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Sample records for affinity constant ka

  1. Automatic gesture analysis using constant affine velocity.

    PubMed

    Cifuentes, Jenny; Boulanger, Pierre; Pham, Minh Tu; Moreau, Richard; Prieto, Flavio

    2014-01-01

    Hand human gesture recognition has been an important research topic widely studied around the world, as this field offers the ability to identify, recognize, and analyze human gestures in order to control devices or to interact with computer interfaces. In particular, in medical training, this approach is an important tool that can be used to obtain an objective evaluation of a procedure performance. In this paper, some obstetrical gestures, acquired by a forceps, were studied with the hypothesis that, as the scribbling and drawing movements, they obey the one-sixth power law, an empirical relationship which connects path curvature, torsion, and euclidean velocity. Our results show that obstetrical gestures have a constant affine velocity, which is different for each type of gesture and based on this idea this quantity is proposed as an appropriate classification feature in the hand human gesture recognition field. PMID:25570332

  2. Determination of proton affinities and acidity constants of sugars.

    PubMed

    Feng, Shuting; Bagia, Christina; Mpourmpakis, Giannis

    2013-06-20

    Proton transfer reactions play a key role in the conversion of biomass derived sugars to chemicals. In this study, we employ high level ab initio theoretical methods, in tandem with solvation effects to calculate the proton affinities (PA) and acidity constants (pKa) of various d-glucose and d-fructose tautomers (protonation-deprotonation processes). In addition, we compare the theoretically derived pH values of sugar solutions against experimentally measured pH values in our lab. Our results demonstrate that the protonation of any of the O atoms of the sugars is thermodynamically preferred without any significant variation in the PA values. Intramolecular hydrogen transfers, dehydration reactions, and ring-opening processes were observed, resulting from the protonation of specific hydroxyl groups on the sugars. Regarding the deprotonation processes (pKa), we found that the sugars' anomeric hydroxyls exhibit the highest acidity. The theoretically calculated pH values of sugar solutions are in excellent agreement with experimental pH measurements at low sugar concentrations. At higher sugar concentrations the calculations predict less acidic solutions than the experiments. In this case, we expect the sugars to act as solvents increasing the proton solvation energy and the acidity of the solutions. We demonstrated through linear relationships that the pKa values are correlated with the relative stability of the conjugate bases. The latter is related to hydrogen bonding and polarization of the C-O(-) bond. A plausible explanation for the good performance of the direct method in calculating the pKa values of sugars can be the presence of intramolecular hydrogen bonds on the conjugate base. Both theory and experiments manifest that fructose is a stronger acid than glucose, which is of significant importance in self-catalyzed biomass-relevant dehydration reactions. PMID:23706015

  3. The fundamental constants of orthotropic affine plate/slab equations

    NASA Technical Reports Server (NTRS)

    Brunelle, E. J.

    1984-01-01

    The global constants associated with orthotropic slab/plate equations are discussed, and the rotational behavior of the modulus/compliance components associated with orthotropic slabs/plates are addressed. It is concluded that one cluster constant is less than or equal to unity for all physically possible materials. Rotationally anomalous behavior is found in two materials, and a simple inequality which can be used to identify regular or anomalous behavior is presented and discussed in detail.

  4. Binding of ionic species: a general approach to measuring binding constants and assessing affinities.

    PubMed

    Roelens, Stefano; Vacca, Alberto; Venturi, Chiara

    2009-03-01

    Bound together: The association of receptors with ionic species cannot be assimilated to the binding of neutral guests. When dealing with salts, both ion pairing and binding to the free and the ion-paired ionic guest determine the actual association pattern (see figure). The general issue of measuring association constants and assessing affinities for ions is addressed and validated in two cases of anion binding.A general approach to the largely underestimated issue of measuring binding constants and assessing affinities in the binding of ionic species is described. The approach is based on a rigorous, nongraphical determination of binding constants in multiequilibrium systems by nonlinear regression of chemical shift data from NMR titrations and on the use of the BC(50) descriptor for assessing affinities and ranking the binding ability of receptors on a common scale. The approach has been validated with two tripodal anion-binding receptors, namely, a ureidic (1) and a pyrrolic (2) receptor, binding to tetramethylammonium chloride in CDCl(3)/CD(3)CN (80:20). A set of five and six formation constants could be measured for 1 and 2, respectively, including, in addition to the ion pair, complexes of the free and the ion-paired anion. The BC(50) values calculated from the measured constants allowed a quantitative assessment of each receptor's binding affinity towards the chloride anion, the pyrrolic receptor showing a 15-fold larger affinity over the ureidic receptor, a figure that quantifies the improvement obtained by replacing the amido-pyrrolic for ureidic binding groups on the tripodal scaffold of the receptor. The results have shown that, in contrast to common practice, neither of the two systems could be appropriately described by a 1:1 association with the anion only, but required the ion-pairing and ion-pair binding equilibria to be taken into account because these contribute substantially to the complexation process. The BC(50) descriptor has also been shown

  5. Determination of stability constants of complexes of neutral analytes with charged cyclodextrins by affinity capillary electrophoresis.

    PubMed

    Beneš, Martin; Zusková, Iva; Svobodová, Jana; Gaš, Bohuslav

    2012-03-01

    A novel procedure for the determination of stability constants in systems with neutral analytes and charged complexation agents by affinity capillary electrophoresis was established. This procedure involves all necessary corrections to achieve precise and reliable data. Temperature, ionic strength, and viscosity corrections were applied. Based on the conductivity measurements, the average temperature of the background electrolyte in the capillary was kept at the constant value of 25°C by decreasing the temperature of the cooling medium. The viscosity correction was performed using the viscosity ratio determined by an external viscosimeter. The electrophoretical measurements were performed, at first, at constant ionic strength. In this case, the increase of ionic strength caused by increasing complexation agent concentration was compensated by changing of the running buffer concentration. Subsequently the dependence of the analyte effective mobility on the complexation agent concentration was measured without the ionic strength compensation (at variable ionic strength). The new procedure for determination of the stability constants even from such data was established. These stability constants are in a very good agreement with those obtained at the constant ionic strength. The established procedure was applied for determination of the thermodynamic stability constants of (R, R)-(+)- and (S, S)-(-)-hydrobenzoin and R- and S-(3-bromo-2-methylpropan-1-ol) complexing with 6-monodeoxy-6-mono(3-hydroxy)propylamino-β-cyclodextrin hydrochloride.

  6. Determining Partition Coefficient (Log P), Distribution Coefficient (Log D) and Ionization Constant (pKa) in Early Drug Discovery.

    PubMed

    Bharate, Sonali S; Kumar, Vikas; Vishwakarma, Ram A

    2016-01-01

    An early prediction of physicochemical properties is highly desirable during drug discovery to find out a viable lead candidate. Although there are several methods available to determine partition coefficient (log P), distribution coefficient (log D) and ionization constant (pKa), none of them involves simple and fixed, miniaturized protocols for diverse set of compounds. Therefore, it is necessary to establish simple, uniform and medium-throughput protocols requiring small sample quantities for the determination of these physicochemical properties. Log P and log D were determined by shake flask method, wherein, the compound was partitioned between presaturated noctanol and water phase (water/PBS pH 7.4) and the concentration of compound in each phase was determined by HPLC. The pKa determination made use of UV spectrophotometric analysis in a 96-well microtiter plate containing a series of aqueous buffers ranging from pH 1.0 to 13.0. The medium-throughput miniaturized protocols described herein, for determination of log P, log D and pKa, are straightforward to set up and require very small quantities of sample (< 5 mg for all three properties). All established protocols were validated using diverse set of compounds.

  7. Determining Partition Coefficient (Log P), Distribution Coefficient (Log D) and Ionization Constant (pKa) in Early Drug Discovery.

    PubMed

    Bharate, Sonali S; Kumar, Vikas; Vishwakarma, Ram A

    2016-01-01

    An early prediction of physicochemical properties is highly desirable during drug discovery to find out a viable lead candidate. Although there are several methods available to determine partition coefficient (log P), distribution coefficient (log D) and ionization constant (pKa), none of them involves simple and fixed, miniaturized protocols for diverse set of compounds. Therefore, it is necessary to establish simple, uniform and medium-throughput protocols requiring small sample quantities for the determination of these physicochemical properties. Log P and log D were determined by shake flask method, wherein, the compound was partitioned between presaturated noctanol and water phase (water/PBS pH 7.4) and the concentration of compound in each phase was determined by HPLC. The pKa determination made use of UV spectrophotometric analysis in a 96-well microtiter plate containing a series of aqueous buffers ranging from pH 1.0 to 13.0. The medium-throughput miniaturized protocols described herein, for determination of log P, log D and pKa, are straightforward to set up and require very small quantities of sample (< 5 mg for all three properties). All established protocols were validated using diverse set of compounds. PMID:27137915

  8. Application of chemometrics in determination of the acid dissociation constants (pKa) of several benzodiazepine derivatives as poorly soluble drugs in the presence of ionic surfactants.

    PubMed

    Shayesteh, Tavakol Heidary; Radmehr, Moojan; Khajavi, Farzad; Mahjub, Reza

    2015-03-10

    In this study, the acid dissociation constants (pKa) of some benzodiazepine derivatives including chlordiazepoxide, clonazepam, lorazepam, and oxazepam in aqueous micellar solution were determined spectrophotometrically at an ionic strength of 0.1M at 25°C. The effect of cetyl trimethylammonium bromide (CTAB) as a cationic and sodium n-dodecyl sulfate(SDS) as an anionic surfactant on the absorption spectra of benzodiazepine drugs at different pH values were studied. The acidity constants of all related species are estimated by considering the surfactant concept and the application of chemometric methods using the whole spectral fitting of the collected data to an established factor analysis model. DATAN® software (Ver. 5.0, Multid Analyses AB, and Goteborg, Sweden) was applied to determine the acidity constants. In this study, a simple and fast method to determine the ionization constant (pKa) of poorly soluble drugs was developed using surfactants. The acidity constant (i.e. pKa) for chlordiazepoxide, clonazepam, lorazepam, and oxazepam were reported as 4.62, pKa1 value of 1.52 and pKa2 value of 10.51, pKa1 value of 1.53 and pKa2 value of 10.92 and pKa1 value 1.63 and pKa2 value of 11.21 respectively. The results showed that the peak values in the spectrophotometric absorption spectra of drugs are influenced by the presence of anionic and cationic surfactants. According to the results, by changing the SDS concentration from 0 to 0.05M, the pKa of chlordiazepoxide was increased to 5.9, the pKa1 of lorazepam was decreased to 0.1 while the pKa2 was increased to 11.5. Increase in SDS concentration has not shown significant alteration in pKa of clonazepam and oxazepam. Results indicate that by Changing the CTAB concentration from 0 to 0.05M, the pKa of chlordiazepoxide was reduced to 4.4, the pKa1 of clonazepam was decreased to 0.1 and the pKa2 was decreased to 9.1, the pKa1 of lorazepam was decreased to 0.4 and the pKa2 was decreased to 9.4, the pKa1 of oxazepam was

  9. Bayesian Estimation of the Active Concentration and Affinity Constants Using Surface Plasmon Resonance Technology.

    PubMed

    Feng, Feng; Kepler, Thomas B

    2015-01-01

    Surface plasmon resonance (SPR) has previously been employed to measure the active concentration of analyte in addition to the kinetic rate constants in molecular binding reactions. Those approaches, however, have a few restrictions. In this work, a Bayesian approach is developed to determine both active concentration and affinity constants using SPR technology. With the appropriate prior probabilities on the parameters and a derived likelihood function, a Markov Chain Monte Carlo (MCMC) algorithm is applied to compute the posterior probability densities of both the active concentration and kinetic rate constants based on the collected SPR data. Compared with previous approaches, ours exploits information from the duration of the process in its entirety, including both association and dissociation phases, under partial mass transport conditions; do not depend on calibration data; multiple injections of analyte at varying flow rates are not necessary. Finally the method is validated by analyzing both simulated and experimental datasets. A software package implementing our approach is developed with a user-friendly interface and made freely available. PMID:26098764

  10. Acidity constants in methanol/water mixtures of polycarboxylic acids used in drug salt preparations. Potentiometric determination of aqueous pKa values of quetiapine formulated as hemifumarate.

    PubMed

    Garrido, Gemma; Ràfols, Clara; Bosch, Elisabeth

    2006-05-01

    The acidic dissociation constants in a number of methanol/water mixtures of mono and polycarboxylic acids commonly used in the preparation of drug salts were determined. These solvent mixtures are usually used to determine the pKa of drugs of low aqueous solubility. However, when these drugs are prepared in salt form, the acid-base equilibria of both the basic drug and the counter-anion are involved in the potentiometric titration curves. In these instances, the inclusion of the pKa of acids as constant values in the curve fitting provides easy computation of the drug pKa without the need of any previous step to get the free base. As an application example, the aqueous pKa values of the quetiapine formulated as hemifumarate (Seroquel) were estimated by extrapolation from the experimental pKa in several methanol/water mixtures, which were then calculated according to the suitable constants of fumaric acid. The estimated aqueous pKa values of quetiapine are compared with those directly obtained in aqueous solution by potentiometry and by capillary electrophoresis.

  11. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    PubMed

    Zheng, Xiliang; Wang, Jin

    2015-04-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  12. The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition

    PubMed Central

    Zheng, Xiliang; Wang, Jin

    2015-01-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  13. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    PubMed

    Zheng, Xiliang; Wang, Jin

    2015-04-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  14. Dissociation constants of weak acids from ab initio molecular dynamics using metadynamics: influence of the inductive effect and hydrogen bonding on pKa values.

    PubMed

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2014-11-26

    The theoretical estimation of the dissociation constant, or pKa, of weak acids continues to be a challenging field. Here, we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pKa value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pKa. We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pKa values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pKa values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pKa values.

  15. Determination of pKa and Hydration Constants for a Series of α-Keto-Carboxylic Acids Using Nuclear Magnetic Resonance Spectrometry.

    PubMed

    Lopalco, Antonio; Douglas, Justin; Denora, Nunzio; Stella, Valentino J

    2016-02-01

    The determination of the acid-base dissociation constants, and thus the pKa values, of α-keto acids such as pyruvic acid is complex because of the existence of these acids in their hydrated and nonhydrated or oxo state. Equilibria involved in the hydration and dehydration of the α-keto group of pyruvic acid and three other α-keto acids, 3-methyl-2-oxobutanoic acid, 4-methyl-2-oxopentanoic acid, and 2-oxo-2-phenylacetic acid, were investigated by proton and carbon nuclear magnetic resonance spectrometry, at constant ionic strength, 0.15, and 25 °C. Dissociation constants for the oxo (pKa(oxo)) and hydrated (pKa(hyd)) acids of each compound were estimated from the change in the degree of hydration with changes in pH and directly from the changes in chemical shifts of various hydrogen and carbons nuclei with pH. α-Keto acids showed greater hydration in their acidic forms than their carboxylate forms. The degree of hydration was sensitive to steric and electronic/resonance factors. As expected, the oxo forms of the acids were stronger acids compared with their hydrated analogs, and their dissociation constants were also sensitive to steric and electronic factors.

  16. Determination of the dissociation constants (pKa) of secondary and tertiary amines in organic media by capillary electrophoresis and their role in the electrophoretic mobility order inversion.

    PubMed

    Cantu, Marcelo Delmar; Hillebranda, Sandro; Carrilho, Emanuel

    2005-03-11

    Non-aqueous capillary electrophoresis (NACE) may provide a selectivity enhancement in separations since the analyte dissociation constants (pKa) in organic media are different from those in aqueous solutions. In this work, we have studied the inversion in mobility order observed in the separation of tertiary (imipramine (IMI) and amitryptiline (AMI)) and secondary amines (desipramine (DES) and nortryptiline (NOR)) in water, methanol, and acetonitrile. We have determined the pKa values in those solvents and the variation of dissociation constants with the temperature. From these data, and applying the Van't Hoff equation, we have calculated the thermodynamic parameters deltaH and deltaS. The pKa values found in methanol for DES, NOR, IMI, and AMI were 10.80, 10.79, 10.38, and 10.33, respectively. On the other hand, in acetonitrile an opposite relation was found since the values were 20.60, 20.67, 20.74, and 20.81 for DES, NOR, IMI, and AMI. This is the reason why a migration order inversion is observed in NACE for these solvents. The thermodynamic parameters were evaluated and presented a tendency that can be correlated with that observed for pKa values.

  17. Comparison of three distinct ELLA protocols for determination of apparent affinity constants between Con A and glycoproteins.

    PubMed

    Mislovičová, D; Katrlík, J; Paulovičová, E; Gemeiner, P; Tkac, J

    2012-06-01

    A procedure for determination of apparent affinity constants K(D)(app) between Concanavalin A (Con A) and naturally d-mannose containing glycoproteins using enzyme-linked lectin assay (ELLA) is reported. Three distinct ELLA protocols are compared to each other with 3 different fitting models used (Liliom, Hill with and without a cooperativity factor). The glycoproteins were physisorbed on a highly charged polystyrene solid surface of immunoassay plates and the amount of lectin bound to the glycoproteins was determined by photometry. The interactions of Con A with five mannose-containing glycoproteins, invertase (INV), glucoamylase (GA), glucose oxidase (GOx), ovalbumin (OVA), and transferrin (TRF) were quantified with apparent affinity constant being in the range 2×10(-7) to 9×10(-6)M. The strength of interaction between Con A and glycoproteins is discussed on the basis of glycan structure/exposure on the protein backbone for each glycoprotein.

  18. Jacalin interaction with human immunoglobulin A1 and bovine immunoglobulin G1: affinity constant determined by piezoelectric biosensoring.

    PubMed

    Pedroso, Mariele M; Pesquero, Naira C; Thomaz, Sandra M O; Roque-Barreira, Maria C; Faria, Ronaldo C; Bueno, Paulo R

    2012-03-01

    The affinity of the D-galactose-binding lectin from Artocarpus heterophyllus lectin, known as jacalin, with immonuglobulins (Igs) was determined by biofunctionalization of a piezoelectric transducer. This piezoelectric biofunctionalized transducer was used as a mass-sensitive analytical tool, allowing the real-time binding analysis of jacalin-human immunoglobulin A1 (IgA(1)) and jacalin-bovine IgG(1) interactions from which the apparent affinity constant was calculated. The strategy was centered in immobilizing jacalin on the gold electrode's surface of the piezoelectric crystal resonator using appropriate procedures based on self-assembling of 11-mercaptoundecanoic acid and 2-mercaptoethanol thiol's mixture, a particular immobilization strategy by which it was possible to avoid cross-interaction between the proteins over electrode's surface. The apparent affinity constants obtained between jacalin-human IgA(1) and jacalin-bovine IgG(1) differed by 1 order of magnitude [(8.0 ± 0.9) 10(5) vs (8.3 ± 0.1) 10(6) L mol(-1)]. On the other hand, the difference found between human IgA(1) and human IgA(2) interaction with jacalin, eight times higher for IgA(1), was attributed to the presence of O-linked glycans in the IgA(1) hinge region, which is absent in IgA(2). Specific interaction of jacalin with O-glycans, proved to be present in the human IgA(1) and hypothetically present in bovine IgG(1) structures, is discussed as responsible for the obtained affinity values.

  19. Thermodynamics of Calcium binding to the Calmodulin N-terminal domain to evaluate site-specific affinity constants and cooperativity.

    PubMed

    Beccia, Maria Rosa; Sauge-Merle, Sandrine; Lemaire, David; Brémond, Nicolas; Pardoux, Romain; Blangy, Stéphanie; Guilbaud, Philippe; Berthomieu, Catherine

    2015-07-01

    Calmodulin (CaM) is an essential Ca(II)-dependent regulator of cell physiology. To understand its interaction with Ca(II) at a molecular level, it is essential to examine Ca(II) binding at each site of the protein, even if it is challenging to estimate the site-specific binding properties of the interdependent CaM-binding sites. In this study, we evaluated the site-specific Ca(II)-binding affinity of sites I and II of the N-terminal domain by combining site-directed mutagenesis and spectrofluorimetry. The mutations had very low impact on the protein structure and stability. We used these binding constants to evaluate the inter-site cooperativity energy and compared it with its lower limit value usually reported in the literature. We found that site I affinity for Ca(II) was 1.5 times that of site II and that cooperativity induced an approximately tenfold higher affinity for the second Ca(II)-binding event, as compared to the first one. We further showed that insertion of a tryptophan at position 7 of site II binding loop significantly increased site II affinity for Ca(II) and the intra-domain cooperativity. ΔH and ΔS parameters were studied by isothermal titration calorimetry for Ca(II) binding to site I, site II and to the entire N-terminal domain. They showed that calcium binding is mainly entropy driven for the first and second binding events. These findings provide molecular information on the structure-affinity relationship of the individual sites of the CaM N-terminal domain and new perspectives for the optimization of metal ion binding by mutating the EF-hand loops sequences.

  20. Determination of the kinetic rate constant of cyclodextrin supramolecular systems by high-performance affinity chromatography.

    PubMed

    Zhang, Jiwen; Li, Haiyan; Sun, Lixin; Wang, Caifen

    2015-01-01

    The kinetics of the association and dissociation are fundamental kinetic processes for the host-guest interactions (such as the drug-target and drug-excipient interactions) and the in vivo performance of supramolecules. With advantages of rapid speed, high precision and ease of automation, the high-performance affinity chromatography (HPAC) is one of the best techniques to measure the interaction kinetics of weak to moderate affinities, such as the typical host-guest interactions of drug and cyclodextrins by using a cyclodextrin-immobilized column. The measurement involves the equilibration of the cyclodextrin column, the upload and elution of the samples (non-retained substances and retained solutes) at different flow rates on the cyclodextrin and control column, and data analysis. It has been indicated that cyclodextrin-immobilized chromatography is a cost-efficient high-throughput tool for the measurement of (small molecule) drug-cyclodextrin interactions as well as the dissociation of other supramolecules with relatively weak, fast, and extensive interactions. PMID:25749964

  1. Photodetachment of an electron from selenide ion - The electron affinity and spin-orbit coupling constant for SeH.

    NASA Technical Reports Server (NTRS)

    Smyth, K. C.; Brauman, J. I.

    1972-01-01

    The relative cross section for the gas phase photodetachment of an electron from SeH(-) was determined in the wavelength region 428 to 578 nm. An ion cyclotron resonance spectrometer was used to generate, trap, and detect the negative ions, and a 1000-W xenon arc lamp with a grating monochromator was employed as the light source. The cross section exhibited two sharp thresholds, whose positions remained unchanged for the photodetachment of SeD(-). As a result of these thresholds, the electron affinity and the spin-orbit coupling constant were evaluated.

  2. Evaluation of equilibrium constants for the interaction of lactate dehydrogenase isoenzymes with reduced nicotinamide-adenine dinucleotide by affinity chromatography.

    PubMed Central

    Brinkworth, R I; Masters, C J; Winzor, D J

    1975-01-01

    Rabbit muscle lactate dehydrogenase was subjected to frontal affinity chromatography on Sepharose-oxamate in the presence of various concentrations of NADH and sodium phosphate buffer (0.05 M, pH 6.8) containing 0.5 M-NaCl. Quantitative interpretation of the results yields an intrinsic association constant of 9.0 x 10 (4)M-1 for the interaction of enzyme with NADH at 5 degrees C, a value that is confirmed by equilibrium-binding measurements. In a second series of experiments, zonal affinity chromatography of a mouse tissue extract under the same conditions was used to evaluate assoication constants of the order 2 x 10(5)M-1, 3 x 10(5)M-1, 4 x 10(5)M-1, 7 x 10(5)M-1 and 2 x 10(6)M-1 for the interaction of NADH with the M4, M3H, M2H2, MH3 and H4 isoenzymes respectively of lactate dehydrogenase. PMID:175784

  3. SNAP-Tag Technology: A Useful Tool To Determine Affinity Constants and Other Functional Parameters of Novel Antibody Fragments.

    PubMed

    Niesen, Judith; Sack, Markus; Seidel, Melanie; Fendel, Rolf; Barth, Stefan; Fischer, Rainer; Stein, Christoph

    2016-08-17

    Antibody derivatives, such as the single chain fragment variable (scFv), can be developed as diagnostic and therapeutic tools in cancer research, especially in the form of fusion proteins. Such derivatives are easier to produce and modify than monoclonal antibodies (mAbs) and achieve better tissue/tumor penetration. The genetic modification of scFvs is also much more straightforward than the challenging chemical modification of mAbs. Therefore, we constructed two scFvs derived from the approved monoclonal antibodies cetuximab (scFv2112) and panitumumab (scFv1711), both of which are specific for the epidermal growth factor receptor (EGFR), a well-characterized solid tumor antigen. Both scFvs were genetically fused to the SNAP-tag, an engineered version of the human DNA repair enzyme O(6)-alkylguanine DNA alkyltransferase that allows the covalent coupling of benzylguanine (BG)-modified substrates such as fluorescent dyes. The SNAP-tag achieves controllable and irreversible protein modification and is an important tool for experimental studies in vitro and in vivo. The affinity constant of a scFv is a key functional parameter, especially in the context of a fusion protein. Therefore, we developed a method to define the affinity constants of scFv-SNAP fusion proteins by surface plasmon resonance (SPR) spectroscopy. We could confirm that both scFvs retained their functionality after fusion to the SNAP-tag in a variety of procedures and assays, including ELISA, flow cytometry, and confocal microscopy. The experimental procedures described herein, and the new protocol for affinity determination by SPR spectroscopy, are suitable for the preclinical evaluation of diverse antibody formats and derivatives. PMID:27391930

  4. The estimation of affinity constants for the binding of model peptides to DNA by equilibrium dialysis.

    PubMed Central

    Standke, K C; Brunnert, H

    1975-01-01

    The binding of lysine model peptides of the type Lys-X-Lys, Lys-X-X-Lys and Lys-X-X-X-Lys (X = different aliphatic and aromatic amino acids) has been studied by equilibrium dialysis. It was shown that the strong electrostatic binding forces generated by protonated amino groups of lysine can be distinguished from the weak forces stemming from neutral and aromatic spacer amino acids. The overall binding strength of the lysine model peptides is modified by these weak binding forces and the apparent binding constants are influenced more by the hydrophobic character of the spacer amino acid side chains than by the chainlength of the spacers. PMID:1187347

  5. Estimation of apparent binding constant of complexes of selected acyclic nucleoside phosphonates with β-cyclodextrin by affinity capillary electrophoresis.

    PubMed

    Šolínová, Veronika; Mikysková, Hana; Kaiser, Martin Maxmilián; Janeba, Zlatko; Holý, Antonín; Kašička, Václav

    2016-01-01

    Affinity capillary electrophoresis (ACE) has been applied to estimation of apparent binding constant of complexes of (R,S)-enantiomers of selected acyclic nucleoside phosphonates (ANPs) with chiral selector β-cyclodextrin (βCD) in aqueous alkaline medium. The noncovalent interactions of five pairs of (R,S)-enantiomers of ANPs-based antiviral drugs and their derivatives with βCD were investigated in the background electrolyte (BGE) composed of 35 or 50 mM sodium tetraborate, pH 10.0, and containing variable concentration (0-25 mM) of βCD. The apparent binding constants of the complexes of (R,S)-enantiomers of ANPs with βCD were estimated from the dependence of effective electrophoretic mobilities of (R,S)-enantiomers of ANPs (measured simultaneously by ACE at constant reference temperature 25°C inside the capillary) on the concentration of βCD in the BGE using different nonlinear and linear calculation methodologies. Nonlinear regression analysis provided more precise and accurate values of the binding constants and a higher correlation coefficient as compared to the regression analysis of the three linearized plots of the effective mobility dependence on βCD concentration in the BGE. The complexes of (R,S)-enantiomers of ANPs with βCD have been found to be relatively weak - their apparent binding constants determined by the nonlinear regression analysis were in the range 13.3-46.4 L/mol whereas the values from the linearized plots spanned the interval 12.3-55.2 L/mol. PMID:26426398

  6. Prediction of the dissociation constant pKa of organic acids from local molecular parameters of their electronic ground state.

    PubMed

    Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2011-09-26

    A quantum chemical method has been developed to estimate the dissociation constant pK(a) of organic acids from their neutral molecular structures by employing electronic structure properties. The data set covers 219 phenols (including 29 phenols with intramolecular H-bonding), 150 aromatic carboxylic acids, 190 aliphatic carboxylic acids, and 138 alcohols, with pK(a) varying by 16 units (0.38-16.80). Optimized ground-state geometries employing the semiempirical AM1 Hamiltonian have been used to quantify the site-specific molecular readiness to donate or accept electron charge in terms of both charge-associated energies and energy-associated charges, augmented by an ortho substitution indicator for aromatic compounds. The resultant regression models yield squared correlation coefficients (r(2)) from 0.82 to 0.90 and root-mean-square errors (rms) from 0.39 to 0.70 pK(a) units, corresponding to an overall (subset-weighted) r(2) of 0.86. Simulated external validation, leave-10%-out cross-validation and target value scrambling demonstrate the statistical robustness and prediction power of the derived model suite. The low intercorrelation with prediction errors from the commercial ACD package provides opportunity for a consensus model approach, offering a pragmatic way for further increasing the confidence in prediction significantly. Interestingly, inclusion of calculated free energies of aqueous solvation does not improve the prediction performance, probably because of the limited precision provided by available continuum-solvation models.

  7. Theoretical calculations of stability constants and pKa values of metal complexes in solution: application to pyridoxamine-copper(II) complexes and their biological implications in AGE inhibition.

    PubMed

    Casasnovas, Rodrigo; Ortega-Castro, Joaquín; Donoso, Josefa; Frau, Juan; Muñoz, Francisco

    2013-10-14

    Accurate prediction of thermodynamic constants of chemical reactions in solution is one of the current challenges in computational chemistry. We report a scheme for predicting stability constants (log β) and pKa values of metal complexes in solution by means of calculating free energies of ligand- and proton-exchange reactions using Density Functional Theory calculations in combination with a continuum solvent model. The accuracy of the predicted log β and pKa values (mean absolute deviations of 1.4 and 0.2 units respectively) is equivalent to the experimental uncertainties. This theoretical methodology provides direct knowledge of log β and pKa values of major and minor species, so it is of potential use in combination with experimental techniques to obtain a detailed description of the microscopic equilibria. In particular, the proposed methodology is shown to be especially useful for obtaining the real acidity constants of those chelates where the metal-ligand coordination changes as a result of ligand deprotonation. The stability and acidity constants of pyridoxamine-Cu(2+) chelates calculated with the proposed methodology show that pyridoxamine is an efficient scavenging agent of Cu(2+) under physiological pH conditions. This is of special interest as Cu(2+) overload is involved in the formation of advanced glycation end-products (AGEs) and their associated degenerative medical conditions. PMID:23999915

  8. Determination of binding constants by affinity capillary electrophoresis, electrospray ionization mass spectrometry and phase-distribution methods

    PubMed Central

    Chen, Zhi; Weber, Stephen G.

    2008-01-01

    Many methods for determining intermolecular interactions have been described in the literature in the past several decades. Chief among them are methods based on spectroscopic changes, particularly those based on absorption or nuclear magnetic resonance (NMR) [especially proton NMR (1H NMR)]. Recently, there have been put forward several new methods that are particularly adaptable, use very small quantities of material, and do not place severe requirements on the spectroscopic properties of the binding partners. This review covers new developments in affinity capillary electrophoresis, electrospray ionization mass spectrometry (ESI-MS) and phasetransfer methods. PMID:19802330

  9. Interpolation method for accurate affinity ranking of arrayed ligand-analyte interactions.

    PubMed

    Schasfoort, Richard B M; Andree, Kiki C; van der Velde, Niels; van der Kooi, Alex; Stojanović, Ivan; Terstappen, Leon W M M

    2016-05-01

    The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)).

  10. Inhibition of ionotropic neurotransmitter receptors by antagonists: strategy to estimate the association and the dissociation rate constant of antagonists with very strong affinity to the receptors.

    PubMed

    Aoshima, H; Inoue, Y; Hori, K

    1992-10-01

    Since binding of an agonist to an ionotropic neurotransmitter receptor causes not only channel opening, but also desensitization of the receptor, inhibition of the receptor by the antagonist sometimes becomes very complicated. The transient state kinetics of ligand association and dissociation, and desensitization of the receptor were considered on the basis of the minimal model proposed by Hess' group, and the following possibilities were proposed. 1) When an agonist is simultaneously applied to the receptor with an antagonist whose affinity to the receptor is extremely strong and different from that of the agonist, it is usually impossible to estimate the real inhibition constant exactly from the responses because desensitization of the receptor proceeds before the equilibrium of the ligand binding. Simultaneous addition of the antagonist with strong affinity to the receptor may apparently accelerate inactivation (desensitization) of the receptor. The association rate constant of the antagonist can be estimated by analyses of the rate of the inactivation in the presence and the absence of the antagonist. 2) A preincubated antagonist with a slow dissociation rate constant, i.e., a very effective inhibitor, may cause apparent noncompetitive inhibition of the receptor, since the receptor is desensitized by an agonist as soon as the antagonist dissociates from the receptor and the dissociation of the antagonist from the receptor becomes the rate-determining step. A nicotinic acetylcholine receptor (nAChR) was expressed in Xenopus oocytes by injecting mRNA prepared from Electrophorus electricus electroplax and used for the experiments on inhibition by an antagonist.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1337082

  11. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae.

    PubMed

    Bianchi, Frans; Klooster, Joury S van 't; Ruiz, Stephanie J; Luck, Katja; Pols, Tjeerd; Urbatsch, Ina L; Poolman, Bert

    2016-01-01

    The import of basic amino acids in Saccharomyces cerevisiae has been reported to be unidirectional, which is not typical of how secondary transporters work. Since studies of energy coupling and transport kinetics are complicated in vivo, we purified the major lysine transporter (Lyp1) of yeast and reconstituted the protein into lipid vesicles. We show that the Michaelis constant (KM) of transport from out-to-in is well in the millimolar range and at least 3 to 4-orders of magnitude higher than that of transport in the opposite direction, disfavoring the efflux of solute via Lyp1. We also find that at low values of the proton motive force, the transport by Lyp1 is comparatively slow. We benchmarked the properties of eukaryotic Lyp1 to that of the prokaryotic homologue LysP and find that LysP has a similar KM for transport from in-to-out and out-to-in, consistent with rapid influx and efflux. We thus explain the previously described unidirectional nature of lysine transport in S. cerevisiae by the extraordinary kinetics of Lyp1 and provide a mechanism and rationale for previous observations. The high asymmetry in transport together with secondary storage in the vacuole allow the cell to accumulate basic amino acids to very high levels. PMID:27550794

  12. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae

    PubMed Central

    Bianchi, Frans; Klooster, Joury S. van ‘t; Ruiz, Stephanie J.; Luck, Katja; Pols, Tjeerd; Urbatsch, Ina L.; Poolman, Bert

    2016-01-01

    The import of basic amino acids in Saccharomyces cerevisiae has been reported to be unidirectional, which is not typical of how secondary transporters work. Since studies of energy coupling and transport kinetics are complicated in vivo, we purified the major lysine transporter (Lyp1) of yeast and reconstituted the protein into lipid vesicles. We show that the Michaelis constant (KM) of transport from out-to-in is well in the millimolar range and at least 3 to 4-orders of magnitude higher than that of transport in the opposite direction, disfavoring the efflux of solute via Lyp1. We also find that at low values of the proton motive force, the transport by Lyp1 is comparatively slow. We benchmarked the properties of eukaryotic Lyp1 to that of the prokaryotic homologue LysP and find that LysP has a similar KM for transport from in-to-out and out-to-in, consistent with rapid influx and efflux. We thus explain the previously described unidirectional nature of lysine transport in S. cerevisiae by the extraordinary kinetics of Lyp1 and provide a mechanism and rationale for previous observations. The high asymmetry in transport together with secondary storage in the vacuole allow the cell to accumulate basic amino acids to very high levels. PMID:27550794

  13. Structure-based model profiles affinity constant of drugs with hPEPT1 for rapid virtual screening of hPEPT1's substrate.

    PubMed

    Sun, L; Meng, S

    2016-08-01

    The human proton-coupled peptide transporter (hPEPT1) with broad substrates is an important route for improving the pharmacokinetic performance of drugs. Thus, it is essential to predict the affinity constant between drug molecule and hPEPT1 for rapid virtual screening of hPEPT1's substrate during lead optimization, candidate selection and hPEPT1 prodrug design. Here, a structure-based in silico model for 114 compounds was constructed based on eight structural parameters. This model was built by the multiple linear regression method and satisfied all the prerequisites of the regression models. For the entire data set, the r(2) and adjusted r(2) values were 0.74 and 0.72, respectively. Then, this model was used to perform substrate/non-substrate classification. For 29 drugs from DrugBank database, all were correctly classified as substrates of hPEPT1. This model was also used to perform substrate/non-substrate classification for 18 drugs and their prodrugs; this QSAR model also can distinguish between the substrate and non-substrate. In conclusion, the QSAR model in this paper was validated by a large external data set, and all results indicated that the developed model was robust, stable, and can be used for rapid virtual screening of hPEPT1's substrate in the early stage of drug discovery. PMID:27586363

  14. ANALYSIS OF DRUG INTERACTIONS WITH HIGH DENSITY LIPOPROTEIN BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY

    PubMed Central

    Chen, Sike; Sobansky, Matthew R.; Hage, David S.

    2009-01-01

    Columns containing immobilized lipoproteins were prepared for the analysis of drug interactions with these particles by high-performance affinity chromatography. This approach was evaluated by using it to examine the binding of high density lipoprotein (HDL) to the drugs propranolol or verapamil. HDL was immobilized by the Schiff base method onto silica and gave HPLC columns with reproducible binding to propranolol over four to five days of continuous operation at pH 7.4. Frontal analysis experiments indicated that two types of interactions were occurring between R/S-propranolol and HDL at 37°C: saturable binding with an association equilibrium constant (Ka) of 1.1–1.9 × 105 M−1, and non-saturable binding with an overall affinity constant (n Ka) of 3.7–4.1 × 104 M−1. Similar results were found at 4 and 27°C. Verapamil also gave similar behavior, with a Ka of 6.0 × 104 M−1 at 37°C for the saturable sites and a n Ka value for the non-saturable sites of 2.5 × 104 M−1. These measured affinities gave good agreement with solution-phase values. The results indicated HPAC can be used to study drug interactions with HDL, providing information that should be valuable in obtaining a better description of how drugs are transported within the body. PMID:19833090

  15. Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation.

    PubMed

    Correa, Agustin; Trajtenberg, Felipe; Obal, Gonzalo; Pritsch, Otto; Dighiero, Guillermo; Oppezzo, Pablo; Buschiazzo, Alejandro

    2013-03-01

    Despite being the most abundant class of immunoglobulins in humans and playing central roles in the adaptive immune response, high-resolution structural data are still lacking for the antigen-binding region of human isotype A antibodies (IgAs). The crystal structures of a human Fab fragment of IgA1 in three different crystal forms are now reported. The three-dimensional organization is similar to those of other Fab classes, but FabA1 seems to be more rigid, being constrained by a hydrophobic core in the interface between the variable and constant domains of the heavy chain (VH-CH1) as well as by a disulfide bridge that connects the light and heavy chains, influencing the relative heavy/light-chain orientation. The crystal structure of the same antibody but with a G-isotype CH1 which is reported to display different antigen affinity has also been solved. The differential structural features reveal plausible mechanisms for constant/variable-domain long-distance effects whereby antibody class switching could alter antigen affinity.

  16. Development of Monopole Interaction Models for Ionic Compounds. Part I: Estimation of Aqueous Henry’s Law Constants for Ions and Gas Phase pKa Values for Acidic Compounds

    EPA Science Inventory

    The SPARC (SPARC Performs Automated Reasoning in Chemistry) physicochemical mechanistic models for neutral compounds have been extended to estimate Henry’s Law Constant (HLC) for charged species by incorporating ionic electrostatic interaction models. Combinations of absolute aq...

  17. Affinity Chromatography.

    ERIC Educational Resources Information Center

    Gray, Gary R.

    1980-01-01

    Presents selected recent advances in immobilization chemistry which have important connections to affinity chromatography. Discusses ligand immobilization and support modification. Cites 51 references. (CS)

  18. Assigning the pKa's of Polyprotic Acids.

    ERIC Educational Resources Information Center

    Bodner, George M.

    1986-01-01

    Discusses (1) polyproptic acids for which the difference between K-a's is large; (2) the Henderson-Hasselbach equation; (3) polyprotic acids for which the difference between K-a's is small; (4) analysis of microscopic dissociation constants for cysteine; and (5) analysis of pK-a data. (JN)

  19. Affinity and efficacy of racemic, (+)-, and (-)-methacholine in muscarinic inhibition of [3H]-noradrenaline release.

    PubMed

    Fuder, H; Jung, B

    1985-02-01

    The right postganglionic sympathetic nerves of rat isolated perfused hearts (previously loaded with [3H]-noradrenaline) were stimulated electrically with 10 trains of 10 pulses at 10 Hz. The inhibition by methacholine of stimulation-evoked [3H]-noradrenaline overflow into the perfusate (determined in the presence of corticosterone, desipramine, phentolamine, and propranolol) was taken as a measure for activation of presynaptic muscarinic receptors. The evoked [3H]-noradrenaline overflow was inhibited by (+)-, racemic, and (-)-methacholine in a reversible and concentration-dependent manner. The concentration causing 50% inhibition (IC50) was 0.1, 0.26, and 65 microM, respectively, resulting in an isomeric potency ratio IC50 (+)/IC50(-) of 650. The dissociation constant KA of the (+/-)- or (+)-methacholine-presynaptic receptor complex was determined after fractional receptor inactivation according to Furchgott & Bursztyn (1967) with phenoxybenzamine or propylbenzilylcholine mustard as irreversible antagonists of muscarinic receptors. KA for (-)-methacholine was estimated according to Mackay (1966). KA of (+)-, (+/-)-, and (-)-methacholine were 2.5, 4 and 440 microM, resulting in an isomeric affinity ratio KA (+)/KA(-) of 180. The discrepancy between the isomeric IC50 ratio and the isomeric KA ratio is explained by a higher intrinsic efficacy of the (+)-enantiomer compared to the (-)-enantiomer. Thus, (+)-methacholine has to occupy fewer receptors to induce a given inhibition of release than its antipode as revealed by a plot of fractional receptor occupancy vs response. The results show that, in the effector system of presynaptic muscarinic inhibition, methacholine enantiomers differ greatly not only in affinity for the receptor, but also to some extent in the efficiency of signal transmission, and both parameters contribute to the high isomeric potency ratio. The activity of the racemate is fully accounted for by the activity of the (+)-enantiomer.

