha..1 subunit (glutamine and asparagine) are somehow involved in ouabain binding.

  12. The 18-kilodalton Chlamydia trachomatis histone H1-like protein (Hc1) contains a potential N-terminal dimerization site and a C-terminal nucleic acid-binding domain

    DEFF Research Database (Denmark)

    Pedersen, Lotte Bang; Birkelund, S; Holm, A

    1996-01-01

    The Chlamydia trachomatis histone H1-like protein (Hc1) is a DNA-binding protein specific for the metabolically inactive chlamydial developmental form, the elementary body. Hc1 induces DNA condensation in Escherichia coli and is a strong inhibitor of transcription and translation. These effects may......-hydroxysuccinimide ester), purified recombinant Hc1 was found to form dimers. The dimerization site was located in the N-terminal part of Hc1 (Hc1(2-57)). Moreover, circular dichroism measurements indicated an overall alpha-helical structure of this region. By using limited proteolysis, Southwestern blotting, and gel...... retardation assays, Hc1(53-125) was shown to contain a domain capable of binding both DNA and RNA. Under the same conditions, Hc1(2-57) had no nucleic acid-binding activity. Electron microscopy of Hc1-DNA and Hc1(53-125)-DNA complexes revealed differences suggesting that the N-terminal part of Hc1 may affect...

  13. Superfund Sites

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This layer represents active Superfund Sites published by the Environmental Protection Agency (EPA). These data were extracted from the Superfund Enterprise...

  14. Site development

    International Nuclear Information System (INIS)

    Noack, J.

    1975-01-01

    The subject of this paper is a general view over all necessary considerations to develop the site after it has been chosen and before starting with the construction of a nuclear power plant. (orig./RW) [de

  15. Site selection

    International Nuclear Information System (INIS)

    Olsen, C.W.

    1983-07-01

    The conditions and criteria for selecting a site for a nuclear weapons test at the Nevada Test Site are summarized. Factors considered are: (1) scheduling of drill rigs, (2) scheduling of site preparation (dirt work, auger hole, surface casing, cementing), (3) schedule of event (when are drill hole data needed), (4) depth range of proposed W.P., (5) geologic structure (faults, Pz contact, etc.), (6) stratigraphy (alluvium, location of Grouse Canyon Tuff, etc.), (7) material properties (particularly montmorillonite and CO 2 content), (8) water table depth, (9) potential drilling problems (caving), (10) adjacent collapse craters and chimneys, (11) adjacent expended but uncollapsed sites, (12) adjacent post-shot or other small diameter holes, (13) adjacent stockpile emplacement holes, (14) adjacent planned events (including LANL), (15) projected needs of Test Program for various DOB's and operational separations, and (16) optimal use of NTS real estate

  16. Semi-quantitative estimation by IR of framework, extraframework and defect Al species of HBEA zeolites.

    Science.gov (United States)

    Marques, João P; Gener, Isabelle; Ayrault, Philippe; Lopes, José M; Ribeiro, F Ramôa; Guisnet, Michel

    2004-10-21

    A simple method based on the characterization (composition, Bronsted and Lewis acidities) of acid treated HBEA zeolites was developed for estimating the concentrations of framework, extraframework and defect Al species.

  17. Site development

    International Nuclear Information System (INIS)

    Gaynor, R.K.

    1989-01-01

    Development of a low-level radioactive waste land disposal facility is little different than any industrial development of similar scope. Consideration must be made for normal business and operations management, security, facility maintenance, traffic control and necessary amenities for personnel. The item specific to the low-level waste site is the handling of radioactive waste materials and the regulatory and environmental protection procedures that must be planned for and accomodated in the site design and development. Each of these elements and the facility as a whole must be designed to be compatible with local land use plans, available transportation and support services, and the social and economic goals of the local community. Plans should also be made for quality control and orderly construction. This chapter deals with those aspects of the facility, its design and construction which are integral parts to the overall performance of the site

  18. Aspartic acid

    Science.gov (United States)

    ... we eat. Aspartic acid is also called asparaginic acid. Aspartic acid helps every cell in the body work. It ... release Normal nervous system function Plant sources of aspartic acid include: avocado, asparagus, and molasses. Animal sources of ...

  19. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    different practices in the construction phase. The research is based on an ethnographic study of a case in Denmark. The empirical data were collected through direct observations and semi-structured interviews with site managers, contract managers, foremen and craftsmen. Findings revealed...... that the construction phase comprises several communities and practices, leading to various uses of the drawings. The results indicated that the craftsmen used drawings to position themselves in the correct location, and that the site managers and contract managers used them as management tools and legal documents...

  20. Differential trace labeling of calmodulin: investigation of binding sites and conformational states by individual lysine reactivities. Effects of beta-endorphin, trifluoperazine, and ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid

    Energy Technology Data Exchange (ETDEWEB)

    Giedroc, D.P.; Sinha, S.K.; Brew, K.; Puett, D.

    1985-11-05

    The CaS -dependent association of beta-endorphin and trifluoperazine with porcine testis calmodulin, as well as the effects of removing CaS by ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) treatment, were investigated by the procedure of differential kinetic labeling. This technique permitted determination of the relative rates of acylation of each of the epsilon-amino groups of the seven lysyl residues on calmodulin by (TH)acetic anhydride under the different conditions. In all cases, less than 0.52 mol of lysyl residue/mol of calmodulin was modified, thus ensuring that the labeling pattern reflects the microenvironments of these groups in the native protein. Lysines 75 and 94 were found to be the most reactive amino groups in CaS -saturated calmodulin. In the presence of CaS and under conditions where beta-endorphin and calmodulin were present at a molar ratio of 2.5:1, the amino groups of lysines 75 and 148 were significantly reduced in reactivity compared to calmodulin alone. At equimolar concentrations of peptides and proteins, essentially the same result was obtained except that the magnitudes of the perturbation of these two lysines were less pronounced. With trifluoperazine, at a molar ratio to calmodulin of 2.5:1, significant perturbations of lysines 75 and 148, as well as Lys 77, were also found. These results further substantiate previous observations of a commonality between phenothiazine and peptide binding sites on calmodulin. Lastly, an intriguing difference in CaS -mediated reactivities between lysines 75 and 77 of calmodulin is demonstrated. In the CaS -saturated form of the protein, both lysines are part of the long connecting helix between the two homologous halves of the protein.

  1. Site selection

    CERN Multimedia

    CERN PhotoLab

    1968-01-01

    To help resolve the problem of site selection for the proposed 300 GeV machine, the Council selected "three wise men" (left to right, J H Bannier of the Netherlands, A Chavanne of Switzerland and L K Boggild of Denmark).

  2. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2001-04-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations.

  3. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2001-01-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations

  4. Cleaving Double-Stranded DNA with Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    1997-01-01

    Peptide nucleic acids and analogues of peptide nucleic acids are used to form duplex, triplex, and other structures with nucleic acids and to modify nucleic acids. The peptide nucleic acids and analogues thereof also are used to modulate protein activity through, for example, transcription arrest......, transcription initiation, and site specific cleavage of nucleic acids....

  5. CATALYTIC PROPERTIES AND ACIDITY OF MODIFIED MCM-41 ...

    African Journals Online (AJOL)

    Adsorption of pyridine and IR spectroscopy indicated various types of Lewis and Brönsted acid sites. The density distribution of acid sites was determined by TPD. Both Lewis and Brönsted acid sites were found to be active in the heptane isomerisation. The presence of aluminium (low Si/Al) combined to the ionic exchange ...

  6. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2002-04-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products.

  7. Mochovce site

    International Nuclear Information System (INIS)

    1997-01-01

    In Mochovce site the construction of four units of WWER 440 NPP with V-213 type of reactor is being carried out. The financing of Mochovce units completion was resolved in April 1996. The completion work commenced at the construction site under leadership of SKODA Prague, the general supplier. The completion work on building part and tests of constructional electric distributions and lightning constructors started. The revisions in technological part were finished, and final protocols from revisions are the basis for starting of completion work. The assembly of transport container anchorage,ventilation system in hermetic areas and hermetic coverage of pools for stored spent nuclear fuel is being carried out. The pre-completion tests of instrumentation and control of ventilation systems, individual dosimetric control in medical station, and tests of nuclear programme according to commissioning and assembling work schedule at the equipment for physical protection of the NPP area started. Inspection activities at Mochovce were performed in accordance with inspection plan for 1996. Evaluation of routine inspections was performed by means of quarterly protocols. Main findings from the inspections performed in Mochovce were in the following areas: (a) deficiencies in the knowledge of the respective regulation and conditions from the Resolution of the state regulatory body, concerning selected employees; (b) training of the selected employees; (c) aim of the measures imposes by inspectors is to eliminate deficiencies in preparation of programmes for pre-completion and completion testing. NRA SR assessment activities at Mochovce NPP were focused mainly on approving and inspecting of design modification to approving programmes for pre-completion and completion testing of system s and equipment and on approving quality assurance programmes. The suggestions of international missions, which reviewed Mochovce safety in the years, were taken into consideration in the programme

  8. Acid Rain

    Science.gov (United States)

    Bricker, Owen P.; Rice, Karen C.

    1995-01-01

    Although acid rain is fading as a political issue in the United States and funds for research in this area have largely disappeared, the acidity of rain in the Eastern United States has not changed significantly over the last decade, and it continues to be a serious environmental problem. Acid deposition (commonly called acid rain) is a term applied to all forms of atmospheric deposition of acidic substances - rain, snow, fog, acidic dry particulates, aerosols, and acid-forming gases. Water in the atmosphere reacts with certain atmospheric gases to become acidic. For example, water reacts with carbon dioxide in the atmosphere to produce a solution with a pH of about 5.6. Gases that produce acids in the presence of water in the atmosphere include carbon dioxide (which converts to carbonic acid), oxides of sulfur and nitrogen (which convert to sulfuric and nitric acids}, and hydrogen chloride (which converts to hydrochloric acid). These acid-producing gases are released to the atmosphere through natural processes, such as volcanic emissions, lightning, forest fires, and decay of organic matter. Accordingly, precipitation is slightly acidic, with a pH of 5.0 to 5.7 even in undeveloped areas. In industrialized areas, most of the acid-producing gases are released to the atmosphere from burning fossil fuels. Major emitters of acid-producing gases include power plants, industrial operations, and motor vehicles. Acid-producing gases can be transported through the atmosphere for hundreds of miles before being converted to acids and deposited as acid rain. Because acids tend to build up in the atmosphere between storms, the most acidic rain falls at the beginning of a storm, and as the rain continues, the acids "wash out" of the atmosphere.

  9. Sulfated polyborate: A mild, efficient catalyst for synthesis of N-tert ...

    Indian Academy of Sciences (India)

    chemsci

    trityl protected amides via Ritter reaction of nitriles with tertiary alcohols in the presence of a sulfated polyborate catalyst under solvent-free conditions is described. The catalyst has the advantage of Lewis as well as Bronsted acidity and.

  10. Desulfurization of Hydrocarbon Fuels at Ambient Conditions Using Supported Silver Oxide-Titania Sorbents

    Science.gov (United States)

    2010-12-13

    Potentiometric titration ------------------------------------------------------------------ 27 II.10 Equilibrium isotherms...chemisorption ------------------------------------------------ 104 VI.1.5 Potentiometric titration ...Figure VI.7. The relationship between bronsted surface acidity measured by potentiometric titration and sulfur adsorption capacity using JP5 fuel (1172

  11. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    International Nuclear Information System (INIS)

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-01-01

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme

  12. Hemoglobin Rahere, a human hemoglobin variant with amino acid substitution at the 2,3-diphosphoglycerate binding site. Functional consequences of the alteration and effects of bezafibrate on the oxygen bindings.

    OpenAIRE

    Sugihara, J; Imamura, T; Nagafuchi, S; Bonaventura, J; Bonaventura, C; Cashon, R

    1985-01-01

    We encountered an abnormal hemoglobin (Rahere), with a threonine residue replacing the beta 82 (EF6) lysine residue at the binding site of 2,3-diphosphoglycerate, which was responsible for overt erythrocytosis in two individuals of a Japanese family. Hemoglobin Rahere shows a lower oxygen affinity on the binding of 2,3-diphosphoglycerate or chloride ions than hemoglobin A. Although a decrease in the positive charge density at the binding sites of 2,3-diphosphoglycerate in hemoglobin Rahere ap...

  13. Amino acids

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/002222.htm Amino acids To use the sharing features on this page, please enable JavaScript. Amino acids are organic compounds that combine to form proteins . ...

  14. Valproic Acid

    Science.gov (United States)

    ... acid is in a class of medications called anticonvulsants. It works by increasing the amount of a ... older (about 1 in 500 people) who took anticonvulsants such as valproic acid to treat various conditions ...

  15. Ascorbic Acid

    Science.gov (United States)

    Ascorbic acid is used to prevent and treat scurvy, a disease caused by a lack of vitamin C in ... Ascorbic acid comes in extended-release (long-acting) capsules and tablets, lozenges, syrup, chewable tablets, and liquid drops to ...

  16. Aminocaproic Acid

    Science.gov (United States)

    Aminocaproic acid is used to control bleeding that occurs when blood clots are broken down too quickly. This type ... the baby is ready to be born). Aminocaproic acid is also used to control bleeding in the ...

  17. Ethacrynic Acid

    Science.gov (United States)

    Ethacrynic acid, a 'water pill,' is used to treat swelling and fluid retention caused by various medical problems. It ... Ethacrynic acid comes as a tablet to take by mouth. It is usually taken once or twice a day ...

  18. Hemoglobin Rahere, a human hemoglobin variant with amino acid substitution at the 2,3-diphosphoglycerate binding site. Functional consequences of the alteration and effects of bezafibrate on the oxygen bindings.

    Science.gov (United States)

    Sugihara, J; Imamura, T; Nagafuchi, S; Bonaventura, J; Bonaventura, C; Cashon, R

    1985-09-01

    We encountered an abnormal hemoglobin (Rahere), with a threonine residue replacing the beta 82 (EF6) lysine residue at the binding site of 2,3-diphosphoglycerate, which was responsible for overt erythrocytosis in two individuals of a Japanese family. Hemoglobin Rahere shows a lower oxygen affinity on the binding of 2,3-diphosphoglycerate or chloride ions than hemoglobin A. Although a decrease in the positive charge density at the binding sites of 2,3-diphosphoglycerate in hemoglobin Rahere apparently shifts the allosteric equilibrium toward the low affinity state, it greatly diminishes the cofactor effects by anions. The oxygen affinity of the patient's erythrocytes is substantially lowered by the presence of bezafibrate, which combines with sites different from those of 2,3-diphosphoglycerate in either hemoglobin Rahere or hemoglobin A.

  19. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  20. Well acidizing

    Energy Technology Data Exchange (ETDEWEB)

    Street, E H

    1980-01-23

    The apparatus relates in particular to a well-treating process in which an aqueous acid solution having a pH of < 2 is injected into a subterranean reservoir in a manner such that materials that contain ferric ions are present in the acid and, as the acid reacts within the reservoir and attains a pH exceeding 3, tend to be precipitated as ferric ion-containing solid materials that may plug the pores of the reservoir. Such a precipitation is prevented by dissolving in the acid solution an amount of 5-sulfosalicylic acid which is at least sufficient to sequester significant proportions of ferric ions when the pH of the acid is from 0.5 to 3 but is less than enough to cause a significant salting-out of solid materials, and an amount of citric acid which is at least sufficient to sequester significant proportions of ferric ions when the pH of the acid is from 3 to 6 but is less than enough to precipitate a significant amount of calcium citrate. The amount of the 5-sulfosalicylic acid may be from 0.01 to 0.05 moles/l and the amount of citric acid is from 0.001 to 0.009 moles/l. 11 claims.