  20. Glycosylation of a VH residue of a monoclonal antibody against alpha (1- ---6) dextran increases its affinity for antigen

    PubMed Central

    1988-01-01

    We have observed that antidextran hybridomas with potential N-linked glycosylation sites in VH have higher affinity for polymeric dextran and for isomaltoheptaose than those lacking potential glycosylation sites. In these studies we have used gene transfection and expression techniques to verify that the carbohydrate addition sites in VH were used. The carbohydrate of the VH region was accessible for binding by the lectin Con A. By ELISA analysis it was demonstrated that the aKa of the antibody for dextran was influenced by the presence of carbohydrate in VH, with the aglycosylated antibody having an aKa 15-fold lower than its untreated counterpart. The aKa for antigen of antibodies that contain carbohydrate only in their constant region was unaffected by lack of carbohydrate. Thus, not only the amino acid sequence of the variable region but also its carbohydrate moieties can determine the magnitude of the antigen-antibody interaction. PMID:2459288

  1. Presynaptic alpha-2 adrenoceptor activation and coupling of the receptor-presynaptic effector system in the perfused rat heart: affinity and efficacy of phenethylamines and imidazoline derivatives.

    PubMed

    Fuder, H; Braun, H J; Schimkus, R

    1986-04-01

    The right sympathetic nerves of perfused rat hearts were stimulated in the presence of inhibitors of neuronal and extraneuronal uptake and propranolol. The inhibition by alpha adrenoceptor agonists of stimulation-evoked (10 pulses, 0.1 Hz) [3H]norepinephrine (NE) overflow into the perfusate was taken as a parameter of presynaptic adrenoceptor activation. Under the present conditions, autoinhibition of NE release is not activated by endogenous NE as evident from ineffectiveness of adrenoceptor antagonists in facilitating evoked [3H]NE overflow. The potency (EC50, -log10), affinity (agonist-presynaptic receptor dissociation constant KA, -log10) and relative efficacies (RE) were determined for phenethylamines (NE or alpha-methylepinephrine) and for imidazoline derivatives. NE (-log EC50, 7.76) was 0.88 log units more potent than alpha-methylepinephrine (-log EC50, 6.88) and about the same difference was observed for the -log KA values (5.92 vs. 4.75). RE were similar (NE, 100%; alpha methylepinephrine, 98%) and 22- to 50-fold higher than efficacies of imidazoline derivatives. Hydroxylations in positions 3 and 4 of the phenyl moiety of phenylaminoimidazoline (-log EC50, less than 5; -log KA, less than 5; RE, less than 1%) resulted in a marked increase in potency (-log EC50, 8.32) of the resulting dihydroxyphenylaminoimidazoline due to a high affinity (-log KA, 8.22) at a low efficacy (2% of NE). In contrast, hydroxylation in positions 3 and 4 of the phenyl ring of tolazoline (no agonist activity under the present conditions; antagonist affinity constant from the literature, 6.4-6.6) produced dihydroxytolazoline, a moderately potent agonist (-log EC50, 7.25) with an efficacy of 3.5% at an affinity (-log KA, 6.92) not much different from that of tolazine.(ABSTRACT TRUNCATED AT 250 WORDS)

  2. HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY AND THE ANALYSIS OF DRUG INTERACTIONS WITH MODIFIED PROTEINS: BINDING OF GLICLAZIDE WITH GLYCATED HUMAN SERUM ALBUMIN

    PubMed Central

    Matsuda, Ryan; Anguizola, Jeanethe; Joseph, K.S.; Hage, David S.

    2011-01-01

    This study used high-performance affinity chromatography (HPAC) to examine the binding of gliclazide (i.e., a sulfonylurea drug used to treat diabetes) with the protein human serum albumin (HSA) at various stages of modification due to glycation. Frontal analysis conducted with small HPAC columns was first used to estimate the number of binding sites and association equilibrium constants (Ka) for gliclazide with normal HSA and glycated HSA. Both normal and glycated HSA interacted with gliclazide according to a two-site model, with a class of high affinity sites (average Ka, 7.1-10 × 104 M−1) and a group of lower affinity sites (average Ka, 5.7-8.9 × 103 M−1) at pH 7.4 and 37°C. Competition experiments indicated that Sudlow sites I and II of HSA were both involved in these interactions, with the Ka values for gliclazide at these sites being 1.9 × 104 M−1 and 6.0 × 104 M−1, respectively, for normal HSA. Two samples of glycated HSA had similar affinities to normal HSA for gliclazide at Sudlow site I, but one sample had a 1.9-fold increase in affinity at this site. All three glycated HSA samples differed from normal HSA in their affinity for gliclazide at Sudlow site II. This work illustrated how HPAC can be used to examine both the overall binding of a drug with normal or modified proteins and the site-specific changes that can occur in these interactions as a result of protein modification. PMID:21922305

  3. CHARACTERIZATION OF THE BINDING OF SULFONYLUREA DRUGS TO HSA BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY

    PubMed Central

    Joseph, K.S.; Hage, David S.

    2010-01-01

    Sulfonylurea drugs are often prescribed as a treatment for type II diabetes to help lower blood sugar levels by stimulating insulin secretion. These drugs are believed to primarily bind in blood to human serum albumin (HSA). This study used high-performance affinity chromatography (HPAC) to examine the binding of sulfonylureas to HSA. Frontal analysis with an immobilized HSA column was used to determine the association equilibrium constants (Ka) and number of binding sites on HSA for the sulfonylurea drugs acetohexamide and tolbutamide. The results from frontal analysis indicated HSA had a group of relatively high affinity binding regions and weaker binding sites for each drug, with average Ka values of 1.3 (± 0.2) × 105 M−1 and 3.5 (± 3.0) × 102 M−1 for acetohexamide and values of 8.7 (± 0.6) × 104 and 8.1 (± 1.7) × 103 M−1 for tolbutamide. Zonal elution and competition studies with site-specific probes were used to further examine the relatively high affinity interactions of these drugs by looking directly at the interactions that were occurring at Sudlow sites I and II of HSA (i.e., the major drug binding sites on this protein). It was found that acetohexamide was able to bind at both Sudlow sites I and II, with Ka values of 1.3 (± 0.1) × 105 and 4.3 (± 0.3) × 104 M−1, respectively, at 37°C. Tolbutamide also appeared to interact with both Sudlow sites I and II, with Ka values of 5.5 (± 0.2) × 104 and 5.3 (± 0.2) × 104 M−1, respectively. The results provide a more quantitative picture of how these drugs bind with HSA and illustrate how HPAC and related tools can be used to examine relatively complex drug-protein interactions. PMID:20435530

  4. Anion-induced increases in the affinity of colcemid binding to tubulin.

    PubMed

    Ray, K; Bhattacharyya, B; Biswas, B B

    1984-08-01

    Colcemid binds tubulin rapidly and reversibly in contrast to colchicine which binds tubulin relatively slowly and essentially irreversibly. At 37 degrees C the association rate constant for colcemid binding is 1.88 X 10(6) M-1 h-1, about 10 times higher than that for colchicine; this is reflected in the activation energies for binding which are 51.4 kJ/mol for colcemid and 84.8 kJ/mol for colchicine. Scatchard analysis indicates two binding sites on tubulin having different affinities for colcemid. The high-affinity site (Ka = 0.7 X 10(5) M-1 at 37 degrees C) is sensitive to temperature and binds both colchicine and colcemid and hence they are mutually competitive inhibitors. The low-affinity site (Kb = 1.2 X 10(4) M-1) is rather insensitive to temperature and binds only colcemid. Like colchicine, 0.6 mol of colcemid are bound/mol of tubulin dimer (at the high-affinity site) and the reaction is entropy driven (163 J K-1 mol-1). Similar to colchicine, colcemid binding to tubulin is stimulated by certain anions (viz. sulfate and tartrate) but by a different mechanism. Colcemid binding affinity at the lower-affinity site of tubulin is increased in the presence of ammonium sulfate. Interestingly, the lower-affinity site on tubulin for colcemid, even when converted to higher affinity in presence of ammonium sulfate, is not recognized by colchicine. We conclude that tubulin possesses two binding sites, one of which specifically recognized the groups present on the B-ring of colchicine molecule and is effected by the ammonium sulfate, whereas the higher-affinity site, which could accommodate both colchicine and colcemid, possibly recognized the A and C ring of colchicine.

  5. ANALYSIS OF DRUG INTERACTIONS WITH MODIFIED PROTEINS BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY: BINDING OF GLIBENCLAMIDE TO NORMAL AND GLYCATED HUMAN SERUM ALBUMIN

    PubMed Central

    Matsuda, Ryan; Anguizola, Jeanethe; Joseph, K.S.; Hage, David S.

    2012-01-01

    High-performance affinity chromatography (HPAC) was used to examine the changes in binding that occur for the sulfonylurea drug glibenclamide with human serum albumin (HSA) at various stages of glycation for HSA. Frontal analysis on columns containing normal HSA or glycated HSA indicated glibenclamide was interacting through both high affinity sites (association equilibrium constant, Ka, 1.4–1.9 × 106 M−1 at pH 7.4 and 37°C) and lower affinity sites (Ka, 4.4–7.2 × 104 M−1). Competition studies were used to examine the effect of glycation at specific binding sites of HSA. An increase in affinity of 1.7- to 1.9-fold was seen at Sudlow site I with moderate to high levels of glycation. An even larger increase of 4.3- to 6.0-fold in affinity was noted at Sudlow site II for all of the tested samples of glycated HSA. A slight decrease in affinity may have occurred at the digitoxin site, but this change was not significant for any individual glycated HSA sample. These results illustrate how HPAC can be used as tool for examining the interactions of relatively non-polar drugs like glibenclamide with modified proteins and should lead to a more complete understanding of how glycation can alter the binding of drugs in blood. PMID:23092871

  6. A comparison of affinity constants for muscarine-sensitive acetylcholine receptors in guinea-pig atrial pacemaker cells at 29 degrees C and in ileum at 29 degrees C and 37 degrees C.

    PubMed Central

    Barlow, R B; Berry, K J; Glenton, P A; Nilolaou, N M; Soh, K S

    1976-01-01

    1 The affinity of 17 compounds for muscarine-sensitive acetylcholine receptors in atrial pacemaker cells and ileum of the guinea-pig has been measured at 29 degrees C in Ringer-Locke solution. Measurements were also made at 37 degrees C with 7 of them. 2 Some of the compounds had much higher affinity for the receptors in the ileum than for those in the atria. For the most selective compound, 4-diphenylacetoxy-N-methylpiperidine methiodide, the difference was approximately 20-fold. The receptors in the atria are therefore different the structure from those in the ileum. 3 The effect of temperature on affinity are not the same for all the compounds, tested indicating different enthalpies and entropies of adsorption and accounting for some of the difficulty experienced in predicting the affinity of new compounds. PMID:1000135

  7. Combination of isothermal titration calorimetry and time-resolved luminescence for high affinity antibody-ligand interaction thermodynamics and kinetics.

    PubMed

    Aweda, Tolulope A; Meares, Claude F

    2012-02-01

    For experiments using synthetic ligands as probes for biological experiments, it is useful to determine the specificity and affinity of the ligands for their receptors. As ligands with higher affinities are developed (K(A)>10(8)M(-1); K(D)<10(-8)M), a new challenge arises: to measure these values accurately. Isothermal titration calorimetry measures heat produced or consumed during ligand binding, and also provides the equilibrium binding constant. However, as normally practiced, its range is limited. Displacement titration, where a competing weaker ligand is used to lower the apparent affinity of the stronger ligand, can be used to determine the binding affinity as well as the complete thermodynamic data for ligand-antibody complexes with very high affinity. These equilibrium data have been combined with kinetic measurements to yield the rate constants as well. We describe this methodology, using as an example antibody 2D12.5, which captures yttrium S-2-(4-aminobenzyl)-1, 4, 7, 10-tetraazacyclododecanetetraacetate.

  8. Microwave spectrum of the Ka = 1 ←

    NASA Astrophysics Data System (ADS)

    Karyakin, E. N.; Fraser, G. T.; Suenram, R. D.

    A 78-118 GHz synthesizer-driven backward-wave oscillator is used together with klystron sources and frequency doublers to measure the electric-resonance optothermal spectrum of the Ka = 1 ← 0 rotation-tunnelling subband of (D2O)2. Transitions are observed originating from each of the six tunnelling states, A+1, B+1, E+1, A-2, B-2, and E-2, allowing an estimate of the largest tunnelling matrix element h4v, characterizing the separation of the A+1, B+1, and E+1 states from the A-2, B-2, and E-2 states. We find the average of h4v for the Ka = 0 and 1 states to be ˜ -8 943 MHz. A comparison of the Ka = 1 ← 0 band origins for the A/B states with the band origin for their E partner gives h2v ˜ -6·9 MHz, where h2v is the tunnelling matrix element responsible for the displacement of the E symmetry levels from the center of their interconversion split A/B partners. Values found for the A rotational constant, A ˜ 124 923 MHz, and h2v are in good agreement with those obtained from the submillimetre measurements of Zwart, E., ter Meulen, J. J., and Meerts, W. L., 1990, Chem. Phys. Lett., 173, 115, on the Ka = 2 ← 1 band of the complex. Estimates are presented for the potential barriers to the 1 → 2, 1 → 5 and 1 → 7 tunnelling processes.

  9. Influence of affinity on antibody determination in microtiter ELISA systems

    SciTech Connect

    Peterman, J.H.; Voss, E.W. Jr.; Butler, J.E.

    1986-03-01

    Theoretically, all immunoassays are affinity (Ka) dependent when the product of the antibody (Ab) Ka and the free epitope concentration is less than 10. Thus, the degree of dependence on Ka depends on the concentration of available antigen in the system. The authors examined the binding of /sup 125/I-anti-fluorescein (a-FLU) monoclonal antibodies of different affinities to FLU-gelatin adsorbed on Immunlon 2 microtiter plates. Data obtained were in general agreement with our theoretical predictions; the percent of /sup 125/I-a-FLU which bound correlated with Ka, as did the shape of the titration curves. Measurement of 5 a-FLU monoclonals by the ELISA showed that the determination of Ab concentrations depends on the FLU-gelatin concentration, epitope density, and on the relationship between the Kas of test samples and the reference standard Ab preparation. Thus the ELISA is Ka dependent and should not be used routinely to estimate the absolute amount to Ab in unknown samples. However, the Ka dependency of the ELISA might provide a convenient assay for the estimation of the relative functional Ka (rfKa) of antibody preparations.

  10. Ka Band Objects: Observation and Monitoring (KaBOOM)

    NASA Astrophysics Data System (ADS)

    Geldzahler, B.

    2012-09-01

    NASA has embarked on a path that will enable the implementation of a high power, high resolution X/Ka band radar system using widely spaced 12m antennas to better track and characterize near Earth objects and orbital debris. This radar system also has applications for cost effective space situational awareness. We shall demonstrate Ka band coherent uplink arraying with real-time atmospheric compensation using three 12m antennas at the Kennedy Space Center (KSC). Our proposed radar system can complement and supplement the activities of the Space Fence. The proposed radar array has the advantages of filling the gap between dusk and dawn and offers the possibility of high range resolution (4 cm) and high spatial resolution (?10 cm at GEO) when used in a VLBI mode. KSC was chosen because [a] of reduced implementation costs, [b] there is a lot of water vapor in the air (not Ka band friendly), and [c] the test satellites have a low elevation adding more attenuation and turbulence to the demonstration. If Ka band coherent uplink arraying can be made to work at KSC, it will work anywhere. We expect to rebaseline X-band in 2013, and demonstrate Ka band uplink arraying in 2014.

  11. Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Walters, Rodney R.

    1985-01-01

    Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

  12. Exploring binding affinity of oxaliplatin and carboplatin, to nucleoprotein structure of chromatin: spectroscopic study and histone proteins as a target.

    PubMed

    Soori, Hosna; Rabbani-Chadegani, Azra; Davoodi, Jamshid

    2015-01-01

    Platinum drugs are potent chemotherapeutic agents widely used in cancer therapy. They exert their biological activity by binding to DNA, producing DNA adducts; however, in the cell nucleus, DNA is complexed with histone proteins into a nucleoprotein structure known as chromatin. The aim of this study was to explore the binding affinity of oxaliplatin and carboplatin to chromatin using spectroscopic as well as thermal denaturation and equilibrium dialysis techniques. The results showed that the drugs quenched with chromophores of chromatin and the quenching effect for oxaliplatin (Ksv = 3.156) was higher than carboplatin (Ksv = 0.28). The binding of the drugs exhibited hypochromicity both in thermal denaturation profiles and UV absorbance at 210 nm. The binding was positive cooperation with spontaneous reaction and oxaliplatin (Ka = 5.3 × 10(3) M(-1), n = 1.7) exhibited higher binding constant and number of binding sites than carboplatin (Ka = 0.33 × 10(3) M(-1), n = 1.0) upon binding to chromatin. Also secondary structure of chromatin proteins was altered upon drugs binding. It is concluded that oxaliplatin represents higher binding affinity to chromatin compared to carboplatin. In chromatin where DNA is compacted into nucleosomes structure with histones, the affinity of the platinated drugs is reduced and histone proteins may play a fundamental role in this binding process.

  13. Ka-band study: 1988

    NASA Technical Reports Server (NTRS)

    Layland, J. W.; Horttor, R. L.; Clauss, R. C.; Wilcher, J. H.; Wallace, R. J.; Mudgway, D. J.

    1989-01-01

    The Ka-band study team was chartered in late 1987 to bring together all the planning elements for establishing 32 GHz (Ka-band) as the primary downlink frequency for deep-space operation, and to provide a stable baseline from which to pursue that development. This article summarizes the results of that study at its conclusion in mid-1988, and corresponds to material presented to NASA's Office of Space Operations on July 14, 1988. For a variety of reasons, Ka-band is the right next major step in deep-space communications. It offers improved radio metric accuracy through reduced plasma sensitivity and increased bandwidth. Because of these improvements, it offers the opportunity to reduce costs in the flight radio system or in the DSN by allocating part of the overall benefits of Ka-band to this cost reduction. A mission scenario is being planned that can drive at least two and possibly all three of the DSN subnets to provide a Ka-band downlink capability by the turn of the century. The implementation scenario devised by the study team is believed to be feasible within reasonable resource expectations, and capable of providing the needed upgrade as a natural follow-on to the technology development which is already underway.

  14. Analysis of Lidocaine Interactions with Serum Proteins Using High-Performance Affinity Chromatography

    PubMed Central

    Soman, Sony; Yoo, Michelle J.; Jang, Yoon Jeong; Hage, David S.

    2010-01-01

    High-performance affinity chromatography was used to study binding by the drug lidocaine to human serum albumin (HSA) and α1–acid glycoprotein (AGP). AGP had strong binding to lidocaine, with an association equilibrium constant (Ka) of 1.1-1.7 × 105 M-1 at 37 °C and pH 7.4. Lidocaine had weak-to-moderate binding to HSA, with a Ka in the range of 103 to 104 M-1. Competitive experiments with site selective probes showed that lidocaine was interacting with Sudlow site II of HSA and the propranolol site of AGP. These results agree with previous observations in the literature and provide a better quantitative understanding of how lidocaine binds to these serum proteins and is transported in the circulation. This study also demonstrates how HPAC can be used to examine the binding of a drug with multiple serum proteins and provide detailed information on the interaction sites and equilibrium constants that are involved in such processes. PMID:20138813

  15. Are Fundamental Constants Really Constant?

    ERIC Educational Resources Information Center

    Swetman, T. P.

    1972-01-01

    Dirac's classical conclusions, that the values of e2, M and m are constants and the quantity of G decreases with time. Evoked considerable interest among researchers and traces historical development by which further experimental evidence points out that both e and G are constant values. (PS)

  16. Analysis of multi-site drug-protein interactions by high-performance affinity chromatography: Binding by glimepiride to normal or glycated human serum albumin.

    PubMed

    Matsuda, Ryan; Li, Zhao; Zheng, Xiwei; Hage, David S

    2015-08-21

    High-performance affinity chromatography (HPAC) was used in a variety of formats to examine multi-site interactions between glimepiride, a third-generation sulfonylurea drug, and normal or in vitro glycated forms of the transport protein human serum albumin (HSA). Frontal analysis revealed that glimepiride interacts with normal HSA and glycated HSA at a group of high affinity sites (association equilibrium constant, or Ka, 9.2-11.8×10(5)M(-1) at pH 7.4 and 37°C) and a group of lower affinity regions (Ka, 5.9-16×10(3)M(-1)). Zonal elution competition studies were designed and carried out in both normal- and reversed-role formats to investigate the binding by this drug at specific sites. These experiments indicated that glimepiride was interacting at both Sudlow sites I and II. Allosteric effects were also noted with R-warfarin at Sudlow site I and with tamoxifen at the tamoxifen site on HSA. The binding at Sudlow site I had a 2.1- to 2.3-fold increase in affinity in going from normal HSA to the glycated samples of HSA. There was no significant change in the affinity for glimepiride at Sudlow site II in going from normal HSA to a moderately glycated sample of HSA, but a slight decrease in affinity was seen in going to a more highly glycated HSA sample. These results demonstrated how various HPAC-based methods can be used to profile and characterize multi-site binding by a drug such as glimepiride to a protein and its modified forms. The information obtained from this study should be useful in providing a better understanding of how drug-protein binding may be affected by glycation and of how separation and analysis methods based on HPAC can be employed to study systems with complex interactions or that involve modified proteins.

  17. Analysis of multi-site drug-protein interactions by high-performance affinity chromatography: Binding by glimepiride to normal or glycated human serum albumin.

    PubMed

    Matsuda, Ryan; Li, Zhao; Zheng, Xiwei; Hage, David S

    2015-08-21

    High-performance affinity chromatography (HPAC) was used in a variety of formats to examine multi-site interactions between glimepiride, a third-generation sulfonylurea drug, and normal or in vitro glycated forms of the transport protein human serum albumin (HSA). Frontal analysis revealed that glimepiride interacts with normal HSA and glycated HSA at a group of high affinity sites (association equilibrium constant, or Ka, 9.2-11.8×10(5)M(-1) at pH 7.4 and 37°C) and a group of lower affinity regions (Ka, 5.9-16×10(3)M(-1)). Zonal elution competition studies were designed and carried out in both normal- and reversed-role formats to investigate the binding by this drug at specific sites. These experiments indicated that glimepiride was interacting at both Sudlow sites I and II. Allosteric effects were also noted with R-warfarin at Sudlow site I and with tamoxifen at the tamoxifen site on HSA. The binding at Sudlow site I had a 2.1- to 2.3-fold increase in affinity in going from normal HSA to the glycated samples of HSA. There was no significant change in the affinity for glimepiride at Sudlow site II in going from normal HSA to a moderately glycated sample of HSA, but a slight decrease in affinity was seen in going to a more highly glycated HSA sample. These results demonstrated how various HPAC-based methods can be used to profile and characterize multi-site binding by a drug such as glimepiride to a protein and its modified forms. The information obtained from this study should be useful in providing a better understanding of how drug-protein binding may be affected by glycation and of how separation and analysis methods based on HPAC can be employed to study systems with complex interactions or that involve modified proteins. PMID:26189669

  18. Analysis of Multi-Site Drug-Protein Interactions by High-Performance Affinity Chromatography: Binding by Glimepiride to Normal or Glycated Human Serum Albumin

    PubMed Central

    Matsuda, Ryan; Li, Zhao; Zheng, Xiwei; Hage, David S.

    2015-01-01

    High-performance affinity chromatography (HPAC) was used in a variety of formats to examine multi-site interactions between glimepiride, a third-generation sulfonylurea drug, and normal or in vitro glycated forms of the transport protein human serum albumin (HSA). Frontal analysis revealed that glimepiride interacts with normal HSA and glycated HSA at a group of high affinity sites (association equilibrium constant, or Ka, 9.2–11.8 × 105 M−1 at pH 7.4 and 37°C) and a group of lower affinity regions (Ka, 5.9–16.2 × 103 M−1). Zonal elution competition studies were designed and carried out in both normal- and reversed-role formats to investigate the binding by this drug at specific sites. These experiments indicated that glimepiride was interacting at both Sudlow sites I and II. Allosteric effects were also noted with R-warfarin at Sudlow site I and with tamoxifen at the tamoxifen site on HSA. The binding at Sudlow site I had a 2.1- to 2.3-fold increase in affinity in going from normal HSA to the glycated samples of HSA. There was no significant change in the affinity for glimepiride at Sudlow site II in going from normal HSA to a moderately glycated sample of HSA, but a slight decrease in affinity was seen in going to a more highly glycated HSA sample. These results demonstrated how various HPAC-based methods can be used to profile and characterize multi-site binding by a drug such as glimepiride to a protein and its modified forms. The information obtained from this study should be useful in providing a better understanding of how drug-protein binding may be affected by glycation and of how separation and analysis methods based on HPAC can be employed to study systems with complex interactions or that involve modified proteins. PMID:26189669

  19. Monoclonal IgM antibody exhibiting high-affinity binding and cryoglobulin properties.

    PubMed Central

    Ballard, D W; Kranz, D M; Voss, E W

    1983-01-01

    A monoclonal IgM antibody (18-2-3) derived from cell fusion of (NZB X NZW) F1 splenocytes following secondary immunization with fluorescein-conjugated keyhole limpet hemocyanin was shown to exhibit high intrinsic binding affinity and cryoinsolubility. Affinity-purified preparations were determined to be IgM by immunochemical, electrophoretic, and chromatographic analyses. An intrinsic association constant (Ka) of 2.9 X 10(10) M-1 (at 2 degrees C) was measured by first-order dissociation-rate analysis. Antibody solubility at low concentration (approximately equal to 50 micrograms/ml) was shown, by absorption spectroscopy, to be temperature dependent between 4 degrees C and 32 degrees C. Insolubility at low temperature (4 degrees C) was reversible in the presence of homologous fluorescyl hapten, indicative of active site involvement in the mechanism of cryoglobulin-18-2-3 complex formation. Characteristics of clone 18-2-3 are discussed in terms of (i) its potential use as a model for examining the mechanism of cryoprecipitation and (ii) the proposed relationship between affinity maturation and the IgM to IgG class switch. Images PMID:6348779

  20. Computational and ESR studies of electron attachment to decafluorocyclopentane, octafluorocyclobutane, and hexafluorocyclopropane: electron affinities of the molecules and the structures of their stable negative ions as determined from 13C and 19F hyperfine coupling constants.

    PubMed

    ElSohly, Adel M; Tschumper, Gregory S; Crocombe, Richard A; Wang, Jih Tzong; Williams, Ffrancon

    2005-08-01

    High-resolution ESR spectra of the ground-state negative ions of hexafluorocyclopropane (c-C3F6*-), octafluorocyclobutane (c-C4F8*-), and decafluorocyclopentane (c-C5F10*-) are reported and their isotropic 19F hyperfine coupling constants (hfcc) of 198.6 +/- 0.4 G, 147.6 +/- 0.4 G, and 117.9 +/- 0.4 G, respectively, are in inverse ratio to the total number of fluorine atoms per anion. Together with the small value of 5.2 +/- 0.4 G determined for the isotropic 13C hfcc of c-C4F8*-, these results indicate that in each case the singly occupied molecular orbital (SOMO) is delocalized over the equivalent fluorines and possesses a nodal plane through the carbon atoms of a time-averaged D(nh) structure. A series of quantum chemical computations were carried out to further characterize these anions and their neutral counterparts. Both the B3LYP density functional and second-order Møller-Plesset perturbation theory (MP2) indicate that c-C3F6*- adopts a D(3h) geometry and a (2)A2'' ground electronic state, that c-C4F8*- adopts a D(4h) geometry and a (2)A2u ground electronic state, and that c-C5F10*- adopts a C(s) structure and a (2)A' electronic state. Moreover, the 19F hyperfine coupling constants computed with the MP2 method and a high quality triple-zeta basis set are within 1% of the experimental values. Also, the values computed for the 13C hfcc of c-C4F8*- are consistent with the experimental value of 5.2 G. Therefore, in keeping with the ESR results, these negative ions derived from first-row elements can be characterized as pi* species. In addition, the hypervalency of these perfluorocycloalkane radical anions has been clarified.

  1. Kinetic analysis of a high-affinity antibody/antigen interaction performed by multiple Biacore users.

    PubMed

    Katsamba, Phinikoula S; Navratilova, Iva; Calderon-Cacia, Maria; Fan, Linsey; Thornton, Kevin; Zhu, Mingde; Bos, Tim Vanden; Forte, Carla; Friend, Della; Laird-Offringa, Ite; Tavares, Gisele; Whatley, John; Shi, Ergang; Widom, Angela; Lindquist, Kevin C; Klakamp, Scott; Drake, Andrew; Bohmann, David; Roell, Marina; Rose, Larry; Dorocke, Jill; Roth, Bruce; Luginbühl, Béatrice; Myszka, David G

    2006-05-15

    To explore the reliability of Biacore-based assays, 22 study participants measured the binding of prostate-specific antigen (PSA) to a monoclonal antibody (mAb). Each participant was provided with the same reagents and a detailed experimental protocol. The mAb was immobilized on the sensor chip at three different densities and a two-step assay was used to determine the kinetic and affinity parameters of the PSA/mAb complex. First, PSA was tested over a concentration range of 2.5-600 nM to obtain k(a) information. Second, to define the k(d) of this stable antigen/antibody complex accurately, the highest PSA concentration was retested with the dissociation phase of each binding cycle monitored for 1h. All participants collected data that could be analyzed to obtain kinetic parameters for the interaction. The association and the extended-dissociation data derived from the three antibody surfaces were globally fit using a simple 1:1 interaction model. The average k(a) and k(d) for the PSA/mAb interaction as calculated from the 22 analyses were (4.1+/-0.6) x 10(4) M(-1) s(-1) and (4.5+/-0.6) x 10(-5) s(-1), respectively. Overall, the experimental standard errors in the rate constants were only approximately 14%. Based on the kinetic rate constants, the affinity (K(D)) of the PSA/mAb interaction was 1.1+/-0.2 nM.

  2. Simultaneous high-throughput determination of interaction kinetics for drugs and cyclodextrins by high performance affinity chromatography with mass spectrometry detection.

    PubMed

    Wang, Caifen; Wang, Xiaobo; Xu, Xiaonan; Liu, Botao; Xu, Xu; Sun, Lixin; Li, Haiyan; Zhang, Jiwen

    2016-02-25

    The individual determination of the apparent dissociation rate constant (kd,app) using high performance affinity chromatography (HPAC) is a tedious process requiring numerous separate tests and massive data fitting, unable to provide the apparent association rate constant (ka) and equilibrium binding constant (Ka). In this study, a HPAC with mass spectrometry detection (HPAC-MS/MS) was employed to determine the drug-cyclodextrin (CD) interaction kinetics with low sample loading quantity (<10 ng per injection for single compound) and high-throughput yield as twenty drugs determined in one injection. The kd,app measured by HPAC-MS/MS approach were 0.89 ± 0.07, 4.34 ± 0.01, 1.48 ± 0.01 and 7.77 ± 0.04 s(-1) for ketoprofen, trimethoprim, indapamide and acetaminophen, with kd,app for acetaminophen consistent with that from the HPAC method with UV detector in our previous studies. For twenty drugs with diverse structures and chemical properties, good correlationship was found between kd,app measured by single compound analysis method and high-throughput HPAC-MS/MS approach, with the correlation coefficient of 0.987 and the significance F less than 0.001. Comprehensive quantification of ka,app, kd,app and Ka values was further performed based on the measurement of kd,app by peak profiling method and Ka by the peak fitting method. And the investigation of the drug-CD interaction kinetics under different conditions indicated that the column temperature and mobile phase composition significantly affected the determination of ka,app, kd,app and Ka while also dependent on the acidity and basicity of drugs. In summary, the high-throughput HPAC-MS/MS approach has been demonstrated high efficiency in determination of the drug-CD primary interaction kinetic parameter, especially, kd,app, being proven as a novel tool in screening the right CD for the solubilization of the right drug. PMID:26851087

  3. Simultaneous high-throughput determination of interaction kinetics for drugs and cyclodextrins by high performance affinity chromatography with mass spectrometry detection.

    PubMed

    Wang, Caifen; Wang, Xiaobo; Xu, Xiaonan; Liu, Botao; Xu, Xu; Sun, Lixin; Li, Haiyan; Zhang, Jiwen

    2016-02-25

    The individual determination of the apparent dissociation rate constant (kd,app) using high performance affinity chromatography (HPAC) is a tedious process requiring numerous separate tests and massive data fitting, unable to provide the apparent association rate constant (ka) and equilibrium binding constant (Ka). In this study, a HPAC with mass spectrometry detection (HPAC-MS/MS) was employed to determine the drug-cyclodextrin (CD) interaction kinetics with low sample loading quantity (<10 ng per injection for single compound) and high-throughput yield as twenty drugs determined in one injection. The kd,app measured by HPAC-MS/MS approach were 0.89 ± 0.07, 4.34 ± 0.01, 1.48 ± 0.01 and 7.77 ± 0.04 s(-1) for ketoprofen, trimethoprim, indapamide and acetaminophen, with kd,app for acetaminophen consistent with that from the HPAC method with UV detector in our previous studies. For twenty drugs with diverse structures and chemical properties, good correlationship was found between kd,app measured by single compound analysis method and high-throughput HPAC-MS/MS approach, with the correlation coefficient of 0.987 and the significance F less than 0.001. Comprehensive quantification of ka,app, kd,app and Ka values was further performed based on the measurement of kd,app by peak profiling method and Ka by the peak fitting method. And the investigation of the drug-CD interaction kinetics under different conditions indicated that the column temperature and mobile phase composition significantly affected the determination of ka,app, kd,app and Ka while also dependent on the acidity and basicity of drugs. In summary, the high-throughput HPAC-MS/MS approach has been demonstrated high efficiency in determination of the drug-CD primary interaction kinetic parameter, especially, kd,app, being proven as a novel tool in screening the right CD for the solubilization of the right drug.

  4. Ka-band MMIC subarray technology program (Ka-Mist)

    NASA Technical Reports Server (NTRS)

    Pottenger, Warren

    1995-01-01

    The broad objective of this program was to demonstrate a proof of concept insertion of Monolithic Microwave Integrated Circuit (MMIC) device technology into an innovative (tile architecture) active phased array antenna application supporting advanced EHF communication systems. Ka-band MMIC arrays have long been considered as having high potential for increasing the capability of space, aircraft, and land mobile communication systems in terms of scan performance, data rate, link margin, and flexibility while offering a significant reduction in size, weight, and power consumption. Insertion of MMIC technology into antenna systems, particularly at millimeter wave frequencies using low power and low noise amplifiers in close proximity to the radiating elements, offers a significant improvement in the array transmit efficiency, receive system noise figure, and overall array reliability. Application of active array technology also leads to the use of advanced beamforming techniques that can improve beam agility, diversity, and adaptivity to complex signal environments.

  5. The affinity and activity of compounds related to nicotine on the rectus abdominis muscle of the frog (Rana pipiens)

    PubMed Central

    Barlow, R. B.; Thompson, G. M.

    1969-01-01

    1. Series of pyridylalkyl- and substituted phenylalkyl-trimethylammonium salts, triethylammonium salts, diethylamines and di-n-propylamines have been made. The substituents in the benzene ring were nitro, chloro, bromo, methoxy, hydroxy and amino groups and the alkyl residues had one, two, or three methylene groups separating the aromatic nucleus from the cationic head. 2. Most of the trimethylammonium compounds caused a contracture of the frog rectus muscle, but some were partial agonists and a few were antagonists. The di-n-propylamines were all antagonists, as were most of the diethylamines and triethylammonium compounds, though some of these were partial agonists and a few triethylammonium compounds were agonists. The affinities of the antagonists and partial agonists for the receptors stimulated by β-pyridylmethyltrimethylammonium (and by nicotine) were measured. The equipotent molar ratios of all the agonists were measured relative to β-pyridylmethyltrimethylammonium. 3. The dissociation constants of the pyridylmethyldiethylamines and substituted benzyldiethylamines were measured. The effects of substituents on the pKa of benzyldiethylamine were similar to their effects on the pKa of aniline, though there were differences with some of the o-substituted compounds, which could be attributed to internal hydrogen-bond formation. 4. There is no obvious correlation between the effects of a substituent on the pKa of benzyldiethylamine and its effects on affinity. Although increasing the size of the cationic group usually increased affinity, it did not always do so. The compounds with the highest affinity, p-hydroxybenzyldiethylamine (log K, 5·90) had about half the affinity of (+)-tubocurarine (log K, 6·11), but the triethylammonium analogue (log K, 4·17) had only about one-fiftieth of the affinity of the tertiary base. The binding of the drug to the receptor appears to involve many factors which include the size of the groups as well as their electron

  6. BC(50): a generalized, unifying affinity descriptor.

    PubMed

    Vacca, Alberto; Francesconi, Oscar; Roelens, Stefano

    2012-12-01

    Assessing binding affinities is an unavoidable step that we come across any time interactions between binding species are investigated. A quantitative evaluation of binding affinities relies on the determination of binding constants but, whilst the binding constant fully defines the affinity of a reagent for a ligand when only one complex species is formed, the same is not true when the interacting partners form more than one complex of different stoichiometry, because all complexes contribute to the overall binding affinity. Unfortunately, this situation is the rule rather than the exception in chemical systems, but a generally accepted solution for this issue has not yet been settled. In this Personal Account, we describe the evolution, from the initial idea to a fully developed stage, of a binding descriptor that has been developed with the aim of filling this gap, thereby providing scientists in all fields of chemistry with a unifying tool for the assessment of binding affinities based on the knowledge of the binding constants in systems that involve any number of complex species.

  7. Fade Mitigation Techniques at Ka-Band

    NASA Technical Reports Server (NTRS)

    Dissanayake, Asoka (Editor)

    1996-01-01

    Rain fading is the dominant propagation impairment affecting Ka-band satellite links and rain fade mitigation is a key element in the design of Ka-band satellite networks. Some of the common fade mitigation techniques include: power control, diversity, adaptive coding, and resource sharing. The Advanced Communications Technology Satellite (ACTS) provides an excellent opportunity to develop and test Ka-band rain impairment amelioration techniques. Up-link power control and diversity are discussed in this paper.

  8. KaVA ESTEMA project

    NASA Astrophysics Data System (ADS)

    Oyadomari, Miyako; Imai, Hiroshi; Cho, Se-Hyung; Asaki, Yoshiharu; Choi, Yoon-Kyong; Kim, Jaeheon; Yun, Youngjoo; Matsumoto, Naoko; Min, Cheul-Hong; Oyama, Tomoaki; Yoon, Sung-Chul; Yoon, Dong-Hwan; Kim, Dong-Jin; Dodson, Richard; Rioja, Maria; Burns, Ross; Orosz, Gabor; Nakagawa, Akiharu; Chibueze O, James; Nakashima, Jun-ichi; Sobolev, Andrey

    2016-07-01

    The ESTEMA (Expanded Study on Stellar Masers) project is one of three Large Programs of the KaVA (the combined array of the Korean VLBI Network and Japanese VLBI Exploration of Radio Astrometry), and conducted in 2015-2016. It aims to publish a database of the largest sample of VLBI images of circumstellar water (H2O) and silicon-monoxide (SiO) maser sources towards circumstellar envelopes (CSEs) of 80 evolved stars in late AGB to early post-AGB phase. Here we present the specifications of the ESTEMA observations and the planned scientific goals in order to share the basic information of the ESTEMA with astronomical community and encourage future collaborations with the ESTEMA and future follow-up observations for the targeted stars.

  9. Affine projective Osserman structures

    NASA Astrophysics Data System (ADS)

    Gilkey, P.; Nikčević, S.

    2013-08-01

    By considering the projectivized spectrum of the Jacobi operator, we introduce the concept of projective Osserman manifold in both the affine and in the pseudo-Riemannian settings. If M is an affine projective Osserman manifold, then the deformed Riemannian extension metric on the cotangent bundle is both spacelike and timelike projective Osserman. Since any rank-1-symmetric space is affine projective Osserman, this provides additional information concerning the cotangent bundle of a rank-1 Riemannian symmetric space with the deformed Riemannian extension metric. We construct other examples of affine projective Osserman manifolds where the Ricci tensor is not symmetric and thus the connection in question is not the Levi-Civita connection of any metric. If the dimension is odd, we use methods of algebraic topology to show the Jacobi operator of an affine projective Osserman manifold has only one non-zero eigenvalue and that eigenvalue is real.

  10. SARAL/AltiKa Project Overview

    NASA Astrophysics Data System (ADS)

    Picot, Nicolas; Sengenes, Pierre; Lambin, Juliette; Noubel, Jocelyne; Mazeau, Sophie; Verron, Jacques

    2015-04-01

    The SARAL-AltiKa satellite mission is an India-France ISRO-CNES joint project. The satellite has been put into orbit by a PSLV vehicle supplied by ISRO, and launched from Sriharikota, the main ISRO launch base, on Feb. 25, 2013. The SARAL (Satellite for ARgos and ALtika) payload consists of an ARGOS instrument, and an altimetry payload including the AltiKa radiometer-altimeter. SARAL/AltiKa is intended to be a gap filler mission between the RA-2 on-board ENVISAT and Sentinel-3. As such, SARAL/AltiKa is flying on the same orbit as ENVISAT. The special feature of SARAL/AltiKa is mainly related to a wideband Ka-band altimeter (35.75 GHz, 500 MHz), which is the very first satellite altimeter dedicated to oceanography to operate at such a high frequency. The AltiKa instrument consists in a Ka-band altimeter based on already developed subsystems inherited from Siral (CRYOSAT) and Poseidon-3 (JASON-2) in particular, and an embedded dual frequency radiometer. The altimeter and the radiometer share the same antenna. Due to the single frequency Ka-band altimeter, the enhanced bandwidth leads to a better vertical resolution. The spatial resolution is also improved, thanks to the Ka-band smaller footprint and the increased PRF. This talk will present the main characteristics of the mission and the main outcome regarding the data availability and overall quality after 2 years of mission. In particular, we will focus on the main advantages and/or drawbacks of the Ka band frequency compared to the classical Ku band used on other missions like Jason-2. A specific point will be performed on the rain attenuation and corresponding impacts on the altimeter data quality.