  1. SiteFind: A software tool for introducing a restriction site as a marker for successful site-directed mutagenesis

    Directory of Open Access Journals (Sweden)

    Evans Paul M

    2005-12-01

    Full Text Available Abstract Background Site-directed mutagenesis is a widely-used technique for introducing mutations into a particular DNA sequence, often with the goal of creating a point mutation in the corresponding amino acid sequence but otherwise leaving the overall sequence undisturbed. However, this method provides no means for verifying its success other than sequencing the putative mutant construct: This can quickly become an expensive method for screening for successful mutations. An alternative to sequencing is to simultaneously introduce a restriction site near the point mutation in manner such that the restriction site has no effect on the translated amino acid sequence. Thus, the novel restriction site can be used as a marker for successful mutation which can be quickly and easily assessed. However, finding a restriction site that does not disturb the corresponding amino acid sequence is a time-consuming task even for experienced researchers. A fast and easy to use computer program is needed for this task. Results We wrote a computer program, called SiteFind, to help us design a restriction site within the mutation primers without changing the peptide sequence. Because of the redundancy of genetic code, a given peptide can be encoded by many different DNA sequences. Since the list of possible restriction sites for a given DNA sequence is not always obvious, SiteFind automates this task. The number of possible sequences a computer program must search through increases exponentially as the sequence length increases. SiteFind uses a novel "moving window" algorithm to reduce the number of possible sequences to be searched to a manageable level. The user enters a nucleotide sequence, specifies what amino acid residues should be changed in the mutation, and SiteFind generates a list of possible restriction sites and what nucleotides must be changed to introduce that site. As a demonstration of its use, we successfully generated a single point mutation

  2. The Degradation of 14C-Glutamic Acid by L-Glutamic Acid Decarboxylase.

    Science.gov (United States)

    Dougherty, Charles M; Dayan, Jean

    1982-01-01

    Describes procedures and semi-micro reaction apparatus (carbon dioxide trap) to demonstrate how a particular enzyme (L-Glutamic acid decarboxylase) may be used to determine the site or sites of labeling in its substrate (carbon-14 labeled glutamic acid). Includes calculations, solutions, and reagents used. (Author/SK)

  3. Caracterização ácido-base da superfície de espécies mistas da alga Spirulina através de titulação potenciométrica e modelo de distribuição de sítios discretos Acid base characterization of the surface of mixed species of algae Spirulin by potentiometric titration and discrete site distribution model

    Directory of Open Access Journals (Sweden)

    Elizabete C. de Lima

    1999-09-01

    Full Text Available Acid base properties of mixed species of the microalgae Spirulina were studied by potentiometric titration in medium of 0.01 and 0.10 mols L-1 NaNO3 at 25.0±0.10 C using modified Gran functions or nonlinear regression techniques for data fitting. The discrete site distribution model was used, permitting the characterization of five classes of ionizable sites in both ionic media. This fact suggests that the chemical heterogeneity of the ionizable sites on the cell surface plays a major role on the acid-base properties of the suspension in comparison to electrostatic effects due to charge-charge interactions. The total of ionizable sites were 1.75±0.10 and 1.86±0.20 mmolsg-1 in ionic media of 0.01 and 0.10 mols L-1 NaNO3, respectively. A major contribution of carboxylic groups was observed with an average 34 and 22% of ionizable sites being titrated with conditional pcKa of 4.0 and 5.4, respectively. The remaining 44% of ionizable sites were divided in three classes with averaged conditional pcKa of 6.9, 8.7 and 10.12, which may be assigned respectively to imidazolic, aminic, and phenolic functionalities.

  4. Potential of amino acid/dipeptide monoester prodrugs of floxuridine in facilitating enhanced delivery of active drug to interior sites of tumors: a two-tier monolayer in vitro study.

    Science.gov (United States)

    Tsume, Yasuhiro; Hilfinger, John M; Amidon, Gordon L

    2011-10-01

    To evaluate the advantages of amino acid/dipeptide monoester prodrugs for cancer treatments by assessing the uptake and cytotoxic effects of floxuridine prodrugs in a secondary cancer cell monolayer following permeation across a primary cancer cell monolayer. The first Capan-2 monolayer was grown on membrane transwell inserts; the second monolayer was grown at the bottom of a plate. The permeation of floxuridine and its prodrugs across the first monolayer and the uptake and cell proliferation assay on secondary layer were sequentially determined. All floxuridine prodrugs exhibited greater permeation across the first Capan-2 monolayer than the parent drug. The correlation between uptake and growth inhibition in the second monolayer with intact prodrug permeating the first monolayer suggests that permeability and enzymatic stability are essential for sustained action of prodrugs in deeper layers of tumors. The correlation of uptake and growth inhibition were vastly superior for dipeptide prodrugs to those obtained with mono amino acid prodrugs. Although a tentative general overall correlation between intact prodrug and uptake or cytotoxic action was obtained, it appears that a mixture of floxuridine prodrugs with varying beneficial characteristics may be more effective in treating tumors.

  5. Nuclear installations sites safety

    International Nuclear Information System (INIS)

    Barber, P.; Candes, P.; Duclos, P.; Doumenc, A.; Faure, J.; Hugon, J.; Mohammadioun, B.

    1988-11-01

    This report is divided into ten parts bearing: 1 Safety analysis procedures for Basis Nuclear Installations sites (BNI) in France 2 Site safety for BNI in France 3 Industrial and transport activities risks for BNI in France 4 Demographic characteristics near BNI sites in France 5 Meteorologic characteristics of BNI sites in France 6 Geological aspects near the BNI sites in France 7 Seismic studies for BNI sites in France 8 Hydrogeological aspects near BNI sites in France 9 Hydrological aspects near BNI sites in France 10 Ecological and radioecological studies of BNI sites in France [fr

  6. Social Media Sites

    Science.gov (United States)

    Media Sites Site Registration Contact Us Search AF.mil: Home > AF Sites > Social Media Sites Social Media Welcome to the Air Force social media directory! The directory is a one-stop shop of official Air Force social media pages across various social media sites. Social media is all about

  7. The 18-kilodalton Chlamydia trachomatis histone H1-like protein (Hc1) contains a potential N-terminal dimerization site and a C-terminal nucleic acid-binding domain

    DEFF Research Database (Denmark)

    Pedersen, LB; Birkelund, Svend; Holm, A

    1996-01-01

    The Chlamydia trachomatis histone H1-like protein (Hc1) is a DNA-binding protein specific for the metabolically inactive chlamydial developmental form, the elementary body. Hc1 induces DNA condensation in Escherichia coli and is a strong inhibitor of transcription and translation. These effects may......-hydroxysuccinimide ester), purified recombinant Hc1 was found to form dimers. The dimerization site was located in the N-terminal part of Hc1 (Hc1(2-57)). Moreover, circular dichroism measurements indicated an overall alpha-helical structure of this region. By using limited proteolysis, Southwestern blotting, and gel...

  8. Formic acid

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, H; Laing, B

    1921-12-03

    The production of formic acid by the oxidation of methane with a metallic oxide or by the interaction of carbon monoxide and water vapor in the presence of a catalyst, preferably a metallic oxide, is described along with the destructive distillation of carbonaceous material in the preesnce of formic acid vapor for the purpose of increasing the yield of condensible hydrocarbons.

  9. Recycling abandoned lead battery sites

    International Nuclear Information System (INIS)

    Montgomery, A.H.

    1993-01-01

    In the past, automobile batteries were recycled principally for their lead content. The waste generated at battery wrecking facilities consisted of spent acid, crushed casings (ebonite and plastic), and where secondary smelting was involved, matte, slag, and carbon from the smelting process. These waste products were generally disposed in an on-site in a landfill or stored in piles. If the facility shut down because further commercial operations were not financially viable, the waste piles remained to be addressed at a later date through remedial action or reclamation programs. There are many of these facilities in the US. Nationally, about 28 sites have been discovered by the US Environmental Protection Agency (EPA) under the Superfund program and are under investigation or administrative orders for remedial action. A major remediation effort is now underway at the Gould Superfund Site in Portland, Oregon, which was operated as a secondary smelting facility between 1949 and 1981. This paper describes the nature of the contamination at the Gould site and the work conducted by Canonie Environmental Services Corp. (Canonie) to develop a process which would treat the waste from battery wrecking operations and produce revenue generating recyclable products while removing the source contamination (lead) from the site. The full-scale commercial plant is now operating and is expected to achieve a throughput rate of between 200 and 250 tons per day in the coming weeks

  10. Ocean Disposal Site Monitoring

    Science.gov (United States)

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.

  11. Promoting Your Web Site.

    Science.gov (United States)

    Raeder, Aggi

    1997-01-01

    Discussion of ways to promote sites on the World Wide Web focuses on how search engines work and how they retrieve and identify sites. Appropriate Web links for submitting new sites and for Internet marketing are included. (LRW)

  12. Particle Physics Education Sites

    Science.gov (United States)

    back to home page Particle Physics Education Sites quick reference Education and Information - National Laboratory Education Programs - Women and Minorities in Physics - Other Physics Sites - Physics Alliance - Accelerators at National Laboratories icon Particle Physics Education and Information sites: top

  13. 5,5'-Dithiobis-(2-nitrobenzoic acid) as a probe for a non-essential cysteine residue at the medium chain acyl-coenzyme A dehydrogenase binding site of the human 'electron transferring flavoprotein' (ETF).

    Science.gov (United States)

    Parker, A; Engel, P C

    1999-01-01

    Human 'electron transferring flavoprotein' (ETF) was inactivated by the thiol-specific reagent 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB). The kinetic profile showed the reaction followed pseudo-first-order kinetics during the initial phase of inactivation. Monitoring the release of 5-thio-2-nitrobenzoate (TNB) showed that modification of 1 cysteine residue was responsible for the loss of activity. The inactivation of ETF by DTNB could be reversed upon incubation with thiol-containing reagents. The loss of activity was prevented by the inclusion of medium chain acyl-CoA dehydrogenase (MCAD) and octanoyl-CoA. Cyanolysis of the DTNB modified-ETF with KCN led to the release of TNB accompanied presumably by the formation of the thio-cyano enzyme and with almost full recovery of activity. Conservation studies and the lack of 100% inactivation, however, suggested that this cysteine residue is not essential for the interaction with MCAD.

  14. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. (Westinghouse Hanford Co., Richland, WA (USA)); Yancey, E.F. (Pacific Northwest Lab., Richland, WA (USA))

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.

  15. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J.; Yancey, E.F.

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs

  16. From Unnatural Amino Acid Incorporation to Artificial Metalloenzymes

    KAUST Repository

    Makki, Arwa

    2016-01-01

    This thesis explores a novel strategy based on the site-selective incorporation of unnatural, metal binding amino acids into a host protein. The unnatural amino acids can either serve directly as metal binding centers can

  17. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  18. Superfund Site Information - Site Sampling Data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes Superfund site-specific sampling information including location of samples, types of samples, and analytical chemistry characteristics of...

  19. Site Closure Strategy Model for Creosote Site

    International Nuclear Information System (INIS)

    Coll, F.R.; Gray, D.R.

    2009-01-01

    In conjunction with RCRA site corrective action at an active wood preserving facility, a risk-based site closure strategy was developed and incorporated the performance of a dense non-aqueous phase liquid (DNAPL) source recovery remedy, a monitored natural attenuation (MNA) remedy for dissolved phase groundwater, and institutional controls. Innovative creosote DNAPL source recovery has been undertaken at the Site since 1998. Pooled creosote DNAPL is present 90 feet below ground within a transmissive sand and gravel aquifer with a saturated thickness of approximately 80 feet. The creosote DNAPL source is situated on the property boundary of the site and has generated a 1/2 mile off-site dissolved phase plume, creating significant NAPL management and remedial technology verification issues. To date, over 120,000 gallons of creosote DNAPL have been recovered from the subsurface utilizing a modified circulation well technology. A mass discharge flux protocol was developed to serve as a major performance metrics for the continuation of source removal efforts and to support the application of monitored natural attenuation as an associated remedial technology for groundwater. The mass removal success has supported the MNA remedy for dissolved phase groundwater and the associated development of institutional controls. The enacted site management strategy outlines the current and future risk management activities for the Site and represents an appropriate site closure strategy for the Site. (authors)

  20. Site specific information in site selection

    International Nuclear Information System (INIS)

    Aeikaes, T.; Hautojaervi, A.

    1998-01-01

    The programme for the siting of a deep repository for final disposal of spent nuclear fuel was started already in 1983 and is carried out today by Posiva Oy which continues the work started by Teollisuuden Voima Oy. The programme aims at site selection by the end of the year 2000. The programme has progressed in successive interim stages with defined goals. After an early phase for site identification, five sites were selected in 1987 for preliminary site characterisation. Three of these were selected and judged to be best suited for the more detailed characterisation in 1992. An additional new site was included into the programme based on a separate feasibility study in the beginning of 1997. Since the year 1983 several safety assessments together with technical plans of the facility have been completed. When approaching the site selection the needs for more detailed consideration of the site specific properties in the safety assessment have been increased. The Finnish regulator STUK has published a proposal for general safety requirements for the final disposal of spent nuclear fuel in Finland. This set of requirements has been projected to be used in conjunction of the decision making by the end 2000. Based on the site evaluation all sites can provide a stable environment and there is evidence that the requirements for the longevity of the canister can be fulfilled at each site. In this manner the four candidate sites do not differ too much from each other. The main difference between the sites is in the salinity of the deep groundwater. The significance of differences in the salinity for the long-term safety cannot be defined yet. The differences may contribute to the discussion of the longevity of the bentonite buffer and also to the modelling of the groundwater flow and transport. The use of the geosphere as a transport barrier is basically culminated on the questions about sparse but fast flow routes and 'how bad channeling can be'. To answer these questions

  1. Alkylation of deoxyribonucleic acid by carcinogens dimethyl sulphate, ethyl methanesulphonate, N-ethyl-N-nitrosourea and N-methyl-N-nitrosourea. Relative reactivity of the phosphodiester site thymidylyl(3'-5')thymidine.

    Science.gov (United States)

    Swenson, D H; Lawley, P D

    1978-01-01

    1. The ethyl phosphotriester of thymidylyl(3'-5')thymidine, dTp(Et)dT, was identified as a product from reaction of DNA with N-ethyl-N-nitrosourea, by procedures parallel to those reported previously for the methyl homologue produced by N-methyl-N-nitrosourea. 2. Enzymic degradation to yield alkyl phosphotriesters from DNA alkylated by these carcinogens and by dimethyl sulphate and ethyl methanesulphonate was studied quantitatively, and the relative yields of the triesters dTp(Alk)dT were determined. The relative reactivity of the phosphodiester group dTpdT to each of the four carcinogens was thus obtained, and compared with that of DNA overall, or with that of the N-7 atom of guanine in DNA. Relative reactivity of the phosphodiester group was lowest towards dimethyl sulphate, the least electrophilic of the reagents used, and was highest towards N-ethyl-N-nitrosourea, the most electrophilic reagent. 3. The nature of the alkyl group transferred also influenced reactivity of the phosphodiester site, since this site was relatively more reactive towards ethylation than would be predicted simply from the known Swain-Scott s values of the alkylating agents. It was therefore suggested that the steric accessibility of the weakly nucleophilic phosphodiester group on the outside of the DNA macromolecule favours its reaction with ethylating, as opposed to methylating, reagents. 4. Taking a value of the Swain-Scott nucleophilicity (n) of 2.5 for an average DNA nucleotide unit [Walles & Ehrenberg (1969) Acta Chem. Scand. 23, 1080-1084], a value of n of about 1 for the phosphodiester group was deduced, and this value was found to be 2-3 units less than that for the N-7 atom of guanine in DNA. 5. The reactivity of DNA overall was markedly high towards the alkylnitrosoureas, despite their relatively low s values. This was ascribed to an electrostatic factor that favoured reaction of the negatively charged polymer with alkyldiazonium cation intermediates. PMID:208508

  2. Preparation and characterization Al3+-bentonite Turen Malang for esterification fatty acid (palmitic acid, oleic acid and linoleic acid)

    Science.gov (United States)

    Abdulloh, Abdulloh; Aminah, Nanik Siti; Triyono, Mudasir, Trisunaryanti, Wega

    2016-03-01

    Catalyst preparation and characterization of Al3+-bentonite for esterification of palmitic acid, oleic acid and linoleic acid has been done. Al3+-bentonite catalyst was prepared from natural bentonite of Turen Malang through cation exchange reaction using AlCl3 solution. The catalysts obtained were characterized by XRD, XRF, pyridine-FTIR and surface area analyser using the BET method. Catalyst activity test of Al3+-bentonite for esterification reaction was done at 65°C using molar ratio of metanol-fatty acid of 30:1 and 0.25 g of Al3+-bentonite catalyst for the period of ½, 1, 2, 3, 4 and 5 hours. Based on the characterization results, the Al3+-bentonite Turen Malang catalyst has a d-spacing of 15.63 Ǻ, acid sites of Brönsted and Lewis respectively of 230.79 µmol/g and 99.39 µmol/g, surface area of 507.3 m2/g and the average of radius pore of 20.09 Å. GC-MS analysis results of the oil phase after esterification reaction showed the formation of biodiesel (FAME: Fatty acid methyl ester), namely methyl palmitate, methyl oleate and methyl linoleate. The number of conversions resulted in esterification reaction using Al3+-bentonite Turen Malang catalyst was 74.61%, 37.75%, and 20, 93% for the esterification of palmitic acid, oleic acid and linoleic acid respectively.

  3. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1993-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP's primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides an existing and future land use plan for the Hanford Site. The HSDP is updated annually in accordance with DOE Order 4320.1B, Site Development Planning, to reflect the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans

  4. Mobilisation of heavy metals and arsenic by acid mine drainage in polluted sites of the Ag-Pb-Zn deposit near Wiesloch; Mobilisierbarkeit von Schwermetallen und Arsen durch saure Grubenabwaesser in Bergbaualtlasten der Ag-Pb-Zn-Lagerstaette in Wiesloch

    Energy Technology Data Exchange (ETDEWEB)

    Kappes, B.A.

    2000-07-01

    2000 years of small scale Ag-Pb-Zn mining has created a legacy of potentially hazardous waste material in Wiesloch. The objective of our study is to investigate the processes to identify the that might lead to a mobilisation of heavy metals and arsenic and their fate at this specific site. The objective of this study is: a) to examine in more detail the chemical and mineralogical composition of ore, dressing and slag material and b) to compare the heavy metal release potential to toxic elements of primary ore versus processing material if subjected to weathering. Three depth profiles due to drilling-operations retrieved mineralogical, chemical and physical data. The three most important pollutants are primary ore, dressing residue and slag. Apart from a chemical characterisation of these materials in order to establish the heavy metal and arsenic content field and laboratory experiments simulated worst case weathering conditions. Elution experiments demonstrated that heavy metal release is very much pH-dependent. The highest release potential was observed in flotation material from the dressing residue whereas primary ore and slag material released 10 times fewer heavy metals and arsenic. (orig.)

  5. Oxidized amino acid residues in the vicinity of Q(A and Pheo(D1 of the photosystem II reaction center: putative generation sites of reducing-side reactive oxygen species.

    Directory of Open Access Journals (Sweden)

    Laurie K Frankel

    Full Text Available Under a variety of stress conditions, Photosystem II produces reactive oxygen species on both the reducing and oxidizing sides of the photosystem. A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem. In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues (239F, (241Q, (242E and the D2 residues (238P, (239T, (242E and (247M and PheoD1 (D1 residues (130E, (133L and (135F. These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.

  6. Region 9 NPL Sites (Superfund Sites 2013)

    Science.gov (United States)

    NPL site POINT locations for the US EPA Region 9. NPL (National Priorities List) sites are hazardous waste sites that are eligible for extensive long-term cleanup under the Superfund program. Eligibility is determined by a scoring method called Hazard Ranking System. Sites with high scores are listed on the NPL. The majority of the locations are derived from polygon centroids of digitized site boundaries. The remaining locations were generated from address geocoding and digitizing. Area covered by this data set include Arizona, California, Nevada, Hawaii, Guam, American Samoa, Northern Marianas and Trust Territories. Attributes include NPL status codes, NPL industry type codes and environmental indicators. Related table, NPL_Contaminants contains information about contaminated media types and chemicals. This is a one-to-many relate and can be related to the feature class using the relationship classes under the Feature Data Set ENVIRO_CONTAMINANT.

  7. Hazardous waste operational plan for site 300

    International Nuclear Information System (INIS)

    Roberts, R.S.

    1982-01-01

    This plan outlines the procedures and operations used at LLNL's Site 300 for the management of the hazardous waste generated. This waste consists primarily of depleted uranium (a by-product of U-235 enrichment), beryllium, small quantities of analytical chemicals, industrial type waste such as solvents, cleaning acids, photographic chemicals, etc., and explosives. This plan details the operations generating this waste, the proper handling of this material and the procedures used to treat or dispose of the hazardous waste. A considerable amount of information found in this plan was extracted from the Site 300 Safety and Operational Manual written by Site 300 Facility personnel and the Hazards Control Department

  8. Fatty acid composition and amino acid profile of two freshwater ...

    African Journals Online (AJOL)

    The proximate, fatty and amino acids composition of two commercially important freshwater fish species Clarias gariepinus and Tilapia zillii. purchased from local fishermen in two landing sites in Lagos State, Nigeria were determined. Live specimens of C. gariepinus were purchased while samples of T. zillii were stored in ...

  9. Chloride binding site of neurotransmitter sodium symporters

    DEFF Research Database (Denmark)

    Kantcheva, Adriana Krassimirova; Quick, Matthias; Shi, Lei

    2013-01-01

    Neurotransmitter:sodium symporters (NSSs) play a critical role in signaling by reuptake of neurotransmitters. Eukaryotic NSSs are chloride-dependent, whereas prokaryotic NSS homologs like LeuT are chloride-independent but contain an acidic residue (Glu290 in LeuT) at a site where eukaryotic NSSs...

  10. Uric acid in multiple sclerosis

    NARCIS (Netherlands)

    Koch, M; De Keyser, J

    Peroxynitrite, a reactive oxidant formed by the reaction of nitric oxide with superoxide at sites of inflammation in multiple sclerosis (MS), is capable of damaging tissues and cells. Uric acid, a natural scavenger of peroxynitrite, reduces inflammatory demyelination in experimental allergic

  11. Koetjapic acid chloroform hemisolvate

    Directory of Open Access Journals (Sweden)

    Z. D. Nassar

    2010-06-01

    Full Text Available The asymmetric unit of the title compound, C30H46O4·0.5CHCl3, consists of one koetjapic acid [systematic name: (3R,4aR,4bS,7S,8S,10bS,12aS-7-(2-carboxyethyl-3,4b,7,10b,12a-pentamethyl-8-(prop-1-en-2-yl-1,2,3,4,4a,4b,5,6,7,8,9,10,10b,11,12,12a-hexadecahydrochrysene-3-carboxylic acid] molecule and one half-molecule of chloroform solvent, which is disordered about a twofold rotation axis. The symmetry-independent component is further disordered over two sites, with occupancies of 0.30 and 0.20. The koetjapic acid contains a fused four-ring system, A/B/C/D. The A/B, B/C and C/D junctions adopt E/trans/cis configurations, respectively. The conformation of ring A is intermediate between envelope and half-chair and ring B adopts an envelope conformation whereas rings C and D adopt chair conformations. A weak intramolecular C—H...O hydrogen bond is observed. The koetjapic acid molecules are linked into dimers by two pairs of intermolecular O—H...O hydrogen bonds. The dimers are stacked along the c axis.

  12. Primary amino acid derivatives: substitution of the 4'-N'-benzylamide site in (R)-N'-benzyl 2-amino-3-methylbutanamide, (R)-N'-benzyl 2-amino-3,3-dimethylbutanamide, and (R)-N'-benzyl 2-amino-3-methoxypropionamide provides potent anticonvulsants with pain-attenuating properties.

    Science.gov (United States)

    King, Amber M; Salomé, Christophe; Salomé-Grosjean, Elise; De Ryck, Marc; Kaminski, Rafal; Valade, Anne; Stables, James P; Kohn, Harold

    2011-10-13

    Recently, we reported that select N'-benzyl 2-substituted 2-amino acetamides (primary amino acid derivatives (PAADs)) exhibited pronounced activities in established whole animal anticonvulsant (i.e., maximal electroshock seizure (MES)) and neuropathic pain (i.e., formalin) models. The anticonvulsant activities of C(2)-hydrocarbon N'-benzyl 2-amino acetamides (MES ED(50) = 13-21 mg/kg) exceeded those of phenobarbital (ED(50) = 22 mg/kg). Two additional studies defining the structure-activity relationship of PAADs are presented in this issue of the journal. In this study, we demonstrated that the anticonvulsant activities of (R)-N'-benzyl 2-amino-3-methylbutanamide and (R)-N'-benzyl 2-amino-3,3-dimethylbutanamide were sensitive to substituents at the 4'-N'-benzylamide site; electron-withdrawing groups retained activity, electron-donating groups led to a loss of activity, and incorporating either a 3-fluorobenzyloxy or 3-fluorophenoxymethyl group using a rationally designed multiple ligand approach improved activity. Additionally, we showed that substituents at the 4'-N'-benzylamide site of (R)-N'-benzyl 2-amino-3-methoxypropionamide also improved anticonvulsant activity, with the 3-fluorophenoxymethyl group providing the largest (∼4-fold) increase in activity (ED(50) = 8.9 mg/kg), a value that surpassed phenytoin (ED(50) = 9.5 mg/kg). Collectively, the pharmacological findings provided new information that C(2)-hydrocarbon PAADs represent a novel class of anticonvulsants.

  13. Methodology of site studies

    International Nuclear Information System (INIS)

    Caries, J.C.; Hugon, J.; Grauby, A.

    1980-01-01

    This methodology consists in an essentially dynamic, estimated and follow-up analysis of the impact of discharges on all the environment compartments, whether natural or not, that play a part in the protection of man and his environment. It applies at two levels, to wit: the choice of site, or the detailed study of the site selected. Two examples of its application will be developed, namely: at the choice of site level in the case of marine sites, and of the detailed study level of the chosen site in that of a riverside site [fr

  14. Lipoic Acid

    Directory of Open Access Journals (Sweden)

    Ramazan Tetikcok

    2015-09-01

    Full Text Available Lipoic acid, which is defined as a miralce antioxidan, is used by many departments. Eventhough clinical using data are very limited , it is used in treatment of diabetic neuropathy, physical therapy and rehabilitation clinic, dermatology clinic, geriatric clinics. It has usage area for cosmetic purposes. Although there are reports there are the direction of the effectiveness in these areas, the works done are not enough. Today lipoic acid , used in many areas ,is evaluated as universal antioxidant [J Contemp Med 2015; 5(3.000: 206-209

  15. NPL Site Locations

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  16. Site Area Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of site boundaries from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and...

  17. NPL Site Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  18. Drupal 7 Multilingual Sites

    CERN Document Server

    Pol, Kristen

    2012-01-01

    A practical book with plenty of screenshots to guide you through the many features of multilingual Drupal. A demo ecommerce site is provided if you want to practice on a sample site, although you can apply the techniques learnt in the book directly to your site too. Any Drupal users who know the basics of building a Drupal site and are familiar with the Drupal UI, will benefit from this book. No previous knowledge of localization or internationalization is required.

  19. Nuclear waste repository siting

    International Nuclear Information System (INIS)

    Soloman, B.D.; Cameron, D.M.

    1987-01-01

    This paper discusses the geopolitics of nuclear waste disposal in the USA. Constitutional choice and social equity perspectives are used to argue for a more open and just repository siting program. The authors assert that every potential repository site inevitably contains geologic, environmental or other imperfections and that the political process is the correct one for determining sites selected

  20. Site Calibration report

    DEFF Research Database (Denmark)

    Yordanova, Ginka; Vesth, Allan

    The report describes site calibration measurements carried out on a site in Denmark. The measurements are carried out in accordance to Ref. [1]. The site calibration is carried out before a power performance measurement on a given turbine to clarify the influence from the terrain on the ratio...

  1. CCS site characterisation criteria

    Energy Technology Data Exchange (ETDEWEB)

    Bachu, S.; Hawkes, C.; Lawton, D.; Pooladi-Darvish, M.; Perkins, E.

    2009-12-15

    IEA GHG recently commissioned the Alberta Research Counil in Canada to conduct a review of storage site selection criteria and site characterisation methods in order to produce a synthesis report. This report reviews the literature on the subject on the site seleciton and characterisation since the publication of the IPCC Special Report on CCS, and provides a synthesis and classification of criteria. 161 refs.

  2. Mefenamic Acid

    Science.gov (United States)

    Mefenamic acid comes as a capsule to take by mouth. It is usually taken with food every 6 hours as needed for up to 1 week. Follow ... pain vomit that is bloody or looks like coffee grounds black, tarry, or bloody stools slowed breathing ...

  3. Acid rain. Les pluies acides

    Energy Technology Data Exchange (ETDEWEB)

    Curren, T

    1979-11-28

    This report was produced for the use of Members of Parliament and House of Commons committees. The document describes the formation of acid rain, emissions of acidifying pollutants in North America, the growth of the problem and its environmental effects on aquatic and terrestrial ecosystems, human health and man-made structures. Areas of Canada which are most susceptible are identified. Actions taken by Parliament are given, including the formation of a sub-committee on acid rain and the passing of Bill C-51 in 1980 to amend the Clean Air Act, bringing it closer to a similar law in the U.S. A chronology of government responses to acid rain at the international, national and provincial level, is given. The most recent government actions included the passing of the US Clean Air Act by the Senate, the amending of the act into law, and commencement of negotiations to develop a Canada-US Air Quality Accord. 10 refs.

  4. Hybrid pine for tough sites

    International Nuclear Information System (INIS)

    Davidson, W.H.

    1994-01-01

    A test planting of 30 first- and second-generation pitch x loblolly pine (pinus rigida x P. taeda) hybrids was established on a West Virginia minesoil in 1985. The site was considered orphaned because earlier attempts at revegetation were unsuccessful. The soil was acid (pH 4.6), lacking in nutrients, and compacted. Vegetation present at the time of planting consisted of a sparse cover of tall fescue (Festuca arundinacea) and poverty grass (Danthonia spicata) and a few sourwood (Oxydendrum arboreum) and mountain laurel (Kalmia latifolia) seedlings. In the planting trial, 30 different hybrids were set out in 4 tree linear plots replicated 5 times. The seedlings had been grown in containers for 1 yr before outplanting. Evaluations made after 6 growing seasons showed overall plantation survival was 93%; six hybrids and one open-pollinated cross survived 100%. Individual tree heights ranged from 50 to 425 cm with a plantation average of 235 cm (7.7 ft). Eleven of the hybrids had average heights that exceeded the plantation average. Another test planting of tree and shrub species on this site has very poor survival. Therefore, pitch x loblolly hybrid pine can be recommended for reclaiming this and similar sites

  5. Site Environmental Report, 1993

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, ``General Environmental Protection Program.`` This 1993 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in the Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here.

  6. Olkiluoto site description 2011

    International Nuclear Information System (INIS)

    2012-12-01

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties

  7. Olkiluoto site description 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-12-15

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties.

  8. Hanford Site Infrastructure Plan

    International Nuclear Information System (INIS)

    1990-01-01

    The Hanford Site Infrastructure Plan (HIP) has been prepared as an overview of the facilities, utilities, systems, and services that support all activities on the Hanford Site. Its purpose is three-fold: to examine in detail the existing condition of the Hanford Site's aging utility systems, transportation systems, Site services and general-purpose facilities; to evaluate the ability of these systems to meet present and forecasted Site missions; to identify maintenance and upgrade projects necessary to ensure continued safe and cost-effective support to Hanford Site programs well into the twenty-first century. The HIP is intended to be a dynamic document that will be updated accordingly as Site activities, conditions, and requirements change. 35 figs., 25 tabs

  9. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1992-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP's primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides a land use plan for the Hanford Site and presents a picture of what is currently known and anticipated in accordance with DOE Order 4320.1B. Site Development Planning. The HSDP wig be updated annually as future decisions further shape the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans

  10. Levulinic acid

    Directory of Open Access Journals (Sweden)

    Barbara Hachuła

    2013-09-01

    Full Text Available The title compound (systematic name: 4-oxopentanoic acid, C5H8O3, is close to planar (r.m.s. deviation = 0.0762 Å. In the crystal, the molecules interact via O—H...O hydrogen bonds in which the hydroxy O atoms act as donors and the ketone O atoms in adjacent molecules as acceptors, forming C(7 chains along [20-1].