  11. Ka-Band MMIC Subarray Technology Program (Ka-Mist)

    NASA Technical Reports Server (NTRS)

    Pottinger, W.

    1995-01-01

    Ka-band monolithic microwave integrated circuit (MMIC) arrays have been considered as having high potential for increasing the capability of space, aircraft, and land mobile communication systems in terms of scan performance, data rate, link margin, and flexibility while offering a significant reduction in size, weight, and power consumption. Insertion of MMIC technology into antenna systems, particularly at millimeter wave frequencies using low power and low noise amplifiers in closed proximity to the radiating elements, offers a significant improvement in the array transmit efficiency, receive system noise figure, and overall array reliability. Application of active array technology also leads to the use of advanced beamforming techniques that can improve beam agility, diversity, and adaptivity to complex signal environments. The objective of this program was to demonstrate the technical feasibility of the 'tile' array packaging architecture at EHF via the insertion of 1990 MMIC technology into a functional tile array or subarray module. The means test of this objective was to demonstrate and deliver to NASA a minimum of two 4 x 4 (16 radiating element) subarray modules operating in a transmit mode at 29.6 GHz. Available (1990) MMIC technology was chosen to focus the program effort on the novel interconnect schemes and packaging requirements rather than focusing on MMIC development. Major technical achievements of this program include the successful integration of two 4 x 4 subarray modules into a single antenna array. This 32 element array demonstrates a transmit EIRP of over 300 watts yielding an effective directive power gain in excess of 55 dB at 29.63 GHz. The array has been actively used as the transmit link in airborne/terrestrial mobile communication experiments accomplished via the ACTS satellite launched in August 1993.

  12. Special Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Parikh, Indu; Cuatrecasas, Pedro

    1985-01-01

    Describes the nature of affinity chromatography and its use in purifying enzymes, studying cell interactions, exploring hormone receptors, and other areas. The potential the technique may have in treating disease is also considered. (JN)

  13. Predicting p Ka values from EEM atomic charges.

    PubMed

    Vařeková, Radka Svobodová; Geidl, Stanislav; Ionescu, Crina-Maria; Skřehota, Ondřej; Bouchal, Tomáš; Sehnal, David; Abagyan, Ruben; Koča, Jaroslav

    2013-04-10

    : The acid dissociation constant p Ka is a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p Ka prediction. We have evaluated the p Ka prediction capabilities of QSPR models based on empirical atomic charges calculated by the Electronegativity Equalization Method (EEM). Specifically, we collected 18 EEM parameter sets created for 8 different quantum mechanical (QM) charge calculation schemes. Afterwards, we prepared a training set of 74 substituted phenols. Additionally, for each molecule we generated its dissociated form by removing the phenolic hydrogen. For all the molecules in the training set, we then calculated EEM charges using the 18 parameter sets, and the QM charges using the 8 above mentioned charge calculation schemes. For each type of QM and EEM charges, we created one QSPR model employing charges from the non-dissociated molecules (three descriptor QSPR models), and one QSPR model based on charges from both dissociated and non-dissociated molecules (QSPR models with five descriptors). Afterwards, we calculated the quality criteria and evaluated all the QSPR models obtained. We found that QSPR models employing the EEM charges proved as a good approach for the prediction of p Ka (63% of these models had R2 > 0.9, while the best had R2 = 0.924). As expected, QM QSPR models provided more accurate p Ka predictions than the EEM QSPR models but the differences were not significant. Furthermore, a big advantage of the EEM QSPR models is that their descriptors (i.e., EEM atomic charges) can be calculated markedly faster than the QM charge descriptors. Moreover, we found that the EEM QSPR models are not so strongly influenced by the selection of the charge calculation approach as the QM QSPR models. The robustness of the EEM QSPR models was subsequently confirmed by cross-validation. The applicability of EEM QSPR models for other chemical classes was illustrated by a case study focused on

  14. Affine group formulation of the Standard Model coupled to gravity

    SciTech Connect

    Chou, Ching-Yi; Ita, Eyo; Soo, Chopin

    2014-04-15

    In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

  15. Development of Methods for the Determination of pKa Values

    PubMed Central

    Reijenga, Jetse; van Hoof, Arno; van Loon, Antonie; Teunissen, Bram

    2013-01-01

    The acid dissociation constant (pKa) is among the most frequently used physicochemical parameters, and its determination is of interest to a wide range of research fields. We present a brief introduction on the conceptual development of pKa as a physical parameter and its relationship to the concept of the pH of a solution. This is followed by a general summary of the historical development and current state of the techniques of pKa determination and an attempt to develop insight into future developments. Fourteen methods of determining the acid dissociation constant are placed in context and are critically evaluated to make a fair comparison and to determine their applications in modern chemistry. Additionally, we have studied these techniques in light of present trends in science and technology and attempt to determine how these trends might affect future developments in the field. PMID:23997574

  16. Analysis of Aged Human Serum Albumin Affinity for Doxazosin.

    PubMed

    Chudzik, Mariola; Równicka-Zubik, Joanna; Pożycka, Jadwiga; Pawelczak, Bartosz; Sulkowska, Anna

    2016-01-01

    Structural changes of human serum albumin (HSA) caused by old age and coexisting diseases result in differences in the binding of doxazosin (DOX). DOX is a postsynaptic α1- adrenoreceptor antagonist used for treatment of hypertension and benign prostatic hyperplasia. In elderly people suffering from various renal or hepatic diseases the significant portion of N-form of human serum albumin (normal) is converted to A-form (aged). The differences in binding of doxazosin to N- and Aform of albumin are an important factor, which may determines therapeutic dosage and toxicity of the test drug. To indicate these differences, the technique of fluorescence spectroscopy was used. The association constant (Ka) obtained from fluorescence quenching demonstrated that doxazosin has higher affinity for AHSA than for HSA. In order to describe the cooperativity in binding process, the values of the Hill's coefficient has been analysed. For DOX-HSA system (λex 295 nm) Hill's coefficient is close to 1 and it indicates that there is a single class of binding sites. For DOX-HSA (λex 275 nm) and DOX-AHSA (λex 275 nm and λex 295 nm) systems we observed positive cooperativity (nH>1). A greater red shift of fluorescence emission maximum of AHSA than HSA in the presence of DOX was observed. This suggests that the binding of DOX to AHSA was accompanied by a stronger increase in polarity around the fluorophores in comparison to HSA. The binding interaction between DOX and HSA has been also studied by molecular docking simulation.

  17. The pKa Distribution of Drugs: Application to Drug Discovery

    PubMed Central

    Manallack, David T.

    2007-01-01

    The acid-base dissociation constant (pKa) of a drug is a key physicochemical parameter influencing many biopharmaceutical characteristics. While this has been well established, the overall proportion of non-ionizable and ionizable compounds for drug-like substances is not well known. Even less well known is the overall distribution of acid and base pKa values. The current study has reviewed the literature with regard to both the proportion of ionizable substances and pKa distributions. Further to this a set of 582 drugs with associated pKa data was thoroughly examined to provide a representative set of observations. This was further enhanced by delineating the compounds into CNS and non-CNS drugs to investigate where differences exist. Interestingly, the distribution of pKa values for single acids differed remarkably between CNS and non-CNS substances with only one CNS compound having an acid pKa below 6.1. The distribution of basic substances in the CNS set also showed a marked cut off with no compounds having a pKa above 10.5. The pKa distributions of drugs are influenced by two main drivers. The first is related to the nature and frequency of occurrence of the functional groups that are commonly observed in pharmaceuticals and the typical range of pKa values they span. The other factor concerns the biological targets these compounds are designed to hit. For example, many CNS targets are based on seven transmembrane G protein-coupled receptors (7TM GPCR) which have a key aspartic acid residue known to interact with most ligands. As a consequence, amines are mostly present in the ligands that target 7TM GPCR’s and this influences the pKa profile of drugs containing basic groups. For larger screening collections of compounds, synthetic chemistry and the working practices of the chemists themselves can influence the proportion of ionizable compounds and consequent pKa distributions. The findings from this study expand on current wisdom in pKa research and have

  18. Calculation of antibody affinity in homogeneous and heterogeneous systems.

    PubMed

    Chalquest, R R

    1988-12-01

    Antibody affinity is an important determinant of all antibody-antigen reactions. A new computer program, AFCRV, was developed to calculate binding constants with data from a radioimmunoassay on most microcomputers in the laboratory by using constant-ratio dilution curves. Evaluation of a homogeneous or heterogeneous antibody in the presence of a single antigen can be accomplished.

  19. Affinity purification of aprotinin from bovine lung.

    PubMed

    Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun

    2015-05-01

    An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462

  20. Direct binding of radioiodinated monoclonal antibody to tumor cells: significance of antibody purity and affinity for drug targeting or tumor imaging

    SciTech Connect

    Kennel, S.J.; Foote, L.J.; Lankford, P.K.; Johnson, M.; Mitchell, T.; Braslawsky, G.R.

    1983-01-01

    For MoAb to be used efficiently for drug targeting and tumor imaging, the fraction of antibody binding to tumor cells must be maximized. The authors have studied the binding of /sup 125/I MoAb in three different tumor systems. The fraction of antibody that could be bound to the cell surface was directly proportional to the antibody purity. The affinity constant also limits the fraction of antibody that can bind to cells at a given antigen concentration. Rearrangement of the standard expression for univalent equilibrium binding between two reactants shows that in antigen excess, the maximum fraction of antibody that can bind =Ka(Ag total)/1 + Ka(Ag total). Binding data using four different MoAb with three cell systems confirm this relationship. Estimates for reasonable concentrations of tumor antigens in vivo indicate that antibodies with binding constants less than 10/sup 8/ M/sup -1/ are not likely to be useful for drug targeting or tumor imaging.

  1. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    NASA Astrophysics Data System (ADS)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  2. IDENTIFICATION AND ANALYSIS OF STEREOSELECTIVE DRUG INTERACTIONS WITH LOW DENSITY LIPOPROTEIN BY HIGH-PERFORMANCE AFFINITY CHROMATOGRAPHY

    PubMed Central

    Sobansky, Matthew R.; Hage, David S.

    2012-01-01

    Columns containing immobilized low density lipoprotein (LDL) were prepared for the analysis of drug interactions with this agent by high-performance affinity chromatography (HPAC). R/S-Propranolol was used as a model drug for this study. The LDL columns gave reproducible binding to propranolol over 60 h of continuous use in the presence of pH 7.4, 0.067 M potassium phosphate buffer. Experiments conducted with this type of column through frontal analysis indicated that two types of interactions were occurring between R-propranolol and LDL, while only a single type of interaction was observed between S-propranolol and LDL. The first type of interaction, which was seen for both enantiomers, involved non-saturable binding; this interaction had an overall affinity (nKa) of 1.9 (± 0.1) × 105 M-1 for R-propranolol and 2.7 (± 0.2) × 105 M-1 for S-propranolol at 37 °C. The second type of interaction was observed only for R-propranolol and involved saturable binding that had an association equilibrium constant (Ka) of 5.2 (± 2.3) × 105 M-1 at 37 °C. Similar differences in binding behavior were found for the two enantiomers at 20 °C and 27 °C. This is the first known example of stereoselective binding of drugs by LDL or other lipoproteins. This work also illustrates the ability of HPAC to be used as a tool for characterizing mixed-mode interactions that involve LDL and related binding agents. PMID:22354572

  3. Affinity purification of metalloprotease from marine bacterium using immobilized metal affinity chromatography.

    PubMed

    Li, Shangyong; Wang, Linna; Yang, Juan; Bao, Jing; Liu, Junzhong; Lin, Shengxiang; Hao, Jianhua; Sun, Mi

    2016-06-01

    In this study, an efficient affinity purification protocol for an alkaline metalloprotease from marine bacterium was developed using immobilized metal affinity chromatography. After screening and optimization of the affinity ligands and spacer arm lengths, Cu-iminmodiacetic acid was chosen as the optimal affinity ligand, which was coupled to Sepharose 6B via a 14-atom spacer arm. The absorption analysis of this medium revealed a desorption constant Kd of 21.5 μg/mL and a theoretical maximum absorption Qmax of 24.9 mg/g. Thanks to this affinity medium, the enzyme could be purified by only one affinity purification step with a purity of approximately 95% pure when analyzed by high-performance liquid chromatography and reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis. The recovery of the protease activity reached 74.6%, which is much higher than the value obtained by traditional protocols (8.9%). These results contribute to the industrial purifications and contribute a significant reference for the purification of other metalloproteases. PMID:27058973

  4. Affinity driven social networks

    NASA Astrophysics Data System (ADS)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  5. High Throughput pharmacokinetic modeling using computationally predicted parameter values: dissociation constants (TDS)

    EPA Science Inventory

    Estimates of the ionization association and dissociation constant (pKa) are vital to modeling the pharmacokinetic behavior of chemicals in vivo. Methodologies for the prediction of compound sequestration in specific tissues using partition coefficients require a parameter that ch...

  6. Calculated pKa Variations Expose Dynamic Allosteric Communication Networks.

    PubMed

    Lang, Eric J M; Heyes, Logan C; Jameson, Geoffrey B; Parker, Emily J

    2016-02-17

    Allosteric regulation of protein function, the process by which binding of an effector molecule provokes a functional response from a distal site, is critical for metabolic pathways. Yet, the way the allosteric signal is communicated remains elusive, especially in dynamic, entropically driven regulation mechanisms for which no major conformational changes are observed. To identify these dynamic allosteric communication networks, we have developed an approach that monitors the pKa variations of ionizable residues over the course of molecular dynamics simulations performed in the presence and absence of an allosteric regulator. As the pKa of ionizable residues depends on their environment, it represents a simple metric to monitor changes in several complex factors induced by binding an allosteric effector. These factors include Coulombic interactions, hydrogen bonding, and solvation, as well as backbone motions and side chain fluctuations. The predictions that can be made with this method concerning the roles of ionizable residues for allosteric communication can then be easily tested experimentally by changing the working pH of the protein or performing single point mutations. To demonstrate the method's validity, we have applied this approach to the subtle dynamic regulation mechanism observed for Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, the first enzyme of aromatic biosynthesis. We were able to identify key communication pathways linking the allosteric binding site to the active site of the enzyme and to validate these findings experimentally by reestablishing the catalytic activity of allosterically inhibited enzyme via modulation of the working pH, without compromising the binding affinity of the allosteric regulator.

  7. Two bradykinin binding sites with picomolar affinities

    SciTech Connect

    Manning, D.C.; Vavrek, R.; Stewart, J.M.; Snyder, S.H.

    1986-05-01

    Bradykinin (BK) and related peptides exert a wide range of effects on several organ systems. We have attempted to sort out these effects by studying the binding interaction of (/sup 3/H)BK at the membrane level with in vitro receptor binding techniques. High specific activity (/sup 3/H)BK and an enzyme inhibitor cocktail has enabled us to label two BK binding sites with different affinity and peptide specificity in several guinea-pig tissues. In the guinea-pig ileum the high-affinity site has an equilibrium dissociation constant (Kd) for (/sup 3/H)BK of 13 pM and a maximal number of binding sites of 8.3 pmol/g of tissue wet weight. The low-affinity guinea-pig ileum site displays a Kd of 910 pM, a maximum number of binding sites of 14 pmol/g of tissue wet weight and shows a greater selectivity for BK analogs over Lysyl-BK analogs. Two similar sites can also be discriminated in kidney and heart. The potencies of a series of BK analogs at the high-affinity guinea-pig ileum site correlate well with their potencies in contracting ileal smooth muscle. The binding of (/sup 3/H)BK in the guinea-pig ileum is inhibited by physiological concentrations of monovalent and divalent cations.

  8. Allowance for antibody bivalence in the determination of association rate constants by kinetic exclusion assay.

    PubMed

    Winzor, Donald J

    2013-10-15

    This investigation completes the amendment of theoretical expressions for the characterization of antigen-antibody interactions by kinetic exclusion assay-an endeavor that has been marred by inadequate allowance for the consequences of antibody bivalence in its uptake by the affinity matrix (immobilized antigen) that is used to ascertain the fraction of free antibody sites in a solution with defined total concentrations of antigen and antibody. A simple illustration of reacted site probability considerations in action confirms that the square root of the fluorescence response ratio, R(Ag)/R₀, needs to be taken in order to determine the fraction of unoccupied antibody sites, which is the parameter employed to describe the kinetics of antigen uptake in the mixture of antigen and antibody with defined initial composition. The approximately 2-fold underestimation of the association rate constant (k(a)) that emanates from the usual practice of omitting the square root factor gives rise to a corresponding overestimate of the equilibrium dissociation constant (K(d))--a situation that is also encountered in the thermodynamic characterization of antigen-antibody interactions by kinetic exclusion assay. PMID:23851342

  9. Determination of dissociation constants of pharmacologically active xanthones by capillary zone electrophoresis with diode array detection.

    PubMed

    Wu, Xiaomu; Gong, Suxuan; Bo, Tao; Liao, Yiping; Liu, Huwei

    2004-12-24

    In this article, the dissociation constants (pKa) of 10 pharmacologically active xanthones isolated from herbal medicine Securidaca inappendiculata were determined by capillary zone electrophoresis with diode array detection. The pKa values determined by the method based on the electrophoretic mobilities (calculated from migration times) have been proved by the method based on UV absorbance calculated from the online spectra corresponding peaks. No conspicuous difference was observed between the two methods with acceptable reproducibility. Two pKa values (pKa1 and pKa2) were found for four xanthones while generally the 10 compounds possess the pKa values ranging from 6.4 to 9.2. PMID:15641365

  10. DNA-binding affinity and sequence permutation preference of the telomere protein from Euplotes crassus

    PubMed Central

    Suzuki, Takahito; McKenzie, Margaret; Ott, Elizabeth; Ilkun, Olesya; Horvath, Martin P.

    2008-01-01

    Telomere end binding proteins from diverse organisms use various forms of an ancient protein structure to recognize and bind with single strand DNA found at the ends of telomeres. To further understand the biochemistry and evolution of these proteins we have characterized the DNA-binding properties of the telomere end binding protein from Euplotes crassus (EcTEBP). EcTEBP and its predicted amino-terminal DNA-binding domain, EcTEBP-N, were expressed in E. coli and purified. Each protein formed stoichiometric (1:1) complexes with single strand DNA oligos derived from the precisely defined d(TTTTGGGGTTTTGG) sequence found at DNA termini in Euplotes. Dissociation constants for DNA•EcTEBP and DNA•EcTEBP-N were comparable, with KD-DNA = 38 ± 2 nM for the full-length protein and KD-DNA = 60 ± 4 nM for the N-terminal domain, indicating that the N-terminal domain retains high affinity for DNA even in the absence of potentially stabilizing moieties located in the C-terminal domain. Rate constants for DNA association and DNA dissociation corroborated a slightly improved DNA binding performance for the full-length protein (ka = 45 ± 4 μM-1 s-1, kd = 0.10 ± 0.02 s-1) relative to the N-terminal domain (ka = 18 ± 1 μM-1 s-1, kd = 0.15 ± 0.01 s-1). Equilibrium dissociation constants measured for sequence permutations of the telomere repeat spanned a 55 – 1400 nM range, with EcTEBP and EcTEBP-N binding most tightly to d(TTGGGGTTTTGG) — the sequence corresponding with that of mature DNA termini. Additionally, competition experiments showed that EcTEBP recognizes and binds the telomere-derived 14-nucleotide DNA in preference to shorter 5′ -truncation variants. Compared with multi-subunit complexes assembled with telomere single strand DNA from Oxytricha nova, our results highlight the relative simplicity of the Euplotes crassus system where a telomere end binding protein has biochemical properties indicating one protein subunit caps the single strand DNA. PMID

  11. Estimated pKa values for the environmentally relevant C1 through C8 perfluorinated sulfonic acid isomers.

    PubMed

    Rayne, Sierra; Forest, Kaya

    2016-10-14

    In order to estimate isomer-specific acidity constants (pKa) for the perfluorinated sulfonic acid (PFSA) environmental contaminants, the parameterization method 6 (PM6) pKa prediction method was extensively validated against a wide range of carbon oxyacids and related sulfonic/sulfinic acids. Excellent pKa prediction performance was observed for the carbon oxyacids using the PM6 method, but this approach was found to have a severe positive bias for sulfonic/sulfinic acids. To overcome this obstacle, a correlation was developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl and halogen-substituted sulfonic acids. Application of this correction to the PM6 values allows for extension of this computational method to a new acid functional group. When used to estimate isomer-specific pKa values for the C1 through C8 PFSAs, the modified PM6 approach suggests an adjusted pKa range from -5.3 to -9.0, indicating that all members of this class of well-known environmental contaminants will be effectively completely dissociated in aquatic systems.

  12. Estimated pKa values for the environmentally relevant C1 through C8 perfluorinated sulfonic acid isomers.

    PubMed

    Rayne, Sierra; Forest, Kaya

    2016-10-14

    In order to estimate isomer-specific acidity constants (pKa) for the perfluorinated sulfonic acid (PFSA) environmental contaminants, the parameterization method 6 (PM6) pKa prediction method was extensively validated against a wide range of carbon oxyacids and related sulfonic/sulfinic acids. Excellent pKa prediction performance was observed for the carbon oxyacids using the PM6 method, but this approach was found to have a severe positive bias for sulfonic/sulfinic acids. To overcome this obstacle, a correlation was developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl and halogen-substituted sulfonic acids. Application of this correction to the PM6 values allows for extension of this computational method to a new acid functional group. When used to estimate isomer-specific pKa values for the C1 through C8 PFSAs, the modified PM6 approach suggests an adjusted pKa range from -5.3 to -9.0, indicating that all members of this class of well-known environmental contaminants will be effectively completely dissociated in aquatic systems. PMID:27389973

  13. A high-affinity estrogen-binding protein in rat placental trophoblast.

    PubMed

    McCormack, S A; Glasser, S R

    1976-09-01

    A high-affinity, low-capacity estradiol-binding molecule (RE) has been demonstrated in the basal zone trophoblast (BZT) of the pregnant rat. On day 11 of pregnancy (day 0 = first sperm-positive day) RE is present in BZT cytosol, where it has a ka of 1.2 X 10(6)M-1 sec-1, t1/2 = 12.7 min, at 20 C. The Kd, under similar conditions, consists of 2 components, 1.3 X 10(-4) sec-1, t1/2 = 90 min, and 5.9 X 10(-5) sec-1, t1/2 = 196 min. When one uses the faster component, the equilibrium constant, Kd, obtained from kd/ka is 1.1 X 10(-10)M, in close agreement with that obtained from Scatchard analysis of specific estradiol (E2) binding at 20 C. On day 11 there were approximately 12,000 sites/cell in BZT cytosol. Scatchard analysis of nuclear RE on day 11 indicated a Kd of 1.85 X 10(-10)M and approximately 21,000 sites/nucleus, but, in day 15 BZT, nuclear RE was undetectable. Neither cytosol nor nuclei prepared from placental labyrinthine zone (LZT) tissue (fetal placenta) showed evidence of high-affinity, low-capacity E2 binding. Sucrose density gradient analysis on 5-20% linear gradients showed the cytosol RE to be approximately 4S whether in high or low-salt conditions. When measured against binding by 3H-labeled estradiol (*E2), the cytosol BTZ RE was competed for strongly (80-90%) by estrone, estriol, diethylstilbestrol, and estradiol-17alpha at 200 times excess. Nafoxidine-HCl, also at 200X excess, competed to approximately 50%. Corticosterone, progesterone, testosterone, dehydroepiandrosterone, and pregnenolone did not compete. The hormone specificity of nuclear BZT RE was similar to that of the comparable cytosol RE with the exception that nafoxidine did not compete. This was probably due to differences in kinetics, nafoxidine requiring a longer time to reach equilibrium than the other estrogens. The size of the nuclear RE by sucrose density gradient analysis was approximately 2S by KCl extraction (which was inefficient) or 4S by trypsin extraction. We conclude that

  14. Affinity enhancement by dendritic side chains in synthetic carbohydrate receptors.

    PubMed

    Destecroix, Harry; Renney, Charles M; Mooibroek, Tiddo J; Carter, Tom S; Stewart, Patrick F N; Crump, Matthew P; Davis, Anthony P

    2015-02-01

    Dendritic side chains have been used to modify the binding environment in anthracene-based synthetic carbohydrate receptors. Control of length, charge, and branching enabled the positioning of side-chain carboxylate groups in such a way that they assisted in binding substrates rather than blocking the cavity. Conformational degeneracy in the dendrimers resulted in effective preorganization despite the flexibility of the system. Strong binding was observed to glucosammonium ions in water, with Ka values up to 7000 M(-1) . Affinities for uncharged substrates (glucose and N-acetylglucosamine) were also enhanced, despite competition from solvent and the absence of electrostatic interactions. PMID:25645064

  15. PHARMACEUTICAL AND BIOMEDICAL APPLICATIONS OF AFFINITY CHROMATOGRAPHY: RECENT TRENDS AND DEVELOPMENTS

    PubMed Central

    Hage, David S.; Anguizola, Jeanethe A.; Bi, Cong; Li, Rong; Matsuda, Ryan; Papastavros, Efthimia; Pfaunmiller, Erika; Vargas, John; Zheng, Xiwei

    2012-01-01

    Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically-related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered. PMID:22305083

  16. Affine differential geometry analysis of human arm movements.

    PubMed

    Flash, Tamar; Handzel, Amir A

    2007-06-01

    Humans interact with their environment through sensory information and motor actions. These interactions may be understood via the underlying geometry of both perception and action. While the motor space is typically considered by default to be Euclidean, persistent behavioral observations point to a different underlying geometric structure. These observed regularities include the "two-thirds power law", which connects path curvature with velocity, and "local isochrony", which prescribes the relation between movement time and its extent. Starting with these empirical observations, we have developed a mathematical framework based on differential geometry, Lie group theory and Cartan's moving frame method for the analysis of human hand trajectories. We also use this method to identify possible motion primitives, i.e., elementary building blocks from which more complicated movements are constructed. We show that a natural geometric description of continuous repetitive hand trajectories is not Euclidean but equi-affine. Specifically, equi-affine velocity is piecewise constant along movement segments, and movement execution time for a given segment is proportional to its equi-affine arc-length. Using this mathematical framework, we then analyze experimentally recorded drawing movements. To examine movement segmentation and classification, the two fundamental equi-affine differential invariants-equi-affine arc-length and curvature are calculated for the recorded movements. We also discuss the possible role of conic sections, i.e., curves with constant equi-affine curvature, as motor primitives and focus in more detail on parabolas, the equi-affine geodesics. Finally, we explore possible schemes for the internal neural coding of motor commands by showing that the equi-affine framework is compatible with the common model of population coding of the hand velocity vector when combined with a simple assumption on its dynamics. We then discuss several alternative explanations

  17. Ka-me: a Voronoi image analyzer

    PubMed Central

    Khiripet, Noppadon; Khantuwan, Wongarnet; Jungck, John R.

    2012-01-01

    Summary: Ka-me is a Voronoi image analyzer that allows users to analyze any image with a convex polygonal tessellation or any spatial point distribution by fitting Voronoi polygons and their dual, Delaunay triangulations, to the pattern. The analytical tools include a variety of graph theoretic and geometric tools that summarize the distribution of the numbers of edges per face, areas, perimeters, angles of Delaunay triangle edges (anglograms), Gabriel graphs, nearest neighbor graphs, minimal spanning trees, Ulam trees, Pitteway tests, circumcircles and convexhulls, as well as spatial statistics (Clark–Evans Nearest Neighborhood and Variance to Mean Ratio) and export functions for standard relationships (Lewis's Law, Desch's Law and Aboav–Weaire Law). Availability: Ka-me: a Voronoi image analyzer is available as an executable with documentation and sample applications from the BioQUEST Library (http://bioquest.org/downloads/kame_1.0.rar). Contact: noppadon.khiripet@nectec.or.th PMID:22556369

  18. Internal standard capillary electrophoresis as a high-throughput method for pKa determination in drug discovery and development.

    PubMed

    Cabot, Joan M; Fuguet, Elisabet; Rosés, Martí

    2014-10-13

    A novel high-throughput method for determining acidity constants (pKa) by capillary electrophoresis (CE) is developed. The method, based on the use of an internal standard (IS-CE), is implemented as a routine method for accurate experimental pKa determination of drugs undergoing physicochemical measurements in drug discovery laboratories. Just two electropherograms at 2 different pH values are needed to calculate an acidity constant. Several ISs can be used in the same buffer and run to enhance precision. With 3 ISs, for example, the pKa of the test compound (TC) can be obtained in triplicate in less than 3 min of electrophoresis. It has been demonstrated that the IS-CE method eliminates some systematic errors, maintaining, or even increasing the precision of the results compared with other methods. Furthermore, pH buffer instability during electrophoretic runs is not a problem in the IS-CE method. It is also proved that after 16 h of electroseparation using the same buffer vial, pH may change by around one unit; but the pKa calculated by the IS-CE method remains constant. Thus, IS-CE is a powerful high-throughput method for pKa determination in drug discovery and development.

  19. pH indicator titration: a novel fast pKa determination method.

    PubMed

    Kong, Xiaole; Zhou, Tao; Liu, Zudong; Hider, Robert C

    2007-10-01

    This study describes a fast spectrophotometic titration method for apparent ionization constant (pKa) determination. In this method, a Universal pH indicator is utilized instead of the conventional pH electrode. An autoburette is set to add HCl at a constant rate to a vigorously stirred 1 cm UV cuvette which contains sample and indicator solution. A spectrophotometer continuously records the spectra. Acquired spectral data are processed by calculating the pH from the indicator spectra in the visible region and extracting sample spectra from the UV region. Five compounds possessing pKa values in the range 2-10 were investigated. These results differed from measurements by conventional spectrophotometric titration by +/-0.05 to +/-0.10 log unit.

  20. Adjoint affine fusion and tadpoles

    NASA Astrophysics Data System (ADS)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  1. Predicting the pKa and stability of organic acids and bases at an oil-water interface.

    PubMed

    Andersson, M P; Olsson, M H M; Stipp, S L S

    2014-06-10

    We have used density functional theory and the implicit solvent model, COSMO-RS, to investigate how the acidity constant, pKa, of organic acids and bases adsorbed at the organic compound-aqueous solution interface changes, compared to its value in the aqueous phase. The pKa determine the surface charge density of the molecules that accumulate at the fluid-fluid interface. We have estimated the pKa by comparing the stability of the protonated and unprotonated forms of a series of molecules in the bulk aqueous solution and at an interface where parts of each molecule reside in the hydrophobic phase and the rest remains in the hydrophilic phase. We found that the pKa for acids is shifted by ∼1 pH unit to higher values compared to the bulk water pKa, whereas they are shifted to lower values by a similar amount for bases. Because this pKa shift is similar in magnitude for each of the molecules studied, we propose that the pKa for molecules at a water-organic compound interface can easily be predicted by adding a small shift to the aqueous pKa. This shift is general and correlates with the functional group. We also found that the relative composition of molecules at the fluid-fluid interface is not the same as in the bulk. For example, species such as carboxylic acids are enriched at the interface, where they can dominate surface properties, even when they are a modest component in the bulk fluid. For high surface concentrations of carboxylic acid groups at an interface, such as a self-assembled monolayer, we have demonstrated that the pKa depends on the degree of deprotonation through direct hydrogen bonding between protonated and deprotonated acidic headgroups.

  2. Validation of GPM Ka-Radar Algorithm Using a Ground-based Ka-Radar System

    NASA Astrophysics Data System (ADS)

    Nakamura, Kenji; Kaneko, Yuki; Nakagawa, Katsuhiro; Furukawa, Kinji; Suzuki, Kenji

    2016-04-01

    GPM led by the Japan Aerospace Exploration Agency (JAXA) and the National Aeronautics and Space Administration of US (NASA) aims to observe global precipitation. The core satellite is equipped with a microwave radiometer (GMI) and a dual-frequency radar (DPR) which is the first spaceborne Ku/Ka-band dual-wavelength radar dedicated for precipitation measurement. In the DPR algorithm, measured radar reflectivity is converted to effective radar reflectivity by estimating the rain attenuation. Here, the scattering/attenuation characteristics of Ka-band radiowaves are crucial, particularly for wet snow. A melting layer observation using a dual Ka-band radar system developed by JAXA was conducted along the slope of Mt. Zao in Yamagata Prefecture, Japan. The dual Ka-band radar system consists of two nearly identical Ka-band FM-CW radars, and the precipitation systems between two radars were observed in opposite directions. From this experiment, equivalent radar reflectivity (Ze) and specific attenuation (k) were obtained. The experiments were conducted for two winter seasons. During the data analyses, it was found that k estimate easily fluctuates because the estimate is based on double difference calculation. With much temporal and spatial averaging, k-Ze relationship was obtained for melting layers. One of the results is that the height of the peak of k seems slightly higher than that of Ze. The results are compared with in-situ precipitation particle measurements.

  3. A MEMS Dielectric Affinity Glucose Biosensor

    PubMed Central

    Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao

    2013-01-01

    Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215

  4. Thiazolium C(2)-proton exchange: structure-reactivity correlations and the pKa of thiamin C(2)-H revisited.

    PubMed

    Washabaugh, M W; Jencks, W P

    1988-07-12

    Rate constants for C(2)-proton exchange from thiamin, N(1')-methylthiamin, and several 3-substituted-4-methylthiazolium ions catalyzed by D2O and deuterioxide ion were determined by 1H NMR at 30 degrees C and ionic strength 2.0 M. Values of pKa for the thiazolium ions, including thiamin itself, were found to be in the range pKa = 17-19; the pKa values for N(1')-protonated thiamin and free thiamin C(2)-H in H2O are 17.7 and 18.0, respectively. The pKa value for N(1')-protonated thiamin was calculated from the observed rate constant for the pD-independent reaction with D2O after correction for a secondary solvent deuterium isotope effect of kH2O/kD2O = 2.6. The pKa value for free thiamin was calculated from the rate constant for catalysis by OD- after correction by a factor of 3.3 = 8/2.4 for an 8-fold negative deviation of kOD from the Brønsted plot of slope 1.0 for general base catalysis and a secondary solvent isotope effect of kOD/kOH = 2.4. Values of k-a = 2 X 10(10) and 3 X 10(9) M-1 s-1 were assumed for diffusion-controlled protonation of the C(2) ylide in the reverse direction by H3O+ and H2O, respectively. The Hammett rho I value for the exchange reaction catalyzed by deuterioxide ion or D2O is 8.4 +/- 0.2. There is no positive deviation of the rate constants for free or N(1')-substituted thiamin analogues in either Hammett correlation. This shows that the aminopyrimidinyl group does not provide significant intramolecular catalysis of nonenzymic C(2)-proton removal in the coenzyme.

  5. Affinity chromatography: a historical perspective.

    PubMed

    Hage, David S; Matsuda, Ryan

    2015-01-01

    Affinity chromatography is one of the most selective and versatile forms of liquid chromatography for the separation or analysis of chemicals in complex mixtures. This method makes use of a biologically related agent as the stationary phase, which provides an affinity column with the ability to bind selectively and reversibly to a given target in a sample. This review examines the early work in this method and various developments that have lead to the current status of this technique. The general principles of affinity chromatography are briefly described as part of this discussion. Past and recent efforts in the generation of new binding agents, supports, and immobilization methods for this method are considered. Various applications of affinity chromatography are also summarized, as well as the influence this field has played in the creation of other affinity-based separation or analysis methods. PMID:25749941

  6. Affine conformal vectors in space-time

    NASA Astrophysics Data System (ADS)

    Coley, A. A.; Tupper, B. O. J.

    1992-05-01

    All space-times admitting a proper affine conformal vector (ACV) are found. By using a theorem of Hall and da Costa, it is shown that such space-times either (i) admit a covariantly constant vector (timelike, spacelike, or null) and the ACV is the sum of a proper affine vector and a conformal Killing vector or (ii) the space-time is 2+2 decomposable, in which case it is shown that no ACV can exist (unless the space-time decomposes further). Furthermore, it is proved that all space-times admitting an ACV and a null covariantly constant vector (which are necessarily generalized pp-wave space-times) must have Ricci tensor of Segré type {2,(1,1)}. It follows that, among space-times admitting proper ACV, the Einstein static universe is the only perfect fluid space-time, there are no non-null Einstein-Maxwell space-times, and only the pp-wave space-times are representative of null Einstein-Maxwell solutions. Otherwise, the space-times can represent anisotropic fluids and viscous heat-conducting fluids, but only with restricted equations of state in each case.

  7. First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale.

    PubMed

    Klamt, Andreas; Eckert, Frank; Diedenhofen, Michael; Beck, Michael E

    2003-11-01

    The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment for more realistic solvation (RS) simulations, has been used for the direct prediction of pKa constants of a large variety of 64 organic and inorganic acids. A highly significant correlation of r(2) = 0.984 with a standard deviation of only 0.49 between the calculated values of the free energies of dissociation and the experimental pKa values was found, without any special adjustment of the method. Thus, we have a theoretical a priori prediction method for pKa, which has the regression constant and the slope as only adjusted parameters. Such a method can be of great value in many areas of physical chemistry, especially in pharmaceutical and agrochemical industry. To our surprise, the slope of pKa vs ΔGdiss is only 58% of the theoretically expected value of 1/RTln(10). A careful analysis with respect to different contributions as well as a comparison with the work of other authors excludes the possibility that the discrepancy is due to weaknesses of the calculation method. Hence, we must conclude that the experimental pKa scale depends differently on the free energy of dissociation than generally assumed. PMID:26313337

  8. High-power Ka-band amplifier

    NASA Technical Reports Server (NTRS)

    Cormier, R.

    1993-01-01

    Development of a high-power tube suitable to power a Ka-band (34.5-GHz) antenna transmitter located at the Goldstone, California, tracking station is continuing. The University of Maryland Laboratory for Plasma Research and JPL are conducting a joint effort to test the feasibility of phase locking a second-harmonic gyrotron both by direct injection at the output cavity and by using a priming cavity to bunch the electrons in the beam. This article describes several design options and the results of computer simulation testing.

  9. The dissociation constant of water at extreme conditions

    NASA Astrophysics Data System (ADS)

    Gonzalez-Vazquez, Otto; Giacomazzi, Luigi; Pinilla, C.; Scandolo, Sandro

    2013-06-01

    Only one out of 107 water molecules is dissociated in liquid water at ambient conditions, but the concentration of dissociated molecules increases with pressure ad temperature, and water eventually reaches a fully dissociated state when pressure exceeds 50-100 GPa and temperature reaches a few thousand Kelvin. The behavior of the dissociation constant of water (pKa) at conditions intermediate between ambient and the fully dissociated state is poorly known. Yet, the water pKa is a parameter of primary importance in the aqueous geochemistry as it controls the solubility of ions in geological fluids. We present results of molecular dynamics calculations of the pKa water at extreme conditions. Free-energy differences between the undissociated and the dissociated state are calculated by thermodynamic integration along the dissociation path. The calculations are based on a recently developed all-atom polarizable force-field for water, parametrized on density-functional theory calculations.

  10. [Effect of low molecular weight organic acids on Pb2+ adsorption and desorption by constant charge soil colloids].

    PubMed

    Yang, Yati; Wang, Xudong; Zhang, Yiping; Qu, Aihua

    2003-11-01

    The isothermal curves of Pb2+ adsorption-desorption by soil colloids followed Freundlich and Langmuir equation. The adsorption constant Ka showed the trend of old manured loessal soil > yellow loessal soil > dark cultivated loessal soil > yellow cinamon soil, which was consistent with surface charge density sigma 0, an indicator of the strength of Pb2+ adsorption by each soil colloid. Low molecular-weight organic acids (LMWOAs) made Pb2+ adsorbed amount decreased and adsorption affinity increased, and the effect of citric acid was larger than that of oxalic acid. The constant Kd of residual Pb2+ adsorption after desorption showed the trend of old manured loessal soil > yellow cinamon soil > dark cultivated loessal soil > yellow loessal soil, which reflected the adsorption strength of residual Pb2+ after desorption, and was related to the contents of organic matter and free ferric oxide. The isothermal curves of Pb2+ desorption from soil colloids were obvious higher than those of Pb2+ adsorption. In NaNO3 and oxalic acid background solution, the isothermal curves of Pb2+ adsorption were far away from those of Pb2+ desorption, showing that the hysteretic degree between adsorption and desorption was very large. The isothermal curves of Pb2+ desorption from soil colloids were closed to those of Pb2+ adsorption in citric acid background solution, which showed that the Pb adsorption and desorption was reversible.

  11. pKa at Quartz/Electrolyte Interfaces.

    PubMed

    Pfeiffer-Laplaud, Morgane; Gaigeot, Marie-Pierre; Sulpizi, Marialore

    2016-08-18

    Acidity of silanol sites at the crystalline quartz/aqueous electrolyte (NaCl, NaI, KCl) interfaces are calculated from ab initio molecular dynamics simulations. pKa's are found to follow a combination of the cationic and anionic Hofmeister series in the order pKa(neat solution) < pKa(NaCl) < pKa(NaI) < pKa(KCl), in agreement with experimental measurements. Rationalization of this ranking is achieved in terms of the microscopic local solvation of the protonated silanols and their conjugated bases, the silanolates SiO(-). The change in the pKa is the result of both water destructuring by alkali halides, as well as of the specific cation/SiO(-) interaction, depending on the electrolyte. Molecular modeling at the atomistic level is required to achieve such comprehension, with ab initio molecular dynamics being able to model complex inhomogeneous charged interfaces and the associated interfacial chemical reactivity. PMID:27483195

  12. On the Khinchin Constant

    NASA Technical Reports Server (NTRS)

    Bailey, David H.; Borwein, Jonathan M.; Crandall, Richard E.; Craw, James M. (Technical Monitor)

    1995-01-01

    We prove known identities for the Khinchin constant and develop new identities for the more general Hoelder mean limits of continued fractions. Any of these constants can be developed as a rapidly converging series involving values of the Riemann zeta function and rational coefficients. Such identities allow for efficient numerical evaluation of the relevant constants. We present free-parameter, optimizable versions of the identities, and report numerical results.