  11. Site characterization plan:

    International Nuclear Information System (INIS)

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in accordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package;and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and developing a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing principles, and organization of this site characterization plan are outlined, and compliance with applicable regulations is discussed

  12. Site characterization plan:

    International Nuclear Information System (INIS)

    1988-01-01

    The Yucca Mountain site in Nevada is one of three candidate sites for the first geologic repository for radioactive waste. On May 28, 1986, it was recommended for detailed study in a program of site characterization. This site characterization plan (SCP) has been prepared in acordance with the requirements of the Nuclear Waste Policy Act to summarize the information collected to date about the geologic conditions at the site;to describe the conceptual designs for the repository and the waste package and to present the plans for obtaining the geologic information necessary to demonstrate the suitability of the site for a repository, to design the repository and the waste package, to prepare an environmental impact statement, and to obtain from the US Nuclear Regulatory Commission (NRC) an authorization to construct the repository. This introduction begins with a brief section on the process for siting and eveloping a repository, followed by a discussion of the pertinent legislation and regulations. A description of site characterization is presented next;it describes the facilities to be constructed for the site characterization program and explains the principal activities to be conducted during the program. Finally, the purpose, content, organizing prinicples, and organization of this site characterization plan are outlined, and compliance with applicable regulations is discussed. 880 refs., 130 figs., 25 tabs

  13. Acid-base characteristics of powdered-activated-carbon surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Reed, B.E. (West Virginia Univ., Morgantown (United States)); Jensen, J.N.; Matsumoto, M.R. (State Univ. of New York, Buffalo (United States))

    Adsorption of heavy metals onto activated carbon has been described using the surface-complex-formation (SCF) model, a chemical equilibrium model. The SCF model requires a knowledge of the amphoteric nature of activated carbon prior to metal adsorption modeling. In the past, a single-diprotic-acid-site model had been employed to describe the amphoteric nature of activated-carbon surfaces. During this study, the amphoteric nature of two powdered activated carbons were investigated, and a three-monoprotic site surface model was found to be a plausible alternative. The single-diprotic-acid-site and two-monoprotic-site models did not describe the acid-base behavior of the two carbons studied adequately. The two-diprotic site was acceptable for only one of the study carbons. The acid-base behavior of activated carbon surfaces seem to be best modeled as a series of weak monoprotic acids.

  14. Integration of Chemical and Biological Catalysis

    DEFF Research Database (Denmark)

    Schwartz, Thomas J.; Goodman, Samuel M.; Osmundsen, Christian Mårup

    2013-01-01

    Furylglycolic acid (FA), a pseudoaromatic hydroxy-acid suitable for copolymerization with lactic acid, can be produced from glucose via enzymatically derived cortalcerone using a combination of Bronsted and Lewis acid catalysts. Cortalcerone is first converted to furylglyoxal hydrate (FH) over a ...

  15. Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation.

    Science.gov (United States)

    Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward; Roger, Andrew J

    2018-03-01

    Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.

  16. Site environmental programs

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, J.W.; Hanf, R.W.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the site environmental programs. Effluent monitoring and environmental surveillance programs monitor for impacts from operations in several areas. The first area consists of the point of possible release into the environment. The second area consists of possible contamination adjacent to DOE facilities, and the third area is the general environment both on and off the site.

  17. Site environmental report summary

    International Nuclear Information System (INIS)

    1992-01-01

    In this summary of the Fernald 1992 Site Environmental Report the authors will describe the impact of the Fernald site on man and the environment and provide results from the ongoing Environmental Monitoring Program. Also included is a summary of the data obtained from sampling conducted to determine if the site complies with DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA) requirements. These requirements are set to protect both man and the environment

  18. Site environmental programs

    International Nuclear Information System (INIS)

    Schmidt, J.W.; Hanf, R.W.

    1995-01-01

    This section of the 1994 Hanford Site Environmental Report summarizes the site environmental programs. Effluent monitoring and environmental surveillance programs monitor for impacts from operations in several areas. The first area consists of the point of possible release into the environment. The second area consists of possible contamination adjacent to DOE facilities, and the third area is the general environment both on and off the site

  19. CERCLA site assessment workbook

    International Nuclear Information System (INIS)

    1994-08-01

    This contains comments for each chapter of exercises (in Vol. 1) which illustrate how to conduct site assessments for CERCLA regulation. A through analysis of the exercises is provided so that work and solutions from Vol 1 can be critiqued and comments are also included on the strategy of site assessment whereas the exercises illustrate the principles involved. Covered exercises include the following: A preliminary assessment of a ground water site; waste characteristics and characterization of sources; documentation of observed releases and actual contamination of targets; the strategy of an SI at a surface water site; the soil exposure pathway; the air pathway

  20. Nuclear site selection studies

    International Nuclear Information System (INIS)

    Gharib, A.; Zohoorian Izadpanah, A.A.; Iranmanesh, H.

    2000-01-01

    It is of special importance, especially from the nuclear safety viewpoint, to select suitable sites for different nuclear structures with the considered future activities. Site selection sometimes involves high costs not necessarily for merely selecting of site but for some preliminary measures to be taken so as the site may have the necessary characteristics. The more suitable the natural characteristics of the site for the considered project, the more successful and efficient the project, the lower the project costs and the longer the project operation period. If so, the project will cause the growth of public culture and sustainable socioeconomic development. This paper is the result of the conclusion of numerous massive reports of this activity in the preliminary phase based on theories, practices and the related safety principles on this ground as well as the application of data and information of the past and a glance to the future. The conception of need for a site for medium structures and nuclear research projects and how to perform this process are presented step by step here with a scientific approach to its selection during the investigations. In this study, it is practically described how the site is selected, by determining and defining the characteristics of research and nuclear projects with medium structures and also its fitting to the optimum site. The discovered sites typically involve the best advantages in technical and economic aspects and no particular contrast with the concerned structures

  1. Meteorology in site operations

    International Nuclear Information System (INIS)

    Anon.

    1986-01-01

    During the site selection and design phases of a plant, meteorological assistance must be based on past records, usually accumulated at stations not actually on the site. These preliminary atadvices will be averages and extremes that might be expected. After a location has been chosen and work has begun, current and forecast weather conditions become of immediate concern. On-site meteorological observations and forecasts have many applications to the operating program of an atomic energy site. Requirements may range from observations of the daily minimum temperatures to forecasts of radiation dosages from airborne clouds

  2. 1994 Site environmental report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-01

    The Fernald site is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the site in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the site. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1994 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here. All information presented in this summary is discussed more fully in the main body of this report.

  3. Decontamination of soil from the research reactor site

    International Nuclear Information System (INIS)

    Won, H. Z.; Kim, K. N.; Choi, W. K.; Jeong, J. H.; Oh, W. J.

    2002-01-01

    The two research reactors (TRIGA MARK II and III) in Korea are to be decommissioned in the near future. When the reactors are completely dismantled, the site may remain contaminated due to the long period of operation. We assume that the site is radioactively contaminated by Co-60. Soils gathered from the research reactor site were artificially contaminated with Co 2+ ion. The desorption characteristics of Co 2+ ion from the soil surface by citric acid solution were investigated. Decontamination performances of citric acid and EDTA on soil stored in the radioactive waste drums was examined. The feasibility test of recycling the citric acid was also performed. We concluded that the radioactive waste volume could be reduced significantly by soil washing with a citric acid solution

  4. PHYSICAL SOLUTIONS FOR ACID MINE DRAINAGE AT REMOTE MINE SITES

    Science.gov (United States)

    After completing extensive bench-scale testing to determine optimum treatment approaches, the technology has been taken to the field. Preliminary results show that calcium hydroxide precipitates the bulk of the arsenic and zinc; the granular ferric hydroxide removes the rest of ...

  5. Savannah River Site's Site Specific Plan

    International Nuclear Information System (INIS)

    1991-01-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering

  6. SITE-94. Mineralogy of the Aespoe site

    International Nuclear Information System (INIS)

    Andersson, Karin

    1996-12-01

    The water composition has several impacts on the repository. It will influence the behaviour of the engineered materials (e.g. corrosion). It may also determine the possible solubility and speciation of released radionuclides. It also acts as a transport medium for the released elements. The groundwater composition and the potential development of the composition due to the presence of the repository as well as due to external variations is thus an important issue in a safety analysis. The development of the groundwater composition is strongly dependent on reactions with the minerals present in water bearing fractures. Here equilibrium chemistry may be of importance, but also reaction kinetics is important to the long-term behaviour. Within the SITE-94 project, a safety analysis is performed for the conditions at the Aespoe site. The mineralogy of the area has been evaluated from drill cores at various places at the site. In this report a recommendation for selection of mineralogy to be used in geochemical modelling of the repository is given. Calcite and iron containing minerals dominate the fracture filling mineralogy at the Aespoe site. Some typical fracture filling mineralogies may be identified in the fractures: epidote, chlorite, calcite, hematite, some illite/smectite + quartz, fluorite, pyrite and goethite. In addition to these a number of minor minerals are found in the fractures. Uncertainties in the fracture filling data may be due to problems when taking out the drill cores. Drilling water may remove important clay minerals and sealed fractures may be reopened mechanically and treated as water conducting fractures. The problem of determining the variability of the mineralogy along the flow paths also remains. This problem will never be solved when the investigation is performed by drilling investigation holes

  7. Preliminary Site Characterization Report, Rulsion Site, Colorado

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-08-01

    This report is a summary of environmental information gathered during a review of the documents pertaining to Project Rulison and interviews with personnel who worked on the project. Project Rulison was part of Operation Plowshare (a program designed to explore peaceful uses for nuclear devices). The project consisted of detonating a 43-kiloton nuclear device on September 10, 1969, in western Colorado to stimulate natural gas production. Following the detonation, a reentry well was drilled and several gas production tests were conducted. The reentry well was shut-in after the last gas production test and was held in standby condition until the general cleanup was undertaken in 1972. A final cleanup was conducted after the emplacement and testing wells were plugged in 1976. However, some surface radiologic contamination resulted from decontamination of the drilling equipment and fallout from the gas flaring during drilling operations. With the exception of the drilling effluent pond, all surface contamination at the Rulison Site was removed during the cleanup operations. All mudpits and other excavations were backfilled, and both upper and lower drilling pads were leveled and dressed. This report provides information regarding known or suspected areas of contamination, previous cleanup activities, analytical results, a review of the regulatory status, the site`s physical environment, and future recommendations for Project Ruhson. Based on this research, several potential areas of contamination have been identified. These include the drilling effluent pond and mudpits used during drilling operations. In addition, contamination could migrate in the gas horizon.

  8. Site-Specific Innovation

    DEFF Research Database (Denmark)

    Reeh, Henrik; Hemmersam, Peter

    2015-01-01

    Currently, cities across the Northern European region are actively redeveloping their former industrial harbours. Indeed, harbours areas are essential in the long-term transition from industrial to information and experience societies; harbours are becoming sites for new businesses and residences...... question is how innovation may contribute to urban life and site-specific qualities....

  9. Criminal Justice Web Sites.

    Science.gov (United States)

    Dodge, Timothy

    1998-01-01

    Evaluates 15 criminal justice Web sites that have been selected according to the following criteria: authority, currency, purpose, objectivity, and potential usefulness to researchers. The sites provide narrative and statistical information concerning crime, law enforcement, the judicial system, and corrections. Searching techniques are also…

  10. The site selection process

    International Nuclear Information System (INIS)

    Kittel, J.H.

    1989-01-01

    One of the most arduous tasks associated with the management of radioactive wastes is the siting of new disposal facilities. Experience has shown that the performance of the disposal facility during and after disposal operations is critically dependent on the characteristics of the site itself. The site selection process consists of defining needs and objectives, identifying geographic regions of interest, screening and selecting candidate sites, collecting data on the candidate sites, and finally selecting the preferred site. Before the site selection procedures can be implemented, however, a formal legal system must be in place that defines broad objectives and, most importantly, clearly establishes responsibilities and accompanying authorities for the decision-making steps in the procedure. Site selection authorities should make every effort to develop trust and credibility with the public, local officials, and the news media. The responsibilities of supporting agencies must also be spelled out. Finally, a stable funding arrangement must be established so that activities such as data collection can proceed without interruption. Several examples, both international and within the US, are given

  11. Siting nuclear power plants

    International Nuclear Information System (INIS)

    Yellin, J.; Joskow, P.L.

    1980-01-01

    The first edition of this journal is devoted to the policies and problems of siting nuclear power plants and the question of how far commercial reactors should be placed from urban areas. The article is divided into four major siting issues: policies, risk evaluation, accident consequences, and economic and physical constraints. One concern is how to treat currently operating reactors and those under construction that were established under less-stringent criteria if siting is to be used as a way to limit the consequences of accidents. Mehanical cost-benefit analyses are not as appropriate as the systematic use of empirical observations in assessing the values involved. Stricter siting rules are justified because (1) opposition because of safety is growing: (2) remote siting will make the industry more stable; (3) the conflict is eliminated between regulatory policies and the probability basis for nuclear insurance; and (4) joint ownership of utilities and power-pooling are increasing. 227 references, 7 tables

  12. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  13. Site decommissioning management plan

    International Nuclear Information System (INIS)

    Fauver, D.N.; Austin, J.H.; Johnson, T.C.; Weber, M.F.; Cardile, F.P.; Martin, D.E.; Caniano, R.J.; Kinneman, J.D.

    1993-10-01

    The Nuclear Regulatory Commission (NRC) staff has identified 48 sites contaminated with radioactive material that require special attention to ensure timely decommissioning. While none of these sites represent an immediate threat to public health and safety they have contamination that exceeds existing NRC criteria for unrestricted use. All of these sites require some degree of remediation, and several involve regulatory issues that must be addressed by the Commission before they can be released for unrestricted use and the applicable licenses terminated. This report contains the NRC staff's strategy for addressing the technical, legal, and policy issues affecting the timely decommissioning of the 48 sites and describes the status of decommissioning activities at the sites

  14. Site decommissioning management plan

    Energy Technology Data Exchange (ETDEWEB)

    Fauver, D.N.; Austin, J.H.; Johnson, T.C.; Weber, M.F.; Cardile, F.P.; Martin, D.E.; Caniano, R.J.; Kinneman, J.D.

    1993-10-01

    The Nuclear Regulatory Commission (NRC) staff has identified 48 sites contaminated with radioactive material that require special attention to ensure timely decommissioning. While none of these sites represent an immediate threat to public health and safety they have contamination that exceeds existing NRC criteria for unrestricted use. All of these sites require some degree of remediation, and several involve regulatory issues that must be addressed by the Commission before they can be released for unrestricted use and the applicable licenses terminated. This report contains the NRC staff`s strategy for addressing the technical, legal, and policy issues affecting the timely decommissioning of the 48 sites and describes the status of decommissioning activities at the sites.

  15. Application of the CPA equation of state to organic acids

    DEFF Research Database (Denmark)

    Derawi, Samer; Zeuthen, Frederik Jacob; Michelsen, Michael Locht

    2004-01-01

    a strong tendency to dimerise in the vapor phase at normal condition resulting in strong non-ideal behavior, even at low pressures. Pure compound parameters have been determined from vapor pressure and liquid density data for the three acids. Among the three tested association schemes (one-site, two......-site, and four-site), only the one-site association scheme describes satisfactorily the association in both the gas and the liquid phase. Second virial coefficients axe predicted well with the proposed one-site model. Excellent binary VLE and acceptable LLE correlations have been obtained for acid + aliphatic...

  16. Understanding Acid Rain

    Science.gov (United States)

    Damonte, Kathleen

    2004-01-01

    The term acid rain describes rain, snow, or fog that is more acidic than normal precipitation. To understand what acid rain is, it is first necessary to know what an acid is. Acids can be defined as substances that produce hydrogen ions (H+), when dissolved in water. Scientists indicate how acidic a substance is by a set of numbers called the pH…

  17. 1994 Site environmental report

    International Nuclear Information System (INIS)

    1995-07-01

    The Fernald site is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the site in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the site. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1994 SER provides the general public as well as scientists and engineers with the results from the site's ongoing Environmental Monitoring Program. Also included in this report is information concerning the site's progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here. All information presented in this summary is discussed more fully in the main body of this report

  18. SITE-94. Radionuclide solubilities for SITE-94

    Energy Technology Data Exchange (ETDEWEB)

    Arthur, R.; Apted, M. [QuantiSci, Denver, CO (United States)

    1996-12-01

    In this report, solubility constraints are evaluated on radioelement source-term concentrations supporting the SITE-94 performance assessment. Solubility models are based on heterogeneous-equilibrium, mass- and charge-balance constraints incorporated into the EQ3/6 geochemical software package, which is used to calculate the aqueous speciation behavior and solubilities of U, Th, Pu, Np, Am, Ni, Ra, Se, Sn, Sr, Tc and Zr in site groundwaters and near-field solutions. The chemical evolution of the near field is approximated using EQ3/6 in terms of limiting conditions at equilibrium, or steady state, in three closed systems representing fully saturated bentonite, Fe{sup o} corrosion products of the canister, and spent fuel. The calculations consider both low-temperature (15 deg C) and high-temperature (80 deg C) conditions in the near field, and the existence of either reducing or strongly oxidizing conditions in each of the bentonite, canister, and spent-fuel barriers. Heterogeneities in site characteristics are evaluated through consideration of a range of initial groundwaters and their interactions with engineered barriers. Aqueous speciation models for many radioelements are constrained by thermodynamic data that are estimated with varying degrees of accuracy. An important question, however, is how accurate do these models need to be for purposes of estimating source-term concentrations? For example, it is unrealistic to expect a high degree of accuracy in speciation models if such models predict solubilities that are below the analytical detection limit for a given radioelement. From a practical standpoint, such models are irrelevant if calculated solubilities cannot be tested by direct comparison to experimental data. In the absence of models that are both accurate and relevant for conditions of interest, the detection limit could define a pragmatic upper limit on radioelement solubility 56 refs, 25 tabs, 10 figs

  19. SITE-94. Radionuclide solubilities for SITE-94

    International Nuclear Information System (INIS)

    Arthur, R.; Apted, M.

    1996-12-01

    In this report, solubility constraints are evaluated on radioelement source-term concentrations supporting the SITE-94 performance assessment. Solubility models are based on heterogeneous-equilibrium, mass- and charge-balance constraints incorporated into the EQ3/6 geochemical software package, which is used to calculate the aqueous speciation behavior and solubilities of U, Th, Pu, Np, Am, Ni, Ra, Se, Sn, Sr, Tc and Zr in site groundwaters and near-field solutions. The chemical evolution of the near field is approximated using EQ3/6 in terms of limiting conditions at equilibrium, or steady state, in three closed systems representing fully saturated bentonite, Fe o corrosion products of the canister, and spent fuel. The calculations consider both low-temperature (15 deg C) and high-temperature (80 deg C) conditions in the near field, and the existence of either reducing or strongly oxidizing conditions in each of the bentonite, canister, and spent-fuel barriers. Heterogeneities in site characteristics are evaluated through consideration of a range of initial groundwaters and their interactions with engineered barriers. Aqueous speciation models for many radioelements are constrained by thermodynamic data that are estimated with varying degrees of accuracy. An important question, however, is how accurate do these models need to be for purposes of estimating source-term concentrations? For example, it is unrealistic to expect a high degree of accuracy in speciation models if such models predict solubilities that are below the analytical detection limit for a given radioelement. From a practical standpoint, such models are irrelevant if calculated solubilities cannot be tested by direct comparison to experimental data. In the absence of models that are both accurate and relevant for conditions of interest, the detection limit could define a pragmatic upper limit on radioelement solubility

  20. Okadaic acid

    DEFF Research Database (Denmark)

    Danielsen, E Michael; Hansen, Gert H; Severinsen, Mai C K

    2014-01-01

    are the hallmark of phospholipidosis, a pathological condition characterized by lysosomal phospholipid accumulation. Phospholipidosis is observed in acquired lysosomal storage diseases and is induced by a large number of cationic amphiphilic drugs. Unlike the latter, however, OA does not act by accumulating...... in acidic organelles, implying a different toxic mechanism of action. We propose that rapid induction of LBs, an indicator of phospholipidosis, should be included in the future toxicity profile of OA....... hyper protein phosphorylation, but no detectable loss of cell polarity or cytoskeletal integrity of the enterocytes. Using a fluorescent membrane marker, FM dye, endocytosis from the brush border was affected by the toxin. Although constitutive uptake into subapical terminal web-localized early...

  1. Acid Sulfate Alteration on Mars

    Science.gov (United States)

    Ming, D. W.; Morris, R. V.

    2016-01-01

    A variety of mineralogical and geochemical indicators for aqueous alteration on Mars have been identified by a combination of surface and orbital robotic missions, telescopic observations, characterization of Martian meteorites, and laboratory and terrestrial analog studies. Acid sulfate alteration has been identified at all three landing sites visited by NASA rover missions (Spirit, Opportunity, and Curiosity). Spirit landed in Gusev crater in 2004 and discovered Fe-sulfates and materials that have been extensively leached by acid sulfate solutions. Opportunity landing on the plains of Meridiani Planum also in 2004 where the rover encountered large abundances of jarosite and hematite in sedimentary rocks. Curiosity landed in Gale crater in 2012 and has characterized fluvial, deltaic, and lacustrine sediments. Jarosite and hematite were discovered in some of the lacustrine sediments. The high elemental abundance of sulfur in surface materials is obvious evidence that sulfate has played a major role in aqueous processes at all landing sites on Mars. The sulfate-rich outcrop at Meridiani Planum has an SO3 content of up to 25 wt.%. The interiors of rocks and outcrops on the Columbia Hills within Gusev crater have up to 8 wt.% SO3. Soils at both sites generally have between 5 to 14 wt.% SO3, and several soils in Gusev crater contain around 30 wt.% SO3. After normalization of major element compositions to a SO3-free basis, the bulk compositions of these materials are basaltic, with a few exceptions in Gusev crater and in lacustrine mudstones in Gale crater. These observations suggest that materials encountered by the rovers were derived from basaltic precursors by acid sulfate alteration under nearly isochemical conditions (i.e., minimal leaching). There are several cases, however, where acid sulfate alteration minerals (jarosite and hematite) formed in open hydrologic systems, e.g., in Gale crater lacustrine mudstones. Several hypotheses have been suggested for the

  2. Comparison and trend study on acidity and acidic buffering capacity of particulate matter in China

    Science.gov (United States)

    Ren, Lihong; Wang, Wei; Wang, Qingyue; Yang, XiaoYang; Tang, Dagang

    2011-12-01

    The acidity of about 2000 particulate matter samples from aircraft and ground-based monitoring is analyzed by the method similar to soil acidity determination. The ground-based samples were collected at about 50 urban or background sites in northern and southern China. Moreover, the acidic buffering capacity of those samples is also analyzed by the method of micro acid-base titration. Results indicate that the acidity level is lower in most northern areas than those in the south, and the acidic buffering capacity showed inverse tendency, correspondingly. This is the most important reason why the pollution of acidic-precipitation is much more serious in Southern China than that in Northern China. The acidity increases and the acidic buffering capacity drops with the decreasing of the particle sizes, indicating that fine particle is the main influencing factor of the acidification. The ionic results show that Ca salt is the main alkaline substance in particulate matter, whereas the acidification of particulate matter is due to the SO 2 and NO x emitted from the fossil fuel burning. And among of them, coal burning is the main contributor of SO 2, however the contribution of NO x that emitted from fuel burning of motor vehicles has increased in recent years. By comparison of the experimental results during the past 20 years, it can be concluded that the acid precipitation of particulate matter has not been well controlled, and it even shows an increasing tendency in China lately. The acid precipitation of particulate matter has begun to frequently attack in part of the northern areas. Multiple regression analysis indicates that coefficient value of the ions is the lowest at the urban sites and the highest at the regional sites, whereas the aircraft measurement results are intermediate between those two kinds of sites.

  3. Site Environmental Report, 1993

    International Nuclear Information System (INIS)

    1994-06-01

    The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, ''General Environmental Protection Program.'' This 1993 SER provides the general public as well as scientists and engineers with the results from the site's ongoing Environmental Monitoring Program. Also included in this report is information concerning the site's progress toward achieving full compliance with requirements set forth by DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in the Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here

  4. The Variable Transition State in Polar Additions to Pi Bonds

    Science.gov (United States)

    Weiss, Hilton M.

    2010-01-01

    A vast majority of polar additions of Bronsted acids to alkynes involve a termolecular transition state. With strong acids, considerable positive charge is developed on carbon and Markovnikov addition predominates. In less acidic solutions, however, the reaction is much slower and the transition state more closely resembles the olefinic product.…

  5. Detection of nucleic acid sequences by invader-directed cleavage

    Science.gov (United States)

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  6. Retroviral integration: Site matters

    Science.gov (United States)

    Demeulemeester, Jonas; De Rijck, Jan

    2015-01-01

    Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co‐opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine‐grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success. PMID:26293289

  7. Siting controversial facilities

    International Nuclear Information System (INIS)

    Baird, R.D.; Blacker, P.B.

    1985-01-01

    There is often significant difficulty involved with siting controversial facilities. The social and political problems are frequently far more difficult to resolve than the technical and economic issues. The tendancy for most developing organizations is to address only technical issues in the search for a technically optimal site, to the exclusion of such weighting considerations as the social and political climate associated with potential sites--an approach which often imperils the success of the project. The site selection processes currently suggested is summarized and two contemporary examples of their application are cited. The difference between developers' real objectives and the objectives they have implicitly assumed by adopting the recommended approaches without augmentation are noted. The resulting morass of public opposition is attributed to the failure to consider the needs of individuals and groups who stand to be negatively impacted by the development. A comprehensive implementation strategy which addresses non-technical consideration in parallel with technical ones is presented and evaluated

  8. Vatwa Resettlement Sites

    International Development Research Centre (IDRC) Digital Library (Canada)

    The BSUP sites, constructed under the Government of India's .... conflicts over paying for maintenance lead to unrepaired water and ... So some women reacted and broke things in the office." ... workplaces, leading many to drop out of work or.

  9. Safety aspects of siting

    International Nuclear Information System (INIS)

    Rosen, M.

    1976-01-01

    Outline of parameters to be considered in site selection, radiation safety, and mechanisms of radiation release. Radiation doses in tablular form for areas at various distances from the plant. (HP) [de

  10. Site Specific Vendor's License

    Data.gov (United States)

    Montgomery County of Maryland — This dataset contains information of a site-specific vendor's license which is required if an individual sells or offers to sell goods or services from a stationary...

  11. Surgical site infections

    African Journals Online (AJOL)

    Surgical site infections (SSIs) are a worldwide problem that has ... deep tissue is found on clinical examination, re-opening, histopathological or radiological investigation ..... Esposito S, Immune system and SSI, Journal of Chemotherapy, 2001.

  12. Superfund Site Information

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes a number of individual data sets related to site-specific information for Superfund, which is governed under the Comprehensive Environmental...

  13. Outdoor Recreation Sites Inventory

    Data.gov (United States)

    Vermont Center for Geographic Information — The RECSITES data layer contains a wide range of recreational sites in Vermont. This point data layer includes parks, ski areas, boat access points, and many other...

  14. Summer Meal Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Information pertaining to Summer Meal Sites, as collected by Citiparks in the City of Pittsburgh Department of Parks and Recreation. This dataset includes the...

  15. Jet Car Track Site

    Data.gov (United States)

    Federal Laboratory Consortium — Located in Lakehurst, New Jersey, the Jet Car Track Site supports jet cars with J57 engines and has a maximum jet car thrust of 42,000 pounds with a maximum speed of...

  16. Site recycling: From Brownfield to football field

    Energy Technology Data Exchange (ETDEWEB)

    Lee, C.; Haas, W.L. [HDR Engineering Inc., Charlotte, NC (United States)

    1995-07-01

    The Carolina Panther`s new home, Carolinas Stadium, will be impressive. It will include a 75,000-seat stadium, about 2,000 parking spaces, and a practice facility equipped with three full-sized football fields, all located on 30 acres bordering the central business district of Charlotte, NC. Fans of the NFL expansion team may never know that, until recently, 13 of those 30 acres were a former state Superfund site contaminated by a commercial scrapyard that had operated from the early 1930s to 1983. The salvage of nonferrous metals from lead-acid batteries, copper from transformers and other electrical equipment, and ferrous metal scrap from junk automobiles at the Smith Metal and Iron (SMI) site had left a complex contamination legacy. The soil contained lead, polychlorinated biphenyls (PCBs), lesser amounts of semivolatiles (polyaromatic hydrocarbons, or PAHs), and volatile organic compounds and petroleum hydrocarbons. The site had remained dormant, like many former industrial sites that have come be called {open_quotes}brownfields,{close_quotes} for nearly a decade when in 1993, Charlotte was selected as the future home of the Carolina Panthers, a National Football League expansion team. The city was able to attract the team in part by offering to redevelop the site, a prime location adjacent to the downtown area. An eight-month-long site remediation effort by HDR Engineering Inc. was completed March 31, on schedule for a June 1996 unveiling of the team`s new facility.

  17. Fusion facility siting considerations

    International Nuclear Information System (INIS)

    Bussell, G.T.

    1985-01-01

    Inherent in the fusion program's transition from hydrogen devices to commercial power machines is a general increase in the size and scope of succeeding projects. This growth will lead to increased emphasis on safety, environmental impact, and the external effects of fusion in general, and of each new device in particular. A critically important consideration in this regard is site selection. The purpose of this paper is to examine major siting issues that may affect the economics, safety, and environmental impact of fusion

  18. Siting of research reactors

    International Nuclear Information System (INIS)

    1987-01-01

    The purpose of this document is to develop criteria for siting and the site-related design basis for research reactors. The concepts presented in this document are intended as recommendations for new reactors and are not suggested for backfitting purposes for facilities already in existence. In siting research reactors serious consideration is given to minimizing the effects of the site on the reactor and the reactor on the site and the potential impact of the reactor on the environment. In this document guidance is first provided on the evaluation of the radiological impact of the installation under normal reactor operation and accident conditions. A classification of research reactors in groups is then proposed, together with a different approach for each group, to take into account the relevant safety problems associated with facilities of different characteristics. Guidance is also provided for both extreme natural events and for man-induced external events which could affect the safe operation of the reactor. Extreme natural events include earthquakes, flooding for river or coastal sites and extreme meteorological phenomena. The feasibility of emergency planning is finally considered for each group of reactors

  19. Site characterization and validation

    International Nuclear Information System (INIS)

    Olsson, O.; Eriksson, J.; Falk, L.; Sandberg, E.

    1988-04-01

    The borehole radar investigation program of the SCV-site (Site Characterization and Validation) has comprised single hole reflection measurements with centre frequencies of 22, 45, and 60 MHz. The radar range obtained in the single hole reflection measurements was approximately 100 m for the lower frequency (22 MHz) and about 60 m for the centre frequency 45 MHz. In the crosshole measurements transmitter-receiver separations from 60 to 200 m have been used. The radar investigations have given a three dimensional description of the structure at the SCV-site. A generalized model of the site has been produced which includes three major zones, four minor zones and a circular feature. These features are considered to be the most significant at the site. Smaller features than the ones included in the generalized model certainly exist but no additional features comparable to the three major zones are thought to exist. The results indicate that the zones are not homogeneous but rather that they are highly irregular containing parts of considerably increased fracturing and parts where their contrast to the background rock is quite small. The zones appear to be approximately planar at least at the scale of the site. At a smaller scale the zones can appear quite irregular. (authors)

  20. Quantitative Autoradiography on [(35)S]TBPS Binding Sites of Gamma- Aminobutyric Acid(A) Receptors in Discrete Brain Regions of High- Alcohol-Drinking and Low-Alcohol- Drinking Rats Selectively Bred forHigh- and Low-Alcohol Preference.

    Science.gov (United States)

    Hwang, B.H.; Kunkler, P.E.; Lumeng, L.