  13. Affine generalization of the Komar complex of general relativity

    NASA Astrophysics Data System (ADS)

    Mielke, Eckehard W.

    2001-02-01

    On the basis of the ``on shell'' Noether identities of the metric-affine gauge approach of gravity, an affine superpotential is derived which comprises the energy- and angular-momentum content of exact solutions. In the special case of general relativity (GR) or its teleparallel equivalent, the Komar or Freud complex, respectively, are recovered. Applying this to the spontaneously broken anti-de Sitter gauge model of McDowell and Mansouri with an induced Euler term automatically yields the correct mass and spin of the Kerr-AdS solution of GR with a (induced) cosmological constant without the factor two discrepancy of the Komar formula.

  14. The hubble constant.

    PubMed

    Huchra, J P

    1992-04-17

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy The Hubble constant is the constant of proportionality between recession velocity and development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution. PMID:17743107

  15. The cosmological constant

    NASA Technical Reports Server (NTRS)

    Carroll, Sean M.; Press, William H.; Turner, Edwin L.

    1992-01-01

    The cosmological constant problem is examined in the context of both astronomy and physics. Effects of a nonzero cosmological constant are discussed with reference to expansion dynamics, the age of the universe, distance measures, comoving density of objects, growth of linear perturbations, and gravitational lens probabilities. The observational status of the cosmological constant is reviewed, with attention given to the existence of high-redshift objects, age derivation from globular clusters and cosmic nuclear data, dynamical tests of Omega sub Lambda, quasar absorption line statistics, gravitational lensing, and astrophysics of distant objects. Finally, possible solutions to the physicist's cosmological constant problem are examined.

  16. p Ka calculation of poliprotic acid: histamine

    NASA Astrophysics Data System (ADS)

    De Abreu, Heitor A.; De Almeida, Wagner B.; Duarte, Hélio A.

    2004-01-01

    Various theoretical studies have been reported addressing the performance of solvation models available to estimate p Ka values. However, no attention has been paid so far to the role played by the electronic, thermal and solvation energy individual contributions to the Gibbs free energy of the deprotonation process. In this work, we decompose the total Gibbs free energy into three distinct terms and then evaluate the dependence of each contribution on the level of theory employed for its determination using different levels of theory. The three possible p Kas of histamine have been estimated and compared with available experimental data. We found that the electronic energy term is sensitive to the level of theory and basis set, and, therefore, could be also a source of error in the theoretical calculation of p Kas.

  17. Determination of acid dissociation constants of warfarin and hydroxywarfarins by capillary electrophoresis.

    PubMed

    Nowak, Paweł; Olechowska, Paulina; Mitoraj, Mariusz; Woźniakiewicz, Michał; Kościelniak, Paweł

    2015-08-10

    In this work the acid dissociation constants--pKa of warfarin and its all important oxidative metabolites have been determined by capillary electrophoresis-based methods. It has resulted in a complete description of two acid-base dissociation equilibria, yet not investigated experimentally for phase I metabolites of warfarin. The capillary electrophoresis (CE) method based on the relation between effective electrophoretic mobilities and pH has proven to be a suitable tool for pKa determination, while the spectrophotometric (CE-DAD) and the internal standard methods (IS-CE), have appeared to be promising alternative approaches. The CE-DAD approach based on the change in absorbance spectra between the acidic and basic forms is a combination between capillary electrophoresis and spectrophotometric titration, and yields very consistent values of pKa1 with CE. The IS-CE, in turn, enables an estimation of pKa1 and pKa2 from only two analytical runs, however, less accurate than CE and CE-DAD. The Debye-Hückel model has been confirmed experimentally as a good predictor of pKa values at various ionic strengths. Therefore, it has been used in determination of thermodynamic pKa1 and pKa2, referring to the zero ionic strength. The results are important from the analytical, pharmacological, and theoretical points of view.

  18. Determination of acid dissociation constants of warfarin and hydroxywarfarins by capillary electrophoresis.

    PubMed

    Nowak, Paweł; Olechowska, Paulina; Mitoraj, Mariusz; Woźniakiewicz, Michał; Kościelniak, Paweł

    2015-08-10

    In this work the acid dissociation constants--pKa of warfarin and its all important oxidative metabolites have been determined by capillary electrophoresis-based methods. It has resulted in a complete description of two acid-base dissociation equilibria, yet not investigated experimentally for phase I metabolites of warfarin. The capillary electrophoresis (CE) method based on the relation between effective electrophoretic mobilities and pH has proven to be a suitable tool for pKa determination, while the spectrophotometric (CE-DAD) and the internal standard methods (IS-CE), have appeared to be promising alternative approaches. The CE-DAD approach based on the change in absorbance spectra between the acidic and basic forms is a combination between capillary electrophoresis and spectrophotometric titration, and yields very consistent values of pKa1 with CE. The IS-CE, in turn, enables an estimation of pKa1 and pKa2 from only two analytical runs, however, less accurate than CE and CE-DAD. The Debye-Hückel model has been confirmed experimentally as a good predictor of pKa values at various ionic strengths. Therefore, it has been used in determination of thermodynamic pKa1 and pKa2, referring to the zero ionic strength. The results are important from the analytical, pharmacological, and theoretical points of view. PMID:25968611

  19. Fundamental Physical Constants

    National Institute of Standards and Technology Data Gateway

    SRD 121 CODATA Fundamental Physical Constants (Web, free access)   This site, developed in the Physics Laboratory at NIST, addresses three topics: fundamental physical constants, the International System of Units (SI), which is the modern metric system, and expressing the uncertainty of measurement results.

  20. Calculation of magnetostriction constants

    NASA Astrophysics Data System (ADS)

    Tatebayashi, T.; Ohtsuka, S.; Ukai, T.; Mori, N.

    1986-02-01

    The magnetostriction constants h1 and h2 for Ni and Fe metals and the anisotropy constants K1 and K2 for Fe metal are calculated on the basis of the approximate d bands obtained by Deegan's prescription, by using Gilat-Raubenheimer's method. The obtained results are compared with the experimental ones.

  1. Thermodynamic mixing of molecular states of the epidermal growth factor receptor modulates macroscopic ligand binding affinity.

    PubMed Central

    Holbrook, M R; Slakey, L L; Gross, D J

    2000-01-01

    The epidermal growth factor receptor (EGFr), when expressed on the cell surface, has long been known to display two distinct affinities for epidermal growth factor (EGF) binding. In addition, the treatment of cells expressing the EGFr with phorbol esters has been shown to cause a loss of the high-affinity binding capacity of the receptor. In the present study, point mutations that alter acidic or phosphorylation sites have been made in an intracellular domain near Tyr-992 (residues 988-992) of the EGFr. Equilibrium (125)I-EGF binding studies demonstrate that the conversion of Tyr-992 into glutamate induces a 4-fold decrease in the EGFr apparent low-affinity dissociation constant, whereas the mutation of two acidic residues, Asp-988 and Glu-991, or the conversion of Tyr-992 into phenylalanine does not alter EGFr affinity. Phorbol ester treatment of EGFr-expressing Chinese hamster ovary cells results in a loss of high-affinity binding and an increase in the apparent low-affinity dissociation constant of the receptor, similar to the effect of a truncation mutant in which the C-terminal 190 residues are deleted. These results are examined in the context of a new model for regulation of the affinity of the EGFr for EGF in which a cytosolic particle stabilizes the high-affinity conformation of the EGFr and a rapid equilibrium exists between EGFr high-affinity and low-affinity conformations. This model demonstrates that the macroscopic affinities of the EGFr can differ from the affinities of individual EGFr molecules and provides a theoretical framework whereby the measured affinities of the EGFr are modulated by intracellular interactions. PMID:11062062

  2. Separate Einstein-Eddington Spaces and the Cosmological Constant

    NASA Astrophysics Data System (ADS)

    Azri, Hemza

    2016-07-01

    In affine variational principle, a symmetric linear connection is taken as a fundamental field. The metric tensor is generated dynamically, and it appears as a canonically conjugate to the connection. From this picture, Einstein's gravity with a cosmological constant can be obtained by a covariant Legendre transformation of the affine Lagrangian. In this talk, we apply this formalism (first proposed by Kijowski) to product spaces and the cosmological constant problem. From pure affine variational principle, we derive the separate Einstein space described by its Ricci tensor. The derived equations spite into two field equations of motion that describe two maximally symmetric spaces with two non independent cosmological constants. We propose that the invariance of the bi-field equations under projections on the separate spaces, may render one of the cosmological constants to zero. We also formulate the model in the presence of matter fields. The resulted separate Einstein-Eddington spaces maybe considered as two states that describe the universe before and after inflation. A possibly interesting affine action for a general perfect fluid is also proposed. It turns out that the condition which leads to zero cosmological constant in the vacuum case, eliminates here the effects of the gravitational mass density of the perfect fluid, and the dynamic of the universe in its final state is governed by only the inertial mass density of the fluid. We present no new solutions to the problems associated with inflation.

  3. Generation of a novel high-affinity monoclonal antibody with conformational recognition epitope on human IgM.

    PubMed

    Sarikhani, Sina; Mirshahi, Manouchehr; Gharaati, Mohammad Reza; Mirshahi, Tooran

    2010-11-01

    As IgM is the first isotype of antibody which appears in blood after initial exposure to a foreign antigen in the pattern of primary response, detection, and quantification of this molecule in blood seems invaluable. To approach these goals, generation, and characterization of a highly specific mAb (monoclonal antibody) against human IgM were investigated. Human IgM immunoglobulins were used to immunize Balb/c mice. Spleen cells taken from the immunized animals were fused with SP2/O myeloma cells using PEG (polyethylene glycol, MW 1450) as fusogen. The hybridomas were cultured in HAT containing medium and supernatants from the growing hybrids were screened by enzyme-linked immunosorbent assay (ELISA) using plates coated with pure human IgM and the positive wells were then cloned at limiting dilutions. The best clone designated as MAN-1, was injected intraperitoneally to some Pristane-injected mice. Anti-IgM mAb was purified from the animals' ascitic fluid by protein-G sepharose followed by DEAE-cellulose ion exchange chromatography. MAN-1 interacted with human IgM with a very high specificity and affinity. The purity of the sample was tested by SDS-PAGE and the affinity constant was measured (K(a) = 3.5 x 10(9)M(-1). Immunoblotting and competitive ELISA were done and the results showed that the harvested antibody recognizes a conformational epitope on the mu chain of human IgM and there was no cross-reactivity with other subclasses of immunoglobulins. Furthermore, isotyping test was done and the results showed the subclass of the obtained mAb which was IgG(1)kappa. PMID:20162378

  4. DARHT 2 kA Cathode Development

    SciTech Connect

    Henestroza, E.; Houck, T.; Kwan, J.W.; Leitner, M.; Miram, G.; Prichard, B.; Roy, P.K.; Waldron, W.; Westenskow, G.; Yu, S.; Bieniosek, F.M.

    2009-03-09

    In the campaign to achieve 2 kA of electron beam current, we have made several changes to the DARHT-II injector during 2006-2007. These changes resulted in a significant increase in the beam current, achieving the 2 kA milestone. Until recently (before 2007), the maximum beam current that was produced from the 6.5-inch diameter (612M) cathode was about 1300 A when the cathode was operating at a maximum temperature of 1140 C. At this temperature level, the heat loss was dominated by radiation which is proportional to temperature to the fourth power. The maximum operating temperature was limited by the damage threshold of the potted filament and the capacity of the filament heater power supply, as well as the shortening of the cathode life time. There were also signs of overheating at other components in the cathode assembly. Thus it was clear that our approach to increase beam current could not be simply trying to run at a higher temperature and the preferred way was to operate with a cathode that has a lower work function. The dispenser cathode initially used was the type 612M made by SpectraMat. According to the manufacturer's bulletin, this cathode should be able to produce more than 10 A/cm{sup 2} of current density (corresponding to 2 kA of total beam current) at our operating conditions. Instead the measured emission (space charge limited) was 6 A/cm{sup 2}. The result was similar even after we had revised the activation and handling procedures to adhere more closely to the recommend steps (taking longer time and nonstop to do the out-gassing). Vacuum was a major concern in considering the cathode's performance. Although the vacuum gauges at the injector vessel indicated 10{sup -8} Torr, the actual vacuum condition near the cathode in the central region of the vessel, where there might be significant out-gassing from the heater region, was never determined. Poor vacuum at the surface of the cathode degraded the emission (by raising the work function value). We

  5. High-affinity Cyclic Peptide Matriptase Inhibitors*

    PubMed Central

    Quimbar, Pedro; Malik, Uru; Sommerhoff, Christian P.; Kaas, Quentin; Chan, Lai Y.; Huang, Yen-Hua; Grundhuber, Maresa; Dunse, Kerry; Craik, David J.; Anderson, Marilyn A.; Daly, Norelle L.

    2013-01-01

    The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase. PMID:23548907

  6. Cesium cation affinities and basicities

    NASA Astrophysics Data System (ADS)

    Gal, Jean-François; Maria, Pierre-Charles; Massi, Lionel; Mayeux, Charly; Burk, Peeter; Tammiku-Taul, Jaana

    2007-11-01

    This review focuses on the quantitative data related to cesium cation interaction with neutral or negatively charged ligands. The techniques used for measuring the cesium cation affinity (enthalpies, CCA), and cesium cation basicities (Gibbs free energies, CCB) are briefly described. The quantum chemical calculations methods that were specifically designed for the determination of cesium cation adduct structures and the energetic aspects of the interaction are discussed. The experimental results, obtained essentially from mass spectrometry techniques, and complemented by thermochemical data, are tabulated and commented. In particular, the correlations between cesium cation affinities and lithium cation affinities for the various kinds of ligands (rare gases, polyatomic neutral molecules, among them aromatic compounds and negative ions) serve as a basis for the interpretation of the diverse electrostatic modes of interaction. A brief account of some recent analytical applications of ion/molecule reactions with Cs+, as well as other cationization approaches by Cs+, is given.

  7. Dating loess up to 800 ka by thermoluminescence

    SciTech Connect

    Berger, G.W. ); Pillans, B.J. ); Palmer, A.S. )

    1992-05-01

    Thermoluminescence (TL) ages agreeing with expected ages have been obtained for 13 loess samples spanning the age range from 20 to 800 ka. The authors samples are from Alaska and North Island, New Zealand, and are unusual in TL dating studies of loess older than 80-100 ka by having independent age assignments that are generally well constrained, from ages of associated tephra beds. With the polymineral fine-silt-sized (4-11 {mu}m) grains the partial-bleach TL technique yielded expected ages up to about 350 ka, whereas the total-bleach method gave accurate ages in the range 100 to 800 ka. Thus, the much disputed upper age limit of 100-150 ka for the TL dating of loess now appears to be sample and worker dependent, rather than a global property of the TL signals in the TL-dominant feldspars.

  8. Space Shuttle astrodynamical constants

    NASA Technical Reports Server (NTRS)

    Cockrell, B. F.; Williamson, B.

    1978-01-01

    Basic space shuttle astrodynamic constants are reported for use in mission planning and construction of ground and onboard software input loads. The data included here are provided to facilitate the use of consistent numerical values throughout the project.

  9. The cosmological constant problem

    SciTech Connect

    Dolgov, A.D.

    1989-05-01

    A review of the cosmological term problem is presented. Baby universe model and the compensating field model are discussed. The importance of more accurate data on the Hubble constant and the Universe age is stressed. 18 refs.

  10. "Clickable" agarose for affinity chromatography.

    PubMed

    Punna, Sreenivas; Kaltgrad, Eiton; Finn, M G

    2005-01-01

    Successful purification of biological molecules by affinity chromatography requires the attachment of desired ligands to biocompatible chromatographic supports. The Cu(I)-catalyzed cycloaddition of azides and alkynes-the premier example of "click chemistry"-is an efficient way to make covalent connections among diverse molecules and materials. Both azide and alkyne units are highly selective in their reactivity, being inert to most chemical functionalities and stable to wide ranges of solvent, temperature, and pH. We show that agarose beads bearing alkyne and azide groups can be easily made and are practical precursors to functionalized agarose materials for affinity chromatography.

  11. Ka-Band Autonomous Formation Flying Sensor

    NASA Technical Reports Server (NTRS)

    Tien, Jeffrey; Purcell, George, Jr.; Srinivasan, Jeffrey; Ciminera, Michael; Srinivasan, Meera; Meehan, Thomas; Young, Lawrence; Aung, MiMi; Amaro, Luis; Chong, Yong; Quirk, Kevin

    2004-01-01

    Ka-band integrated range and bearing-angle formation sensor called the Autonomous Formation Flying (AFF) Sensor has been developed to enable deep-space formation flying of multiple spacecraft. The AFF Sensor concept is similar to that of the Global Positioning System (GPS), but the AFF Sensor would not use the GPS. The AFF Sensor would reside in radio transceivers and signal-processing subsystems aboard the formation-flying spacecraft. A version of the AFF Sensor has been developed for initial application to the two-spacecraft StarLight optical-interferometry mission, and several design investigations have been performed. From the prototype development, it has been concluded that the AFF Sensor can be expected to measure distances and directions with standard deviations of 2 cm and 1 arc minute, respectively, for spacecraft separations ranging up to about 1 km. It has also been concluded that it is necessary to optimize performance of the overall mission through design trade-offs among the performance of the AFF Sensor, the field of view of the AFF Sensor, the designs of the spacecraft and the scientific instruments that they will carry, the spacecraft maneuvers required for formation flying, and the design of a formation-control system.

  12. High power Ka band TWT amplifier

    SciTech Connect

    Golkowski, C.; Ivers, J.D.; Nation, J.A.; Wang, P.; Schachter, L.

    1999-07-01

    Two high power 35 GHz TWT amplifiers driven by a relativistic pencil, 850 kV, 200A electron beam have been assembled and tested. The first had a dielectric slow wave structure and was primarily used to develop diagnostics, and to gain experience in working with high power systems in Ka band. The source of the input power for the amplifier was a magnetron producing a 30 kW, 200ns long pulse of which 10 kW as delivered to the experiment. The 30 cm long dielectric (Teflon) amplifier produced output power levels of about 1 MW with a gain of about 23 dB. These results are consistent with expectations from PIC code simulations for this arrangement. The second amplifier, which is a single stage disk loaded slow wave structure, has been designed. It consists of one hundred uniform cells with two sets of ten tapered calls at the ends to lower the reflection coefficient. The phase advance per cell is {pi}/2. The amplifier passband extends from 28 to 40 GHz. It is designed to increase the output power to about 20 MW. The amplifier is in construction and will be tested in the near future. Details of the design of both systems will be provided and initial results from the new amplifier presented.

  13. Constant potential pulse polarography

    USGS Publications Warehouse

    Christie, J.H.; Jackson, L.L.; Osteryoung, R.A.

    1976-01-01

    The new technique of constant potential pulse polarography, In which all pulses are to be the same potential, is presented theoretically and evaluated experimentally. The response obtained is in the form of a faradaic current wave superimposed on a constant capacitative component. Results obtained with a computer-controlled system exhibit a capillary response current similar to that observed In normal pulse polarography. Calibration curves for Pb obtained using a modified commercial pulse polarographic instrument are in good accord with theoretical predictions.

  14. Overview of affinity tags for protein purification.

    PubMed

    Kimple, Michelle E; Brill, Allison L; Pasker, Renee L

    2013-01-01

    Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:24510596

  15. Coenzyme-like ligands for affinity isolation of cholesterol oxidase.

    PubMed

    Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu

    2016-05-15

    Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%. PMID:26856529

  16. Fluorogen-Activating-Proteins as Universal Affinity Biosensors for Immunodetection

    PubMed Central

    Gallo, Eugenio; Vasilev, Kalin V.; Jarvik, Jonathan

    2014-01-01

    Fluorogen-activating-proteins (FAPs) are a novel platform of fluorescence biosensors utilized for protein discovery. The technology currently demands molecular manipulation methods that limit its application and adaptability. Here, we highlight an alternative approach based on universal affinity reagents for protein detection. The affinity reagents were engineered as bi-partite fusion proteins, where the specificity moiety is derived from IgG-binding proteins –Protein-A or Protein-G – and the signaling element is a FAP. In this manner, primary antibodies provide the antigenic selectivity against a desired protein in biological samples, while FAP affinity reagents target the constant region (Fc) of antibodies and provide the biosensor component of detection. Fluorescence results using various techniques indicate minimal background and high target specificity for exogenous and endogenous proteins in mammalian cells. Additionally, FAP-based affinity reagents provide enhanced properties of detection previously absent using conventional affinity systems. Distinct features explored in this report include: (1) unfixed signal wavelengths (excitation and emission) determined by the particular fluorogen chosen, (2) real-time user controlled fluorescence on-set and off-set, (3) signal wavelength substitution while performing live analysis, and (4) enhanced resistance to photobleaching. PMID:24122476

  17. Measurements of p Ka of organic molecules using third-order nonlinear optics

    NASA Astrophysics Data System (ADS)

    de Araujo, R. E.; Gomes, A. S. L.; de Araújo, Cid B.

    2000-11-01

    We report the use of the Z-scan method, which is a nonlinear optical technique, as a general method to determine a chemical parameter, the p Ka, which characterizes the equilibrium constant in acid-base reactions. The measurements were performed with picosecond pulses at 532 nm in aqueous solution of methyl orange, C 14H 14N 3O 3S -. The experimental results agree well with a phenomenological description of the molecule nonlinearity as well as with the results predicted using the Henderson-Hasselbalch equation.

  18. Quantifying Affinity among Chinese Dialects.

    ERIC Educational Resources Information Center

    Cheng, Chin-Chuan

    A study of the relationships between Chinese dialects based on a quantitative measure of dialect affinity is summarized. First, tone values in all the dialect localities available in the early 1970s were used to calculate the dialectal differences in terms of tone height with respect to the "yin and yang" split. In the late 1970s, calculations of…

  19. Affine Contractions on the Plane

    ERIC Educational Resources Information Center

    Celik, D.; Ozdemir, Y.; Ureyen, M.

    2007-01-01

    Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…

  20. Variation of Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Flambaum, V. V.

    2006-11-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. The spatial variation can explain a fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence. We present a review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra. Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance.

  1. Determination of acid dissociation constants of triazole fungicides by pressure assisted capillary electrophoresis.

    PubMed

    Konášová, Renáta; Dytrtová, Jana Jaklová; Kašička, Václav

    2015-08-21

    Pressure assisted capillary electrophoresis was applied to determination of acid dissociation constants (pKa) of six widely used triazole fungicides (cyproconazole, epoxiconazole, flusilazole, tebuconazole, penconazole and propiconazole) in aqueous medium. The pKa values were determined from the dependence of effective electrophoretic mobility of the triazole fungicides on p[H(+)] of the background electrolyte (BGE) using non-linear regression analysis. The p[H(+)] was used instead of pH to reflect the increased ionic strength of the strongly acidic BGEs (pH<1.75) as compared to the BGEs at pH equal to or greater than 1.75. Prior to the pKa calculation, the measured effective electrophoretic mobilities were corrected to the reference temperature (25°C) and constant ionic strength (25mM). The regression function was modified to allow the determination of pKa in the BGEs of varying ionic strength. The electrophoretic measurements showed that the above triazole fungicides are very weak bases - their pKa values were found to be in the range 1.05-1.97 and were in a good agreement with the values calculated by SPARC online pKa calculator.

  2. History of Larix decidua Mill. (European larch) since 130 ka

    NASA Astrophysics Data System (ADS)

    Wagner, Stefanie; Litt, Thomas; Sánchez-Goñi, Maria-Fernanda; Petit, Rémy J.

    2015-09-01

    Retrospective studies focussing on forest dynamics using fossil and genetic data can provide important keys to prepare forests for the future. In this study we analyse the impact of past climate and anthropogenic changes on Larix decidua Mill. (European larch) populations based on a new range-wide fossil compilation encompassing the last 130 ka and on recently produced genetic data (nuclear, mitochondrial). Results demonstrate that during the last 130 ka L. decidua persisted close to its current distribution range and colonized vast areas outside this range during the first two early Weichselian interstadials (c. 87-109 ka and c. 83-78 ka), reaching a distributional maxima in the north-central European lowlands. Some fossil sites point to notably rapid responses to some abrupt climate events (Dansgaard-Oeschger cycles and Heinrich Events). Combined fossil and genetic data identify at least six MIS 2 refuges and postglacial recolonization pathways. The establishment of extant L. decidua forests dates back to the first two millennia of the Holocene (c. 11.5-9.5 ka) and the onset of anthropogenic impact was inferred since the late Neolithic (c. 6 ka), with major changes occurring since the Bronze Age (c. 4 ka). During the last 300 years human-induced translocations resulted in recent admixture of populations originating from separate refuges. Altogether, the results of this study provide valuable clues for developing sustainable conservation and management strategies targeting ancient genetic lineages and for studying evolutionary issues.

  3. On the development of protein pKa calculation algorithms

    SciTech Connect

    Carstensen, Tommy; Farrell, Damien; Huang, Yong; Baker, Nathan A.; Nielsen, Jens E.

    2011-12-01

    Protein pKa calculation algorithms are typically developed to reproduce experimental pKa values and provide us with a better understanding of the fundamental importance of electrostatics for protein structure and function. However, the approximations and adjustable parameters employed in almost all pKa calculation methods means that there is the risk that pKa calculation algorithms are 'over-fitted' to the available datasets, and that these methods therefore do not model protein physics realistically. We employ simulations of the protein pKa calculation algorithm development process to show that careful optimization procedures and non-biased experimental datasets must be applied to ensure a realistic description of the underlying physical terms. We furthermore investigate the effect of experimental noise and find a significant effect on the pKa calculation algorithm optimization landscape. Finally, we comment on strategies for ensuring the physical realism of protein pKa calculation algorithms and we assess the overall state of the field with a view to predicting future directions of development.

  4. Entrapment of alpha1-acid glycoprotein in high-performance affinity columns for drug-protein binding studies.

    PubMed

    Bi, Cong; Jackson, Abby; Vargas-Badilla, John; Li, Rong; Rada, Giana; Anguizola, Jeanethe; Pfaunmiller, Erika; Hage, David S

    2016-05-15

    A slurry-based method was developed for the entrapment of alpha1-acid glycoprotein (AGP) for use in high-performance affinity chromatography to study drug interactions with this serum protein. Entrapment was achieved based on the physical containment of AGP in hydrazide-activated porous silica supports and by using mildly oxidized glycogen as a capping agent. The conditions needed for this process were examined and optimized. When this type of AGP column was used in binding studies, the association equilibrium constant (Ka) measured by frontal analysis at pH 7.4 and 37°C for carbamazepine with AGP was found to be 1.0 (±0.5)×10(5)M(-1), which agreed with a previously reported value of 1.0 (±0.1)×10(5)M(-1). Binding studies based on zonal elution were conducted for several other drugs with such columns, giving equilibrium constants that were consistent with literature values. An entrapped AGP column was also used in combination with a column containing entrapped HSA in a screening assay format to compare the binding of various drugs to AGP and HSA. These results also agreed with previous data that have been reported in literature for both of these proteins. The same entrapment method could be extended to other proteins and to the investigation of additional types of drug-protein interactions. Potential applications include the rapid quantitative analysis of biological interactions and the high-throughput screening of drug candidates for their binding to a given protein.

  5. Elastic constants of calcite

    USGS Publications Warehouse

    Peselnick, L.; Robie, R.A.

    1962-01-01

    The recent measurements of the elastic constants of calcite by Reddy and Subrahmanyam (1960) disagree with the values obtained independently by Voigt (1910) and Bhimasenachar (1945). The present authors, using an ultrasonic pulse technique at 3 Mc and 25??C, determined the elastic constants of calcite using the exact equations governing the wave velocities in the single crystal. The results are C11=13.7, C33=8.11, C44=3.50, C12=4.82, C13=5.68, and C14=-2.00, in units of 1011 dyncm2. Independent checks of several of the elastic constants were made employing other directions and polarizations of the wave velocities. With the exception of C13, these values substantially agree with the data of Voigt and Bhimasenachar. ?? 1962 The American Institute of Physics.

  6. Aspartate embedding depth affects pHLIP's insertion pKa.

    PubMed

    Fendos, Justin; Barrera, Francisco N; Engelman, Donald M

    2013-07-01

    We have used the pHlow insertion peptide (pHLIP) family to study the role of aspartate embedding depth in pH-dependent transmembrane peptide insertion. pHLIP binds to the surface of a lipid bilayer as a largely unstructured monomer at neutral pH. When the pH is lowered, pHLIP inserts spontaneously across the membrane as a spanning α-helix. pHLIP insertion is reversible when the pH is adjusted back to a neutral value. One of the critical events facilitating pHLIP insertion is the protonation of aspartates in the spanning domain of the peptide: the negative side chains of these residues convert to uncharged, polar forms, facilitating insertion by altering the hydrophobicity of the spanning domain. To examine this protonation mechanism further, we created pHLIP sequence variants in which the two spanning aspartates (D14 and D25) were moved up or down in the sequence. We hypothesized that the aspartate depth in the inserted state would directly affect the proton affinity of the acidic side chains, altering the pKa of pH-dependent insertion. To this end, we also mutated the arginine at position 11 to determine whether arginine snorkeling modulates the insertion pKa by affecting the aspartate depth. Our results indicate that both types of mutations change the insertion pKa, supporting the idea that the aspartate depth is a participating parameter in determining the pH dependence. We also show that pHLIP's resistance to aggregation can be altered with our mutations, identifying a new criterion for improving the performance of pHLIP in vivo when targeting acidic disease tissues such as cancer and inflammation. PMID:23721379

  7. A hemispherically scanning X/Ka band mirror antenna

    NASA Astrophysics Data System (ADS)

    Hollenbeck, Kurt; Kesler, Oren

    1987-02-01

    Texas Instruments, under contract to Naval Surface Weapons Center (NSWC), have delivered the first proof of concept, prototype X and Ka band Mirror Scanning Antenna to the Navy. This antenna is a candidate for the Navy's new generation of ship self defense weapon systems and culminates over two years of work by Texas Instruments' Antenna Department. Several unique operational features are offered by the Mirror Scanning Antenna. These features include full hemispherical scan coverage, simultaneous X and Ka band dual plane monopulse tracking, rapid scan rates, variable scan modes, high Ka band power handling ability, and an integral weather-tight protective radome.

  8. NASA SCaN Overview and Ka-Band Actvities

    NASA Technical Reports Server (NTRS)

    Stegeman, James D.; Midon, Marco Mario; Davarian, Faramaz; Geldzahler, Barry

    2014-01-01

    The Ka- and Broadband Communications Conference is an international forum attended by worldwide experts in the area of Ka-Band Propagation and satellite communications. Since its inception, NASA has taken the initiative of organizing and leading technical sections on RF Propagation and satellite communications, solidifying its worldwide leadership in the aforementioned areas. Consequently, participation in this conference through the contributions described below will maintain NASA leadership in Ka- and above RF Propagation as it relates to enhancing current and future satellite communication systems supporting space exploration.

  9. The Hubble constant

    NASA Technical Reports Server (NTRS)

    Huchra, John P.

    1992-01-01

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy radial velocities and distances. Although there has been considerable progress in the development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution.

  10. Onboard Interferometric SAR Processor for the Ka-Band Radar Interferometer (KaRIn)

    NASA Technical Reports Server (NTRS)

    Esteban-Fernandez, Daniel; Rodriquez, Ernesto; Peral, Eva; Clark, Duane I.; Wu, Xiaoqing

    2011-01-01

    An interferometric synthetic aperture radar (SAR) onboard processor concept and algorithm has been developed for the Ka-band radar interferometer (KaRIn) instrument on the Surface and Ocean Topography (SWOT) mission. This is a mission- critical subsystem that will perform interferometric SAR processing and multi-look averaging over the oceans to decrease the data rate by three orders of magnitude, and therefore enable the downlink of the radar data to the ground. The onboard processor performs demodulation, range compression, coregistration, and re-sampling, and forms nine azimuth squinted beams. For each of them, an interferogram is generated, including common-band spectral filtering to improve correlation, followed by averaging to the final 1 1-km ground resolution pixel. The onboard processor has been prototyped on a custom FPGA-based cPCI board, which will be part of the radar s digital subsystem. The level of complexity of this technology, dictated by the implementation of interferometric SAR processing at high resolution, the extremely tight level of accuracy required, and its implementation on FPGAs are unprecedented at the time of this reporting for an onboard processor for flight applications.

  11. Compassion is a constant.

    PubMed

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands.

  12. XrayOpticsConstants

    2005-06-20

    This application (XrayOpticsConstants) is a tool for displaying X-ray and Optical properties for a given material, x-ray photon energy, and in the case of a gas, pressure. The display includes fields such as the photo-electric absorption attenuation length, density, material composition, index of refraction, and emission properties (for scintillator materials).

  13. Compassion is a constant.

    PubMed

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands. PMID:26542898

  14. Determination of acidity constants of enolisable compounds by capillary electrophoresis.

    PubMed

    Mofaddel, N; Bar, N; Villemin, D; Desbène, P L

    2004-10-01

    Research on the structure-activity relationships of molecules with acidic carbon atoms led us to undertake a feasibility study on the determination of their acidity constants by capillary electrophoresis (CE). The studied molecules had diverse structures and were tetronic acid, acetylacetone, diethylmalonate, Meldrum's acid, 3-methylrhodanine, nitroacetic acid ethyl ester, pyrimidine-2,4,6-trione, 3-oxo-3-phenylpropionic acid ethyl ester, 1-phenylbutan-1,3-dione, 5,5-dimethylcyclohexan-1,3-dione and homophthalic anhydride. The p Ka range explored by CE was therefore very large (from 3 to 12) and p Ka values near 12 were evaluated by mathematical extrapolations. The analyses were carried out in CZE mode using a fused silica capillary grafted (or not) with hexadimethrine. Owing to the electrophoretic behaviour of these compounds according to the pH, their acidity constants could be evaluated and appeared in perfect agreement with the literature data obtained, a few decades ago, by means of potentiometry, spectrometry or conductimetry. The p Ka of homophthalic anhydride and 3-methylrhodanine were evaluated for the first time.

  15. Mars Telecommunications Orbiter Ka-band system design and operations

    NASA Technical Reports Server (NTRS)

    Noreen, Gary; Komarek, Tomas; Diehl, Roger; Shambayati, Shervin; Breidenthal, Julian; Lopez, Saturnino; Jordan, Frank

    2003-01-01

    NASA's Mars Telecommunications Orbiter (MTO) will relay broadband communications from landers, rovers and spacecraft in the vicinity of Mars to Earth. This paper describes the MTO communications system and how the MTO Ka-band system will be operated.

  16. A 20-ka climate record from Central Himalayan loess deposits

    NASA Astrophysics Data System (ADS)

    Pant, R. K.; Basavaiah, N.; Juyal, N.; Saini, N. K.; Yadava, M. G.; Appel, E.; Singhvi, A. K.

    2005-07-01

    The southwest monsoon that dominated Central Himalaya has preserved loessic silt deposits preserved in patches that are proximal to periglacial areas. The occurrence of such silts suggests contemporary prevalence of cold and dry northwesterly winds. Field stratigraphy, geochemistry, mineral magnetism, infrared stimulated luminescence (IRSL) and radiocarbon dating has enabled reconstruction of an event chronology during the past 20 ka. Three events of loess accretion could be identified. The first two events of loess deposition occurred betweem 20 and 9 ka and were separated by a phase of moderate weathering. Pedogenesis at the end of this event gave rise to a well-developed soil that was bracketed around 9 to > 4 ka. This was followed by the third phase of loess accretion that occurred around 4 to > 1 ka. Episodes of loess deposition and soil formation are interpreted in terms of changes in the strength of the Indian southwest monsoon. Copyright

  17. A comparative study of RADAR Ka-band backscatter

    NASA Astrophysics Data System (ADS)

    Mapelli, D.; Pierdicca, N.; Guerriero, L.; Ferrazzoli, Paolo; Calleja, Eduardo; Rommen, B.; Giudici, D.; Monti Guarnieri, A.

    2014-10-01

    Ka-band RADAR frequency range has not yet been used for Synthetic Aperture Radar (SAR) from space so far, although this technology may lead to important applications for the next generation of SAR space sensors. Therefore, feasibility studies regarding a Ka-band SAR instrument have been started [1][2], for the next generation of SAR space sensors. In spite of this, the lack of trusted references on backscatter at Ka-band revealed to be the main limitation for the investigation of the potentialities of this technology. In the framework of the ESA project "Ka-band SAR backscatter analysis in support of future applications", this paper is aimed at the study of wave interaction at Ka-band for a wide range of targets in order to define a set of well calibrated and reliable Ka-band backscatter coefficients for different kinds of targets. We propose several examples of backscatter data resulting from a critical survey of available datasets at Ka-band, focusing on the most interesting cases and addressing both correspondences and differences. The reliability of the results will be assessed via a preliminary comparison with ElectroMagnetic (EM) theoretical models. Furthermore, in support of future technological applications, we have designed a prototypal software acting as a "library" of earth surface radar response. In our intention, the output of the study shall contribute to answer to the need of a trustworthy Ka-Band backscatter reference. It will be of great value for future technological applications, such as support to instrument analysis, design and requirements' definition (e.g.: Signal to Noise Ratio, Noise Equivalent Sigma Zero).

  18. The Mars Observer Ka-band link experiment

    NASA Technical Reports Server (NTRS)

    Rebold, T. A.; Kwok, A.; Wood, G. E.; Butman, S.

    1994-01-01

    The Ka-Band Link Experiment was the first demonstration of a deep-space communications link in the 32- to 35-GHz band (Ka-band). It was carried out using the Mars Observer spacecraft while the spacecraft was in the cruise phase of its mission and using a 34-meter beam-waveguide research and development antenna at the Goldstone complex of the DSN. The DSN has been investigating the performance benefits of a shift from X-band (8.4 GHz) to Ka-band (32 GHz) for deep-space communications. The fourfold increase in frequency is expected to offer a factor of 3 to 10 improvement (5 to 10 dB) in signal strength for a given spacecraft transmitter power and antenna size. Until recently, the expected benefits were based on performance studies, with an eye to implementing such a link, but theory was transformed to reality when a 33.7-GHz Ka-band signal was received from the spacecraft by DSS 13. This article describes the design and implementation of the Ka-Band Link Experiment from the spacecraft to the DSS-13 system, as well as results from the Ka-band telemetry demonstration, ranging demonstration, and long-term tracking experiment. Finally, a preliminary analysis of comparative X- and Ka-band tracking results is included. These results show a 4- to 7-dB advantage for Ka-band using the system at DSS 13, assuming such obstacles as antenna pointing loss and power conversion loss are overcome.

  19. Lectin affinity chromatography of glycolipids

    SciTech Connect

    Torres, B.V.; Smith, D.F.

    1987-05-01

    Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.

  20. Wall of fundamental constants

    SciTech Connect

    Olive, Keith A.; Peloso, Marco; Uzan, Jean-Philippe

    2011-02-15

    We consider the signatures of a domain wall produced in the spontaneous symmetry breaking involving a dilatonlike scalar field coupled to electromagnetism. Domains on either side of the wall exhibit slight differences in their respective values of the fine-structure constant, {alpha}. If such a wall is present within our Hubble volume, absorption spectra at large redshifts may or may not provide a variation in {alpha} relative to the terrestrial value, depending on our relative position with respect to the wall. This wall could resolve the contradiction between claims of a variation of {alpha} based on Keck/Hires data and of the constancy of {alpha} based on Very Large Telescope data. We derive the properties of the wall and the parameters of the underlying microscopic model required to reproduce the possible spatial variation of {alpha}. We discuss the constraints on the existence of the low-energy domain wall and describe its observational implications concerning the variation of the fundamental constants.

  1. Recent Results From The Mars Global Surveyor Ka-Band Link Experiment (MGS/KaBLE-II)

    NASA Technical Reports Server (NTRS)

    Morabito, D.; Butman, S.; Shambayati, S.

    1998-01-01

    The Mars Global Surveyor (MGS) spacecraft, launched on November 7, 1996, carries an experimental space-to-ground telecommunications link at Ka-Band (32 GHz) along with the primary X-band (8.4 GHz) downlink.

  2. Varying constants quantum cosmology

    SciTech Connect

    Leszczyńska, Katarzyna; Balcerzak, Adam; Dabrowski, Mariusz P. E-mail: abalcerz@wmf.univ.szczecin.pl

    2015-02-01

    We discuss minisuperspace models within the framework of varying physical constants theories including Λ-term. In particular, we consider the varying speed of light (VSL) theory and varying gravitational constant theory (VG) using the specific ansätze for the variability of constants: c(a) = c{sub 0} a{sup n} and G(a)=G{sub 0} a{sup q}. We find that most of the varying c and G minisuperspace potentials are of the tunneling type which allows to use WKB approximation of quantum mechanics. Using this method we show that the probability of tunneling of the universe ''from nothing'' (a=0) to a Friedmann geometry with the scale factor a{sub t} is large for growing c models and is strongly suppressed for diminishing c models. As for G varying, the probability of tunneling is large for G diminishing, while it is small for G increasing. In general, both varying c and G change the probability of tunneling in comparison to the standard matter content (cosmological term, dust, radiation) universe models.

  3. Multiple GPCR conformations and signalling pathways: implications for antagonist affinity estimates

    PubMed Central

    Baker, Jillian G.; Hill, Stephen J.