    1997-01-01

    It has been documented that ethanol can potentiate brain gamma-aminobutyric acid (GABA)ergic function, and there is a close link between the GABA(A) receptor complex and effects of ethanol, including reinforcement of alcohol which is a fundamental element of alcohol preference. However, it is unknown in what discrete brain regions GABA(A) receptors might be associated with alcohol preference. In the present study, [(35)S]t-butylbicyclophosphorothionate ([(35)S]TBPS) was used to localize GABA(A) receptors in high-alcohol-drinking (HAD) rats and low-alcohol-drinking (LAD) rats which were selectively bred for high and low alcohol preference, respectively. Initial qualitative observations indicated that [(35)S]TBPS binding sites were abundant in many brain areas including the cerebral cortex, hypothalamus and amygdala of HAD and LAD rats. Furthermore, the quantitative autoradiographic analysis revealed fewer [(35)S]TBPS binding sites of GABA(A) receptors in the amygdaloid complex, central medial thalamic nucleus, lateral hypothalamic nucleus and anterior hypothalamic nucleus of HAD rats than LAD rats. Collectively, this study has indicated that HAD rats selectively bred for high alcohol preference possess lower [(35)S]TBPS binding in the brain. Since lower TBPS binding has been proposed to reflect enhanced GABAergic function, as evidenced in rats with seizure or under alcohol withdrawal, the results from the present study suggest that HAD rats might have an enhanced GABAergic function. It is thus likely that enhanced GABAergic function in the brain might be related to high alcohol preference which is characteristic in HAD rats. In addition, the present result showing no difference of [(35)S]TBPS binding in the nucleus accumbens is also in agreement with a notion that [(35)S]TBPS binding may represent only a small spectrum of the GABA(A) receptor complex which is constituted of a sophisticated subunit combination whose functional compositions are still unknown. In

  1. Imprinting of molecular recognition sites combined with π-donor-acceptor interactions using bis-aniline-crosslinked Au-CdSe/ZnS nanoparticles array on electrodes: Development of electrochemiluminescence sensor for the ultrasensitive and selective detection of 2-methyl-4-chlorophenoxyacetic acid.

    Science.gov (United States)

    Yang, Yukun; Fang, Guozhen; Wang, Xiaomin; Liu, Guiyang; Wang, Shuo

    2016-03-15

    A novel strategy is reported for the fabrication of bis-aniline-crosslinked Au nanoparticles (NPs)-CdSe/ZnS quantum dots (QDs) array composite by facil one-step co-electropolymerization of thioaniline-functionalized AuNPs and thioaniline-functionalized CdSe/ZnS QDs onto thioaniline-functionalized Au elctrodes (AuE). Stable and enhanced cathodic electrochemiluminescence (ECL) of CdSe/ZnS QDs is observed on the modified electrode in neutral solution, suggesting promising applications in ECL sensing. An advanced ECL sensor is explored for detection of 2-methyl-4-chlorophenoxyacetic acid (MCPA) which quenches the ECL signal through electron-transfer pathway. The sensitive determination of MCPA with limit of detection (LOD) of 2.2 nmolL(-1) (S/N=3) is achieved by π-donor-acceptor interactions between MCPA and the bis-aniline bridging units. Impressively, the imprinting of molecular recognition sites into the bis-aniline-crosslinked AuNPs-CdSe/ZnS QDs array yields a functionalized electrode with an extremely sensitive response to MCPA in a linear range of 10 pmolL(-1)-50 μmolL(-1) with a LOD of 4.3 pmolL(-1 ()S/N=3). The proposed ECL sensor with high sensitivity, good selectivity, reproducibility and stability has been successfully applied for the determination of MCPA in real samples with satisfactory recoveries. In this study, ECL sensor combined the merits of QDs-ECL and molecularly imprinting technology is reported for the first time. The developed ECL sensor holds great promise for the fabrication of QDs-based ECL sensors with improved sensitivity and furthermore opens the door to wide applications of QDs-based ECL in food safety and environmental monitoring. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Dehydration of alcohols using solid acid catalysts

    OpenAIRE

    Cholerton, Mary

    2014-01-01

    Solid acid catalysts were prepared through silicon substitution into aluminophosphate frameworks. Silicon incorporation was confirmed using solid state nuclear magnetic resonance spectroscopy. The nature of the acid sites generated was determined using Fourier Transform infrared spectroscopy. These materials were tested as catalysts for the dehydration of ethanol to ethylene at low operating temperatures. The materials were active for dehydration of ethanol to ethylene with significant differ...

  3. The 11C-radioisotopic study of methanol conversion on V-MCM-41; the influence of methyl iodide on the transformation

    International Nuclear Information System (INIS)

    Sarkadi-Priboczki, E.; Szelecsenyi, F.; Kovacs, Z.; Solmaz, A.; Balci, S.; Dogu, T.

    2007-01-01

    Complete text of publication follows. The MCM-41 mesoporous material has Lewis and even Bronsted acid sites to produce dimethyl ether with some hydrocarbons, while over metal modified MCM-41 mostly formaldehyde and dimethoxy methane (i.e. methylal) or methyl formate are produced. In present experiments V incorporated basically mild acid sites of MCM-41 was prepared by low temperature direct synthesis. The V-MCM-41 has enough main active Lewis sites (by V-) to form formaldehyde and also light Bronsted acid sites to let the adsorbed formaldehyde eliminate and afterwards, with methanol, to form dimethoxy methane in nonoxidative environment. This V-MCM-41 has been tested by ethanol conversion in non-oxidative environments too and diethoxy methane as main product was detected. In present work the methanol conversion, as well as the methanol co-reaction with methyl iodide are studied from the same V-MCM-41 sample using 11 C-technique. The 11 C-labelled radioactive methanol has been already applied for determination of methanol conversion rates on Cu-modified MCM-41. The V-MCM-41 was prepared by direct hydrothermal synthesis method. The adsorption rate of 11 C-methanol and, after the reaction, the desorption rate of the remaining 11 C-derivatives on catalyst were continuously detected by gamma detectors. The derivatives were analyzed by radio-gas chromatography (gas chromatograph with FID coupled on-line with a radioactivity detector). Both dimethyl ether and hydrocarbon formation are also in slight degrees according to weak Lewis and Bronsted acidities. Since the conversion was carried out without added oxygen gas, only the frame oxygen can take part into catalysis. In presence of non-radioactive methyl iodide, the radioactive methanol is converted to radioactive methyl iodide on V-MCM-41. The radio-GC analysis confirmed that the iodide induced change of the reaction performance was reversible i.e. the radioactive methyl iodide was regenerated to non-radioactive methyl

  4. Acid monolayer functionalized iron oxide nanoparticle catalysts

    Science.gov (United States)

    Ikenberry, Myles

    Superparamagnetic iron oxide nanoparticle functionalization is an area of intensely active research, with applications across disciplines such as biomedical science and heterogeneous catalysis. This work demonstrates the functionalization of iron oxide nanoparticles with a quasi-monolayer of 11-sulfoundecanoic acid, 10-phosphono-1-decanesulfonic acid, and 11-aminoundecanoic acid. The carboxylic and phosphonic moieties form bonds to the iron oxide particle core, while the sulfonic acid groups face outward where they are available for catalysis. The particles were characterized by thermogravimetric analysis (TGA), transmission electron microscopy (TEM), potentiometric titration, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), inductively coupled plasma optical emission spectrometry (ICP-OES), X-ray photoelectron spectrometry (XPS), and dynamic light scattering (DLS). The sulfonic acid functionalized particles were used to catalyze the hydrolysis of sucrose at 80° and starch at 130°, showing a higher activity per acid site than the traditional solid acid catalyst Amberlyst-15, and comparing well against results reported in the literature for sulfonic acid functionalized mesoporous silicas. In sucrose catalysis reactions, the phosphonic-sulfonic nanoparticles (PSNPs) were seen to be incompletely recovered by an external magnetic field, while the carboxylic-sulfonic nanoparticles (CSNPs) showed a trend of increasing activity over the first four recycle runs. Between the two sulfonic ligands, the phosphonates produced a more tightly packed monolayer, which corresponded to a higher sulfonic acid loading, lower agglomeration, lower recoverability through application of an external magnetic field, and higher activity per acid site for the hydrolysis of starch. Functionalizations with 11-aminoundecanoic acid resulted in some amine groups binding to the surfaces of iron oxide nanoparticles. This amine binding is commonly ignored in iron oxide

  5. Experimental site and design

    Energy Technology Data Exchange (ETDEWEB)

    Guenette, C. C. [SINTEF Applied Cemistry, Trondheim (Norway)

    1999-08-01

    Design and site selection criteria for the Svalbard oil spill experiments are described. All three experimental sites have coarse and mixed sediment beaches of sand and pebble; within each site wave exposure is very similar; along-shore and across-shore sediment characteristics are also relatively homogeneous. Tidal range is in the order of 0.6 m at neaps, and 1.8 m at springs. All three sites are open to wave action and are ice-free during the experimental period of mid-July to mid-October. Study plots at each site were selected for different treatments from within the continuous stretch of oiled shoreline, with oiled buffer zones between plots and at either end of the oiled zone. Treatments included mixing (tilling), sediment relocation (surf washing) and bioremediation (nutrient enrichment). Measurements and observations were carried out during the summers of 1997 and 1998. The characteristics measured were: wave and wind conditions; beach topography and elevation; sediment grain size distribution; mineral fines size distribution and mineral composition; background hydrocarbons; concentration of oil within experimental plots and the rate of oil loss over time; depth of oil penetration and thickness of the oiled sediment layer; oil concentration and toxicity of near-shore benthic sediments; mineral composition of suspended particulate material captured in sub-tidal sediment traps; and oil-fines interaction in near-shore water samples. 1 fig.

  6. Experimental site and design

    Energy Technology Data Exchange (ETDEWEB)

    Guenette, C. C. [SINTEF Applied Cemistry, Trondheim (Norway)

    1999-07-01

    Design and site selection criteria for the Svalbard oil spill experiments are described. All three experimental sites have coarse and mixed sediment beaches of sand and pebble; within each site waveexposure is very similar; along-shore and across-shore sediment characteristics are also relatively homogeneous. Tidal range is in the order of 0.6 m at neaps, and 1.8 m at springs. All three sites are open to wave action and are ice-free during the experimental period of mid-July to mid-October. Study plots at each site were selected for different treatments from within the continuous stretch of oiled shoreline, with oiled buffer zones between plots and at either end of the oiled zone. Treatments included mixing (tilling), sediment relocation (surf washing) and bioremediation (nutrient enrichment). Measurements and observations were carried out during the summers of 1997 and 1998. The characteristics measured were: wave and wind conditions; beach topography and elevation; sediment grain size distribution; mineral fines size distribution and mineral composition; background hydrocarbons; concentration of oil within experimental plots and the rate of oil loss over time; depth of oil penetration and thickness of the oiled sediment layer; oil concentration and toxicity of near-shore benthic sediments; mineral composition of suspended particulate material captured in sub-tidal sediment traps; and oil-fines interaction in near-shore water samples. 1 fig.

  7. Criteria of site assessment

    International Nuclear Information System (INIS)

    Gibbs, P.; Fuchs, H.

    1975-01-01

    The criteria which lead to the choice of a particular site for a nuclear power station are in general very similar to those which would apply to any other type of power station. The principal differences derive from the simpler transport problems for the fuel compared with, say, solid fuel and the special safety considerations which attach to nuclear reactors. The search for a suitable site obviously starts by considering where the power is needed, i.e. where the load centers are and also the existing transmission network which may help to bring the power from a more remote site to the load centers. This economic incentive to put the plant close to loads conflicts directly with the nuclear safety argument which favours more remote siting, and part of the problem of site selection is to reconcile these two matters. In addition, there are many other important matters which will be considered later concerning the adequacy of cooling water supplies, foundation conditions, etc., all of which must be examined in considerable detail. (orig./TK) [de

  8. Repository site characterization

    International Nuclear Information System (INIS)

    Voss, J.W.; Pentz, D.L.

    1987-01-01

    The characterization of candidate repository sites has a number of programmatic objectives. Principal among these is the acquisition of data: a) to determine the suitability of a site relative to the DOE repository siting guidelines, b) to support model development and calculations to determine the suitability of a site relative to the post closure criteria of the NRC and EPA, c) to support the design of a disposal system, including the waste package and the engineered barrier system, as well as the shafts and underground openings of the repository. In meeting the gaols of site characterization, the authors have an obligation to conduct their investigations within an appropriate budget and schedule. This mandates that a well-constructed and systematic plan for field investigations be developed. Such a plan must fully account for the mechanisms which will control the radiologic performance in the repository. The plan must also flexibly and dynamically respond to the results of each step of field investigation, responding to the spatial variability of earth as well as to enhanced understandings of the performance of the disposal system. Such a plan must ensure that sufficient data are available to support the necessary probabilistic calculations of performance. This paper explores the planning for field data acquisition with specific reference to requirements for demonstrations of the acceptable performance for disposal systems

  9. Site 300 SPCC Plan

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-11-23

    This Spill Prevention, Control, and Countermeasure (SPCC) Plan describes the measures that are taken at Lawrence Livermore National Laboratory’s (LLNL) Experimental Test Site (Site 300) near Tracy, California, to prevent, control, and handle potential spills from aboveground containers that can contain 55 gallons or more of oil. This SPCC Plan complies with the Oil Pollution Prevention regulation in Title 40 of the Code of Federal Regulations, Part 112 (40 CFR 112) and with 40 CFR 761.65(b) and (c), which regulates the temporary storage of polychlorinated biphenyls (PCBs). This Plan has also been prepared in accordance with Division 20, Chapter 6.67 of the California Health and Safety Code (HSC 6.67) requirements for oil pollution prevention (referred to as the Aboveground Petroleum Storage Act [APSA]), and the United States Department of Energy (DOE) Order No. 436.1. This SPCC Plan establishes procedures, methods, equipment, and other requirements to prevent the discharge of oil into or upon the navigable waters of the United States or adjoining shorelines for aboveground oil storage and use at Site 300. This SPCC Plan has been prepared for the entire Site 300 facility and replaces the three previous plans prepared for Site 300: LLNL SPCC for Electrical Substations Near Buildings 846 and 865 (LLNL 2015), LLNL SPCC for Building 883 (LLNL 2015), and LLNL SPCC for Building 801 (LLNL 2014).

  10. Modulation of the acidity of niobic acid by ion-doping: Effects of nature and amount of the dopant ions

    Energy Technology Data Exchange (ETDEWEB)

    Carniti, Paolo [Dipartimento di Chimica, Università degli Studi di Milano (UNIMI), Milano (Italy); Gervasini, Antonella, E-mail: antonella.gervasini@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano (UNIMI), Milano (Italy); Marzo, Matteo [Dipartimento di Chimica, Università degli Studi di Milano (UNIMI), Milano (Italy); Auroux, Aline [Université Lyon 1, CNRS, UMR 5256, (IRCELYON), Villeurbanne (France)

    2013-09-10

    Highlights: ► Mitigation of the surface acidity of niobic acid was pursued by K-, Ba-, and Nd-doping. ► Thermal techniques of study were effective for the acidity study. ► The nature of the dopant influences the effectiveness of the acidity tuning of niobic acid. ► The acidity of the doped surfaces decreased with increasing the dopant species added to niobic acid. ► The samples showed different acidity when measured in gas–solid phase (intrinsic acidity) and water (effective acidity). - Abstract: The acidity of niobic acid (NBO) has been successfully mitigated and tuned by addition of K{sup +}, Ba{sup 2+} and Nd{sup 3+} dopant species in amounts from 1 to 15 atom nm{sup −2}. The characterization of the intrinsic acid properties of the samples was performed by adsorption of NH{sub 3} in a volumetric–microcalorimetric coupled line and by temperature programmed desorption (TPD) of 2-phenylethylamine in a thermogravimetric apparatus. The K-dopant was more effective in decreasing the acidity of niobic acid than the Ba- and Nd-dopants. Complementary measurements of the effective acidity of the samples in water by base titrations with 2-phenylethylamine completed the study and revealed a different picture of the effect of the three dopants on the NBO acidity in water. All the results indicated that the K-dopant targeted more selectively the Brønsted acid sites, acting as an ion-exchanger, while Ba- and Nd-species predominantly acted on the Lewis acid sites of the NBO surface.

  11. Superfund and Toxic Release Inventory Sites - MDC_ContaminatedSite

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — A point feature class of open DERM Contaminated sites - see phase code for status of site. Contaminated sites identifies properties where environmental contamination...

  12. SLAC site design aesthetics

    International Nuclear Information System (INIS)

    Hall, F.F.