    2007-01-01

    Antagonist affinity measurements have traditionally been considered important in characterizing the cell-surface receptors present in a particular cell or tissue. A central assumption has been that antagonist affinity is constant for a given receptor–antagonist interaction, regardless of the agonist used to stimulate that receptor or the downstream response that is measured. As a consequence, changes in antagonist affinity values have been taken as initial evidence for the presence of novel receptor subtypes. Emerging evidence suggests, however, that receptors can possess multiple binding sites and the same receptor can show different antagonist affinity measurements under distinct experimental conditions. Here, we discuss several mechanisms by which antagonists have different affinities for the same receptor as a consequence of allosterism, coupling to different G proteins, multiple (but non-interacting) receptor sites, and signal-pathway-dependent pharmacology (where the pharmacology observed varies depending on the signalling pathway measured). PMID:17629959

  4. General approach for characterizing in vitro selected peptides with protein binding affinity.

    PubMed

    Larsen, Andrew C; Gillig, Annabelle; Shah, Pankti; Sau, Sujay P; Fenton, Kathryn E; Chaput, John C

    2014-08-01

    In vitro selection technologies are important tools for identifying high affinity peptides to proteins of broad medical and biological interest. However, the technological advances that have made it possible to generate long lists of candidate peptides have far outpaced our ability to characterize the binding properties of individual peptides. Here, we describe a low cost strategy to rapidly synthesize, purify, screen, and characterize peptides for high binding affinity. Peptides are assayed in a 96-well dot blot apparatus using membranes that enable partitioning of bound and unbound peptide-protein complexes. We have validated the binding affinity constants produced by this method using known peptide ligands and applied this process to discover five new peptides with nanomolar affinity to human α-thrombin. Given the need for new analytical tools that can accelerate peptide discovery and characterization, we feel that this approach would be useful to a wide range of technologies that utilize high affinity peptides.

  5. Two-parameter twisted quantum affine algebras

    NASA Astrophysics Data System (ADS)

    Jing, Naihuan; Zhang, Honglian

    2016-09-01

    We establish Drinfeld realization for the two-parameter twisted quantum affine algebras using a new method. The Hopf algebra structure for Drinfeld generators is given for both untwisted and twisted two-parameter quantum affine algebras, which include the quantum affine algebras as special cases.

  6. Native Elution of Yeast Protein Complexes Obtained by Affinity Capture.

    PubMed

    LaCava, John; Fernandez-Martinez, Javier; Rout, Michael P

    2016-01-01

    This protocol describes two options for the native (nondenaturing) elution of protein complexes obtained by affinity capture. The first approach involves the elution of complexes purified through a tag that includes a human rhinovirus 3C protease (PreScission protease) cleavage site sequence between the protein of interest and the tag. Incubation with the protease cleaves immobilized complexes from the affinity medium. The second approach involves the release of protein A-tagged protein complexes using a competitive elution reagent called PEGylOx. The degree of purity of the native assemblies eluted is sample dependent and strongly influenced by the affinity capture. It should be noted that the efficiency of native elution is commonly lower than that of elution by a denaturing agent (e.g., SDS) and the release of the complex will be limited by the activity of the protease or the inhibition constant (Ki) of the competitive release agent. However, an advantage of native release is that some nonspecifically bound materials tend to stay adsorbed to the affinity medium, providing an eluted fraction of higher purity. Finally, keep in mind that the presence of the protease or elution peptide could potentially affect downstream applications; thus, their removal should be considered. PMID:27371597

  7. A chirality change in XPC- and Sfi1-derived peptides affects their affinity for centrin.

    PubMed

    Grecu, Dora; Irudayaraj, Victor Paul Raj; Martinez-Sanz, Juan; Mallet, Jean-Maurice; Assairi, Liliane

    2016-04-01

    The Ca(2+)-binding protein centrin binds to a hydrophobic motif (W(1)xxL(4)xxxL(8)) included in the sequence of several cellular targets: XPC (xeroderma pigmentosum group C protein), Sfi1 (suppressor of fermentation-induced loss of stress resistance protein1), and Sac3 [the central component of the transcription and mRNA export (TREX-2) complex]. However, centrin binding occurs in a reversed orientation (L(8)xxxL(4)xxW(1)) for Sfi1 and Sac3 compared with XPC. Because D-peptides have been investigated for future therapeutic use, we analyzed their centrin-binding properties. Their affinity for centrin was measured using isothermal titration calorimetry. The chirality change in the target-derived peptides affected their ability to bind centrin in a specific manner depending on the sequence orientation of the centrin-binding motif. In contrast to L-XPC-P10, D-XPC-P10 bound C-HsCen1 in a Ca(2+)-dependent manner and to a lesser extent. D-XPC-P10 exhibited a reduced affinity for C-HsCen1 (Ka=0.064 × 10(6) M(-1)) by a factor of 2000 compared with L-XPC-P10 (Ka=132 × 10(6) M(-1)). D-peptides have a lower affinity than L-peptides for centrin, and the strength of this affinity depends on the sequence orientation of the target-derived peptides. The residual affinity observed for D-XPC suggests that the use of d-peptides represents a promising strategy for inhibiting centrin binding to its targets.

  8. Binding affinities of anti-acetylcholine receptor autoantibodies in myasthenia gravis

    SciTech Connect

    Bray, J.J.; Drachman, D.B.

    1982-01-01

    Antibodies directed against acetylcholine (ACh) receptors are present in the sera of nearly 90% of patients with myasthenia gravis (MG), and are involved in the pathogenesis of this autoimmune disease. However, the antibody titers measured by the standard radioimmunoassay correspond poorly with the clinical severity of the disease. To determine whether this disparity could be accounted for by differences in the binding affinities of anti-ACh receptor antibodies in different patients, we have measured the binding affinities of these autoantibodies in 15 sera from MG patients. The affinity constants (K/sub o/), as determined by Scatchard analysis, were all in the range of 10/sup 10/ M/sup -1/, comparable to the highest values reported in immunized animals. The affinity constants were truly representative of the population of autoantibodies detected by the radioimmunoassay, as shown by the remarkable linearity of the Scatchard plots (r/sup 2/>0.90) and the close correlation between the antibody titers determined by extrapolation of the Scatchard plots and by saturation analysis (r = 0.99; p < 0.001). There was only a 6-fold variation in affinity constants measured in this series of patients despite widely differing antibody titers and severity of the disease. Factors other than the titer and affinity of anti-ACh receptor antibodies may correlate better with the clinical manifestations of MG.

  9. Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers.

    PubMed

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2015-03-01

    Estimation of the dissociation constant, or pKa, of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pKa values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pKa, the acid dissociation constant. We show that the method predicts the pKa value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pKa values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data. PMID:25652329

  10. Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers.

    PubMed

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2015-03-01

    Estimation of the dissociation constant, or pKa, of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pKa values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pKa, the acid dissociation constant. We show that the method predicts the pKa value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pKa values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

  11. Germline variable region gene segment derivation of human monoclonal anti-Rh(D) antibodies. Evidence for affinity maturation by somatic hypermutation and repertoire shift.

    PubMed Central

    Bye, J M; Carter, C; Cui, Y; Gorick, B D; Songsivilai, S; Winter, G; Hughes-Jones, N C; Marks, J D

    1992-01-01

    To date, there has been no systematic study of the process of affinity maturation of human antibodies. We therefore sequenced the variable region genes (V genes) of 14 human monoclonal antibodies specific for the erythrocyte Rh(D) alloantigen and determined the germline gene segments of origin and extent of somatic hypermutation. These data were correlated with determinations of antibody affinity. The four IgM antibodies (low affinity) appear to be derived from two germline heavy chain variable region gene segments and one or two germline light chain variable region gene segments and were not extensively mutated. The 10 IgG antibodies (higher affinity) appear to be derived from somatic hypermutation of these V gene segments and by use of new V gene segments or V gene segment combinations (repertoire shift). Affinity generally increased with increasing somatic hypermutation; on average, there were 8.9 point mutations in the V gene segments of the four IgM antibodies (Ka = 1-4 x 10(7)/M-1) compared with 19 point mutations in the V gene segments of the 10 IgG antibodies. The four highest affinity antibodies (Ka = 0.9-3 x 10(9)/M-1) averaged 25.5 point mutations. The use of repertoire shift and somatic hypermutation in affinity maturation of human alloantibodies is similar to data obtained in inbred mice immunized with haptens. PMID:1469099

  12. Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site.

    PubMed

    Song, Xiangfei; Wang, Yefei; Zhang, Shujun; Yan, Shihai; Li, Tong; Yao, Lishan

    2015-07-27

    An attempt is made to evaluate the dielectric constant of the Trichoderma reesei Cel7B active site. Through kinetic measurements, the pKa value of the catalytic acid E201 is determined. Mutations (away from E201) with net charge changes are introduced to perturb the E201 pKa. It is shown that the mutation with a +1 charge change (including G225R, G230R, and A335R) decreases the pKa of E201, whereas the mutation with a -1 charge change (including Q149E, A222D, G225D, and G230D) increases the pKa. This effect is consistent with the electrostatic interaction between the changed charge and the E201 side chain. The fitting of the experimental data yields an apparent dielectric constant of 25-80. Molecular dynamics simulations with explicit water molecules indicate that the high solvent accessibility of the active site contributes largely to the high dielectric constant. ONIOM calculations show that high dielectric constant benefits the catalysis through decreasing the energy of the transition state relative to that of the enzyme substrate complex. PMID:26114648

  13. Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site.

    PubMed

    Song, Xiangfei; Wang, Yefei; Zhang, Shujun; Yan, Shihai; Li, Tong; Yao, Lishan

    2015-07-27

    An attempt is made to evaluate the dielectric constant of the Trichoderma reesei Cel7B active site. Through kinetic measurements, the pKa value of the catalytic acid E201 is determined. Mutations (away from E201) with net charge changes are introduced to perturb the E201 pKa. It is shown that the mutation with a +1 charge change (including G225R, G230R, and A335R) decreases the pKa of E201, whereas the mutation with a -1 charge change (including Q149E, A222D, G225D, and G230D) increases the pKa. This effect is consistent with the electrostatic interaction between the changed charge and the E201 side chain. The fitting of the experimental data yields an apparent dielectric constant of 25-80. Molecular dynamics simulations with explicit water molecules indicate that the high solvent accessibility of the active site contributes largely to the high dielectric constant. ONIOM calculations show that high dielectric constant benefits the catalysis through decreasing the energy of the transition state relative to that of the enzyme substrate complex.

  14. Analysis of agonist dissociation constants as assessed by functional antagonism in guinea pig left atria

    SciTech Connect

    Molenaar, P.; Malta, E.

    1986-04-01

    In electrically driven guinea pig left atria, positive inotropic responses to (-)-isoprenaline and the selective beta 1-adrenoceptor agonist RO363 were obtained in the absence and in the presence of the functional antagonists adenosine, carbachol, gallopamil, nifedipine, and Ro 03-7894. Each of the functional antagonists reduced the maximum response to both agonists and produced nonparallel rightward shifts in the cumulative concentration effect curves. For both agonists, dissociation constants (KA) were calculated using the equation described by Furchgott (1966) for irreversible antagonism. For RO363, which is a partial agonist with high agonist activity, the equations outlined for functional interaction by Mackay (1981) were also employed to calculate KA values. The KA values obtained by each method were compared with the dissociation constants (KD) for the two agonists determined from their ability to displace the radioligand (-)-(/sup 125/I)iodocyanopindolol from beta 1-adrenoceptors in guinea pig left atrial membrane preparations. The estimates of KA varied substantially from KD values. The KD values were taken as more accurate estimates of the true values for the dissociation constants because a high degree of correlation exists between pKD and pD2 values for a number of other beta-adrenoceptor agonists that behave as partial agonists and between pKD and pKB values for a number of beta-adrenoceptor antagonists. Thus, it appears that there are serious limitations in the current theory for using functional antagonism as a means of obtaining agonist dissociation constants.

  15. Change is a Constant.

    PubMed

    Lubowitz, James H; Provencher, Matthew T; Brand, Jefferson C; Rossi, Michael J; Poehling, Gary G

    2015-06-01

    In 2015, Henry P. Hackett, Managing Editor, Arthroscopy, retires, and Edward A. Goss, Executive Director, Arthroscopy Association of North America (AANA), retires. Association is a positive constant, in a time of change. With change comes a need for continuing education, research, and sharing of ideas. While the quality of education at AANA and ISAKOS is superior and most relevant, the unique reason to travel and meet is the opportunity to interact with innovative colleagues. Personal interaction best stimulates new ideas to improve patient care, research, and teaching. Through our network, we best create innovation.

  16. Cosmology with varying constants.

    PubMed

    Martins, Carlos J A P

    2002-12-15

    The idea of possible time or space variations of the 'fundamental' constants of nature, although not new, is only now beginning to be actively considered by large numbers of researchers in the particle physics, cosmology and astrophysics communities. This revival is mostly due to the claims of possible detection of such variations, in various different contexts and by several groups. I present the current theoretical motivations and expectations for such variations, review the current observational status and discuss the impact of a possible confirmation of these results in our views of cosmology and physics as a whole.

  17. Complex high affinity interactions occur between MHCI and superantigens

    NASA Technical Reports Server (NTRS)

    Chapes, S. K.; Herpich, A. R.; Spooner, B. S. (Principal Investigator)

    1998-01-01

    Staphylococcal enterotoxins A and C1 (SEA or SEC1) bound to major histocompatibility-I (MHCI) molecules with high affinity (binding constants ranging from 1.1 microM to 79 nM). SEA and SEC1 directly bound MHCI molecules that had been captured by monoclonal antibodies specific for H-2Kk, H-2Dk, or both. In addition, MHCI-specific antibodies inhibited the binding of SEC1 to LM929 cells and SEA competitively inhibited SEC1 binding; indicating that the superantigens bound to MHCI on the cell surface. The affinity and number of superantigen binding sites differed depending on whether MHCI was expressed in the membrane of LM929 cells or whether it was captured. These data support the hypothesis that MHCI molecules can serve as superantigen receptors.

  18. Affinity screening using competitive binding with fluorine-19 hyperpolarized ligands.

    PubMed

    Kim, Yaewon; Hilty, Christian

    2015-04-13

    Fluorine-19 NMR and hyperpolarization form a powerful combination for drug screening. Under a competitive equilibrium with a selected fluorinated reporter ligand, the dissociation constant (K(D)) of other ligands of interest is measurable using a single-scan Carr-Purcell-Meiboom-Gill (CPMG) experiment, without the need for a titration. This method is demonstrated by characterizing the binding of three ligands with different affinities for the serine protease trypsin. Monte Carlo simulations show that the highest accuracy is obtained when about one-half of the bound reporter ligand is displaced in the binding competition. Such conditions can be achieved over a wide range of affinities, allowing for rapid screening of non-fluorinated compounds when a single fluorinated ligand for the binding pocket of interest is known.

  19. Banach frames in the affine synthesis problem

    NASA Astrophysics Data System (ADS)

    Terekhin, Pavel A.

    2009-10-01

    We consider the problem of representing functions f\\in L^p(\\mathbb R^d) by a series in elements of the affine system \\displaystyle \\psi_{j,k}(x)=\\lvert\\det a_j\\rvert^{1/2}\\psi(a_jx-bk), \\qquad j\\in\\mathbb N, \\quad k\\in\\mathbb Z^d. The corresponding representation theorems are established on the basis of the frame inequalities \\displaystyle A\\Vert g\\Vert _q\\le\\Vert\\{(g,\\psi_{j,k})\\}\\Vert _Y\\le B\\Vert g\\Vert _q for the Fourier coefficients \\displaystyle(g,\\psi_{j,k})=\\int_{\\mathbb R^d}g(x)\\psi_{j,k}(x)\\,dx of functions g\\in L^q(\\mathbb R^d), 1/p+1/q=1, where {\\Vert\\cdot\\Vert}_Y is the norm in some Banach space of number families \\{y_{j,k}\\} and 0 are constants. In particular, it is proved that if the integral of a function \\psi\\in L^1\\cap L^p(\\mathbb R^d), 1, is nonzero, so \\displaystyle\\int_{\\mathbb R^d}\\psi(x)\\,dx\

  20. THE CURRENT STAR FORMATION RATE OF K+A GALAXIES

    SciTech Connect

    Nielsen, Danielle M.; Ridgway, Susan E.; De Propris, Roberto; Goto, Tomotsugu

    2012-12-20

    We derive the stacked 1.4 GHz flux from the FIRST survey for 811 K+A galaxies selected from the Sloan Digital Sky Survey Data Release 7. For these objects we find a mean flux density of 56 {+-} 9 {mu}Jy. A similar stack of radio-quiet white dwarfs yields an upper limit of 43 {mu}Jy at a 5{sigma} significance to the flux in blank regions of the sky. This implies an average star formation rate of 1.6 {+-} 0.3 M{sub Sun} yr{sup -1} for K+A galaxies. However, the majority of the signal comes from {approx}4% of K+A fields that have aperture fluxes above the 5{sigma} noise level of the FIRST survey. A stack of the remaining galaxies shows little residual flux consistent with an upper limit on star formation of 1.3 M{sub Sun} yr{sup -1}. Even for a subset of 456 'young' (spectral ages <250 Myr) K+A galaxies, we find that the stacked 1.4 GHz flux is consistent with no current star formation. Our data suggest that the original starburst has been terminated in the majority of K+A galaxies, but that this may represent part of a duty cycle where a fraction of these galaxies may be active at a given moment with dusty starbursts and active galactic nuclei being present.

  1. Sea surface temperatures in the North Atlantic Ocean from 30ka to 10ka

    NASA Astrophysics Data System (ADS)

    Barrack, Kerr; Greenop, Rosanna; Burke, Andrea; Barker, Stephen; Chalk, Thomas; Crocker, Anya

    2016-04-01

    Some of the most striking features of the Late Pleistocene interval are the rapid changes in climate between warmer interstadial and cold stadial periods which, when coupled, are termed Dansgaard-Oeschger (D-O) events. This shift between warm and cold climates has been interpreted to result from changes in the thermohaline circulation (Broecker et al., 1985) triggered by, for instance, freshwater input from the collapse of the Laurentide ice sheet (Zahn et al., 1997). However, a recent study suggests that major ice rafting events cannot be the 'trigger' for the centennial to millennial scale cooling events identified over the past 500kyr (Barker at al., 2015). Polar planktic foraminiferal and lithogenic/terrigenous grain counts reveal that the southward migration of the polar front occurs before the deposition of ice rafted debris and therefore the rafting of ice during stadial periods. Based upon this evidence, Barker et al. suggest that the transition to a stadial state is a non-linear response to gradual cooling in the region. In order to test this hypothesis, our study reconstructs sea surface temperature across D-O events and the deglaciation in the North Atlantic between 30ka and 10ka using Mg/ Ca paleothermometry in Globigerina bulloides at ODP Sites 980 and 983 (the same sites as used in Barker et al., 2015) with an average sampling resolution of 300 years. With our new record we evaluate the timing of surface ocean temperature change, frontal shift movement, and ice rafting to investigate variations in the temperature gradient across the polar front over D-O events. References: Barker, S., Chen, J., Gong, X., Jonkers, L., Knorr, G., Thornalley, D., 2015. Icebergs not the trigger for North Atlantic cold events. Nature, 520(7547), pp.333-336. Broecker, W.S., Peteer, D.M., Rind, D., 1985. Does the ocean-atmosphere system have more than one stable mode of operation? Nature, 315 (6014), pp.21-26. Zahn, R., Schönfeld, J., Kudrass, H.-R., Park, M

  2. High affinity DNA-microtubule associated protein interaction.

    PubMed

    Marx, K A

    1992-07-01

    We have isolated the MAP/tau proteins from twice-cycled chick brain microtubule preparations and demonstrated that they are responsible for the nitrocellulose DNA binding activity we and others have measured. Using the isolated MAP/tau proteins we then measured the apparent affinity constant K(app) for the homologous chick DNA interaction and found evidence for two equilibrium affinity classes-a K(app) = 6 x 10(7) M-1, responsible for the bulk of the DNA binding activity and a small (less than 10%) higher affinity K(app) = 10(8) - 10(9) M-1, likely due to sequence specific binding protein species. Using the same chick brain MAP-tau protein, a heterologous interaction with D. melanogaster DNA, was found to possess just the lower affinity class-K(app) = 2 x 10(7) M-1. Under stringent binding conditions we carried out equilibrium nitrocellulose filter binding experiments in a ternary reaction mixture at constant MAP/tau protein and 35S radiolabelled chick DNA concentration using increasing and excess concentrations of competitor DNAs of different sources. The order of competitor strengths found was-chick DNA greater than mouse DNA greater than D. melanogaster = E. coli. DNA. These data and specifically the homologous DNA: protein case being the strongest competitor corroborate our previous studies using total microtubule protein and provide new evidence for a conserved interaction of a small DNA sequence class with MAP/tau protein species. Moreover, these data allow us to conclude that the conserved DNA sequence: MAP/tau protein interactions do not critically depend upon any energetic feature co-involving tubulin for their properties since tubulin is absent from these preparations.

  3. About variable constants

    NASA Astrophysics Data System (ADS)

    Blichert-Toft, J.; Albarede, F.

    2011-12-01

    When only modern isotope compositions are concerned, the choice of normalization values is inconsequential provided that their values are universally accepted. No harm is done as long as large amounts of standard reference material with known isotopic differences with respect to the reference value ('anchor point') can be maintained under controlled conditions. For over five decades, the scientific community has been referring to an essentially unavailable SMOW for stable O and H isotopes and to a long-gone belemnite sample for carbon. For radiogenic isotopes, the isotope composition of the daughter element, the parent-daughter ratio, and a particular value of the decay constant are all part of the reference. For the Lu-Hf system, for which the physical measurements of the decay constant have been particularly defective, the reference includes the isotope composition of Hf and the Lu/Hf ratio of an unfortunately heterogeneous chondrite mix that has been successively refined by Patchett and Tatsumoto (1981), Blichert-Toft and Albarede (1997, BTA), and Bouvier et al. (2008, BVP). The \\varepsilonHf(T) difference created by using BTA and BVP is nearly within error (+0.45 epsilon units today and -0.36 at 3 Ga) and therefore of little or no consequence. A more serious issue arises when the chondritic reference is taken to represent the Hf isotope evolution of the Bulk Silicate Earth (BSE): the initial isotope composition of the Solar System, as determined by the indistinguishable intercepts of the external eucrite isochron (Blichert-Toft et al., 2002) and the internal angrite SAH99555 isochron (Thrane et al., 2010), differs from the chondrite value of BTA and BVP extrapolated to 4.56 Ga by ~5 epsilon units. This difference and the overestimated value of the 176Lu decay constant derived from the slopes of these isochrons, have been interpreted as reflecting irradiation of the solar nebula by either gamma (Albarede et al., 2006) or cosmic rays (Thrane et al., 2010) during

  4. Measurement of the solar constant

    NASA Technical Reports Server (NTRS)

    Crommelynck, D.

    1981-01-01

    The absolute value of the solar constant and the long term variations that exist in the absolute value of the solar constant were measured. The solar constant is the total irradiance of the Sun at a distance of one astronomical unit. An absolute radiometer removed from the effects of the atmosphere with its calibration tested in situ was used to measure the solar constant. The importance of an accurate knowledge of the solar constant is emphasized.

  5. Ka-band MMIC microstrip array for high rate communications

    NASA Technical Reports Server (NTRS)

    Lee, R. Q.; Raquet, C. A.; Tolleson, J. B.; Sanzgiri, S. M.

    1991-01-01

    In a recent technology assessment of alternative communication systems for the space exploration initiative (SEI), Ka-band (18 to 40 GHz) communication technology was identified to meet the mission requirements of telecommunication, navigation, and information management. Compared to the lower frequency bands, Ka-band antennas offer higher gain and broader bandwidths; thus, they are more suitable for high data rate communications. Over the years, NASA has played an important role in monolithic microwave integrated circuit (MMIC) phased array technology development, and currently, has an ongoing contract with Texas Instrument (TI) to develop a modular Ka-band MMIC microstrip subarray (NAS3-25718). The TI contract emphasizes MMIC integration technology development and stipulates using existing MMIC devices to minimize the array development cost. The objective of this paper is to present array component technologies and integration techniques used to construct the subarray modules.

  6. The Hubble constant.

    PubMed

    Tully, R B

    1993-06-01

    Five methods of estimating distances have demonstrated internal reproducibility at the level of 5-20% rms accuracy. The best of these are the cepheid (and RR Lyrae), planetary nebulae, and surface-brightness fluctuation techniques. Luminosity-line width and Dn-sigma methods are less accurate for an individual case but can be applied to large numbers of galaxies. The agreement is excellent between these five procedures. It is determined that Hubble constant H0 = 90 +/- 10 km.s-1.Mpc-1 [1 parsec (pc) = 3.09 x 10(16) m]. It is difficult to reconcile this value with the preferred world model even in the low-density case. The standard model with Omega = 1 may be excluded unless there is something totally misunderstood about the foundation of the distance scale or the ages of stars. PMID:11607391

  7. When constants are important

    SciTech Connect

    Beiu, V.

    1997-04-01

    In this paper the authors discuss several complexity aspects pertaining to neural networks, commonly known as the curse of dimensionality. The focus will be on: (1) size complexity and depth-size tradeoffs; (2) complexity of learning; and (3) precision and limited interconnectivity. Results have been obtained for each of these problems when dealt with separately, but few things are known as to the links among them. They start by presenting known results and try to establish connections between them. These show that they are facing very difficult problems--exponential growth in either space (i.e. precision and size) and/or time (i.e., learning and depth)--when resorting to neural networks for solving general problems. The paper will present a solution for lowering some constants, by playing on the depth-size tradeoff.

  8. The Hubble constant.

    PubMed Central

    Tully, R B

    1993-01-01

    Five methods of estimating distances have demonstrated internal reproducibility at the level of 5-20% rms accuracy. The best of these are the cepheid (and RR Lyrae), planetary nebulae, and surface-brightness fluctuation techniques. Luminosity-line width and Dn-sigma methods are less accurate for an individual case but can be applied to large numbers of galaxies. The agreement is excellent between these five procedures. It is determined that Hubble constant H0 = 90 +/- 10 km.s-1.Mpc-1 [1 parsec (pc) = 3.09 x 10(16) m]. It is difficult to reconcile this value with the preferred world model even in the low-density case. The standard model with Omega = 1 may be excluded unless there is something totally misunderstood about the foundation of the distance scale or the ages of stars. PMID:11607391

  9. Unitaxial constant velocity microactuator

    DOEpatents

    McIntyre, Timothy J.

    1994-01-01

    A uniaxial drive system or microactuator capable of operating in an ultra-high vacuum environment. The mechanism includes a flexible coupling having a bore therethrough, and two clamp/pusher assemblies mounted in axial ends of the coupling. The clamp/pusher assemblies are energized by voltage-operated piezoelectrics therewithin to operatively engage the shaft and coupling causing the shaft to move along its rotational axis through the bore. The microactuator is capable of repeatably positioning to sub-manometer accuracy while affording a scan range in excess of 5 centimeters. Moreover, the microactuator generates smooth, constant velocity motion profiles while producing a drive thrust of greater than 10 pounds. The system is remotely controlled and piezoelectrically driven, hence minimal thermal loading, vibrational excitation, or outgassing is introduced to the operating environment.

  10. Unitaxial constant velocity microactuator

    DOEpatents

    McIntyre, T.J.

    1994-06-07

    A uniaxial drive system or microactuator capable of operating in an ultra-high vacuum environment is disclosed. The mechanism includes a flexible coupling having a bore therethrough, and two clamp/pusher assemblies mounted in axial ends of the coupling. The clamp/pusher assemblies are energized by voltage-operated piezoelectrics therewithin to operatively engage the shaft and coupling causing the shaft to move along its rotational axis through the bore. The microactuator is capable of repeatably positioning to sub-nanometer accuracy while affording a scan range in excess of 5 centimeters. Moreover, the microactuator generates smooth, constant velocity motion profiles while producing a drive thrust of greater than 10 pounds. The system is remotely controlled and piezoelectrically driven, hence minimal thermal loading, vibrational excitation, or outgassing is introduced to the operating environment. 10 figs.

  11. Constant attitude orbit transfer

    NASA Astrophysics Data System (ADS)

    Cress, Peter; Evans, Michael

    A two-impulse orbital transfer technique is described in which the spacecraft attitude remains constant for both burns, eliminating the need for attitude maneuvers between the burns. This can lead to significant savings in vehicle weight, cost and complexity. Analysis is provided for a restricted class of applications of this transfer between circular orbits. For those transfers with a plane change less than 30 deg, the total velocity cost of the maneuver is less than twelve percent greater than that of an optimum plane split Hohmann transfer. While this maneuver does not minimize velocity requirement, it does provide a means of achieving necessary transfer while substantially reducing the cost and complexity of the spacecraft.

  12. A Constant Pressure Bomb

    NASA Technical Reports Server (NTRS)

    Stevens, F W

    1924-01-01

    This report describes a new optical method of unusual simplicity and of good accuracy suitable to study the kinetics of gaseous reactions. The device is the complement of the spherical bomb of constant volume, and extends the applicability of the relationship, pv=rt for gaseous equilibrium conditions, to the use of both factors p and v. The method substitutes for the mechanical complications of a manometer placed at some distance from the seat of reaction the possibility of allowing the radiant effects of reaction to record themselves directly upon a sensitive film. It is possible the device may be of use in the study of the photoelectric effects of radiation. The method makes possible a greater precision in the measurement of normal flame velocities than was previously possible. An approximate analysis shows that the increase of pressure and density ahead of the flame is negligible until the velocity of the flame approaches that of sound.

  13. Analysis of free drug fractions in human serum by ultrafast affinity extraction and two-dimensional affinity chromatography.

    PubMed

    Zheng, Xiwei; Podariu, Maria; Matsuda, Ryan; Hage, David S

    2016-01-01

    Ultrafast affinity extraction and a two-dimensional high performance affinity chromatographic system were used to measure the free fractions for various drugs in serum and at typical therapeutic concentrations. Pooled samples of normal serum or serum from diabetic patients were utilized in this work. Several drug models (i.e., quinidine, diazepam, gliclazide, tolbutamide, and acetohexamide) were examined that represented a relatively wide range of therapeutic concentrations and affinities for human serum albumin (HSA). The two-dimensional system consisted of an HSA microcolumn for the extraction of a free drug fraction, followed by a larger HSA analytical column for the further separation and measurement of this fraction. Factors that were optimized in this method included the flow rates, column sizes, and column switching times that were employed. The final extraction times used for isolating the free drug fractions were 333-665 ms or less. The dissociation rate constants for several of the drugs with soluble HSA were measured during system optimization, giving results that agreed with reference values. In the final system, free drug fractions in the range of 0.7-9.5% were measured and gave good agreement with values that were determined by ultrafiltration. Association equilibrium constants or global affinities were also estimated by this approach for the drugs with soluble HSA. The results for the two-dimensional system were obtained in 5-10 min or less and required only 1-5 μL of serum per injection. The same approach could be adapted for work with other drugs and proteins in clinical samples or for biomedical research. PMID:26462924

  14. Towards radiocarbon calibration beyond 28 ka using speleothems from the Bahamas

    NASA Astrophysics Data System (ADS)

    Hoffmann, Dirk L.; Beck, J. Warren; Richards, David A.; Smart, Peter L.; Singarayer, Joy S.; Ketchmark, Tricia; Hawkesworth, Chris J.

    2010-01-01

    We present a new speleothem record of atmospheric Δ 14C between 28 and 44 ka that offers considerable promise for resolving some of the uncertainty associated with existing radiocarbon calibration curves for this time period. The record is based on a comprehensive suite of AMS 14C ages, using new low-blank protocols, and U-Th ages using high precision MC-ICPMS procedures. Atmospheric Δ 14C was calculated by correcting 14C ages with a constant dead carbon fraction (DCF) of 22.7 ± 5.9%, based on a comparison of stalagmite 14C ages with the IntCal04 ( Reimer et al., 2004) calibration curve between 15 and 11 ka. The new Δ 14C speleothem record shows similar structure and amplitude to that derived from Cariaco Basin foraminifera (Hughen et al., 2004, 2006), and the match is further improved if the latter is tied to the most recent Greenland ice core chronology ( Svensson et al., 2008). These data are however in conflict with a previously published 14C data set for a stalagmite record from the Bahamas — GB-89-24-1 ( Beck et al., 2001), which likely suffered from 14C analytical blank subtraction issues in the older part of the record. The new Bahamas speleothem ∆ 14C data do not show the extreme shifts between 44 and 40 ka reported in the previous study ( Beck et al., 2001). Causes for the observed structure in derived atmospheric Δ 14C variation based on the new speleothem data are investigated with a suite of simulations using an earth system model of intermediate complexity. Data-model comparison indicates that major fluctuations in atmospheric ∆ 14C during marine isotope stage 3 is primarily a function of changes in geomagnetic field intensity, although ocean-atmosphere system reorganisation also played a supporting role.

  15. Cold climate deglaciation prior to termination 2 implied by new evidence for high sea-levels at 132 KA

    SciTech Connect

    Johnson, R.G. . Dept. of Geology and Geophysics)

    1992-01-01

    Radioisotope dating of corals from reefs and beaches suggests a high sea stand just prior to termination 2. Lack of precision in the ages, stratigraphic uncertainties, and possible diagenetic alterations in the corals have prevented a widespread acceptance of this sea stand. These disadvantages can be avoided by an approach that uses differential uplift measurements to determine the duration of the interval of generally high sea-levels. The last interglacial terrace on Barbados has features indicating two intervals of constant sea-level: an older wave-cut at the inshore edge of the terrace, and a younger cut formed near present eustatic sea-level, below the crest, and just before the earliest Wisconsin glacial buildup. The differential uplift between these two features, measured at five locations having uplift rates between 0.18 and 0.39m/ka, yields a eustatic sea-level differences of 5.4m and a minimal duration of 12.1 [+-] 0.6ka between the two still stands. The assigned age of the younger wave-cut is 120 [+-] 0.5ka, based on sea-level regression due to ice sheet buildup implied by a Little Ice Age analog and rapidly falling Milankovitch summer insolation. The resulting minimal age of the first high sea-stand is 132.1 [+-] 1.1ka, about 7ka before termination 2. This age implies a major early deglaciation caused by a deficit of moisture transported to the great ice sheets, and occurring under relatively cold climate conditions.

  16. The Determination of "Apparent" pKa's. Part II: An Experiment Using Very Weak Acids (pKa's > 11.4).

    ERIC Educational Resources Information Center

    Cawley, John J.

    1995-01-01

    Presents an experiment designed to show students that the Henderson-Hasselbalch equation will fail when they use this particular one-half titration technique for acids with large pKa's. Involves determining the apparent pKa for such acids and using that to calculate the true pKa. (JRH)

  17. X-/Ka-band dichroic plate noise temperature reduction

    NASA Technical Reports Server (NTRS)

    Veruttipong, W.; Lee, P.

    1994-01-01

    The X-/Ka-band (8.4 GHz/32.0 GHz) dichroic plate installed as DSS 13 contributes an estimated 3 K to the system noise temperature at 32.0 GHz. Approximately 1 percent of the Ka-band incident field is reflected by the plate into the 300-K environment of the DSS-13 pedestal room. A low-cost, easily implemented method of reducing the noise temperature is presented. Using a curved reflector, the reflected field can be re-focused into an 80-K cold load, reducing the noise temperature contribution of the dichroic plate by about 2 K.

  18. The Ka-Band Propagation Measurements campaign at JPL

    NASA Technical Reports Server (NTRS)

    Chakraborty, D.; Davarian, Faramaz; Stutzman, Warren L.

    1993-01-01

    The objectives of the JPL-managed Propagation Program are discussed, and the types of activities performed to meet these objectives are described. Particular consideration is given to activities of the NASA-sponsored Ka-Band Propagation Measurement campaign, which was established to investigate the applicability of using the Ka-band (20/30 GHz) for satellite telecommunications via ESA's OLYMPUS satellite, which is a precursor to NASA's ACTS. The basic physics involved in this problem are discussed, and the OLYMPUS-program data collected to date are reviewed.

  19. Satellite-borne QPSK Direct Modulator for Ka Band

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Li, Changsheng

    2016-02-01

    Ka band is referred to a microwave band whose frequency range is from 24.6 GHz to 40 GHz, it shares a wide available bandwidth, high frequency reuse rate and strong ability of anti-jamming. This paper presents a novel method to design a modulator for Ka-band satellite communication. Using QPSK to improve the ability of anti-jamming, using direct modulation to reduce the weight, volume and cost of electronic equipment, using sub-harmonic mixer to cut the LO power leakage, excellent modulation results are obtained.

  20. The maximal affinity of ligands

    PubMed Central

    Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A.

    1999-01-01

    We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of ≈−1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin–avidin. PMID:10468550

  1. Engineering antibody affinity and specificity.

    PubMed

    Webster, D M; Roberts, S; Cheetham, J C; Griest, R; Rees, A R

    1988-01-01

    A combination of ab initio calculations, "knowledge-based prediction", molecular graphics and site-directed mutagenesis has enabled us to probe the molecular details of antibody:antigen recognition and binding and to alter the affinity and specificity of an antibody for its antigen. The significance of electrostatic hydrogen bonding, hydrophilic/hydrophobic patch matching and van der Waals interactions as well as CDR:CDR interactions are discussed in relation to the results of site-directed mutagenesis experiments on the anti-lysozyme antibody Gloop2. The ability to generate reconstructed antibodies, chimeric antibodies, catalytic antibodies and the use of modelled antibodies for the design of drugs is discussed. PMID:3209295

  2. Proton affinities of hydrated molecules

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes

    2016-09-01

    Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.

  3. Complex Affine Toda Theories and Soliton Solutions

    NASA Astrophysics Data System (ADS)

    Zhu, Zhiqing

    1995-01-01

    Toda field theories (TFT's) constitute a large class of integrable (1 + 1)-dimensional field theories that are relativistically invariant: included are conformal field theories and integrable deformations away from conformality. Because they are soluble, for example, by the inverse scattering method, and because they are related to many other areas of field theory, they have been studied extensively in recent years. Hirota's method is a straightforward procedure to obtain soliton solutions to non-linear integrable equations. In Hirota's method, one first writes the nonlinear equations in Hirota's bilinear form, and then expands the so called tau-functions as a power series in an arbitrary parameter. The power series terminates at some finite order, thus the solutions obtained are exact. For an N-soliton solution, the number of terms in the expansion grows exponentially with N, making direct calculation of N-soliton solutions difficult. We extend Hirota's one -parameter expansion to an N-parameter expansion. In the new expansion series, many terms are identical to those in the (N - 1)-soliton solutions, and new terms grow only linearly with N. Furthermore, we note that the expansion must terminate at some finite order, thus the vanishing of higher order terms can be used as constraints on these new terms. It turns out that these constraints can be used to determine the new terms completely. We used this extended Hirota's method to find N-soliton solutions for complex affine TFT's based on a simply-laced Kac-Moody algebra. Soliton solutions for non-simply-laced complex ATFT's can be obtained for those of simply-laced complex ATFT's by folding or twisting. Even though some soliton solutions have already been obtained for complex ATFT's by various methods, the physical implications of these solutions have not yet been thoroughly discussed. There are infinitely many distinct topological solitons in any given complex affine Toda field theory and most of them have complex

  4. High affinity of water-soluble cryptophanes for cesium cations.

    PubMed

    Brotin, Thierry; Montserret, Roland; Bouchet, Aude; Cavagnat, Dominique; Linares, Mathieu; Buffeteau, Thierry

    2012-01-20

    Exceptionally high affinity for cesium cations was achieved in aqueous solution using two enantiopure cryptophanes. Complexation of cesium was evidenced by (133)Cs NMR spectroscopy and by electronic circular dichroism (ECD). Binding constants as high as 6 × 10(9) M(-1) have been measured by isothermal titration calorimetry (ITC). Very strong complexation of rubidium cations (K ~10(6) M(-1)) has also been measured. Chiral hosts allowed the detection of the two cations at low concentrations (μM) using ECD.

  5. Modified gravity in three dimensional metric-affine scenarios

    NASA Astrophysics Data System (ADS)

    Bambi, Cosimo; Ghasemi-Nodehi, M.; Rubiera-Garcia, D.

    2015-08-01

    We consider metric-affine scenarios where a modified gravitational action is sourced by electrovacuum fields in a three dimensional space-time. We first study the case of f (R ) theories, finding deviations near the center as compared to the solutions of general relativity. We then consider Born-Infeld gravity, which has raised a lot of interest in the last few years regarding its applications in astrophysics and cosmology, and show that new features always arise at a finite distance from the center. Several properties of the resulting space-times, in particular in presence of a cosmological constant term, are discussed.

  6. Analyzing a kinetic titration series using affinity biosensors.

    PubMed

    Karlsson, Robert; Katsamba, Phinikoula S; Nordin, Helena; Pol, Ewa; Myszka, David G

    2006-02-01

    The classical method of measuring binding constants with affinity-based biosensors involves testing several analyte concentrations over the same ligand surface and regenerating the surface between binding cycles. Here we describe an alternative approach to collecting kinetic binding data, which we call "kinetic titration." This method involves sequentially injecting an analyte concentration series without any regeneration steps. Through a combination of simulation and experimentation, we show that this method can be as robust as the classical method of analysis. In addition, kinetic titrations can be more efficient than the conventional data collection method and allow us to fully characterize analyte binding to ligand surfaces that are difficult to regenerate.

  7. Conformal field theory on affine Lie groups

    SciTech Connect

    Clubok, K.S.

    1996-04-01

    Working directly on affine Lie groups, we construct several new formulations of the WZW model, the gauged WZW model, and the generic affine-Virasoro action. In one formulation each of these conformal field theories (CFTs) is expressed as a one-dimensional mechanical system whose variables are coordinates on the affine Lie group. When written in terms of the affine group element, this formulation exhibits a two-dimensional WZW term. In another formulation each CFT is written as a two-dimensional field theory, with a three- dimensional WZW term, whose fields are coordinates on the affine group. On the basis of these equivalent formulations, we develop a translation dictionary in which the new formulations on the affine Lie group are understood as mode formulations of the conventional formulations on the Lie group. Using this dictionary, we also express each CFT as a three-dimensional field theory on the Lie group with a four-dimensional WZW term. 36 refs.