    1985-10-01

    Stanford Linear Accelerator Center (SLAC) is a single mission laboratory dedicated to basic research in high energy particle physics. SLAC site also houses Stanford Synchrotron Radiation Laboratory (SSRL) which is a multi-mission laboratory for research using beams of ultraviolet light and low energy photons as emitted tangentially from SLAC colliding beam facilities. This paper discusses various aspects of SLAC site design aesthetics under the following headings: (1) imposed footprint of SLAC, (2) description of selected site, (3) use of earth cover for radiation and sight screens, (4) use of landscaping for cosmetic purposes, (5) use of exterior paint colors to soften SLAC impact on neighbors, (6) relocation of SLAC main entrance, (7) relocation of SLAC collider arcs and experimental hall, (8) parking lots and storage yards, and (9) land use zoning at SLAC

  13. Siting and public acceptance

    International Nuclear Information System (INIS)

    De Lise, Pasquale.

    1977-01-01

    The paper discusses the problem of nuclear power plant siting according to presently applicable legislation in Italy, taking into account urban and environmental aspects. Act No 393 of 2 August 1975 on the siting of nuclear plants introduced a significant change in that prior to its adoption, the competence to license nuclear installations was divided amongst so many bodies that approval was inevitably delayed. Act No. 393 lays down the siting procedure which involves authorities at regional and State level and provides a step by step consultation of the Communes concerned and gives them a time limit for replying to the proposed project, while enabling the necessary scientific, environmental and urban investigations to be made. Thus although ultimate decisions rest with the State, the regional bodies representing the public have a voice in them. In such planning the authorities must take into account the public interest, from the environmental and social angles as well as political and economic interests. (NEA) [fr

  14. Measuring site occupancy

    DEFF Research Database (Denmark)

    Rogowska-Wrzesinska, Adelina; Wojdyla, Katarzyna; Williamson, James

    2014-01-01

    occupancy of the modification site. We show that, on one hand, heavily modified cysteines are not necessarily involved in the response to oxidative stress. On the other hand residues with low modification level can be dramatically affected by mild oxidative imbalance. We make use of high resolution mass...... peptides corresponding to 90 proteins. Only 6 modified peptides changed significantly under mild oxidative stress. Quantitative information allowed us to determine relative modification site occupancy of each identified modified residue and pin point heavily modified ones. The method proved to be precise...... and sensitive enough to detect and quantify endogenous levels of oxidative stress on proteome-wide scale and brings a new perspective on the role of the modification site occupancy in cellular redox response....

  15. YUCCA MOUNTAIN SITE DESCRIPTION

    International Nuclear Information System (INIS)

    Simmons, A.M.

    2004-01-01

    The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work done at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel

  16. YUCCA MOUNTAIN SITE DESCRIPTION

    Energy Technology Data Exchange (ETDEWEB)

    A.M. Simmons

    2004-04-16

    The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work done at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel.

  17. [Teichoic acids from lactic acid bacteria].

    Science.gov (United States)

    Livins'ka, O P; Harmasheva, I L; Kovalenko, N K

    2012-01-01

    The current view of the structural diversity of teichoic acids and their involvement in the biological activity of lactobacilli has been reviewed. The mechanisms of effects of probiotic lactic acid bacteria, in particular adhesive and immunostimulating functions have been described. The prospects of the use of structure data of teichoic acid in the assessment of intraspecific diversity of lactic acid bacteria have been also reflected.

  18. Hydroelectric generating site signage

    Energy Technology Data Exchange (ETDEWEB)

    Bentley, K [British Columbia Hydro, Vancouver, BC (Canada)

    1997-04-01

    Recreational sites have been developed at several BC Hydro reservoirs. These sites are visited by approximately 800,000 people annually and therefore, require consistent control measures to ensure public safety and to restrict public access to hazardous areas. BC Hydro is in the process of establishing a province-wide standard in which layout, colour, description of hazards, BC Hydro identity and sign placement would follow an established set of criteria. Proposed signs would consist of a pictograph and a printed warning below. Preliminary designs for 16 of the signs were presented. 16 figs.

  19. PhosphoSiteAnalyzer

    DEFF Research Database (Denmark)

    Bennetzen, Martin V; Cox, Jürgen; Mann, Matthias

    2012-01-01

    an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility......Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites...... and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net ....

  20. Multi-Sited Resilience

    DEFF Research Database (Denmark)

    Olwig, Mette Fog

    2012-01-01

    with natural disasters and climate change. In a globalized world, however, it is hard to discern what is “local” as global organizations play an increasingly visible and powerful role. This paper will argue that local understandings and practices of resilience cannot be disentangled from global understandings...... flooding in northern Ghana, this paper examines the mutual construction of “local” and “global” notions and practices of resilience through multi-sited processes. It is based on interviews and participant observation in multiple sites at the “local,” “regional” and “global” levels....

  1. Plasma amino acids

    Science.gov (United States)

    Amino acids blood test ... types of methods used to determine the individual amino acid levels in the blood. ... test is done to measure the level of amino acids in the blood. An increased level of a ...

  2. Uric acid - urine

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003616.htm Uric acid urine test To use the sharing features on ... are no risks with this test. Images Uric acid test Uric acid crystals References Burns CM, Wortmann RL. Clinical ...

  3. Uric acid test (image)

    Science.gov (United States)

    Uric acid urine test is performed to check for the amount of uric acid in urine. Urine is collected over a 24 ... for testing. The most common reason for measuring uric acid levels is in the diagnosis or treatment of ...

  4. Methylmalonic acid blood test

    Science.gov (United States)

    ... medlineplus.gov/ency/article/003565.htm Methylmalonic acid blood test To use the sharing features on this page, please enable JavaScript. The methylmalonic acid blood test measures the amount of methylmalonic acid in the ...

  5. Facts about Folic Acid

    Science.gov (United States)

    ... Information For… Media Policy Makers Facts About Folic Acid Language: English (US) Español (Spanish) Recommend on Facebook ... of the baby’s brain and spine. About folic acid Folic acid is a B vitamin. Our bodies ...

  6. Ligand exchange chromatography of free amino acids and proteins on porous microparticulate zirconium oxide

    International Nuclear Information System (INIS)

    Blackwell, J.A.; Carr, P.W.

    1992-01-01

    The Lewis acid sites present on the underlying zirconium oxide particles are responsible for the unusual elution sequence for amino acids on copper loaded, phosphated zirconium oxide supports reported in an earlier study. To more thoroughly examine the effect of these strong Lewis acid sites in this paper. The authors have studied ligand exchange chromatography on copper loaded zirconium oxide particles. It is shown here that carboxylate functional groups on amino acid solutes strongly interact with surface Lewis acid sites. Addition of competing hard Lewis bases to the eluent attenuates these specific interactions. The result is a chromatographic system with high selectivity which is also suitable for ligand exchange chromatography of proteins

  7. Allegheny County Illegal Dump Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Illegal Dump Site dataset includes information on illegal dump sites, their type of trash, and the estimate tons of trash at each site. The information was...

  8. Sites and Enactments

    DEFF Research Database (Denmark)

    Korsgaard, Steffen T.; Neergaard, Helle

    2008-01-01

    is formulated where opportunities are seen as dynamic in the sense that they are enacted in different social practices at different sites. The method is illustrated through an analysis of the birth of The Republic of Tea, a very successful tea company, as presented in the book "The Republic of Tea"....

  9. Hanford site environment

    International Nuclear Information System (INIS)

    Isaacson, R.E.

    1976-01-01

    A synopsis is given of the detailed characterization of the existing environment at Hanford. The following aspects are covered: demography, land use, meteorology, geology, hydrology, and seismology. It is concluded that Hanford is one of the most extensively characterized nuclear sites

  10. Mathematics. [SITE 2002 Section].

    Science.gov (United States)

    Connell, Michael L., Ed.; Lowery, Norene Vail, Ed.; Harnisch, Delwyn L., Ed.

    This document contains the following papers on mathematics from the SITE (Society for Information Technology & Teacher Education) 2002 conference: (1) "Teachers' Learning of Mathematics in the Presence of Technology: Participatory Cognitive Apprenticeship" (Mara Alagic); (2) "A Fractal Is a Pattern in Your Neighborhood" (Craig N. Bach); (3)…

  11. 2014 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    Paquette, Douglas [Brookhaven National Lab. (BNL), Upton, NY (United States); Remien, Jason [Brookhaven National Lab. (BNL), Upton, NY (United States); Foley, Brian [Brookhaven National Lab. (BNL), Upton, NY (United States); Burke, John [Brookhaven National Lab. (BNL), Upton, NY (United States); Dorsch, William [Brookhaven National Lab. (BNL), Upton, NY (United States); Ratel, Karen [Brookhaven National Lab. (BNL), Upton, NY (United States); Howe, Robert [Brookhaven National Lab. (BNL), Upton, NY (United States); Welty, Tim [Brookhaven National Lab. (BNL), Upton, NY (United States); Williams, Jeffrey [Brookhaven National Lab. (BNL), Upton, NY (United States); Pohlpt, Peter [Brookhaven National Lab. (BNL), Upton, NY (United States); Lagattolla, Richard [Brookhaven National Lab. (BNL), Upton, NY (United States); Metz, Robert [Brookhaven National Lab. (BNL), Upton, NY (United States); Milligan, James [Brookhaven National Lab. (BNL), Upton, NY (United States); Lettieri, Lawrence [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-10-01

    BNL prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1B, Environment, Safety and Health Reporting. The report is written to inform the public, regulators, employees, and other stakeholders of the Laboratory’s environmental performance during the calendar year in review.

  12. Dataset of cocoa aspartic protease cleavage sites

    Directory of Open Access Journals (Sweden)

    Katharina Janek

    2016-09-01

    Full Text Available The data provide information in support of the research article, “The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors” (Janek et al., 2016 [1]. Three different protein substrates were partially digested with the aspartic protease isolated from cocoa beans and commercial pepsin, respectively. The obtained peptide fragments were analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS/MS and identified using the MASCOT server. The N- and C-terminal ends of the peptide fragments were used to identify the corresponding in-vitro cleavage sites by comparison with the amino acid sequences of the substrate proteins. The same procedure was applied to identify the cleavage sites used by the cocoa aspartic protease during cocoa fermentation starting from the published amino acid sequences of oligopeptides isolated from fermented cocoa beans. Keywords: Aspartic protease, Cleavage sites, Cocoa, In-vitro proteolysis, Mass spectrometry, Peptides

  13. Small Wind Site Assessment Guidelines

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Tim [Advanced Energy Systems LLC, Eugene, OR (United States); Preus, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    Site assessment for small wind energy systems is one of the key factors in the successful installation, operation, and performance of a small wind turbine. A proper site assessment is a difficult process that includes wind resource assessment and the evaluation of site characteristics. These guidelines address many of the relevant parts of a site assessment with an emphasis on wind resource assessment, using methods other than on-site data collection and creating a small wind site assessment report.

  14. Acid distribution in phosphoric acid fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Okae, I.; Seya, A.; Umemoto, M. [Fuji Electric Co., Ltd., Chiba (Japan)

    1996-12-31

    Electrolyte acid distribution among each component of a cell is determined by capillary force when the cell is not in operation, but the distribution under the current load conditions had not been clear so far. Since the loss of electrolyte acid during operation is inevitable, it is necessary to store enough amount of acid in every cell. But it must be under the level of which the acid disturbs the diffusion of reactive gases. Accordingly to know the actual acid distribution during operation in a cell is very important. In this report, we carried out experiments to clarify the distribution using small single cells.

  15. Strong activation of bile acid-sensitive ion channel (BASIC) by ursodeoxycholic acid

    Science.gov (United States)

    Wiemuth, Dominik; Sahin, Hacer; Lefèvre, Cathérine M.T.; Wasmuth, Hermann E.; Gründer, Stefan

    2013-01-01

    Bile acid-sensitive ion channel (BASIC) is a member of the DEG/ENaC gene family of unknown function. Rat BASIC (rBASIC) is inactive at rest. We have recently shown that cholangiocytes, the epithelial cells lining the bile ducts, are the main site of BASIC expression in the liver and identified bile acids, in particular hyo- and chenodeoxycholic acid, as agonists of rBASIC. Moreover, it seems that extracellular divalent cations stabilize the resting state of rBASIC, because removal of extracellular divalent cations opens the channel. In this addendum, we demonstrate that removal of extracellular divalent cations potentiates the activation of rBASIC by bile acids, suggesting an allosteric mechanism. Furthermore, we show that rBASIC is strongly activated by the anticholestatic bile acid ursodeoxycholic acid (UDCA), suggesting that BASIC might mediate part of the therapeutic effects of UDCA. PMID:23064163

  16. 300 Area waste acid treatment system closure plan. Revision 1

    International Nuclear Information System (INIS)

    1996-03-01

    This section provides a description of the Hanford Site, identifies the proposed method of 300 Area Waste Acid Treatment System (WATS) closure, and briefly summarizes the contents of each chapter of this plan

  17. 300 Area waste acid treatment system closure plan. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    This section provides a description of the Hanford Site, identifies the proposed method of 300 Area Waste Acid Treatment System (WATS) closure, and briefly summarizes the contents of each chapter of this plan.

  18. Wismut sites regeneration: Flooding of the former leaching mine 'Koenigstein'

    International Nuclear Information System (INIS)

    Runge, W.

    2001-01-01

    Flooding of abandoned mines was part of the regeneration programme for the Wismut sites. In January 2001, flooding was started at the Koenigstein mine, the easternmost site of the Wismut in Sachsen. The operations are scheduled for 5 - 6 years. Since 1984, this mine was operated in a leaching process involving sulphuric acid, so that a number of measures had to be taken to ensure that polluted flooding water will not contaminate the groundwater in this area [de

  19. Olkiluoto site description 2006

    International Nuclear Information System (INIS)

    Andersson, J.; Ahokas, H.; Hudson, J.A.

    2007-03-01

    This second version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2004 (Posiva 2005) with the data and knowledge obtained up to December 2005. The main product of the modelling has been to develop a descriptive model of the site (the Site Descriptive Model), i.e. a model describing the geometry, properties of the bedrock and the water and the associated interacting processes and mechanisms. For practical reasons, the Site Descriptive Model is divided into five parts: surface system, geology, rock mechanics, hydrogeology and hydrogeochemistry, which are presented in individual chapters. Four separated models are presented: the geological, rock mechanics, hydrogeological and hydrogeochemical models. The consistency between the hydrogeological and hydrogeochemical models is assessed in a joint chapter. Chapter 1 presents an outline of the report, explains the background to its development and sets out its objectives and scope. It is also introduces and explains the integrated modelling methodology, the nomenclature used in the descriptions of the models and the prediction/outcome studies. Chapter 2 provides a brief overview of the data used for producing the Site Description. Chapters 3 to 8 present the descriptive modelling, which involves interpreting data, interpolating or extrapolating between measurement points and calibrating the model against data, based on the various assumptions made about each conceptual model. Chapter 9 presents the results of the prediction/outcome studies performed during 2005 and Chapter 10 the overall consistency and confidence assessment. Overall conclusions are provided in Chapter 11. The main advances since Site Report 2004 are: A new geological model is presented in Chapter 4, representing a significant change from Bedrock Model 2003/1. There has been extensive use of geological data, whereas hydrogeological data have deliberately not been used and more

  20. Acid precipitation literature review

    Energy Technology Data Exchange (ETDEWEB)

    Seip, H M; Andersen, B; Andersson, G; Hov, Oe; Kucera, V; Moseholm, L

    1986-01-01

    There is an increasing number of publications on acid deposition and related phenomena. Interest in these topics has also been reflected in a considerable number of meetings and conferences in this field. The largest of these in 1985 was the ''International Symposium on Acidic Precipitation'' (Muskoka, Ontario). Most work so far has been carried out in North America and Europe. There is, however, an increasing interest in obtaining a better picture of sensitive areas and possible acidification in other parts of the world. Anthropogenic SO/sub 2/ emissions have been estimated to be (in TgSyr/sup -1/): 2.4 (Africa), 4.1 (South America), 0.7 (Ocenia), and 18.3 (Asia). The largest increase during the last decade has been in Asia. Based on Studies of precipitation in remote areas it has been suggested that the natural background concentration for sulphate in many areas should be about 6 ..mu..eq 1/sup -1/. A new study of sulphate and nitrate in Greenland snow showed that both ions increased by a factor of about 2 from 1895 to 1978. The concentrations of SO/sub 2/ at Norwegian rural sites show a decreasing trend since late 1970s, while concentrations of sulphate in air show no clear trend. More reliable models for transformation, transport and deposition of chemicals are being developed, including three-dimensional grid models to describe episodes of elevated pollution levels lasting for a few days. Model calculations indicate that control of hydrocarbon (HC) emissions is much more efficient in reducing the ozone level in southern Scandinavia in episodes influenced by long-range transported pollutants than NO/sub x/ control of combined NO/sub x/ and HC control. 36 refs. (EG).