  8. Characterization of a constant current charge detector.

    PubMed

    Mori, Masanobu; Chen, Yongjing; Ohira, Shin-Ichi; Dasgupta, Purnendu K

    2012-12-15

    Ion exchangers are ionic equivalents of doped semiconductors, where cations and anions are equivalents of holes and electrons as charge carriers in solid state semiconductors. We have previously demonstrated an ion exchange membrane (IEM) based electrolyte generator which behaves similar to a light-emitting diode and a charge detector (ChD) which behaves analogous to a p-i-n photodiode. The previous work on the charge detector, operated at a constant voltage, established its unique ability to respond to the charge represented by the analyte ions regardless of their redox properties, rather than to their conductivities. It also suggested that electric field induced dissociation (EFID) of water occurs at one or both ion exchange membranes. A logical extension is to study the behavior of the same device, operated in a constant current mode (ChD(i)). The evidence indicates that in the present operational mode the device also responds to the charge represented by the analytes and not their conductivity. Injection of a base into a charge detector operated in the constant voltage mode was not previously examined; in the constant current mode, base injection appears to inhibit EFID. The effects of applied current, analyte residence time and outer channel fluid composition were individually examined; analyte ions of different mobilities as well as affinities for the respective IEMs were used. While the exact behavior is somewhat dependent on the applied current, strong electrolytes, both acids and salts, respond the highest and in a near-uniform fashion, weak acids and their salts respond in an intermediate fashion and bases produce the lowest responses. A fundamentally asymmetric behavior is observed. Injected bases but not injected acids produce a poor response; the effects of incorporating a strong base as the electrolyte in the anion exchange membrane (AEM) compartment is far greater than incorporating an acid in the cation exchange membrane (CEM) compartment. These

  9. Differential Mobility Spectrometry: Preliminary Findings on Determination of Fundamental Constants

    NASA Technical Reports Server (NTRS)

    Limero, Thomas; Cheng, Patti; Boyd, John

    2007-01-01

    The electron capture detector (ECD) has been used for 40+ years (1) to derive fundamental constants such as a compound's electron affinity. Given this historical perspective, it is not surprising that differential mobility spectrometry (DMS) might be used in a like manner. This paper will present data from a gas chromatography (GC)-DMS instrument that illustrates the potential capability of this device to derive fundamental constants for electron-capturing compounds. Potential energy curves will be used to provide possible explanation of the data.

  10. FERROELECTRIC SWITCH FOR A HIGH-POWER Ka-BAND ACTIVE PULSE COMPRESSOR

    SciTech Connect

    Hirshfield, Jay L.

    2013-12-18

    Results are presented for design of a high-power microwave switch for operation at 34.3 GHz, intended for use in an active RF pulse compressor. The active element in the switch is a ring of ferroelectric material, whose dielectric constant can be rapidly changed by application of a high-voltage pulse. As envisioned, two of these switches would be built into a pair of delay lines, as in SLED-II at SLAC, so as to allow 30-MW μs-length Ka-band pulses to be compressed in time by a factor-of-9 and multiplied in amplitude to generate 200 MW peak power pulses. Such high-power pulses could be used for testing and evaluation of high-gradient mm-wave accelerator structures, for example. Evaluation of the switch design was carried out with an X-band (11.43 GHz) prototype, built to incorporate all the features required for the Ka-band version.

  11. Multi-Step Ka/Ka Dichroic Plate with Rounded Corners for NASA's 34m Beam Waveguide Antenna

    NASA Technical Reports Server (NTRS)

    Veruttipong, Watt; Khayatian, Behrouz; Hoppe, Daniel; Long, Ezra

    2013-01-01

    A multi-step Ka/Ka dichroic plate Frequency Selective Surface (FSS structure) is designed, manufactured and tested for use in NASA's Deep Space Network (DSN) 34m Beam Waveguide (BWG) antennas. The proposed design allows ease of manufacturing and ability to handle the increased transmit power (reflected off the FSS) of the DSN BWG antennas from 20kW to 100 kW. The dichroic is designed using HFSS and results agree well with measured data considering the manufacturing tolerances that could be achieved on the dichroic.

  12. Structural determinants of sigma receptor affinity

    SciTech Connect

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

  13. Non-affine deformations in polymer hydrogels

    PubMed Central

    Wen, Qi; Basu, Anindita; Janmey, Paul A.; Yodh, A. G.

    2012-01-01

    Most theories of soft matter elasticity assume that the local strain in a sample after deformation is identical everywhere and equal to the macroscopic strain, or equivalently that the deformation is affine. We discuss the elasticity of hydrogels of crosslinked polymers with special attention to affine and non-affine theories of elasticity. Experimental procedures to measure non-affine deformations are also described. Entropic theories, which account for gel elasticity based on stretching out individual polymer chains, predict affine deformations. In contrast, simulations of network deformation that result in bending of the stiff constituent filaments generally predict non-affine behavior. Results from experiments show significant non-affine deformation in hydrogels even when they are formed by flexible polymers for which bending would appear to be negligible compared to stretching. However, this finding is not necessarily an experimental proof of the non-affine model for elasticity. We emphasize the insights gained from experiments using confocal rheoscope and show that, in addition to filament bending, sample micro-inhomogeneity can be a significant alternative source of non-affine deformation. PMID:23002395

  14. A Novel Vertex Affinity for Community Detection

    SciTech Connect

    Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot

    2015-10-05

    We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.

  15. Microbial communities involved in Kaşar cheese ripening.

    PubMed

    Aydemir, Oğuz; Harth, Henning; Weckx, Stefan; Dervişoğlu, Muhammet; De Vuyst, Luc

    2015-04-01

    The microbiota of non-starter lactic acid bacteria (NSLAB) and their concomitant community dynamics during cheese ripening were investigated for traditional Turkish Kaşar cheeses made from raw cows' milk. Five batches of 15 Kaşar cheeses produced in different dairy plants located in Kars were analysed during their whole ripening phase up to 180 days. Lactobacilli and lactococci were determined as the prevailing microbial groups. The molecular classification and identification of 594 LAB isolates during Kaşar cheese ripening were performed through (GTG)5-PCR fingerprinting of their genomic DNA followed by verification of the (GTG)5-PCR clusters obtained after numerical analysis through 16S rRNA gene sequencing of representative isolates. Lactobacillus casei (247 isolates, 41.6%), Lactobacillus plantarum (77 isolates, 13.0%), and Pediococcus acidilactici (58 isolates, 9.8%) were the prevailing NSLAB species in all Kaşar cheeses of the different dairy plants investigated throughout cheese ripening. The data of the present study contribute to the inventory of unique cheese varieties to enable the prevention of losses of microbial biodiversity and the selection of starter cultures for controlled cheese manufacturing.

  16. Anatomically modern human in Southeast Asia (Laos) by 46 ka.

    PubMed

    Demeter, Fabrice; Shackelford, Laura L; Bacon, Anne-Marie; Duringer, Philippe; Westaway, Kira; Sayavongkhamdy, Thongsa; Braga, José; Sichanthongtip, Phonephanh; Khamdalavong, Phimmasaeng; Ponche, Jean-Luc; Wang, Hong; Lundstrom, Craig; Patole-Edoumba, Elise; Karpoff, Anne-Marie

    2012-09-01

    Uncertainties surround the timing of modern human emergence and occupation in East and Southeast Asia. Although genetic and archeological data indicate a rapid migration out of Africa and into Southeast Asia by at least 60 ka, mainland Southeast Asia is notable for its absence of fossil evidence for early modern human occupation. Here we report on a modern human cranium from Tam Pa Ling, Laos, which was recovered from a secure stratigraphic context. Radiocarbon and luminescence dating of the surrounding sediments provide a minimum age of 51-46 ka, and direct U-dating of the bone indicates a maximum age of ~63 ka. The cranium has a derived modern human morphology in features of the frontal, occipital, maxillae, and dentition. It is also differentiated from western Eurasian archaic humans in aspects of its temporal, occipital, and dental morphology. In the context of an increasingly documented archaic-modern morphological mosaic among the earliest modern humans in western Eurasia, Tam Pa Ling establishes a definitively modern population in Southeast Asia at ~50 ka cal BP. As such, it provides the earliest skeletal evidence for fully modern humans in mainland Southeast Asia.

  17. Measurement techniques for cryogenic Ka-band microstrip antennas

    NASA Technical Reports Server (NTRS)

    Richard, M. A.; Bhasin, K. B.; Gilbert, C.; Metzler, S.; Claspy, P. C.

    1991-01-01

    The measurement of cryogenic antennas poses unique logistical problems since the antenna under test must be embedded in a cooling chamber. A method of measuring the performance of cryogenic microstrip antennas using a closed cycle gas cooled refrigerator in a far field range is described. Antenna patterns showing the performance of gold and superconducting Ka-band microstrip antennas at various temperatures are presented.

  18. Modified Wilkinson Power Dividers For K And Ka Bands

    NASA Technical Reports Server (NTRS)

    Antsos, Dimitrios

    1995-01-01

    Modified configuration for Wilkinson power dividers devised for operating frequencies in K and Ka bands (18 to 27 and 27 to 40 GHz, respectively). Overcomes some difficulties associated with increasing frequency, making possible to design and accurately predict performances of unequal-split power dividers for frequencies above X-band.

  19. Mars Global Surveyor Ka-Band Frequency Data Analysis

    NASA Technical Reports Server (NTRS)

    Morabito, D.; Butman, S.; Shambayati, S.

    2000-01-01

    The Mars Global Surveyor (MGS) spacecraft, launched on November 7, 1996, carries an experimental space-to-ground telecommunications link at Ka-band (32 GHz) along with the primary X-band (8.4 GHz) downlink. The signals are simultaneously transmitted from a 1.5-in diameter parabolic high gain antenna (HGA) on MGS and received by a beam-waveguide (BWG) R&D 34-meter antenna located in NASA's Goldstone Deep Space Network (DSN) complex near Barstow, California. The projected 5-dB link advantage of Ka-band relative to X-band was confirmed in previous reports using measurements of MGS signal strength data acquired during the first two years of the link experiment from December 1996 to December 1998. Analysis of X-band and Ka-band frequency data and difference frequency (f(sub x)-f(sub ka)/3.8) data will be presented here. On board the spacecraft, a low-power sample of the X-band downlink from the transponder is upconverted to 32 GHz, the Ka-band frequency, amplified to I-W using a Solid State Power Amplifier, and radiated from the dual X/Ka HGA. The X-band signal is amplified by one of two 25 W TWTAs. An upconverter first downconverts the 8.42 GHz X-band signal to 8 GHz and then multiplies using a X4 multiplier producing the 32 GHz Ka-band frequency. The frequency source selection is performed by an RF switch which can be commanded to select a VCO (Voltage Controlled Oscillator) or USO (Ultra-Stable Oscillator) reference. The Ka-band frequency can be either coherent with the X-band downlink reference or a hybrid combination of the USO and VCO derived frequencies. The data in this study were chosen such that the Ka-band signal is purely coherent with the X-band signal, that is the downconverter is driven by the same frequency source as the X-band downlink). The ground station used to acquire the data is DSS-13, a 34-meter BWG antenna which incorporates a series of mirrors inside beam waveguide tubes which guide the energy to a subterranean pedestal room, providing a stable

  20. Anatomically modern human in Southeast Asia (Laos) by 46 ka

    PubMed Central

    Demeter, Fabrice; Shackelford, Laura L.; Bacon, Anne-Marie; Duringer, Philippe; Westaway, Kira; Sayavongkhamdy, Thongsa; Braga, José; Sichanthongtip, Phonephanh; Khamdalavong, Phimmasaeng; Ponche, Jean-Luc; Wang, Hong; Lundstrom, Craig; Patole-Edoumba, Elise; Karpoff, Anne-Marie

    2012-01-01

    Uncertainties surround the timing of modern human emergence and occupation in East and Southeast Asia. Although genetic and archeological data indicate a rapid migration out of Africa and into Southeast Asia by at least 60 ka, mainland Southeast Asia is notable for its absence of fossil evidence for early modern human occupation. Here we report on a modern human cranium from Tam Pa Ling, Laos, which was recovered from a secure stratigraphic context. Radiocarbon and luminescence dating of the surrounding sediments provide a minimum age of 51–46 ka, and direct U-dating of the bone indicates a maximum age of ∼63 ka. The cranium has a derived modern human morphology in features of the frontal, occipital, maxillae, and dentition. It is also differentiated from western Eurasian archaic humans in aspects of its temporal, occipital, and dental morphology. In the context of an increasingly documented archaic–modern morphological mosaic among the earliest modern humans in western Eurasia, Tam Pa Ling establishes a definitively modern population in Southeast Asia at ∼50 ka cal BP. As such, it provides the earliest skeletal evidence for fully modern humans in mainland Southeast Asia. PMID:22908291

  1. Marine04 Marine radiocarbon age calibration, 26 ? 0 ka BP

    SciTech Connect

    Hughen, K; Baille, M; Bard, E; Beck, J; Bertrand, C; Blackwell, P; Buck, C; Burr, G; Cutler, K; Damon, P; Edwards, R; Fairbanks, R; Friedrich, M; Guilderson, T; Kromer, B; McCormac, F; Manning, S; Bronk-Ramsey, C; Reimer, P; Reimer, R; Remmele, S; Southon, J; Stuiver, M; Talamo, S; Taylor, F; der Plicht, J v; Weyhenmeyer, C

    2004-11-01

    New radiocarbon calibration curves, IntCal04 and Marine04, have been constructed and internationally ratified to replace the terrestrial and marine components of IntCal98. The new calibration datasets extend an additional 2000 years, from 0-26 ka cal BP (Before Present, 0 cal BP = AD 1950), and provide much higher resolution, greater precision and more detailed structure than IntCal98. For the Marine04 curve, dendrochronologically dated tree-ring samples, converted with a box-diffusion model to marine mixed-layer ages, cover the period from 0-10.5 ka cal BP. Beyond 10.5 ka cal BP, high-resolution marine data become available from foraminifera in varved sediments and U/Th-dated corals. The marine records are corrected with site-specific {sup 14}C reservoir age information to provide a single global marine mixed-layer calibration from 10.5-26.0 ka cal BP. A substantial enhancement relative to IntCal98 is the introduction of a random walk model, which takes into account the uncertainty in both the calendar age and the radiocarbon age to calculate the underlying calibration curve. The marine datasets and calibration curve for marine samples from the surface mixed layer (Marine04) are discussed here. The tree-ring datasets, sources of uncertainty, and regional offsets are presented in detail in a companion paper by Reimer et al.

  2. Beyond the Hubble Constant

    NASA Astrophysics Data System (ADS)

    1995-08-01

    about the distances to galaxies and thereby about the expansion rate of the Universe. A simple way to determine the distance to a remote galaxy is by measuring its redshift, calculate its velocity from the redshift and divide this by the Hubble constant, H0. For instance, the measured redshift of the parent galaxy of SN 1995K (0.478) yields a velocity of 116,000 km/sec, somewhat more than one-third of the speed of light (300,000 km/sec). From the universal expansion rate, described by the Hubble constant (H0 = 20 km/sec per million lightyears as found by some studies), this velocity would indicate a distance to the supernova and its parent galaxy of about 5,800 million lightyears. The explosion of the supernova would thus have taken place 5,800 million years ago, i.e. about 1,000 million years before the solar system was formed. However, such a simple calculation works only for relatively ``nearby'' objects, perhaps out to some hundred million lightyears. When we look much further into space, we also look far back in time and it is not excluded that the universal expansion rate, i.e. the Hubble constant, may have been different at earlier epochs. This means that unless we know the change of the Hubble constant with time, we cannot determine reliable distances of distant galaxies from their measured redshifts and velocities. At the same time, knowledge about such change or lack of the same will provide unique information about the time elapsed since the Universe began to expand (the ``Big Bang''), that is, the age of the Universe and also its ultimate fate. The Deceleration Parameter q0 Cosmologists are therefore eager to determine not only the current expansion rate (i.e., the Hubble constant, H0) but also its possible change with time (known as the deceleration parameter, q0). Although a highly accurate value of H0 has still not become available, increasing attention is now given to the observational determination of the second parameter, cf. also the Appendix at the

  3. Structure of classical affine and classical affine fractional W-algebras

    SciTech Connect

    Suh, Uhi Rinn

    2015-01-15

    We introduce a classical BRST complex (See Definition 3.2.) and show that one can construct a classical affine W-algebra via the complex. This definition clarifies that classical affine W-algebras can be considered as quasi-classical limits of quantum affine W-algebras. We also give a definition of a classical affine fractional W-algebra as a Poisson vertex algebra. As in the classical affine case, a classical affine fractional W-algebra has two compatible λ-brackets and is isomorphic to an algebra of differential polynomials as a differential algebra. When a classical affine fractional W-algebra is associated to a minimal nilpotent, we describe explicit forms of free generators and compute λ-brackets between them. Provided some assumptions on a classical affine fractional W-algebra, we find an infinite sequence of integrable systems related to the algebra, using the generalized Drinfel’d and Sokolov reduction.

  4. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display.

    PubMed

    Hanes, J; Schaffitzel, C; Knappik, A; Plückthun, A

    2000-12-01

    Here we applied ribosome display to in vitro selection and evolution of single-chain antibody fragments (scFvs) from a large synthetic library (Human Combinatorial Antibody Library; HuCAL) against bovine insulin. In three independent ribosome display experiments different clusters of closely related scFvs were selected, all of which bound the antigen with high affinity and specificity. All selected scFvs had affinity-matured up to 40-fold compared to their HuCAL progenitors, by accumulating point mutations during the ribosome display cycles. The dissociation constants of the isolated scFvs were as low as 82 pM, which validates the design of the naïve library and the power of this evolutionary method. We have thus mimicked the process of antibody generation and affinity maturation with a synthetic library in a cell-free system in just a few days, obtaining molecules with higher affinities than most natural antibodies.

  5. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity.

    PubMed

    Boder, E T; Midelfort, K S; Wittrup, K D

    2000-09-26

    Single-chain antibody mutants have been evolved in vitro with antigen-binding equilibrium dissociation constant K(d) = 48 fM and slower dissociation kinetics (half-time > 5 days) than those for the streptavidin-biotin complex. These mutants possess the highest monovalent ligand-binding affinity yet reported for an engineered protein by over two orders of magnitude. Optimal kinetic screening of randomly mutagenized libraries of 10(5)-10(7) yeast surface-displayed antibodies enabled a >1,000-fold decrease in the rate of dissociation after four cycles of affinity mutagenesis and screening. The consensus mutations are generally nonconservative by comparison with naturally occurring mouse Fv sequences and with residues that do not contact the fluorescein antigen in the wild-type complex. The existence of these mutants demonstrates that the antibody Fv architecture is not intrinsically responsible for an antigen-binding affinity ceiling during in vivo affinity maturation.

  6. Purification of muscarinic acetylcholine receptors by affinity chromatography.

    PubMed Central

    André, C; De Backer, J P; Guillet, J C; Vanderheyden, P; Vauquelin, G; Strosberg, A D

    1983-01-01

    Calf forebrain homogenates contain 2.8 pM muscarinic acetylcholine receptors per mg of protein. [3H]Antagonist saturation binding experiments under equilibrium conditions revealed a single class of sites with equilibrium dissociation constants of 0.82 nM for [3H]dexetimide and 0.095 nM for [3H]quinuclidinyl benzilate. Displacement binding studies with agonists revealed the presence of low and high affinity sites. Here we describe the solubilization of muscarinic acetylcholine receptors with digitonin and their purification by affinity chromatography using an affinity gel which consisted of dexetimide coupled to Affi-Gel 10 (i.e., carboxy N-hydroxysuccinimide esters linked via a 1 nm spacer arm to agarose beads). Purified proteins were obtained by specific elution with muscarinic drugs, i.e., the antagonist atropine and the irreversible ligand propylbenzilylcholine mustard. SDS-polyacrylamide gel electrophoresis of the radioiodinated purified preparations revealed a major 70-K protein. Images Fig. 3. PMID:6605245

  7. Selective retention of basic compounds by metal aquo-ion affinity chromatography.

    PubMed

    Asakawa, Yoshiki; Yamamoto, Eiichi; Asakawa, Naoki

    2014-10-01

    A novel metal aquo-ion affinity chromatography has been developed for the analysis of basic compounds using heat-treated silica gel containing hydrated metal cations (metal aquo-ions) as the packing material. The packing materials of the metal aquo-ion affinity chromatography were prepared by the immobilization of a single metal component such as Fe(III), Al(III), Ag(I), and Ni(II) on silica gel followed by extensive heat treatment. The immobilized metals form aquo-ions to present cation-exchange ability for basic analytes and the cation-exchange ability for basic analytes depends on pKa of the immobilized metal species. In the present study, to evaluate the retention characteristics of metal aquo-ion affinity chromatography, the on-line solid-phase extraction of drugs was investigated. Obtained data clearly evidence the selective retention capability of metal aquo-ion affinity chromatography for basic analytes with sufficient capacity. PMID:25044622

  8. Methods for Improving Aptamer Binding Affinity.

    PubMed

    Hasegawa, Hijiri; Savory, Nasa; Abe, Koichi; Ikebukuro, Kazunori

    2016-01-01

    Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers. PMID:27043498

  9. Mars Global Surveyor Ka-Band Frequency Data Analysis

    NASA Astrophysics Data System (ADS)

    Morabito, D.; Butman, S.; Shambayati, S.

    2000-01-01

    The Mars Global Surveyor (MGS) spacecraft, launched on November 7, 1996, carries an experimental space-to-ground telecommunications link at Ka-band (32 GHz) along with the primary X-band (8.4 GHz) downlink. The signals are simultaneously transmitted from a 1.5-in diameter parabolic high gain antenna (HGA) on MGS and received by a beam-waveguide (BWG) R&D 34-meter antenna located in NASA's Goldstone Deep Space Network (DSN) complex near Barstow, California. The projected 5-dB link advantage of Ka-band relative to X-band was confirmed in previous reports using measurements of MGS signal strength data acquired during the first two years of the link experiment from December 1996 to December 1998. Analysis of X-band and Ka-band frequency data and difference frequency (fx-fka)/3.8 data will be presented here. On board the spacecraft, a low-power sample of the X-band downlink from the transponder is upconverted to 32 GHz, the Ka-band frequency, amplified to I-W using a Solid State Power Amplifier, and radiated from the dual X/Ka HGA. The X-band signal is amplified by one of two 25 W TWTAs. An upconverter first downconverts the 8.42 GHz X-band signal to 8 GHz and then multiplies using a X4 multiplier producing the 32 GHz Ka-band frequency. The frequency source selection is performed by an RF switch which can be commanded to select a VCO (Voltage Controlled Oscillator) or USO (Ultra-Stable Oscillator) reference. The Ka-band frequency can be either coherent with the X-band downlink reference or a hybrid combination of the USO and VCO derived frequencies. The data in this study were chosen such that the Ka-band signal is purely coherent with the X-band signal, that is the downconverter is driven by the same frequency source as the X-band downlink). The ground station used to acquire the data is DSS-13, a 34-meter BWG antenna which incorporates a series of mirrors inside beam waveguide tubes which guide the energy to a subterranean pedestal room, providing a stable environment

  10. Improving image segmentation by learning region affinities

    SciTech Connect

    Prasad, Lakshman; Yang, Xingwei; Latecki, Longin J

    2010-11-03

    We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

  11. A global benchmark study using affinity-based biosensors.

    PubMed

    Rich, Rebecca L; Papalia, Giuseppe A; Flynn, Peter J; Furneisen, Jamie; Quinn, John; Klein, Joshua S; Katsamba, Phini S; Waddell, M Brent; Scott, Michael; Thompson, Joshua; Berlier, Judie; Corry, Schuyler; Baltzinger, Mireille; Zeder-Lutz, Gabrielle; Schoenemann, Andreas; Clabbers, Anca; Wieckowski, Sebastien; Murphy, Mary M; Page, Phillip; Ryan, Thomas E; Duffner, Jay; Ganguly, Tanmoy; Corbin, John; Gautam, Satyen; Anderluh, Gregor; Bavdek, Andrej; Reichmann, Dana; Yadav, Satya P; Hommema, Eric; Pol, Ewa; Drake, Andrew; Klakamp, Scott; Chapman, Trevor; Kernaghan, Dawn; Miller, Ken; Schuman, Jason; Lindquist, Kevin; Herlihy, Kara; Murphy, Michael B; Bohnsack, Richard; Andrien, Bruce; Brandani, Pietro; Terwey, Danny; Millican, Rohn; Darling, Ryan J; Wang, Liann; Carter, Quincy; Dotzlaf, Joe; Lopez-Sagaseta, Jacinto; Campbell, Islay; Torreri, Paola; Hoos, Sylviane; England, Patrick; Liu, Yang; Abdiche, Yasmina; Malashock, Daniel; Pinkerton, Alanna; Wong, Melanie; Lafer, Eileen; Hinck, Cynthia; Thompson, Kevin; Primo, Carmelo Di; Joyce, Alison; Brooks, Jonathan; Torta, Federico; Bagge Hagel, Anne Birgitte; Krarup, Janus; Pass, Jesper; Ferreira, Monica; Shikov, Sergei; Mikolajczyk, Malgorzata; Abe, Yuki; Barbato, Gaetano; Giannetti, Anthony M; Krishnamoorthy, Ganeshram; Beusink, Bianca; Satpaev, Daulet; Tsang, Tiffany; Fang, Eric; Partridge, James; Brohawn, Stephen; Horn, James; Pritsch, Otto; Obal, Gonzalo; Nilapwar, Sanjay; Busby, Ben; Gutierrez-Sanchez, Gerardo; Gupta, Ruchira Das; Canepa, Sylvie; Witte, Krista; Nikolovska-Coleska, Zaneta; Cho, Yun Hee; D'Agata, Roberta; Schlick, Kristian; Calvert, Rosy; Munoz, Eva M; Hernaiz, Maria Jose; Bravman, Tsafir; Dines, Monica; Yang, Min-Hsiang; Puskas, Agnes; Boni, Erica; Li, Jiejin; Wear, Martin; Grinberg, Asya; Baardsnes, Jason; Dolezal, Olan; Gainey, Melicia; Anderson, Henrik; Peng, Jinlin; Lewis, Mark; Spies, Peter; Trinh, Quyhn; Bibikov, Sergei; Raymond, Jill; Yousef, Mohammed; Chandrasekaran, Vidya; Feng, Yuguo; Emerick, Anne; Mundodo, Suparna; Guimaraes, Rejane; McGirr, Katy; Li, Yue-Ji; Hughes, Heather; Mantz, Hubert; Skrabana, Rostislav; Witmer, Mark; Ballard, Joshua; Martin, Loic; Skladal, Petr; Korza, George; Laird-Offringa, Ite; Lee, Charlene S; Khadir, Abdelkrim; Podlaski, Frank; Neuner, Phillippe; Rothacker, Julie; Rafique, Ashique; Dankbar, Nico; Kainz, Peter; Gedig, Erk; Vuyisich, Momchilo; Boozer, Christina; Ly, Nguyen; Toews, Mark; Uren, Aykut; Kalyuzhniy, Oleksandr; Lewis, Kenneth; Chomey, Eugene; Pak, Brian J; Myszka, David G

    2009-03-15

    To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.

  12. Identification of an Orthogonal Peptide Binding Motif for Biarsenical Multiuse Affinity Probes

    SciTech Connect

    Chen, Baowei; Cao, Haishi; Yan, Ping; Mayer, M. Uljana; Squier, Thomas C.

    2007-07-01

    Biarsenical multiuse affinity probes (MAPs) complexed with ethanedithiol (EDT) permit the selective cellular labeling of proteins engineered with tetracysteine motifs, but are limited by the availability of a single binding motif (i.e., CCPGCC or PG tag) that prevents the differential labeling of co-expressed proteins. To overcome this problem, we have used a high-throughput peptide screen to identify an alternate binding motif (i.e., CCKACC or KA tag), which has a similar brightness to the classical sequence upon MAP binding, but displays altered rates and affinities of association that permit the differential labeling of these peptide sequences by the red probe 4,5-bis(1,3,2-dithiarsolan-2-yl)-resorufin (ReAsH-EDT2) or its green cognate 4’,5’-bis(1,3,2-dithoarsolan-2-yl)fluorescein-(1,2-ethanedithiol)2 (FLAsH-EDT2). The utility of this labeling strategy was demonstrated following the expression of PG- and KA-tagged subunits of RNA polymerase expressed in E. coli. Specific labeling of two subunits of RNA polymerase in cellular lysates was achieved, whereby ReAsH-EDT2 is shown to selectively label the PG-tag on RNA polymerase alpha subunit prior to the labeling of the KA-tag sequence of the beta subunit of RNA polymerase with FlAsH-EDT2. These results demonstrate the ability to selectively label multiple individual proteins with orthogonal sequence tags in complex cellular lystates with spectroscopically distinct MAPs, and indicate the absolute specificity of ReAsH to target expressed proteins with essentially no nonspecific binding interactions.

  13. New Quasar Studies Keep Fundamental Physical Constant Constant

    NASA Astrophysics Data System (ADS)

    2004-03-01

    Very Large Telescope sets stringent limit on possible variation of the fine-structure constant over cosmological time Summary Detecting or constraining the possible time variations of fundamental physical constants is an important step toward a complete understanding of basic physics and hence the world in which we live. A step in which astrophysics proves most useful. Previous astronomical measurements of the fine structure constant - the dimensionless number that determines the strength of interactions between charged particles and electromagnetic fields - suggested that this particular constant is increasing very slightly with time. If confirmed, this would have very profound implications for our understanding of fundamental physics. New studies, conducted using the UVES spectrograph on Kueyen, one of the 8.2-m telescopes of ESO's Very Large Telescope array at Paranal (Chile), secured new data with unprecedented quality. These data, combined with a very careful analysis, have provided the strongest astronomical constraints to date on the possible variation of the fine structure constant. They show that, contrary to previous claims, no evidence exist for assuming a time variation of this fundamental constant. PR Photo 07/04: Relative Changes with Redshift of the Fine Structure Constant (VLT/UVES) A fine constant To explain the Universe and to represent it mathematically, scientists rely on so-called fundamental constants or fixed numbers. The fundamental laws of physics, as we presently understand them, depend on about 25 such constants. Well-known examples are the gravitational constant, which defines the strength of the force acting between two bodies, such as the Earth and the Moon, and the speed of light. One of these constants is the so-called "fine structure constant", alpha = 1/137.03599958, a combination of electrical charge of the electron, the Planck constant and the speed of light. The fine structure constant describes how electromagnetic forces hold

  14. Calibration of the radiocarbon time scale at 37ka BP

    SciTech Connect

    Southon, J.R.; Deino, A.L.; Orsi, G.

    1995-12-01

    Results from radiocarbon and U-Th measurements on corals have provided a radiocarbon calibration beyond the range covered by tree ring series, but the uncertainties in the measurements beyond 20ka BP are very large. We have obtained new calibration data from radiocarbon dates on material associated with the catastrophic Campanian Ignimbrite eruption from the Phlegrean Fields near Naples. The eruption has been well dated by {sup 40}Ar/{sup 39}Ar to 37ka BP. Radiocarbon measurements were carried out on charcoal from a carbonized branch exposed within the ignimbrite tuff on the wall of an active quarry. The sample was split and analyzed at both the Naples and Lawrence Livermore AMS facilities. The offset between the Ar-Ar data and the radiocarbon results (recalculated using the true 5730-year half life for {sup 14}C) is consistent with predictions from paleomagnetic data and carbon cycle modeling.

  15. Compact 810 kA Linear Transformer Driver Cavity

    NASA Astrophysics Data System (ADS)

    Woodworth, J. R.; Fowler, W. E.; Stoltzfus, B. S.; Stygar, W. A.; Sceiford, M. E.; Mazarakis, M. G.; Anderson, H. D.; Harden, M. J.; Blickem, J. R.; White, R.; Kim, A. A.

    2011-04-01

    We are performing experiments with a 92-kV, 810-kA, 74.6-GW linear transformer driver (LTD) cavity. This cavity generates a ˜100ns power pulse from DC-charged capacitors in a single step. Our experiments start with an existing 100-kV, 490-kA LTD cavity and are making a number of improvements to it that are aimed at increasing the cavity’s peak output power and better understanding its operation. We are making improvements to the gas switches, the capacitors, and the magnetic toroids as well as heavily instrumenting the cavity. These experiments have increased the cavity’s output current into a matched load by 65% without increasing its volume.

  16. Ka-band MMIC arrays for ACTS Aero Terminal Experiment

    NASA Technical Reports Server (NTRS)

    Raquet, C.; Zakrajsek, R.; Lee, R.; Turtle, J.

    1992-01-01

    An antenna system consisting of three experimental Ka-band active arrays using GaAs MMIC devices at each radiating element for electronic beam steering and distributed power amplification is presented. The MMIC arrays are to be demonstrated in the ACTS Aeronautical Terminal Experiment, planned for early 1994. The experiment is outlined, with emphasis on a description of the antenna system. Attention is given to the way in which proof-of-concept MMIC arrays featuring three different state-of-the-art approaches to Ka-band MMIC insertion are being incorporated into an experimental aircraft terminal for the demonstration of an aircraft-to-satellite link, providing a basis for follow-on MMIC array development.

  17. Measurement techniques for cryogenic Ka-band microstrip antennas

    NASA Technical Reports Server (NTRS)

    Richard, M. A.; Bhasin, Kul B.; Gilbert, C.; Metzler, S.; Claspy, P. C.

    1992-01-01

    The measurement of cryogenic antennas poses unique logistical problems since the antenna under test must be embedded in the cooling chamber. A method for measuring the performance of cryogenic microstrip antennas using a closed cycle gas-cooled refrigerator in a far field range is described. Antenna patterns showing the performance of gold and superconducting Ka-band microstrip antennas at various temperatures are presented.

  18. Determination of the dissociation constants of sulfonated azo dyes by capillary zone electrophoresis and spectrophotometry methods.

    PubMed

    Pérez-Urquiza, M; Beltrán, J L

    2001-05-11

    The dissociation constants of 10 sulfonated azo dyes, six of the most common food colours used as additives (Food Yellow 4, Food Yellow 3, Food Red 9, Food Red 7, Food Red 17 and Food Blue 5), and four commonly used as textile dyes (Acid Orange 7, Acid Orange 12, Acid Red 26 and Acid Red 88), have been determined by two different systems, one by using capillary electrophoresis (CE) with diode array detection and the other by using UV-visible absorption spectrophotometry, which has been used as reference method to obtain the pKa values. The pKa values obtained by CE were determined in two ways, first on the basis of the electrophoretic mobilities (calculated from the migration times), and after we propose a new methodology, in which the dissociation constants are determined from the spectra corresponding to the maxima of electrophoretic peaks. The pKa values obtained by using these CE methods have been compared with those obtained by using the spectrophotometric method. The results show that the pKa values obtained by the CE proposed method are in general closer to the reference values than those obtained from the electrophoretic mobilities. Moreover, the proposed method retains the advantages of CE, as the possibility of working with small amounts of sample, despite its purity.

  19. X/Ka Celestial Frame Improvements: Vision to Reality

    NASA Technical Reports Server (NTRS)

    Jacobs, C. S.; Bagri, D. S.; Britcliffe, M. J.; Clark, J. E.; Franco, M. M.; Garcia-Miro, C.; Goodhart, C. E.; Horiuchi, S.; Lowe, S. T.; Moll, V. E.; Navarro, R.; Rogstad, S. P.; Proctor, R. C.; Sigman, E. H.; Skjerve, L. J.; Soriano, M. A.; Sovers, O. J.; Tucker, B. C.; Wang, D.; White, L. A.

    2010-01-01

    In order to extend the International Celestial Reference Frame from its S/X-band (2.3/8.4 GHz) basis to a complementary frame at X/Ka-band (8.4/32 GHz), we began in mid-2005 an ongoing series of X/Ka observations using NASA s Deep Space Network (DSN) radio telescopes. Over the course of 47 sessions, we have detected 351 extra-galactic radio sources covering the full 24 hours of right ascension and declinations down to -45 degrees. Angular source position accuracy is at the part-per-billion level. We developed an error budget which shows that the main errors arise from limited sensitivity, mismodeling of the troposphere, uncalibrated instrumental effects, and the lack of a southern baseline. Recent work has improved sensitivity by improving pointing calibrations and by increasing the data rate four-fold. Troposphere calibration has been demonstrated at the mm-level. Construction of instrumental phase calibrators and new digital baseband filtering electronics began in recent months. We will discuss the expected effect of these improvements on the X/Ka frame.

  20. Rain Fade Compensation Alternatives for Ka Band Communication Satellites

    NASA Technical Reports Server (NTRS)

    Acosta, Roberto J.

    1997-01-01

    Future satellite communications systems operating in Ka-band frequency band are subject to degradation produced by the troposphere which is much more severe than those found at lower frequency bands. These impairments include signal absorption by rain, clouds and gases, and amplitude scintillation's arising from refractive index irregularities. For example, rain attenuation at 20 GHz is almost three times that at 11 GHz. Although some of these impairments can be overcome by oversizing the ground station antennas and high power amplifiers, the current trend is using small (less than 20 inches apertures), low-cost ground stations (less than $1000) that can be easily deployed at user premises. As a consequence, most Ka-band systems are expected to employ different forms of fade mitigation that can be implemented relatively easily and at modest cost. The rain fade mitigation approaches are defined by three types of Ka-band communications systems - a low service rate (less than 1.5 Mb/s), a moderate service rate (1.5 to 6 Mb/s) system and a high service rate (greater than 43 Mb/s) system. The ACTS VSAT network, which includes an adaptive rain fade technique, is an example of a moderate service rate.

  1. Late Paleogene terrestrial fauna and paleoenvironments in Eastern Anatolia: New insights from the Kağızman-Tuzluca Basin

    NASA Astrophysics Data System (ADS)

    Métais, Grégoire; Sen, Sevket; Sözeri, Koray; Peigné, Stéphane; Varol, Baki

    2015-08-01

    In Eastern Turkey, relatively little work has been undertaken to characterize the sedimentologic and stratigraphical context of the Kağızman-Tuzluca Basin until now. Extending across the Turkey-Armenian border, this basin documents the syn- and post-collisional evolution of Eastern Anatolia, resulting from the closure of the Neotethyan Seaways and the final collision of the Afro-Arabian and Eurasian plates. From detailed sedimentological and paleontological studies, we propose an interpretation of the lithology and depositional environment of the Late Paleogene Alhan Formation located on the western bank of the Aras River. This sequence of terrestrial clastics rests directly and unconformably onto the ophiolitic mélange, and it documents several depositional sequences deposited in alluvial plain and lacustrine environments. At this stage, the age of the Alhan Formation can only be calibrated by fossil evidence. Several stratigraphic levels yielding fossil data along the section have been identified, but these poor assemblages of fauna and flora hamper extensive comparisons with roughly contemporaneous localities of Central and Southern Asia. Carnivorous and ruminant mammal remains are reported for the first time from the supposed Late Oligocene Güngörmez Formation. The identified fossil mammal taxa reveal biogeographic affinities between Central Anatolia and southern Asia, thus suggesting dispersal between these areas during the Oligocene or earlier. Further studies of the fossil assemblages from the Kağızman-Tuzluca Basin and other basins of Eastern Anatolia and lesser Caucasus regions are needed to better constrain the paleobiogeographic models.

  2. Affinity Proteomics in the mountains: Alpbach 2015.

    PubMed

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  3. Aptamers in Affinity Separations: Stationary Separation

    NASA Astrophysics Data System (ADS)

    Ravelet, Corinne; Peyrin, Eric

    The use of DNA or RNA aptamers as tools in analytical chemistry is a very promising field of research because of their capabilities to bind specifically the target molecules with an affinity similar to that of antibodies. Notably, they appear to be of great interest as target-specific ligands for the separation and capture of various analytes in affinity chromatography and related affinity-based methods such as magnetic bead technology. In this chapter, the recent developments of these aptamer-based separation/capture approaches are addressed.

  4. The role of reaction affinity and secondary minerals in regulating chemical weathering rates at the Santa Cruz Soil Chronosequence, California

    SciTech Connect

    Maher, K.; Steefel, C. I.; White, A.F.; Stonestrom, D.A.

    2009-02-25

    In order to explore the reasons for the apparent discrepancy between laboratory and field weathering rates and to determine the extent to which weathering rates are controlled by the approach to thermodynamic equilibrium, secondary mineral precipitation and flow rates, a multicomponent reactive transport model (CrunchFlow) was used to interpret soil profile development and mineral precipitation and dissolution rates at the 226 ka marine terrace chronosequence near Santa Cruz, CA. Aqueous compositions, fluid chemistry, transport, and mineral abundances are well characterized (White et al., 2008, GCA) and were used to constrain the reaction rates for the weathering and precipitating minerals in the reactive transport modeling. When primary mineral weathering rates are calculated with either of two experimentally determined rate constants, the nonlinear, parallel rate law formulation of Hellmann and Tisser and [2006] or the aluminum inhibition model proposed by Oelkers et al. [1994], modeling results are consistent with field-scale observations when independently constrained clay precipitation rates are accounted for. Experimental and field rates, therefore, can be reconciled at the Santa Cruz site. Observed maximum clay abundances in the argillic horizons occur at the depth and time where the reaction fronts of the primary minerals overlap. The modeling indicates that the argillic horizon at Santa Cruz can be explained almost entirely by weathering of primary minerals and in situ clay precipitation accompanied by undersaturation of kaolinite at the top of the profile. The rate constant for kaolinite precipitation was also determined based on model simulations of mineral abundances and dissolved Al, SiO{sub 2}(aq) and pH in pore waters. Changes in the rate of kaolinite precipitation or the flow rate do not affect the gradient of the primary mineral weathering profiles, but instead control the rate of propagation of the primary mineral weathering fronts and thus total

  5. AltiKa: a Ka-band Altimetry Payload and System for Operational Altimetry during the GMES Period

    PubMed Central

    Vincent, Patrick; Steunou, Nathalie; Caubet, Eric; Phalippou, Laurent; Rey, Laurent; Thouvenot, Eric; Verron, Jacques

    2006-01-01

    This paper describes the Ka-band altimetry payload and system that has been studied for several years by CNES, ALCATEL SPACE and some science laboratories. Altimetry is one of the major elements of the ocean observing system to be made sustainable through the GEOSS (Global Earth Observation System of Systems) and GMES (Global Monitoring of the Environment and Security) programs. A short review of some mission objectives to be fulfilled in terms of mesoscale oceanography in the frame of the GEOSS and GMES programs is performed. To answer the corresponding requirements, the approach consisting in a constellation of nadir altimeter is discussed. A coupled Ka-band altimeter-radiometer payload is then described; technical items are detailed to explain how this payload shall meet the science and operational requirements, and expected performances are displayed. The current status of the payload development and flight perspectives are given.

  6. NMR determination of lysine pKa values in the Pol lambda lyase domain: mechanistic implications.

    PubMed

    Gao, Guanghua; DeRose, Eugene F; Kirby, Thomas W; London, Robert E

    2006-02-14

    The base excision repair (BER) process requires removal of an abasic deoxyribose-5-phosphate group, a catalytic activity that has been demonstrated for the N-terminal 8 kDa domain of DNA polymerase beta (Pol beta), and for the homologous domain of DNA polymerase lambda (Pol lambda). Previous studies have demonstrated that this activity results from formation of a Schiff base adduct of the abasic deoxyribose C-1' with a lysine residue (K312 in the case of Pol lambda), followed by a beta-elimination reaction. To better understand the underlying chemistry, we have determined pKa values for the lysine residues in the Pol lambda lyase domain labeled with [epsilon-13C]lysine. At neutral pH, the H(epsilon) protons on 3 of the 10 lysine residues in this domain, K287, K291, and K312, exhibit chemical shift inequivalence that results from immobilization of the lysyl side chains. For K287 and K291, this results from the K287-E261 and K291-E298 salt bridge interactions, while for K312, immobilization apparently results from steric and hydrogen-bonding interactions that constrain the position of the lysine side chain. The pKa value of K312 is depressed to 9.58, a value indicating that at physiological pH K312 will exist predominantly in the protonated form. Titration of the domain with hairpin DNA containing a 5'-tetrahydrofuran terminus to model the abasic site produced shifts of the labeled lysine resonances that were in fast exchange but appeared to be complete at a stoichiometry of approximately 1:1.3, consistent with a dissociation constant of approximately 1 microM. The epsilon-proton shifts of K273 were the most sensitive to the addition of the DNA, apparently due to changes in the relative orientation between K273 and W274 in the DNA complex. The average pKa values increased by 0.55, consistent with the formation of some DNA-lysine salt bridges and with the general pH increase expected to result from a reduction in the net positive charge of the complex. A general

  7. Constant-Pressure Hydraulic Pump

    NASA Technical Reports Server (NTRS)

    Galloway, C. W.

    1982-01-01

    Constant output pressure in gas-driven hydraulic pump would be assured in new design for gas-to-hydraulic power converter. With a force-multiplying ring attached to gas piston, expanding gas would apply constant force on hydraulic piston even though gas pressure drops. As a result, pressure of hydraulic fluid remains steady, and power output of the pump does not vary.

  8. PRINCIPLES OF AFFINITY-BASED BIOSENSORS

    EPA Science Inventory

    Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applic...

  9. Visualizing Antibody Affinity Maturation in Germinal Centers

    PubMed Central

    Tas, Jeroen M.J.; Mesin, Luka; Pasqual, Giulia; Targ, Sasha; Jacobsen, Johanne T.; Mano, Yasuko M.; Chen, Casie S.; Weill, Jean-Claude; Reynaud, Claude-Agnès; Browne, Edward P.; Meyer-Hermann, Michael; Victora, Gabriel D.

    2016-01-01

    Antibodies somatically mutate to attain high affinity in germinal centers (GCs). There, competition between B cell clones and among somatic mutants of each clone drives an increase in average affinity across the population. The extent to which higher-affinity cells eliminating competitors restricts clonal diversity is unknown. By combining multiphoton microscopy and sequencing, we show that tens to hundreds of distinct B cell clones seed each GC, and that GCs lose clonal diversity at widely disparate rates. Furthermore, efficient affinity maturation can occur in the absence of homogenizing selection, ensuring that many clones can mature in parallel within the same GC. Our findings have implications for development of vaccines in which antibodies with non-immunodominant specificities must be elicited, as is the case for HIV-1 and influenza. PMID:26912368

  10. Protein purification using PDZ affinity chromatography.

    PubMed

    Walkup, Ward G; Kennedy, Mary B

    2015-01-01

    PDZ domains function in nature as protein-binding domains within scaffold and membrane-associated proteins. They comprise approximately 90 residues and undergo specific, high-affinity interactions with complementary C-terminal peptide sequences, other PDZ domains, and/or phospholipids. We have previously shown that the specific, strong interactions of PDZ domains with their ligands make them well suited for use in affinity chromatography. This unit provides protocols for the PDZ affinity chromatography procedure that are applicable for the purification of proteins that contain PDZ domains or PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We detail the preparation of affinity resins composed of PDZ domains or PDZ domain peptide ligands coupled to solid supports. These resins can be used to purify proteins containing endogenous or genetically introduced PDZ domains or ligands, eluting the proteins with free PDZ domain peptide ligands. PMID:25829303

  11. Designing Chaotic Systems by Piecewise Affine Systems

    NASA Astrophysics Data System (ADS)

    Wu, Tiantian; Li, Qingdu; Yang, Xiao-Song

    Based on mathematical analysis, this paper provides a methodology to ensure the existence of homoclinic orbits in a class of three-dimensional piecewise affine systems. In addition, two chaotic generators are provided to illustrate the effectiveness of the method.

  12. Affinity Electrophoresis Using Ligands Attached To Polymers

    NASA Technical Reports Server (NTRS)

    Van Alstine, James M.; Snyder, Robert S.; Harris, J. M.; Brooks, D. E.

    1990-01-01

    In new technique, reduction of electrophoretic mobilities by addition of polyethylene glycol to ligands increases electrophoretic separabilities. In immuno-affinity electrophoresis, modification of ligands extends specificity of electrophoretic separation to particles having surface electric-charge structures otherwise making them electrophoretically inseparable. Modification of antibodies by polyethylene glycol greatly reduces ability to aggregate while enhancing ability to affect electrophoretic mobilities of cells. In hydrophobic-affinity electrophoresis, addition of polyethylene glycol reduces tendency toward aggregation of cells or macromolecules.

  13. First Airswot Ka-Band Radar Backscatter Returns over a Complex California Wetland

    NASA Astrophysics Data System (ADS)

    Baney, O. N.; Smith, L. C.; Pitcher, L. H.; Gleason, C. J.; Chu, V. W.; Bennett, M. M.; Pavelsky, T.; Sadowy, G. A.

    2014-12-01

    In anticipation of the launch of the NASA Surface Water Ocean Topography (SWOT) mission, this project was conducted around the Piute Ponds of Edwards Air Force Base within the Mojave Desert, California to characterize ground conditions simultaneously with two AirSWOT flights collected May 14th, 2014. Both SWOT and AirSWOT employ a Ka-band interferometer to map water surface elevations and extent, but the ability of Ka-band radar to discriminate shorelines and flooded vegetation is not well known. Presumed bright returns from moist soils surrounding surface water bodies have also been speculated to confound interpretation of SWOT/AirSWOT data. The Piute Ponds are a dynamic area of constantly changing water conditions, providing a convenient test site for field studies to assess open water, dry shorelines, vegetation edges, islands, flooded vegetation and soil moisture in conjunction with AirSWOT backscatter and visible/near-infrared camera imagery. Islands were characterized into dry islands and flooded vegetation stands including species such as bulrush (Scripus acutus) and tamarisk (Tammarix ramosissima). Results demonstrate that full water extent can be determined by near-range backscatter returns which are strong for both open water and flooded vegetation. Far-range backscatter returns over open water were unreliable for flooded extent. Comparing near-range and far-range backscatter results to the soil moisture transect shows correlation, however as soil moisture increases, discriminating between wet sediment and water becomes difficult. In sum, first results suggest near-return backscatter results prove most useful in distinguishing open water from non-water, with a strong correlation between soil moisture and backscatter returns.

  14. EF5 Is the High-Affinity Mg(2+) Site in ALG-2.

    PubMed

    Tanner, John J; Frey, Benjamin B; Pemberton, Travis; Henzl, Michael T

    2016-09-13

    The penta-EF-hand (PEF) protein ALG-2 (apoptosis-linked gene 2) has been implicated in several important physiological processes, including endoplasmic reticulum-Golgi vesicular transport and endosomal biogenesis/transport. ALG-2 was recently shown to harbor a metal ion-binding site with a high affinity for Mg(2+) and a low affinity for Ca(2+). We herein present the X-ray structure of Mg(2+)-bound ALG-2des23(wt). Although the C(α) trace is nearly indistinguishable from that of the Ca(2+)-free protein, the orientation of the C-terminal helix differs in the two structures. Consistent with that observation, replacement of the +x ligand in EF5, D169, with alanine eliminates high-affinity Mg(2+) binding. It also eliminates the low-affinity Ca(2+) site and lowers the affinity of the remaining Ca(2+)-binding sites, EF3 and EF1. The coordination environment in EF5 approaches ideal Mg(2+) octahedral geometry. The ligand array, consisting of three carboxylates (+x, +y, +z), a backbone carbonyl (-y), and two water molecules (-x, -z), may offer a recipe for a high-affinity, high-selectivity Mg(2+)-binding site. Sequence data for other PEF proteins indicate that select calpain large subunits, notably CAPN1 and CAPN8, may also possess a high-affinity Mg(2+)-binding site. In Mg(2+)-bound ALG-2, the carbonyl of F188 and the C-terminal carboxylate of V191 interact with the ε-ammonium group of K137 in the opposing subunit, suggesting that Mg(2+) binding could have an impact on dimerization. Interestingly, EF1 and EF3 are also occupied in the crystal, despite having modest affinity for Mg(2+). The results of a calorimetry-based analysis indicate that their Mg(2+) binding constants are 2 orders of magnitude lower than that determined for EF5. PMID:27541325

  15. Constants and Variables of Nature

    SciTech Connect

    Sean Carroll

    2009-04-03

    It is conventional to imagine that the various parameters which characterize our physical theories, such as the fine structure constant or Newton’s gravitational constant, are truly “constant”, in the sense that they do not change from place to place or time to time. Recent developments in both theory and observation have led us to re-examine this assumption, and to take seriously the possibility that our supposed constants are actually gradually changing. I will discuss why we might expect these parameters to vary, and what observation and experiment have to say about the issue.

  16. Low cost, Ka-band microstrip patch monopulse antenna

    NASA Astrophysics Data System (ADS)

    Jackson, Charles M.; Newman, Jeffrey

    1987-07-01

    A monopulse antenna is a novel concept which combines the theory of an interferometer with the practical application of pulsed radar to obtain the angle and altitude of an object in a single radar pulse; four antennas receive signals that are combined to obtain information about the elevation, azimuth, and distance of an object. This paper describes the design and test of a low-cost Ka-band microstrip antenna. Performance results are examined for 35 GHz (twice the rated frequency), and the antenna patterns are considered.

  17. Ka-Band ARM Zenith Radar (KAZR) Instrument Handbook

    SciTech Connect

    Widener, K; Bharadwaj, N; Johnson, K

    2012-03-06

    The Ka-band ARM zenith radar (KAZR) is a zenith-pointing Doppler cloud radar operating at approximately 35 GHz. The KAZR is an evolutionary follow-on radar to ARM's widely successful millimeter-wavelength cloud radar (MMCR). The main purpose of the KAZR is to provide vertical profiles of clouds by measuring the first three Doppler moments: reflectivity, radial Doppler velocity, and spectra width. At the sites where the dual-polarization measurements are made, the Doppler moments for the cross-polarization channel are also available. In addition to the moments, velocity spectra are also continuously recorded for each range gate.

  18. Design and construction of a Ka-band scatterometer

    NASA Astrophysics Data System (ADS)

    Zoll, Michael

    1994-10-01

    This report provides documentation of a Ka-band scatterometer designed and constructed for the Corps of Engineers Waterways Experiment Station. The system is designed to work in conjunction with a Hewlett-Packard 8510 network analyzer to provide fully polarimetric measurements of back-scatter from terrain. It operates over a 2-GHz bandwidth and can be operated in a monostatic, quasimonostatic, or bistatic configuration. The design, theory of operation, and characteristics are provided as a means to assist the operator or to provide information to others wishing to construct their own.

  19. Estimating the acidity of transition metal hydride and dihydrogen complexes by adding ligand acidity constants.

    PubMed

    Morris, Robert H

    2014-02-01

    A simple equation (pKa(THF) = ∑AL + Ccharge + Cnd + Cd6) can be used to obtain an estimate of the pKa of diamagnetic transition metal hydride and dihydrogen complexes in tetrahydrofuran, and, by use of conversion equations, in other solvents. It involves adding acidity constants AL for each of the ligands in the 5-, 6-, 7-, or 8-coordinate conjugate base complex of the hydride or dihydrogen complex along with a correction for the charge (Ccharge = -15, 0 or 30 for x = +1, 0 or -1 charge, respectively) and the periodic row of the transition metal (Cnd = 0 for 3d or 4d metal, 2 for 5d metal) as well as a correction for d(6) octahedral acids (Cd6 = 6 for d(6) metal ion in the acid, 0 for others) that are not dihydrogen complexes. Constants AL are provided for 13 commonly occurring ligand types; of these, nine neutral ligands are correlated with Lever's electrochemical ligand parameters EL. This method gives good estimates of the over 170 literature pKa values that range from less than zero to 50 with a standard deviation of 3 pKa units for complexes of the metals chromium to nickel, molybdenum, ruthenium to palladium, and tungsten to platinum in the periodic table. This approach allows a quick assessment of the acidity of hydride complexes found in nature (e.g., hydrogenases) and in industry (e.g., catalysis and hydrogen energy applications). The pKa values calculated for acids that have bulky or large bite angle chelating ligands deviate the most from this correlation. The method also provides an estimate of the base strength of the deprotonated form of the complex.

  20. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

    PubMed Central

    2015-01-01

    We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values. PMID:25061443

  1. Estimating the acidity of transition metal hydride and dihydrogen complexes by adding ligand acidity constants.

    PubMed

    Morris, Robert H

    2014-02-01

    A simple equation (pKa(THF) = ∑AL + Ccharge + Cnd + Cd6) can be used to obtain an estimate of the pKa of diamagnetic transition metal hydride and dihydrogen complexes in tetrahydrofuran, and, by use of conversion equations, in other solvents. It involves adding acidity constants AL for each of the ligands in the 5-, 6-, 7-, or 8-coordinate conjugate base complex of the hydride or dihydrogen complex along with a correction for the charge (Ccharge = -15, 0 or 30 for x = +1, 0 or -1 charge, respectively) and the periodic row of the transition metal (Cnd = 0 for 3d or 4d metal, 2 for 5d metal) as well as a correction for d(6) octahedral acids (Cd6 = 6 for d(6) metal ion in the acid, 0 for others) that are not dihydrogen complexes. Constants AL are provided for 13 commonly occurring ligand types; of these, nine neutral ligands are correlated with Lever's electrochemical ligand parameters EL. This method gives good estimates of the over 170 literature pKa values that range from less than zero to 50 with a standard deviation of 3 pKa units for complexes of the metals chromium to nickel, molybdenum, ruthenium to palladium, and tungsten to platinum in the periodic table. This approach allows a quick assessment of the acidity of hydride complexes found in nature (e.g., hydrogenases) and in industry (e.g., catalysis and hydrogen energy applications). The pKa values calculated for acids that have bulky or large bite angle chelating ligands deviate the most from this correlation. The method also provides an estimate of the base strength of the deprotonated form of the complex. PMID:24410025

  2. Filling the gap. Human cranial remains from Gombore II (Melka Kunture, Ethiopia; ca. 850 ka) and the origin of Homo heidelbergensis.

    PubMed

    Profico, Antonio; Di Vincenzo, Fabio; Gagliardi, Lorenza; Piperno, Marcello; Manzi, Giorgio

    2016-06-20

    African archaic humans dated to around 1,0 Ma share morphological affinities with Homo ergaster and appear distinct in cranio-dental morphology from those of the Middle Pleistocene that are referred to Homo heidelbergensis. This observation suggests a taxonomic and phylogenetic discontinuity in Africa that ranges across the Matuyama/Brunhes reversal (780 ka). Yet, the fossil record between roughly 900 and 600 ka is notoriously poor. In this context, the Early Stone Age site of Gombore II, in the Melka Kunture formation (Upper Awash, Ethiopia), provides a privileged case-study. In the Acheulean layer of Gombore II, somewhat more recent than 875 ±10 ka, two large cranial fragments were discovered in 1973 and 1975 respectively: a partial left parietal (Melka Kunture 1) and a right portion of the frontal bone (Melka Kunture 2), which probably belonged to the same cranium. We present here the first detailed description and computer-assisted reconstruction of the morphology of the cranial vault pertaining to these fossil fragments. Our analysis suggest that the human fossil specimen from Gombore II fills a phenetic gap between Homo ergaster and Homo heidelbergensis. This appears in agreement with the chronology of such a partial cranial vault, which therefore represents at present one of the best available candidates (if any) for the origin of Homo heidelbergensis in Africa.

  3. Filling the gap. Human cranial remains from Gombore II (Melka Kunture, Ethiopia; ca. 850 ka) and the origin of Homo heidelbergensis.

    PubMed

    Profico, Antonio; Di Vincenzo, Fabio; Gagliardi, Lorenza; Piperno, Marcello; Manzi, Giorgio

    2016-06-20

    African archaic humans dated to around 1,0 Ma share morphological affinities with Homo ergaster and appear distinct in cranio-dental morphology from those of the Middle Pleistocene that are referred to Homo heidelbergensis. This observation suggests a taxonomic and phylogenetic discontinuity in Africa that ranges across the Matuyama/Brunhes reversal (780 ka). Yet, the fossil record between roughly 900 and 600 ka is notoriously poor. In this context, the Early Stone Age site of Gombore II, in the Melka Kunture formation (Upper Awash, Ethiopia), provides a privileged case-study. In the Acheulean layer of Gombore II, somewhat more recent than 875 ±10 ka, two large cranial fragments were discovered in 1973 and 1975 respectively: a partial left parietal (Melka Kunture 1) and a right portion of the frontal bone (Melka Kunture 2), which probably belonged to the same cranium. We present here the first detailed description and computer-assisted reconstruction of the morphology of the cranial vault pertaining to these fossil fragments. Our analysis suggest that the human fossil specimen from Gombore II fills a phenetic gap between Homo ergaster and Homo heidelbergensis. This appears in agreement with the chronology of such a partial cranial vault, which therefore represents at present one of the best available candidates (if any) for the origin of Homo heidelbergensis in Africa. PMID:26583275

  4. Characterization of a dockerin-based affinity tag: application for purification of a broad variety of target proteins.

    PubMed

    Demishtein, Alik; Karpol, Alon; Barak, Yoav; Lamed, Raphael; Bayer, Edward A

    2010-01-01

    Cellulose, a major component of plant matter, is degraded by a cell surface multiprotein complex called the cellulosome produced by several anaerobic bacteria. This complex coordinates the assembly of different glycoside hydrolases, via a high-affinity Ca(2+)-dependent interaction between the enzyme-borne dockerin and the scaffoldin-borne cohesin modules. In this study, we characterized a new protein affinity tag, ΔDoc, a truncated version (48 residues) of the Clostridium thermocellum Cel48S dockerin. The truncated dockerin tag has a binding affinity (K(A)) of 7.7 × 10(8)M(-1), calculated by a competitive enzyme-linked assay system. In order to examine whether the tag can be used for general application in affinity chromatography, it was fused to a range of target proteins, including Aequorea victoria green fluorescent protein (GFP), C. thermocellum β-glucosidase, Escherichia coli thioesterase/protease I (TEP1), and the antibody-binding ZZ-domain from Staphylococcus aureus protein A. The results of this study significantly extend initial studies performed using the Geobacillus stearothermophilus xylanase T-6 as a model system. In addition, the enzymatic activity of a C. thermocellum β-glucosidase, purified using this approach, was tested and found to be similar to that of a β-glucosidase preparation (without the ΔDoc tag) purified using the standard His-tag. The truncated dockerin derivative functioned as an effective affinity tag through specific interaction with a cognate cohesin, and highly purified target proteins were obtained in a single step directly from crude cell extracts. The relatively inexpensive beaded cellulose-based affinity column was reusable and maintained high capacity after each cycle. This study demonstrates that deletion into the first Ca(2+)-binding loop of the dockerin module results in an efficient and robust affinity tag that can be generally applied for protein purification. PMID:21038354

  5. Varying Constants, Gravitation and Cosmology

    NASA Astrophysics Data System (ADS)

    Uzan, Jean-Philippe

    2011-12-01

    Fundamental constants are a cornerstone of our physical laws. Any constant varying in space and/or time would reflect the existence of an almost massless field that couples to matter. This will induce a violation of the universality of free fall. Thus, it is of utmost importance for our understanding of gravity and of the domain of validity of general relativity to test for their constancy. We detail the relations between the constants, the tests of the local position invariance and of the universality of free fall. We then review the main experimental and observational constraints that have been obtained from atomic clocks, the Oklo phenomenon, solar system observations, meteorite dating, quasar absorption spectra, stellar physics, pulsar timing, the cosmic microwave background and big bang nucleosynthesis. At each step we describe the basics of each system, its dependence with respect to the constants, the known systematic effects and the most recent constraints that have been obtained. We then describe the main theoretical frameworks in which the low-energy constants may actually be varying and we focus on the unification mechanisms and the relations between the variation of different constants. To finish, we discuss the more speculative possibility of understanding their numerical values and the apparent fine-tuning that they confront us with.

  6. Characterization of methacrylate chromatographic monoliths bearing affinity ligands.

    PubMed

    Černigoj, Urh; Vidic, Urška; Nemec, Blaž; Gašperšič, Jernej; Vidič, Jana; Lendero Krajnc, Nika; Štrancar, Aleš; Podgornik, Aleš

    2016-09-16

    We investigated effect of immobilization procedure and monolith structure on chromatographic performance of methacrylate monoliths bearing affinity ligands. Monoliths of different pore size and various affinity ligands were prepared and characterized using physical and chromatographic methods. When testing protein A monoliths with different protein A ligand densities, a significant nonlinear effect of ligand density on dynamic binding capacity (DBC) for IgG was obtained and accurately described by Langmuir isotherm curve enabling estimation of protein A utilization as a function of ligand density. Maximal IgG binding capacity was found to be at least 12mg/mL exceeding theoretical monolayer adsorption value of 7.8mg/mL assuming hexagonal packing and IgG hydrodynamic diameter of 11nm. Observed discrepancy was explained by shrinkage of IgG during adsorption on protein A experimentally determined through calculated adsorbed IgG layer thickness of 5.4nm from pressure drop data. For monoliths with different pore size maximal immobilized densities of protein A as well as IgG dynamic capacity linearly correlates with monolith surface area indicating constant ligand utilization. Finally, IgGs toward different plasma proteins were immobilized via the hydrazide coupling chemistry to provide oriented immobilization. DBC was found to be flow independent and was increasing with the size of bound protein. Despite DBC was lower than IgG capacity to immobilized protein A, ligand utilization was higher. PMID:27554023

  7. Advances in affinity ligand-functionalized nanomaterials for biomagnetic separation.

    PubMed

    Fields, Conor; Li, Peng; O'Mahony, James J; Lee, Gil U

    2016-01-01

    The downstream processing of proteins remains the most significant cost in protein production, and is largely attributed to rigorous chromatographic purification protocols, where the stringency of purity for biopharmaceutical products sometimes exceeds 99%. With an ever burgeoning biotechnology market, there is a constant demand for alternative purification methodologies, to ameliorate the dependence on chromatography, while still adhering to regulatory concerns over product purity and safety. In this article, we present an up-to-date view of bioseparation, with emphasis on magnetic separation and its potential application in the field. Additionally, we discuss the economic and performance benefits of synthetic ligands, in the form of peptides and miniaturized antibody fragments, compared to full-length antibodies. We propose that adoption of synthetic affinity ligands coupled with magnetic adsorbents, will play an important role in enabling sustainable bioprocessing in the future.

  8. Advances in affinity ligand-functionalized nanomaterials for biomagnetic separation.

    PubMed

    Fields, Conor; Li, Peng; O'Mahony, James J; Lee, Gil U

    2016-01-01

    The downstream processing of proteins remains the most significant cost in protein production, and is largely attributed to rigorous chromatographic purification protocols, where the stringency of purity for biopharmaceutical products sometimes exceeds 99%. With an ever burgeoning biotechnology market, there is a constant demand for alternative purification methodologies, to ameliorate the dependence on chromatography, while still adhering to regulatory concerns over product purity and safety. In this article, we present an up-to-date view of bioseparation, with emphasis on magnetic separation and its potential application in the field. Additionally, we discuss the economic and performance benefits of synthetic ligands, in the form of peptides and miniaturized antibody fragments, compared to full-length antibodies. We propose that adoption of synthetic affinity ligands coupled with magnetic adsorbents, will play an important role in enabling sustainable bioprocessing in the future. PMID:26032605

  9. Classification of neocortical interneurons using affinity propagation

    PubMed Central

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  10. Classification of neocortical interneurons using affinity propagation.

    PubMed

    Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  11. Classification of neocortical interneurons using affinity propagation.

    PubMed

    Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  12. Rationalization of the pKa values of alcohols and thiols using atomic charge descriptors and its application to the prediction of amino acid pKa's.

    PubMed

    Ugur, Ilke; Marion, Antoine; Parant, Stéphane; Jensen, Jan H; Monard, Gerald

    2014-08-25

    In a first step toward the development of an efficient and accurate protocol to estimate amino acids' pKa's in proteins, we present in this work how to reproduce the pKa's of alcohol and thiol based residues (namely tyrosine, serine, and cysteine) in aqueous solution from the knowledge of the experimental pKa's of phenols, alcohols, and thiols. Our protocol is based on the linear relationship between computed atomic charges of the anionic form of the molecules (being either phenolates, alkoxides, or thiolates) and their respective experimental pKa values. It is tested with different environment approaches (gas phase or continuum solvent-based approaches), with five distinct atomic charge models (Mulliken, Löwdin, NPA, Merz-Kollman, and CHelpG), and with nine different DFT functionals combined with 16 different basis sets. Moreover, the capability of semiempirical methods (AM1, RM1, PM3, and PM6) to also predict pKa's of thiols, phenols, and alcohols is analyzed. From our benchmarks, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the CPCM model at the B3LYP/3-21G and M062X/6-311G levels for alcohols (R(2) = 0.995) and thiols (R(2) = 0.986), respectively. The applicability of the suggested protocol is tested with tyrosine and cysteine amino acids, and precise pKa predictions are obtained. The stability of the amino acid pKa's with respect to geometrical changes is also tested by MM-MD and DFT-MD calculations. Considering its strong accuracy and its high computational efficiency, these pKa prediction calculations using atomic charges indicate a promising method for predicting amino acids' pKa in a protein environment.

  13. Rationalization of the pKa values of alcohols and thiols using atomic charge descriptors and its application to the prediction of amino acid pKa's.

    PubMed

    Ugur, Ilke; Marion, Antoine; Parant, Stéphane; Jensen, Jan H; Monard, Gerald

    2014-08-25

    In a first step toward the development of an efficient and accurate protocol to estimate amino acids' pKa's in proteins, we present in this work how to reproduce the pKa's of alcohol and thiol based residues (namely tyrosine, serine, and cysteine) in aqueous solution from the knowledge of the experimental pKa's of phenols, alcohols, and thiols. Our protocol is based on the linear relationship between computed atomic charges of the anionic form of the molecules (being either phenolates, alkoxides, or thiolates) and their respective experimental pKa values. It is tested with different environment approaches (gas phase or continuum solvent-based approaches), with five distinct atomic charge models (Mulliken, Löwdin, NPA, Merz-Kollman, and CHelpG), and with nine different DFT functionals combined with 16 different basis sets. Moreover, the capability of semiempirical methods (AM1, RM1, PM3, and PM6) to also predict pKa's of thiols, phenols, and alcohols is analyzed. From our benchmarks, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the CPCM model at the B3LYP/3-21G and M062X/6-311G levels for alcohols (R(2) = 0.995) and thiols (R(2) = 0.986), respectively. The applicability of the suggested protocol is tested with tyrosine and cysteine amino acids, and precise pKa predictions are obtained. The stability of the amino acid pKa's with respect to geometrical changes is also tested by MM-MD and DFT-MD calculations. Considering its strong accuracy and its high computational efficiency, these pKa prediction calculations using atomic charges indicate a promising method for predicting amino acids' pKa in a protein environment. PMID:25089727

  14. Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors

    PubMed Central

    Duan, Xuexin; Li, Yue; Rajan, Nitin K.; Routenberg, David A.; Modis, Yorgo; Reed, Mark A.

    2014-01-01

    Monitoring the binding affinities and kinetics of protein interactions is important in clinical diagnostics and drug development because such information is used to identify new therapeutic candidates. Surface plasmon resonance is at present the standard method used for such analysis, but this is limited by low sensitivity and low-throughput analysis. Here, we show that silicon nanowire field-effect transistors can be used as biosensors to measure protein–ligand binding affinities and kinetics with sensitivities down to femtomolar concentrations. Based on this sensing mechanism, we develop an analytical model to calibrate the sensor response and quantify the molecular binding affinities of two representative protein–ligand binding pairs. The rate constant of the association and dissociation of the protein–ligand pair is determined by monitoring the reaction kinetics, demonstrating that silicon nanowire field-effect transistors can be readily used as high-throughput biosensors to quantify protein interactions. PMID:22635097

  15. Measurement of affinity of viral monoclonal antibodies by ELISA titration of free antibody in equilibrium mixtures.

    PubMed

    Azimzadeh, A; Van Regenmortel, M H

    1991-08-01

    The binding affinity of a monoclonal antibody (Mab) to tobacco mosaic virus (TMV) was determined by measuring, in an enzyme-linked immunosorbent assay, the amount of free antibody present after ultracentrifugation of virus-antibody complexes at equilibrium. In antibody excess, univalent binding of Mabs was observed and the affinity constant was K = 3.2 +/- 0.4 10(8) l/mol; in antigen excess, bivalent antibody binding was observed and the antibody avidity was about 15 times higher. In antigen excess, it was imperative to correct experimental data for the presence of 0.55% inactive molecules in the immunopurified antibody preparation. Modelling studies suggest that in the case of antibodies of increasing affinity, it becomes increasingly important to correct for the presence of inactive antibody in the binding assay.

  16. Influence of the galloyl moiety in tea catechins on binding affinity for human serum albumin.

    PubMed

    Minoda, Kanako; Ichikawa, Tatsuya; Katsumata, Tomoharu; Onobori, Ken-ichi; Mori, Taiki; Suzuki, Yukiko; Ishii, Takeshi; Nakayama, Tsutomu

    2010-01-01

    The major catechins of green tea extract are (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECg), and (-)-epigallocatechin gallate (EGCg). Recent research has indicated that catechins form complexes with human serum albumin (HSA) in blood, and differences in their binding affinity toward HSA are believed to modulate their bioavailability. In this study, we kinetically investigated the interaction between the catechins and HSA immobilized on a quartz-crystal microbalance (QCM). The association constants obtained from the frequency changes of QCM revealed interactions of ECg and EGCg with HSA that are 100 times stronger than those of EC and EGC. Furthermore, comparisons of these catechins by native-gel electrophoresis/blotting with redox-cycling staining revealed that, in a phosphate buffer, ECg and EGCg have a higher binding affinity toward HSA than EC and EGC. These observations indicate that catechins with a galloyl moiety have higher binding affinities toward HSA than catechins lacking a galloyl moiety.

  17. Impedance-derived electrochemical capacitance spectroscopy for the evaluation of lectin-glycoprotein binding affinity.

    PubMed

    Santos, Adriano; Carvalho, Fernanda C; Roque-Barreira, Maria-Cristina; Bueno, Paulo R

    2014-12-15

    Characterization of lectin-carbohydrate binding using label-free methods such as impedance-derived electrochemical capacitance spectroscopy (ECS) is desirable to evaluate specific interactions, for example, ArtinM lectin and horseradish peroxidase (HRP) glycoprotein, used here as a model for protein-carbohydrate binding affinity. An electroactive molecular film comprising alkyl ferrocene as a redox probe and ArtinM as a carbohydrate receptive center to target HRP was successfully used to determine the binding affinity between ArtinM and HRP. The redox capacitance, a transducer signal associated with the alkyl ferrocene centers, was obtained by ECS and used in the Langmuir adsorption model to obtain the affinity constant (1.6±0.6)×10(8) L mol(-1). The results shown herein suggest the feasibility of ECS application for lectin glycoarray characterization. PMID:24994505

  18. One-step surface modification of polyurethane using affinity binding peptides for enhanced fouling resistance.

    PubMed

    Wang, Yibing; Yu, Yong; Zhang, Liting; Qin, Peng; Wang, Ping

    2015-01-01

    Affinity binding peptides were examined for surface fabrication of synthetic polymeric materials. Peptides possessing strong binding affinities toward polyurethane (PU) were discovered via biopanning of M13 phage peptide library. The apparent binding constant (K(app)) was as high as 2.68 × 10(9) M(-1) with surface peptide density exceeded 1.8 μg/cm(2). Structural analysis showed that the ideal peptide had a high content (75%) of H-donor amino acid residues, and that intensified hydrogen bond interaction was the key driving force for the highly stable binding of peptides on PU. PU treated with such affinity peptides promises applications as low-fouling materials, as peptides increased its wettability and substantially reduced protein adsorption and cell adhesion. These results demonstrated a facile but highly efficient one-step strategy for surface property modification of polymeric materials for biotechnological applications. PMID:25732121

  19. Impedance-derived electrochemical capacitance spectroscopy for the evaluation of lectin-glycoprotein binding affinity.

    PubMed

    Santos, Adriano; Carvalho, Fernanda C; Roque-Barreira, Maria-Cristina; Bueno, Paulo R

    2014-12-15

    Characterization of lectin-carbohydrate binding using label-free methods such as impedance-derived electrochemical capacitance spectroscopy (ECS) is desirable to evaluate specific interactions, for example, ArtinM lectin and horseradish peroxidase (HRP) glycoprotein, used here as a model for protein-carbohydrate binding affinity. An electroactive molecular film comprising alkyl ferrocene as a redox probe and ArtinM as a carbohydrate receptive center to target HRP was successfully used to determine the binding affinity between ArtinM and HRP. The redox capacitance, a transducer signal associated with the alkyl ferrocene centers, was obtained by ECS and used in the Langmuir adsorption model to obtain the affinity constant (1.6±0.6)×10(8) L mol(-1). The results shown herein suggest the feasibility of ECS application for lectin glycoarray characterization.

  20. Ultra Small Aperture Terminal for Ka-Band SATCOM

    NASA Technical Reports Server (NTRS)

    Acosta, Roberto; Reinhart, Richard; Lee, Richard; Simons, Rainee

    1997-01-01

    An ultra small aperture terminal (USAT) at Ka-band frequency has been developed by Lewis Research Center (LeRC) for data rates up to 1.5 Mbps in the transmit mode and 40 Mbps in receive mode. The terminal consists of a 35 cm diameter offset-fed parabolic antenna which is attached to a solid state power amplifier and low noise amplifier. A single down converter is used to convert the Ka-band frequency to 70 MHz intermediate frequency (IF). A variable rate (9.6 Kbps to 10 Mbps) commercial modem with a standard RS-449/RS-232 interface is used to provide point-to-point digital services. The terminal has been demonstrated numerous times using the Advanced Communications Technology Satellite (ACTS) and the 4.5 in Link Evaluation Terminal (LET) in Cleveland. A conceptual design for an advanced terminal has also been developed. This advanced USAT utilizes Microwave Monolithic Integrated Circuit (MMIC) and flat plate array technologies. This terminal will be self contained in a single package which will include a 1 watt solid state amplifier (SSPA), low noise amplifier (LNA) and a modem card located behind the aperture of the array. The advanced USAT will be light weight, transportable, low cost and easy to point to the satellite. This paper will introduce designs for the reflector based and array based USAT's.

  1. Ka-Band, Multi-Gigabit-Per-Second Transceiver

    NASA Technical Reports Server (NTRS)

    Simons, Rainee N.; Wintucky, Edwin G.; Smith, Francis J.; Harris, Johnny M.; Landon, David G.; Haddadin, Osama S.; McIntire, William K.; Sun, June Y.

    2011-01-01

    A document discusses a multi-Gigabit-per-second, Ka-band transceiver with a software-defined modem (SDM) capable of digitally encoding/decoding data and compensating for linear and nonlinear distortions in the end-to-end system, including the traveling-wave tube amplifier (TWTA). This innovation can increase data rates of space-to-ground communication links, and has potential application to NASA s future spacebased Earth observation system. The SDM incorporates an extended version of the industry-standard DVB-S2, and LDPC rate 9/10 FEC codec. The SDM supports a suite of waveforms, including QPSK, 8-PSK, 16-APSK, 32- APSK, 64-APSK, and 128-QAM. The Ka-band and TWTA deliver an output power on the order of 200 W with efficiency greater than 60%, and a passband of at least 3 GHz. The modem and the TWTA together enable a data rate of 20 Gbps with a low bit error rate (BER). The payload data rates for spacecraft in NASA s integrated space communications network can be increased by an order of magnitude (>10 ) over current state-of-practice. This innovation enhances the data rate by using bandwidth-efficient modulation techniques, which transmit a higher number of bits per Hertz of bandwidth than the currently used quadrature phase shift keying (QPSK) waveforms.

  2. K/Ka-band channel characterization for mobile satellite systems

    NASA Technical Reports Server (NTRS)

    Pinck, Deborah S.; Rice, Michael D.

    1995-01-01

    Mobile satellite systems allow truly ubiquitous wireless communications to users anywhere and anytime. NASA's Advanced Communications Technology Satellite (ACTS) provides an ideal space-based platform for the measurement of K/Ka band propagation characteristics in a land mobile satellite application. Field tests conducted in Southern California during the first seven months of 1994 using JPL's ACTS Mobile Terminal (AMT) provided channel characterization data for the K/Ka-band link. A pilot tone was transmitted from a fixed station in Cleveland, Ohio through the satellite and downlinked at 20 GHz in the Southern California spot beam. The AMT was equipped with a narrow beam, high gain antenna which tracked the satellite in azimuth for a fixed elevation angle (46 degrees for this case). The field tests were conducted in three basic environments: clear line-of-sight (LOS) highways, lightly shadowed suburban, and heavily shadowed suburban. Preliminary results of these field tests indicate very little multipath for rural environments and for clear LOS links (as expected with a narrow beam antenna). Deep fades were experienced in shadowed areas, especially those where tree canopies covered the road.

  3. ITIL and Grid services at GridKa

    NASA Astrophysics Data System (ADS)

    Marten, H.; Koenig, T.

    2010-04-01

    The Steinbuch Centre for Computing (SCC) is a new organizational unit of the Karlsruhe Institute of Technology (KIT). Founded in February 2008 as a merger of the previous Institute for Scientific Computing of Forschungszentrum Karlsruhe and the Computing Centre of the Technical University Karlsruhe, SCC provides a broad spectrum of IT services for 8.000 employees and 18.000 students and carries out research and development in key areas of information technology under the same roof. SCC is also known to host the German WLCG [1] Tier-1 centre GridKa. In order to accompany the merging of the two existing computing centres located at a distance of about 10 km and to provide common first class services for science, SCC has selected the IT service management according to the industrial quasi-standard "IT Infrastructure Library (ITIL)" [3] as a strategic element. The paper discusses the implementation of a few ITIL key components from the perspective of a Scientific Computing Centre using examples of Grid services at GridKa.

  4. CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

    PubMed Central

    2013-01-01

    A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has currently obtained data from Abbott, GlaxoSmithKline, and Vertex and is working on obtaining data from several others. Combined with our in-house projects, we are providing a data set consisting of 6 protein targets, 647 compounds with biological affinities, and 82 crystal structures. Multiple congeneric series are available for several targets with a few representative crystal structures of each of the series. These series generally contain a few inactive compounds, usually not available in the literature, to provide an upper bound to the affinity range. The affinity ranges are typically 3–4 orders of magnitude per series. For our in-house projects, we have had compounds synthesized for biological testing. Affinities were measured by Thermofluor, Octet RED, and isothermal titration calorimetry for the most soluble. This allows the direct comparison of the biological affinities for those compounds, providing a measure of the variance in the experimental affinity. It appears that there can be considerable variance in the absolute value of the affinity, making the prediction of the absolute value ill-defined. However, the relative rankings within the methods are much better, and this fits with the observation that predicting relative ranking is a more tractable problem computationally. For those in-house compounds, we also have measured the following physical properties: logD, logP, thermodynamic solubility, and pKa. This data set also provides a substantial decoy set for each target consisting of diverse conformations covering the entire active site for all of the 58 CSAR-quality crystal structures. The CSAR data sets (CSAR-NRC HiQ and the 2012 release) provide substantial, publically

  5. Identity, Affinity, Reality: Making the Case for Affinity Groups in Elementary School

    ERIC Educational Resources Information Center

    Parsons, Julie; Ridley, Kimberly

    2012-01-01

    Affinity groups are places where students build connections and process "ouch" moments from their classes. Children talk about the isolation they sometimes feel. The relationships students gain through race-based affinity groups enable them to feel less alone with their emotions and help them build a stronger sense of self. At the same time,…

  6. Stepparents' Affinity-Seeking and Affinity-Maintaining Strategies with Stepchildren.

    ERIC Educational Resources Information Center

    Ganong, Lawrence; Coleman, Marilyn; Fine, Mark; Martin, Patricia

    1999-01-01

    Examines the strategies that stepparents use to develop and maintain affinity with stepchildren and the effects that these strategies have on the development of stepparent-stepchildren relationships. Thirty-one affinity-seeking strategies are identified. Results show that dyadic activities worked best, but it is important that stepchildren…

  7. Constant fields and constant gradients in open ionic channels.

    PubMed

    Chen, D P; Barcilon, V; Eisenberg, R S

    1992-05-01

    Ions enter cells through pores in proteins that are holes in dielectrics. The energy of interaction between ion and charge induced on the dielectric is many kT, and so the dielectric properties of channel and pore are important. We describe ionic movement by (three-dimensional) Nemst-Planck equations (including flux and net charge). Potential is described by Poisson's equation in the pore and Laplace's equation in the channel wall, allowing induced but not permanent charge. Asymptotic expansions are constructed exploiting the long narrow shape of the pore and the relatively high dielectric constant of the pore's contents. The resulting one-dimensional equations can be integrated numerically; they can be analyzed when channels are short or long (compared with the Debye length). Traditional constant field equations are derived if the induced charge is small, e.g., if the channel is short or if the total concentration gradient is zero. A constant gradient of concentration is derived if the channel is long. Plots directly comparable to experiments are given of current vs voltage, reversal potential vs. concentration, and slope conductance vs. concentration. This dielectric theory can easily be tested: its parameters can be determined by traditional constant field measurements. The dielectric theory then predicts current-voltage relations quite different from constant field, usually more linear, when gradients of total concentration are imposed. Numerical analysis shows that the interaction of ion and channel can be described by a mean potential if, but only if, the induced charge is negligible, that is to say, the electric field is spatially constant.