  1. Intestinal metabolism of sulfur amino acids

    Science.gov (United States)

    The gastrointestinal tract (GIT) is a metabolically significant site of sulfur amino acid (SAA) metabolism in the body and metabolizes approx. 20% of the dietary methionine intake that is mainly transmethylated to homocysteine and transsulfurated to cysteine. The GIT accounts for approx. 25% of the ...

  2. Geotechnical site assessment methodology

    International Nuclear Information System (INIS)

    Tunbridge, L.W.; Richards, L.R.

    1985-09-01

    A final report summarizing the research conducted on geotechnical site assessment methodology at the Carwynnen test mine in Cornwall. The geological setting of the test site in the Cornubian granite batholith is described. The effect of structure imposed by discontinuities on the engineering behaviour of rock masses is discussed and the scanline survey method of obtaining data on discontinuities in the rock mass is described. The applicability of some methods of statistical analysis for discontinuity data is reviewed. The requirement for remote geophysical methods of characterizing the mass is discussed and experiments using seismic and ultrasonic velocity measurements are reported. Methods of determining the in-situ stresses are described and the final results of a programme of in-situ stress measurements using the overcoring and hydrofracture methods are reported. (author)

  3. Shaft siting decision

    International Nuclear Information System (INIS)

    1987-08-01

    This study identifies and establishes relative guidelines to be used for siting of repository shafts. Weights were determined for the significant factors that impact the selection of shaft locations for a nuclear waste repository in salt. The study identified a total of 45 factors. A panel of experienced mining people utilized the Kepner-Tregoe (K-T) Decision Analysis Process to perform a structured evaluation of each significant shaft siting factor. The evaluation determined that 22 of the factors were absolute constraints and that the other 23 factors were desirable characteristics. The group established the relative weights for each of the 23 desirable characteristics by using a paired comparison method. 8 refs., 2 figs., 5 tabs

  4. IOs as Social Sites

    DEFF Research Database (Denmark)

    Park, Susan M.; Vetterlein, Antje

    Norms research has made significant inroads into examining their emergence and influence in international relations, while recognizing international organizations (IOs) as key social sites for norms to be created and/or disseminated. This paper interrogates how IOs as “organizational platforms......” (Finnemore 1996) influence the norm building process. Going beyond state-centric approaches to norm construction, it argues that the process of taking up a norm by an IO does affect the norm’s power. A norm’s strength is determined by the extent to which it is uncontested and taken for granted as appropriate...... the norm building process in this way provides insight into the effect of IOs as social sites in strengthening a norm....

  5. Web Site Optimisation

    OpenAIRE

    Petrželka, Jiří

    2007-01-01

    This BSc Project was performed during a study stay at the Coventry University, UK. The goal of this project is to enhance the accessibility and usability of an existing company presentation located at http://www.hcc.cz, boost the site's traffic and so increase the company's revenues. The project follows these steps to accomplish this: a ) A partial refactoring of the back-end (PHP scripts). b ) Transformation of the website contents according to the recommendations of the World Wide Web conso...

  6. Doping phosphoric acid in polybenzimidazole membranes for high temperature proton exchange membrane fuel cells

    DEFF Research Database (Denmark)

    He, Ronghuan; Li, Qingfeng; Jensen, Jens Oluf

    2007-01-01

    Polybenzimidazole (PBI) membranes were doped in phosphoric acid solutions of different concentrations at room temperature. The doping chemistry was studied using the Scatchard method. The energy distribution of the acid complexation in polymer membranes is heterogeneous, that is, there are two...... different types of sites in PBI for the acid doping. The protonation constants of PBI by phosphoric acid are found to be 12.7 L mol(-1) (K-1) for acid complexing sites with higher affinity, and 0.19 L mol(-1) (K-2) for the sites with lower affinity. The dissociation constants for the complexing acid onto...... these two types of PBI sites are found to be 5.4 X 10(-4) and 3.6 X 10(-2), respectively, that is, about 10 times smaller than that of aqueous phosphoric acid in the first case but 5 times higher in the second. The proton conducting mechanism is also discussed....

  7. 1999 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    ENGEL-COX,J.; ZIMMERMAN,E.; LEE,R.; WILLIAMS,J.; GREEN,T.; PAQUETTE,D.; HOODA,B.; SCARPITTA,S.; GENZER,P.; ET AL

    2000-09-01

    Throughout the scientific community, Brookhaven National Laboratory (BNL) is renowned for its leading-edge research in physics, medicine, chemistry, biology, materials, and the environment. BNL is committed to supporting its world-class scientific research with an internationally recognized environmental protection program. The 1999 Site Environmental Report (SER) summarizes the status of the Laboratory's environmental programs and performance, including the steady progress towards cleaning up the site and fully integrating environmental stewardship into all facets of the Laboratory's mission. BNL is located on 5,265 acres of pine barrens in Suffolk County in the center of Long Island, New York. The Laboratory is situated above a sole source aquifer at the headwaters of the Peconic River; therefore, protecting ground and surface water quality is a special concern. Approximately 3,600 acres of the site are undeveloped and serve as habitat for a wide variety of animals and plants, including one New York State endangered species, the tiger salamander, and two New York State threatened species, the banded sunfish and the stiff goldenrod. Monitoring, preserving, and restoring these ecological resources is a high priority for the Laboratory.

  8. Site specific plan

    International Nuclear Information System (INIS)

    Hutchison, J.; Jernigan, G.

    1989-12-01

    The Environmental Restoration and Waste Management Five-Year Plan (FYP) covers the period for FY 1989 through FY 1995. The plan establishes a Department of Energy -- Headquarters (DOE-HQ) agenda for cleanup and compliance against which overall progress can be measured. The FYP covers three areas: Corrective Activities, Environmental Restoration, and Waste Management Operations. Corrective Activities are those activities necessary to bring active or standby facilities into compliance with local, state, and federal environmental regulations. Environmental restoration activities include the assessment and cleanup of surplus facilities and inactive waste sites. Waste management operations includes the treatment, storage, and disposal of wastes which are generated as a result of ongoing operations. This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show how environmental restoration and waste management activities that were identified during the preparation of the FYP will be implemented, tracked, and reported. The SSP describes DOE Savannah River (DOE-SR) and operating contractor, Westinghouse Savannah River Company (WSRC), organizations that are responsible, for undertaking the activities identified in this plan. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. 8 refs., 46 figs., 23 tabs

  9. Citric acid urine test

    Science.gov (United States)

    Urine - citric acid test; Renal tubular acidosis - citric acid test; Kidney stones - citric acid test; Urolithiasis - citric acid test ... No special preparation is necessary for this test. But the results ... test is usually done while you are on a normal diet. Ask your ...

  10. Silica-supported sulfonic acids as recyclable catalyst for esterification of levulinic acid with stoichiometric amounts of alcohols

    Directory of Open Access Journals (Sweden)

    Raimondo Maggi

    2016-10-01

    Full Text Available Converting biomass into value-added chemicals holds the key to sustainable long-term carbon resource management. In this context, levulinic acid, which is easily obtained from cellulose, is valuable since it can be transformed into a variety of industrially relevant fine chemicals. Here we present a simple protocol for the selective esterification of levulinic acid using solid acid catalysts. Silica supported sulfonic acid catalysts operate under mild conditions and give good conversion and selectivity with stoichiometric amounts of alcohols. The sulfonic acid groups are tethered to the support using organic tethers. These tethers may help in preventing the deactivation of the active sites in the presence of water.

  11. NOAA History - About This Site

    Science.gov (United States)

    NOAA History Banner gold bar divider home - takes you to index page about the site contacts noaa - takes you to the noaa home page search this site white divider about this site The NOAA History site is the result of the work of many individuals throughout 3d history page NOAA who have been inspired by

  12. Implementing Site-based Budgeting.

    Science.gov (United States)

    Sielke, Catherine C.

    2001-01-01

    Discusses five questions that must be answered before implementing site-based budgeting: Why are we doing this? What budgeting decisions will be devolved to the school site? How do dollars flow from the central office to the site? Who will be involved at the site? How will accountability be achieved? (Author/PKP)

  13. Effects of water on the esterification of free fatty acids by acid catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Park, Ji-Yeon; Kim, Deog-Keun; Lee, Jin-Suk [Korea Institute of Energy Research, 71-2, Jang-dong, Yuseong-gu, Daejeon 305-343 (Korea); Wang, Zhong-Ming [Guangzhou Institute of Energy Conversion, No. 2 Nengyuan Rd, Wushan, Tianhe, Guangzhou 510-640 (China)

    2010-03-15

    To maximize the production of biodiesel from soybean soapstock, the effects of water on the esterification of high-FFA (free fatty acid) oils were investigated. Oleic acid and high acid acid oil (HAAO) were esterified by reaction with methanol in the presence of Amberlyst-15 as a heterogeneous catalyst or sulfuric acid as a homogeneous catalyst. The yield of fatty acid methyl ester (FAME) was studied at oil to methanol molar ratios of 1:3 and 1:6 and reaction temperatures of 60 and 80 C. The rate of esterification of oleic acid significantly decreased as the initial water content increased to 20% of the oil. The activity of Amberlyst-15 decreased more rapidly than that of sulfuric acid, due to the direct poisoning of acid sites by water. Esterification using sulfuric acid was not affected by water until there was a 5% water addition at a 1:6 molar ratio of oil to methanol. FAME content of HAAO prepared from soapstock rapidly increased for the first 30 min of esterification. Following the 30-min mark, the rate of FAME production decreased significantly due to the accumulation of water. When methanol and Amberlyst-15 were removed from the HAAO after 30 min of esterification and fresh methanol and a catalyst were added, the time required to reach 85% FAME content was reduced from 6 h to 1.8 h. (author)

  14. Contamination by perfluorinated compounds in water near waste recycling and disposal sites in Vietnam.

    Science.gov (United States)

    Kim, Joon-Woo; Tue, Nguyen Minh; Isobe, Tomohiko; Misaki, Kentaro; Takahashi, Shin; Viet, Pham Hung; Tanabe, Shinsuke

    2013-04-01

    There are very few reports on the contamination by perfluorinated chemicals (PFCs) in the environment of developing countries, especially regarding their emission from waste recycling and disposal sites. This is the first study on the occurrence of a wide range of PFCs (17 compounds) in ambient water in Vietnam, including samples collected from a municipal dumping site (MD), an e-waste recycling site (ER), a battery recycling site (BR) and a rural control site. The highest PFC concentration was found in a leachate sample from MD (360 ng/L). The PFC concentrations in ER and BR (mean, 57 and 16 ng/L, respectively) were also significantly higher than those detected in the rural control site (mean, 9.4 ng/L), suggesting that municipal solid waste and waste electrical and electronic equipment are potential contamination sources of PFCs in Vietnam. In general, the most abundant PFCs were perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluoroundecanoic acid (PFUDA; waste materials.

  15. Aluminium release from acidic forest soil following deforestation and ...

    African Journals Online (AJOL)

    Acidic tropical soils often have high Al3+ concentrations in soil solutions, which can be toxic to plants and, thereby, reduce agricultural yields. This study focuses on the impact of deforestation and cultivation on the short and long-term Al geochemistry of acidic soils in Ghana, West Africa. Site-specific investigations were ...

  16. Examining the role of glutamic acid 183 in chloroperoxidase catalysis

    NARCIS (Netherlands)

    Yi, X.; Conesa, A.; Punt, P.J.; Hager, L.P.

    2003-01-01

    Site-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in

  17. Nickel Inhibits Mitochondrial Fatty Acid Oxidation

    Science.gov (United States)

    Uppala, Radha; McKinney, Richard W.; Brant, Kelly A.; Fabisiak, James P.; Goetzman, Eric S.

    2015-01-01

    Nickel exposure is associated with changes in cellular energy metabolism which may contribute to its carcinogenic properties. Here, we demonstrate that nickel strongly represses mitochondrial fatty acid oxidation—the pathway by which fatty acids are catabolized for energy—in both primary human lung fibroblasts and mouse embryonic fibroblasts. At the concentrations used, nickel suppresses fatty acid oxidation without globally suppressing mitochondrial function as evidenced by increased glucose oxidation to CO2. Pre-treatment with L-carnitine, previously shown to prevent nickel-induced mitochondrial dysfunction in neuroblastoma cells, did not prevent the inhibition of fatty acid oxidation. The effect of nickel on fatty acid oxidation occurred only with prolonged exposure (>5 hr), suggesting that direct inhibition of the active sites of metabolic enzymes is not the mechanism of action. Nickel is a known hypoxia-mimetic that activates hypoxia inducible factor-1α (HIF1α). Nickel-induced inhibition of fatty acid oxidation was blunted in HIF1α knockout fibroblasts, implicating HIF1α as one contributor to the mechanism. Additionally, nickel down-regulated the protein levels of the key fatty acid oxidation enzyme very long-chain acyl-CoA dehydrogenase (VLCAD) in a dose-dependent fashion. In conclusion, inhibition of fatty acid oxidation by nickel, concurrent with increased glucose metabolism, represents a form of metabolic reprogramming that may contribute to nickel-induced carcinogenesis. PMID:26051273

  18. Amino acid analogs for tumor imaging

    International Nuclear Information System (INIS)

    Goodman, M.M.; Shoup, T.

    1998-01-01

    The invention provides novel amino acid compounds of use in detecting and evaluating brain and body tumors. These compounds combine the advantageous properties of 1-amino-cycloalkyl-1-carboxylic acids, namely, their rapid uptake and prolonged retention in tumors with the properties of halogen substituents, including certain useful halogen isotopes including fluorine-18, iodine-123, iodine-125, iodine-131, bromine-75, bromine-76, bromine-77 and bromine-82. In one aspect, the invention features amino acid compounds that have a high specificity for target sites when administered to a subject in vivo. Preferred amino acid compounds show a target to non-target ratio of at least 5:1, are stable in vivo and substantially localized to target within 1 hour after administration. An especially preferred amino acid compound is [ 18 F]-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC). In another aspect, the invention features pharmaceutical compositions comprised of an α-amino acid moiety attached to either a four, five, or a six member carbon-chain ring. In addition, the invention features analogs of α-aminoisobutyric acid

  19. Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

    Science.gov (United States)

    Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika

    2016-03-04

    Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.

  20. The Acid-Base Balance Between Organic Acids and Circumneutral Ground Waters in Large Peatlands

    Science.gov (United States)

    Siegel, D. I.; Glaser, P. H.; So, J.

    2006-05-01

    Organic acids supply most of the acidity in the surface waters of bogs in peatlands. Yet, the fundamental geochemical properties of peatland organic acids are still poorly known. To assess the geochemical properties of typical organic acid assemblages in peatlands, we used a triprotic analog model for peat pore waters and surface waters in the Glacial Lake Agassiz Peatlands, optimizing on charge balance and calibrated to estimates of mole site density in DOC and triprotic acid dissociation constants. Before the calibration process, all bog waters and 76% of fen waters had more than +20% charge imbalance. After calibration, most electrochemically balanced within 20%. In the best calibration, the mole site denisty of bog DOC was estimated as ~0.05 mmol/mmol C., approximately 6 times smaller than that for fen DOC or the DOC in the fen deeper fen peats that underlie bogs. The three modeled de-protonation constants were; pKa1 = ~3.0, pKa2 = ~4.5 and pKa3 = ~7.0 for the bog DOC, and; pKa1 = ~5.2, pKa2 =~ 6.5 and pKa3 = ~7.0 for the fen DOC. Bog DOC, behaves as a strong acid despite its small mole site density. The DOC in bog runoff can therefore theoretically acidify the surface waters in adjacent fens wherever these waters do not receive sufficient buffering alkalinity from active groundwater seepage.