  8. Constant fields and constant gradients in open ionic channels.

    PubMed Central

    Chen, D P; Barcilon, V; Eisenberg, R S

    1992-01-01

    Ions enter cells through pores in proteins that are holes in dielectrics. The energy of interaction between ion and charge induced on the dielectric is many kT, and so the dielectric properties of channel and pore are important. We describe ionic movement by (three-dimensional) Nemst-Planck equations (including flux and net charge). Potential is described by Poisson's equation in the pore and Laplace's equation in the channel wall, allowing induced but not permanent charge. Asymptotic expansions are constructed exploiting the long narrow shape of the pore and the relatively high dielectric constant of the pore's contents. The resulting one-dimensional equations can be integrated numerically; they can be analyzed when channels are short or long (compared with the Debye length). Traditional constant field equations are derived if the induced charge is small, e.g., if the channel is short or if the total concentration gradient is zero. A constant gradient of concentration is derived if the channel is long. Plots directly comparable to experiments are given of current vs voltage, reversal potential vs. concentration, and slope conductance vs. concentration. This dielectric theory can easily be tested: its parameters can be determined by traditional constant field measurements. The dielectric theory then predicts current-voltage relations quite different from constant field, usually more linear, when gradients of total concentration are imposed. Numerical analysis shows that the interaction of ion and channel can be described by a mean potential if, but only if, the induced charge is negligible, that is to say, the electric field is spatially constant. Images FIGURE 1 PMID:1376159

  9. Effective cosmological constant induced by stochastic fluctuations of Newton's constant

    NASA Astrophysics Data System (ADS)

    de Cesare, Marco; Lizzi, Fedele; Sakellariadou, Mairi

    2016-09-01

    We consider implications of the microscopic dynamics of spacetime for the evolution of cosmological models. We argue that quantum geometry effects may lead to stochastic fluctuations of the gravitational constant, which is thus considered as a macroscopic effective dynamical quantity. Consistency with Riemannian geometry entails the presence of a time-dependent dark energy term in the modified field equations, which can be expressed in terms of the dynamical gravitational constant. We suggest that the late-time accelerated expansion of the Universe may be ascribed to quantum fluctuations in the geometry of spacetime rather than the vacuum energy from the matter sector.

  10. Concurrent low- and high-affinity sulfate reduction kinetics in marine sediment

    NASA Astrophysics Data System (ADS)

    Harder Tarpgaard, Irene; Røy, Hans; Jørgensen, Bo Barker

    Bacterial sulfate reduction in marine sediments generally occurs in the presence of high millimolar concentrations of sulfate. Published data indicate that low sulfate concentrations may limit sulfate reduction rates below 0.2-2 mM. Yet, high sulfate reduction rates occur in the 1-100 μM range in freshwater sediments and at the sulfate-methane transition in marine sediments. Through a combination of 35S-tracer experiments, including initial velocity experiments and time course experiments, we searched for different sulfate affinities in the mixed community of sulfate reducers in a marine sediment. We supported the radiotracer experiments with a highly sensitive ion chromatographic technique for sulfate with a detection limit of 0.15 μM SO 42- in marine pore water. Our results showed that high and low affinities for sulfate co-occur and that the applied experimental approach may determine the observed apparent half saturation constant, Km. Our experimental and model data both show that sulfate reduction in the studied marine sediment could be explained by two dominating affinities for sulfate: a low affinity with a mean half saturation constant, Km, of 430 μM SO 42- and a high affinity with a mean Km of 2.6 μM SO 42-. The high-affinity sulfate reduction was thermodynamically un-constrained down to <1 μM SO 42-, both in our experiments and under in situ conditions. The reduction of radio-labeled sulfate was partly reversible due to concurrent re-oxidation of sulfide by Fe(III) and possibly due to a reversibility of the enzymatic pathway of sulfate reduction. A literature survey of apparent Km values for sediments and pure cultures is presented and discussed.

  11. Affinity chromatography of bacterial lactate dehydrogenases.

    PubMed Central

    Kelly, N; Delaney, M; O'Carra, P

    1978-01-01

    The affinity system used was the immobilized oxamate derivative previously used to purify mammalian lactate dehydrogenases. The bacterial dehydrogenases specific for the L-stereoisomer of lactate behaved in the same way as the mammalian enzymes, binding strongly in the presence of NADH. The D-lactate-specific enzymes, however, did not show any biospecific affinity for this gel. The L-specific enzymes could be purified to homogeneity in one affinity-chromatographic step. The D-specific enzymes could be efficiently separated from the L-specific ones and could then be further purified on an immobilized NAD derivative. The mechanism of activation of the lactate dehydrogenase from Streptococcus faecalis by fructose 1,6-bisphosphate was investigated by using the immobilized oxamate gel. PMID:666726

  12. Affinity chromatography of bacterial lactate dehydrogenases.

    PubMed

    Kelly, N; Delaney, M; O'Carra, P

    1978-06-01

    The affinity system used was the immobilized oxamate derivative previously used to purify mammalian lactate dehydrogenases. The bacterial dehydrogenases specific for the L-stereoisomer of lactate behaved in the same way as the mammalian enzymes, binding strongly in the presence of NADH. The D-lactate-specific enzymes, however, did not show any biospecific affinity for this gel. The L-specific enzymes could be purified to homogeneity in one affinity-chromatographic step. The D-specific enzymes could be efficiently separated from the L-specific ones and could then be further purified on an immobilized NAD derivative. The mechanism of activation of the lactate dehydrogenase from Streptococcus faecalis by fructose 1,6-bisphosphate was investigated by using the immobilized oxamate gel. PMID:666726

  13. The role of reaction affinity and secondary minerals in regulating chemical weathering rates at the Santa Cruz Soil Chronosequence, California

    NASA Astrophysics Data System (ADS)

    Maher, Kate; Steefel, Carl I.; White, Art F.; Stonestrom, Dave A.

    2009-05-01

    In order to explore the reasons for the apparent discrepancy between laboratory and field weathering rates and to determine the extent to which weathering rates are controlled by the approach to thermodynamic equilibrium, secondary mineral precipitation, and flow rates, a multicomponent reactive transport model (CrunchFlow) was used to interpret soil profile development and mineral precipitation and dissolution rates at the 226 ka Marine Terrace Chronosequence near Santa Cruz, CA. Aqueous compositions, fluid chemistry, transport, and mineral abundances are well characterized [White A. F., Schulz M. S., Vivit D. V., Blum A., Stonestrom D. A. and Anderson S. P. (2008) Chemical weathering of a Marine Terrace Chronosequence, Santa Cruz, California. I: interpreting the long-term controls on chemical weathering based on spatial and temporal element and mineral distributions. Geochim. Cosmochim. Acta72 (1), 36-68] and were used to constrain the reaction rates for the weathering and precipitating minerals in the reactive transport modeling. When primary mineral weathering rates are calculated with either of two experimentally determined rate constants, the nonlinear, parallel rate law formulation of Hellmann and Tisserand [Hellmann R. and Tisserand D. (2006) Dissolution kinetics as a function of the Gibbs free energy of reaction: An experimental study based on albite feldspar. Geochim. Cosmochim. Acta70 (2), 364-383] or the aluminum inhibition model proposed by Oelkers et al. [Oelkers E. H., Schott J. and Devidal J. L. (1994) The effect of aluminum, pH, and chemical affinity on the rates of aluminosilicate dissolution reactions. Geochim. Cosmochim. Acta58 (9), 2011-2024], modeling results are consistent with field-scale observations when independently constrained clay precipitation rates are accounted for. Experimental and field rates, therefore, can be reconciled at the Santa Cruz site. Additionally, observed maximum clay abundances in the argillic horizons occur at the

  14. The role of reaction affinity and secondary minerals in regulating chemical weathering rates at the Santa Cruz Soil Chronosequence, California

    USGS Publications Warehouse

    Maher, K.; Steefel, Carl; White, A.F.; Stonestrom, D.A.

    2009-01-01

    In order to explore the reasons for the apparent discrepancy between laboratory and field weathering rates and to determine the extent to which weathering rates are controlled by the approach to thermodynamic equilibrium, secondary mineral precipitation, and flow rates, a multicomponent reactive transport model (CrunchFlow) was used to interpret soil profile development and mineral precipitation and dissolution rates at the 226 ka Marine Terrace Chronosequence near Santa Cruz, CA. Aqueous compositions, fluid chemistry, transport, and mineral abundances are well characterized [White A. F., Schulz M. S., Vivit D. V., Blum A., Stonestrom D. A. and Anderson S. P. (2008) Chemical weathering of a Marine Terrace Chronosequence, Santa Cruz, California. I: interpreting the long-term controls on chemical weathering based on spatial and temporal element and mineral distributions. Geochim. Cosmochim. Acta 72 (1), 36-68] and were used to constrain the reaction rates for the weathering and precipitating minerals in the reactive transport modeling. When primary mineral weathering rates are calculated with either of two experimentally determined rate constants, the nonlinear, parallel rate law formulation of Hellmann and Tisserand [Hellmann R. and Tisserand D. (2006) Dissolution kinetics as a function of the Gibbs free energy of reaction: An experimental study based on albite feldspar. Geochim. Cosmochim. Acta 70 (2), 364-383] or the aluminum inhibition model proposed by Oelkers et al. [Oelkers E. H., Schott J. and Devidal J. L. (1994) The effect of aluminum, pH, and chemical affinity on the rates of aluminosilicate dissolution reactions. Geochim. Cosmochim. Acta 58 (9), 2011-2024], modeling results are consistent with field-scale observations when independently constrained clay precipitation rates are accounted for. Experimental and field rates, therefore, can be reconciled at the Santa Cruz site. Additionally, observed maximum clay abundances in the argillic horizons occur at

  15. European and international collaboration in affinity proteomics.

    PubMed

    Stoevesandt, Oda; Taussig, Michael J

    2012-06-15

    In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New

  16. Displacement phenomena in lectin affinity chromatography.

    PubMed

    Cho, Wonryeon

    2015-10-01

    The work described here examines displacement phenomena that play a role in lectin affinity chromatography and their potential to impact reproducibility. This was achieved using Lycopersicon esculentum lectin (LEL), a lectin widely used in monitoring cancer. Four small identical LEL columns were coupled in series to form a single affinity chromatography system with the last in the series connected to an absorbance detector. The serial affinity column set (SACS) was then loaded with human plasma proteins. At the completion of loading, the column set was disassembled, the four columns were eluted individually, the captured proteins were trypsin digested, the peptides were deglycosylated with PNGase F, and the parent proteins were identified through mass spectral analyses. Significantly different sets of glycoproteins were selected by each column, some proteins appearing to be exclusively bound to the first column while others were bound further along in the series. Clearly, sample displacement chromatography (SDC) occurs. Glycoproteins were bound at different places in the column train, identifying the presence of glycoforms with different affinity on a single glycoprotein. It is not possible to see these phenomena in the single column mode of chromatography. Moreover, low abundance proteins were enriched, which facilitates detection. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Displacement phenomena are concluded to be a significant component of the separation mechanism in heavily loaded lectin affinity chromatography columns. This further suggests that care must be exercised in sample loading of lectin columns to prevent analyte displacement with nonretained proteins. PMID:26348026

  17. The dynamics of metric-affine gravity

    SciTech Connect

    Vitagliano, Vincenzo; Sotiriou, Thomas P.; Liberati, Stefano

    2011-05-15

    Highlights: > The role and the dynamics of the connection in metric-affine theories is explored. > The most general second order action does not lead to a dynamical connection. > Including higher order invariants excites new degrees of freedom in the connection. > f(R) actions are also discussed and shown to be a non- representative class. - Abstract: Metric-affine theories of gravity provide an interesting alternative to general relativity: in such an approach, the metric and the affine (not necessarily symmetric) connection are independent quantities. Furthermore, the action should include covariant derivatives of the matter fields, with the covariant derivative naturally defined using the independent connection. As a result, in metric-affine theories a direct coupling involving matter and connection is also present. The role and the dynamics of the connection in such theories is explored. We employ power counting in order to construct the action and search for the minimal requirements it should satisfy for the connection to be dynamical. We find that for the most general action containing lower order invariants of the curvature and the torsion the independent connection does not carry any dynamics. It actually reduces to the role of an auxiliary field and can be completely eliminated algebraically in favour of the metric and the matter field, introducing extra interactions with respect to general relativity. However, we also show that including higher order terms in the action radically changes this picture and excites new degrees of freedom in the connection, making it (or parts of it) dynamical. Constructing actions that constitute exceptions to this rule requires significant fine tuned and/or extra a priori constraints on the connection. We also consider f(R) actions as a particular example in order to show that they constitute a distinct class of metric-affine theories with special properties, and as such they cannot be used as representative toy theories to

  18. Optical constants of solid methane

    NASA Technical Reports Server (NTRS)

    Khare, Bishun N.; Thompson, W. R.; Sagan, C.; Arakawa, E. T.; Bruel, C.; Judish, J. P.; Khanna, R. K.; Pollack, J. B.

    1989-01-01

    Methane is the most abundant simple organic molecule in the outer solar system bodies. In addition to being a gaseous constituent of the atmospheres of the Jovian planets and Titan, it is present in the solid form as a constituent of icy surfaces such as those of Triton and Pluto, and as cloud condensate in the atmospheres of Titan, Uranus, and Neptune. It is expected in the liquid form as a constituent of the ocean of Titan. Cometary ices also contain solid methane. The optical constants for both solid and liquid phases of CH4 for a wide temperature range are needed for radiative transfer calculations, for studies of reflection from surfaces, and for modeling of emission in the far infrared and microwave regions. The astronomically important visual to near infrared measurements of solid methane optical constants are conspicuously absent from the literature. Preliminary results are presented of the optical constants of solid methane for the 0.4 to 2.6 micron region. K is reported for both the amorphous and the crystalline (annealed) states. Using the previously measured values of the real part of the refractive index, n, of liquid methane at 110 K n is computed for solid methane using the Lorentz-Lorentz relationship. Work is in progress to extend the measurements of optical constants n and k for liquid and solid to both shorter and longer wavelengths, eventually providing a complete optical constants database for condensed CH4.

  19. Affine Invariant Character Recognition by Progressive Removing

    NASA Astrophysics Data System (ADS)

    Iwamura, Masakazu; Horimatsu, Akira; Niwa, Ryo; Kise, Koichi; Uchida, Seiichi; Omachi, Shinichiro

    Recognizing characters in scene images suffering from perspective distortion is a challenge. Although there are some methods to overcome this difficulty, they are time-consuming. In this paper, we propose a set of affine invariant features and a new recognition scheme called “progressive removing” that can help reduce the processing time. Progressive removing gradually removes less feasible categories and skew angles by using multiple classifiers. We observed that progressive removing and the use of the affine invariant features reduced the processing time by about 60% in comparison to a trivial one without decreasing the recognition rate.

  20. Negative Electron Affinity Mechanism for Diamond Surfaces

    NASA Technical Reports Server (NTRS)

    Krainsky, I. L.; Asnin, V. M.

    1998-01-01

    The energy distribution of the secondary electrons for chemical vacuum deposited diamond films with Negative Electron Affinity (NEA) was investigated. It was found that while for completely hydrogenated diamond surfaces the negative electron affinity peak in the energy spectrum of the secondary electrons is present for any energy of the primary electrons, for partially hydrogenated diamond surfaces there is a critical energy above which the peak is present in the spectrum. This critical energy increases sharply when hydrogen coverage of the diamond surface diminishes. This effect was explained by the change of the NEA from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surfaces.

  1. Adsorption affinity of anions on metal oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Pechenyuk, S. I.; Semushina, Yu. P.; Kuz'mich, L. F.

    2013-03-01

    The dependences of anion (phosphate, carbonate, sulfate, chromate, oxalate, tartrate, and citrate) adsorption affinity anions from geometric characteristics, acid-base properties, and complex forming ability are generalized. It is shown that adsorption depends on the nature of both the anions and the ionic medium and adsorbent. It is established that anions are generally grouped into the following series of adsorption affinity reduction: PO{4/3-}, CO{3/2-} > C2O{4/2-}, C(OH)(CH2)2(COO){3/3-}, (CHOH)2(COO){2/2-} > CrO{4/2-} ≫ SO{4/2-}.

  2. New unitary affine-Virasoro constructions

    SciTech Connect

    Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M. ); Yamron, J.P. )

    1990-06-20

    This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g.

  3. Screening of high-affinity scFvs from a ribosome displayed library using BIAcore biosensor.

    PubMed

    Yuan, Qing; Wang, Zhongkang; Nian, Siji; Yin, Youping; Chen, Gang; Xia, Yuxian

    2009-02-01

    An experimental protocol was developed to screen high-affinity single-chain Fv antibody fragments (scFvs) from a Xanthomonas axonopodis pv. citri (Xac) immunized ribosome display library using BIAcore biosensor. The screening methods involved immobilizing antigen [lipopolysaccharides (LPS) of Xac] on sensor chip HPA and then unpurified expression products of scFvs flowing over the immobilized sensor chip. The affinity-improved scFvs were selected based on dissociation rate constants (k (d)). Thirty-five enzyme-linked immunosorbent assay-positive scFvs were analyzed by BIAcore, and three of those (scFv A1, B2, and C5) with lower k (d) were screened. To demonstrate the accuracy of the screening method, the three scFvs were expressed in Escherichia coli HB2151 and purified. The purified scFvs were subsequently further identified according to association rate and affinity constants. The results showed that the three scFvs (A1, B2, and C5) had high affinity for LPS of Xac (3.51 x 10(-11), 1.13 x 10(-10), 5.06 x 10(-10) M, respectively). Furthermore, the scFv B2 was highly specific for LPS of Xac and had no any cross-reactions with bovine serum albumin and LPS from Xac-related bacteria. This provided evidence that the information from the BIAcore screening assay could be accurate. PMID:18574567

  4. Superconformal Chern-Simons partition functions of affine D-type quiver from Fermi gas

    NASA Astrophysics Data System (ADS)

    Moriyama, Sanefumi; Nosaka, Tomoki

    2015-09-01

    We consider the partition function of the superconformal Chern-Simons theories with the quiver diagram being the affine D-type Dynkin diagram. Rewriting the partition function into that of a Fermi gas system, we show that the perturbative expansions in 1 /N are summed up to an Airy function, as in the ABJM theory or more generally the theories of the affine A-type quiver. As a corollary, this provides a proof for the previous proposal in the large N limit. For special values of the Chern-Simons levels, we further identify three species of the membrane instantons and also conjecture an exact expression of the overall constant, which corresponds to the constant map in the topological string theory. [Figure not available: see fulltext.

  5. Evaluating North America Paleoclimate Simulations using Simulated and Observed Paleovegetation Data for 6 ka and 21 ka

    NASA Astrophysics Data System (ADS)

    Shafer, S. L.; Bartlein, P. J.; Thompson, R. S.; Anderson, K.; Izumi, K.; Strickland, L. E.; Pelltier, R.

    2013-12-01

    An important use of paleoclimate data is to evaluate climate models that simulate future climate. We used paleoclimate simulations from the Paleoclimate Modelling Intercomparison Project phase 3 (PMIP3) and Coupled Model Intercomparison Project phase 5 (CMIP5) database to evaluate simulated and observed vegetation agreement for 6 ka and 21 ka. The paleoclimate simulations were downscaled to a 10-km grid of North America following the PMIP3 vegetation simulation protocol. The downscaled climate data were used with BIOME4, an equilibrium vegetation model, to simulate paleovegetation for each time period. The simulated paleovegetation was compared with observed paleovegetation data from the BIOME 6000 (ver. 4.2) dataset and the U.S. Geological Survey/NOAA North American Packrat Midden Database (ver. 3). We evaluated the magnitude and spatial patterns of agreement and disagreement of the observed and simulated paleovegetation. The results were analyzed for individual climate model simulations and paleovegetation types. Some simulated paleovegetation types (e.g., needleleaf evergreen forest) showed good agreement with observed paleovegetation data while other simulated paleovegetation types (e.g., open conifer woodland) showed relatively poor agreement. The analyses provide insights into climate and vegetation model performance and suggest opportunities for improving both model simulations and interpretations of observed paleovegetation data.

  6. Measurements of relative binding of cohesin and dockerin mutants using an advanced ELISA technique for high-affinity interactions.

    PubMed

    Slutzki, Michal; Barak, Yoav; Reshef, Dan; Schueler-Furman, Ora; Lamed, Raphael; Bayer, Edward A

    2012-01-01

    The cellulosome is a large bacterial extracellular multienzyme complex able to degrade crystalline cellulosic substrates. The complex contains catalytic and noncatalytic subunits, interconnected by high-affinity cohesin-dockerin interactions. In this chapter, we introduce an optimized method for comparative binding among different cohesins or cohesin mutants to the dockerin partner. This assay offers advantages over other methods (such as ELISA, cELIA, SPR, and ITC) for particularly high-affinity binding interactions. In this approach, the high-affinity interaction of interest occurs in the liquid phase during the equilibrated binding step, whereas the interaction with the immobilized phase is used only for detection of the unbound dockerins that remain in the solution phase. Once equilibrium conditions are reached, the change in free energy of binding (ΔΔG(binding)), as well as the affinity constant of mutants, can be estimated against the known affinity constant of the wild-type interaction. In light of the above, we propose this method as a preferred alternative for the relative quantification of high-affinity protein interactions. PMID:22608739

  7. Increased Antibody Affinity Confers Broad In Vitro Protection against Escape Mutants of Severe Acute Respiratory Syndrome Coronavirus

    PubMed Central

    Rani, Mridula; Bolles, Meagan; Donaldson, Eric F.; Van Blarcom, Thomas; Baric, Ralph; Iverson, Brent

    2012-01-01

    Even though the effect of antibody affinity on neutralization potency is well documented, surprisingly, its impact on neutralization breadth and escape has not been systematically determined. Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the neutralizing antibody 80R followed by bacterial display screening using anchored periplasmic expression (APEx) were used to generate a number of higher-affinity variants of the severe acute respiratory syndrome coronavirus (SARS-CoV)-neutralizing antibody 80R with equilibrium dissociation constants (KD) as low as 37 pM, a >270-fold improvement relative to that of the parental 80R single-chain variable fragment (scFv). As expected, antigen affinity was shown to correlate directly with neutralization potency toward the icUrbani strain of SARS-CoV. Additionally, the highest-affinity antibody fragment displayed 10-fold-increased broad neutralization in vitro and completely protected against several SARS-CoV strains containing substitutions associated with antibody escape. Importantly, higher affinity also led to the suppression of viral escape mutants in vitro. Escape from the highest-affinity variant required reduced selective pressure and multiple substitutions in the binding epitope. Collectively, these results support the hypothesis that engineered antibodies with picomolar dissociation constants for a neutralizing epitope can confer escape-resistant protection. PMID:22696652

  8. Optical constants of solid methane

    NASA Technical Reports Server (NTRS)

    Khare, Bishun N.; Thompson, W. R.; Sagan, C.; Arakawa, E. T.; Bruel, C.; Judish, J. P.; Khanna, R. K.; Pollack, J. B.

    1990-01-01

    Methane is the most abundant simple organic molecule in the outer solar system bodies. In addition to being a gaseous constituent of the atmospheres of the Jovian planets and Titan, it is present in the solid form as a constituent of icy surfaces such as those of Triton and Pluto, and as cloud condensate in the atmospheres of Titan, Uranus, and Neptune. It is expected in the liquid form as a constituent of the ocean of Titan. Cometary ices also contain solid methane. The optical constants for both solid and liquid phases of CH4 for a wide temperature range are needed for radiative transfer calculations, for studies of reflection from surfaces, and for modeling of emission in the far infrared and microwave regions. The astronomically important visual to near infrared measurements of solid methane optical constants are conspicuously absent from the literature. Preliminary results are presented on the optical constants of solid methane for the 0.4 to 2.6 micrometer region. Deposition onto a substrate at 10 K produces glassy (semi-amorphous) material. Annealing this material at approximately 33 K for approximately 1 hour results in a crystalline material as seen by sharper, more structured bands and negligible background extinction due to scattering. The constant k is reported for both the amorphous and the crystalline (annealed) states. Typical values (at absorption maxima) are in the .001 to .0001 range. Below lambda = 1.1 micrometers the bands are too weak to be detected by transmission through the films less than or equal to 215 micrometers in thickness, employed in the studies to date. Using previously measured values of the real part of the refractive index, n, of liquid methane at 110 K, n is computed for solid methane using the Lorentz-Lorenz relationship. Work is in progress to extend the measurements of optical constants n and k for liquid and solid to both shorter and longer wavelengths, eventually providing a complete optical constants database for

  9. Ka-Band Multibeam Aperture Phased Array Being Developed

    NASA Technical Reports Server (NTRS)

    Reinhart, Richard C.; Kacpura, Thomas J.

    2004-01-01

    Phased-array antenna systems offer many advantages to low-Earth-orbiting satellite systems. Their large scan angles and multibeam capabilities allow for vibration-free, rapid beam scanning and graceful degradation operation for high rate downlink of data to users on the ground. Technology advancements continue to reduce the power, weight, and cost of these systems to make phased arrays a competitive alternative in comparison to the gimbled reflector system commonly used in science missions. One effort to reduce the cost of phased arrays is the development of a Ka-band multibeam aperture (MBA) phased array by Boeing Corporation under a contract jointly by the NASA Glenn Research Center and the Office of Naval Research. The objective is to develop and demonstrate a space-qualifiable dual-beam Ka-band (26.5-GHz) phased-array antenna. The goals are to advance the state of the art in Ka-band active phased-array antennas and to develop and demonstrate multibeam transmission technology compatible with spacecraft in low Earth orbit to reduce the cost of future missions by retiring certain development risks. The frequency chosen is suitable for space-to-space and space-to-ground communication links. The phased-array antenna has a radiation pattern designed by combining a set of individual radiating elements, optimized with the type of radiating elements used, their positions in space, and the amplitude and phase of the currents feeding the elements. This arrangement produces a directional radiation pattern that is proportional to the number of individual radiating elements. The arrays of interest here can scan the main beam electronically with a computerized algorithm. The antenna is constructed using electronic components with no mechanical parts, and the steering is performed electronically, without any resulting vibration. The speed of the scanning is limited primarily by the control electronics. The radiation performance degrades gracefully if a portion of the elements

  10. Malama I Ka `Aina: Fostering the Culture-Science connection

    NASA Astrophysics Data System (ADS)

    Bruno, B.; Chinn, P.

    2005-12-01

    The Malama I Ka `Aina Project (Caring for the land, or sustainability) aims to improve and expand the education of Hawai`i's children by developing and disseminating standards-based, culturally relevant science curricular materials based on an understanding and appreciation of the ways in which traditional Hawaiians interacted with their environment for sustainability. Key concepts include the role of water and the ahupua`a (traditional Hawaiian system of land management), and a culture-based sense of place that includes knowledge of and connection to the land. Elementary, middle, high school and University of Hawai`i teachers work together to develop and implement curricula that are especially relevant to a particular school's science program and issues, e.g., invasive species, students, community and/or geographical location. Participants (typically a mix of teachers, education majors and science majors) enroll in Malama I Ka `Aina, a three-credit course offered through the University of Hawai`i`s Dept. of Curriculum Studies and applicable toward a Bachelor's or Master's degree. This course (team taught by scientists, cultural experts and educational professionals) enables participants to: (1) Study Hawai`i`s unique geology, geography and environmental issues in the context of Hawaiian culture and post Western contact; (2) Use course knowledge to develop, teach and assess Hawaii-oriented, project-based, inquiry activities that address the Hawaii Science Content Standards; (3) Gain an appreciation for the scientific method, and the curiosity that drives science (4) Use educational technology such as PowerPoint, graphing packages and web authoring software to develop electronic resources for educational activities. A sample of the lessons developed by course participants can be found on http://malama.hawaii.edu/schools/index2.html. This project is based at the University of Hawai`i College of Education and funded by an award to P. Chinn by the US Department of

  11. Cosmologies with variable gravitational constant

    SciTech Connect

    Narkikar, J.V.

    1983-03-01

    In 1937 Dirac presented an argument, based on the socalled large dimensionless numbers, which led him to the conclusion that the Newtonian gravitational constant G changes with epoch. Towards the end of the last century Ernst Mach had given plausible arguments to link the property of inertia of matter to the large scale structure of the universe. Mach's principle also leads to cosmological models with a variable gravitational constant. Three cosmologies which predict a variable G are discussed in this paper both from theoretical and observational points of view.

  12. Elastic constants for 8-OCB

    NASA Astrophysics Data System (ADS)

    Czechowski, Grzegorz; Zywucki, B.; Jadzyn, Jan

    1993-10-01

    The Frederiks transitions for the n-octyloxycyanobiphenyl (8-OCB) placed in the external magnetic and electric field as a function of the temperature have been studied. On the basis of threshold values Bc and Uc, the elastic constants for splay, bend and twist modes are determined. The magnetic anisotropy of 8-OCB as a function of temperature has been determined. The K11 and K33 elastic constants show the pretransitional nematic- smectic A effect. The values of critical exponents obtained from the temperature dependence of K11 and K33 in the vicinity of N-SA phase transition are discussed.

  13. Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution.

    PubMed

    Ahmad, Kareem M; Xiao, Yi; Soh, H Tom

    2012-12-01

    Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (K(d)) <10 pM, representing a ∼200-fold improvement in binding affinity over the monomeric aptamers and a ∼15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.

  14. On the binding affinity of macromolecular interactions: daring to ask why proteins interact

    PubMed Central

    Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

    2013-01-01

    Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition. PMID:23235262

  15. Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry.

    PubMed

    Krainer, Georg; Keller, Sandro

    2015-04-01

    Isothermal titration calorimetry (ITC) is the gold standard for dissecting the thermodynamics of a biomolecular binding process within a single experiment. However, reliable determination of the dissociation constant (KD) from a single titration is typically limited to the range 100 μM>KD>1 nM. Interactions characterized by a lower KD can be assessed indirectly by so-called competition or displacement assays, provided that a suitable competitive ligand is available whose KD falls within the directly accessible window. However, this protocol is limited by the fact that it necessitates at least two titrations to characterize one high-affinity inhibitor, resulting in considerable consumption of both sample material and time. Here, we introduce a fast and efficient ITC displacement assay that allows for the simultaneous characterization of both a high-affinity ligand and a moderate-affinity ligand competing for the same binding site on a receptor within a single experiment. The protocol is based on a titration of the high-affinity ligand into a solution containing the moderate-affinity ligand bound to the receptor present in excess. The resulting biphasic binding isotherm enables accurate and precise determination of KD values and binding enthalpies (ΔH) of both ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation, explore its potential and limitations with the aid of simulations and statistical analyses, and elaborate on potential applications to protein-inhibitor interactions.

  16. High-affinity host-guest chemistry of large-ring cyclodextrins.

    PubMed

    Assaf, Khaleel I; Gabel, Detlef; Zimmermann, Wolfgang; Nau, Werner M

    2016-08-10

    The host-guest chemistry of large-ring cyclodextrins (LRCDs) has been largely unexplored due to the lack of suitable guest molecules that bind with significant affinities to enable potential applications. Herein, we report their complexation with dodecaborate anions (B12X12(2-)), a novel class of guest molecules. The binding constants of the inorganic guests (10(4)-10(6) M(-1)) allow their classification as the first tight binders for LRCDs. PMID:27456317

  17. Determination of chromatographic dissociation constants of some carbapenem group antibiotics and quantification of these compounds in human urine.

    PubMed

    Çubuk Demiralay, Ebru; Koç, Duygu; Daldal, Y Doğan; Alsancak, Güleren; Ozkan, Sibel A

    2014-05-01

    The dissociation constant values (s (s) pKa ) of some carbapenem group drugs (ertapenem, meropenem, doripenem) in different percentages of methanol-water binary mixtures (18, 20 and 22%, v/v) were determined from the mobile phase pH dependence of their retention factor. Evaluation of these data was performed using the NLREG program. From calculated pKa values, the aqueous pKa values of these subtances were calculated by different approaches. Moreover, the correlation established between retention factor and the pH of the water-methanol mobile phase was used to determine the optimum separation conditions. In order to validate the optimized conditions, these drugs were studied in human urine. The chromatographic separation was realized using a Gemini NX C18 column (250 × 4.6 mm i.d., 5 µm particles) and UV detector set at 220 and 295 nm.

  18. ACTIVE GALACTIC NUCLEI AND THE TRUNCATION OF STAR FORMATION IN K+A GALAXIES

    SciTech Connect

    Brown, Michael J. I.; Palamara, David; Moustakas, John; Caldwell, Nelson; Cool, Richard J.; Zaritsky, Dennis; Dey, Arjun; Jannuzi, Buell T.; Hickox, Ryan C.; Murray, Stephen S.

    2009-09-20

    We have searched for active galactic nuclei (AGNs) in K+A galaxies, using multiwavelength imaging and spectroscopy in the Booetes field of the NOAO Deep Wide-Field Survey. The K+A galaxies, which have had their star formation rapidly truncated, are selected via their strong Balmer absorption lines and weak Halpha emission. Our sample consists of 24 K+A galaxies selected from 6594 0.10 < z < 0.35 galaxies brighter than I = 20 with optical spectroscopy from the AGN and Galaxy Evolution Survey. Two thirds of the K+A galaxies are likely ongoing galaxy mergers, with nearby companion galaxies or tidal tails. Galaxy mergers may be responsible for the truncation of star formation, or we are observing the aftermath of merger triggered starbursts. As expected, the optical colors of K+A galaxies largely fall between blue galaxies with ongoing star formation and red passive galaxies. However, only 1% of the galaxies with colors between the red and blue populations are K+A galaxies, and we conclude that the truncation of star formation in K+A galaxies must have been unusually abrupt ({approx}<100 Myr). We examined the AGN content of K+A galaxies with both optical emission-line ratios (BPT diagrams) and Chandra X-ray imaging. At least half of all K+A galaxies display the optical emission-line ratios of AGNs, and a third of M{sub R} < -22 K+A galaxies host AGNs with X-ray luminosities of {approx}10{sup 42} erg s{sup -1}. The faintest K+A galaxies do not show clear evidence for hosting AGNs, having emission-line ratios consistent with photoionization by massive stars and few X-ray detections. We speculate that two mechanisms may be responsible for the truncation of star formation in K+A galaxies, with AGN feedback only playing a role in M{sub R} {approx}< -20.5 galaxies.

  19. Modern affinity reagents: Recombinant antibodies and aptamers.

    PubMed

    Groff, Katherine; Brown, Jeffrey; Clippinger, Amy J

    2015-12-01

    Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.

  20. Fan Affinity Laws from a Collision Model

    ERIC Educational Resources Information Center

    Bhattacharjee, Shayak

    2012-01-01

    The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…

  1. Advanced Ka-Band Transceiver With Monopulse Tracking

    NASA Technical Reports Server (NTRS)

    Khan, Abdur; Hoppe, Dan; Epp, Larry; Perez, Raul

    2006-01-01

    A proposed Ka-band transmitting/ receiving system would embody a unique combination of established and semi-proven design features. The proposed system (see figure) would include a monopulse receiving feedback loop and a mirror that could be moved by piezoelectric actuators in the feedback loop to adjust the aim of the transmitted and received radio beams. Unlike in a phased-array tracking system, phase shifters (which can be complex and expensive) would not be needed in this monopulse tracking system. Moreover, the monopulse-tracking loop could be combined with other subsystems used in established subreflector and antenna designs. The final transmitter power amplifier in the proposed system would be a quasi-optical power amplifier (QOPA) -- a combination of a planar array of 25 amplifiers and corresponding planar arrays of antenna elements, such that free-space power combining would take place at the output.

  2. A personal communications network using a Ka-band satellite

    NASA Technical Reports Server (NTRS)

    Palmer, Larry C.; Laborde, Enrique; Stern, Alan; Sohn, Philip Y.

    1992-01-01

    The feasibility of a personal communications network using portable terminals that can provide 4.8-kb/s voice communications to a hub station via a Ka-band geosynchronous satellite has been investigated. Tradeoffs are examined so that the combined system of hub and gateway earth stations, the satellite, and the personal terminals can provide a competitive service in terms of cost, availability, and quality. A baseline system that uses a spacecraft with approximately 140 spot beams to cover the contiguous US (CONUS) and 5-W power amplifiers in each beam is described. Satellite access in both the forward and return directions uses frequency-division multiple-access/code-division multiple-access (FDMA/CDMA) with a chip rate of 2.5 Mchip/s.

  3. The intrinsic pKa values for phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine in monolayers deposited on mercury electrodes.

    PubMed Central

    Moncelli, M R; Becucci, L; Guidelli, R

    1994-01-01

    The intrinsic pKa values of the phosphate groups of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) and of the phosphate and carboxyl groups of phosphatidylserine (PS) in self-organized monolayers deposited on a hanging mercury drop electrode were determined by a novel procedure based on measurements of the differential capacity C of this lipid-coated electrode. In view of the Gouy-Chapman theory, plots of 1/C at constant bulk pH and variable KCl concentration against the reciprocal of the calculated diffuse-layer capacity Cd,0 at zero charge exhibit slopes that decrease from an almost unit value to vanishingly low values as the absolute value of the charge density on the lipid increases from zero to approximately 2 microC cm-2. The intrinsic pKa values so determined are 0.5 for PE and 0.8 for PC. The plots of 1/C against 1/Cd,0 for pure PS exhibit slopes that pass from zero to a maximum value and then back to zero as pH is varied from 7.5 to 3, indicating that the charge density of the lipid film passes from slight negative to slight positive values over this pH range. An explanation for this anomalous behavior, which is ascribed to the phosphate group of PS, is provided. Interdispersion of PS and PC molecules in the film decreases the "formal" pKa value of the latter group by about three orders of magnitude. PMID:8075331

  4. Miniaturized Ka-Band Dual-Channel Radar

    NASA Technical Reports Server (NTRS)

    Hoffman, James P.; Moussessian, Alina; Jenabi, Masud; Custodero, Brian

    2011-01-01

    Smaller (volume, mass, power) electronics for a Ka-band (36 GHz) radar interferometer were required. To reduce size and achieve better control over RFphase versus temperature, fully hybrid electronics were developed for the RF portion of the radar s two-channel receiver and single-channel transmitter. In this context, fully hybrid means that every active RF device was an open die, and all passives were directly attached to the subcarrier. Attachments were made using wire and ribbon bonding. In this way, every component, even small passives, was selected for the fabrication of the two radar receivers, and the devices were mounted relative to each other in order to make complementary components isothermal and to isolate other components from potential temperature gradients. This is critical for developing receivers that can track each other s phase over temperature, which is a key mission driver for obtaining ocean surface height. Fully hybrid, Ka-band (36 GHz) radar transmitter and dual-channel receiver were developed for spaceborne radar interferometry. The fully hybrid fabrication enables control over every aspect of the component selection, placement, and connection. Since the two receiver channels must track each other to better than 100 millidegrees of RF phase over several minutes, the hardware in the two receivers must be "identical," routed the same (same line lengths), and as isothermal as possible. This level of design freedom is not possible with packaged components, which include many internal passive, unknown internal connection lengths/types, and often a single orientation of inputs and outputs.

  5. Microcantilever-Based Label-Free Characterization of Temperature-Dependent Biomolecular Affinity Binding

    PubMed Central

    Wang, Bin; Huang, Fengliang; Nguyen, ThaiHuu; Xu, Yong; Lin, Qiao

    2014-01-01

    This paper presents label-free characterization of temperature-dependent biomolecular affinity binding on solid surfaces using a microcantilever-based device. The device consists of a Parylene cantilever one side of which is coated with a gold film and functionalized with molecules as an affinity receptor to a target analyte. The cantilever is located in a poly(dimethylsiloxane) (PDMS) microfluidic chamber that is integrated with a transparent indium tin oxide (ITO) resistive temperature sensor on the underlying substrate. The ITO sensor allows for real-time measurements of the chamber temperature, as well as unobstructed optical access for reflection-based optical detection of the cantilever deflection. To test the temperature-dependent binding between the target and receptor, the temperature of the chamber is maintained at a constant setpoint, while a solution of unlabeled analyte molecules is continuously infused through the chamber. The measured cantilever deflection is used to determine the target-receptor binding characteristics. We demonstrate label-free characterization of temperature-dependent binding kinetics of the platelet-derived growth factor (PDGF) protein with an aptamer receptor. Affinity binding properties including the association and dissociation rate constants as well as equilibrium dissociation constant are obtained, and shown to exhibit significant dependencies on temperature. PMID:24723743

  6. Effects of alkyl chain length and solvents on thermodynamic dissociation constants of the ionic liquids with one carboxyl group in the alkyl chain of imidazolium cations.

    PubMed

    Chen, Yuehua; Wang, Huiyong; Wang, Jianji

    2014-05-01

    Thermodynamic dissociation constants of the Brønsted acidic ionic liquids (ILs) are important for their catalytic and separation applications. In this work, a series of imidazolium bromides with one carboxylic acid substitute group in their alkyl chain ([{(CH2)nCOOH}mim]Br, n = 1,3,5,7) have been synthesized, and their dissociation constants (pKa) at different ionic strengths have been determined in aqueous and aqueous organic solvents at 0.1 mole fraction (x) of ethanol, glycol, iso-propanol, and dimethyl sulfoxide by potentiometric titrations at 298.2 K. The standard thermodynamic dissociation constants (pKa(T)) of the ILs in these solvents were calculated from the extended Debye-Hückel equation. It was found that the pKa values increased with the increase of ionic strength of the media and of the addition of organic solvent in water. The pKa(T) values also increased with the increase of the alkyl chain length of cations of the ILs. In addition, the effect of solvent nature on pKa(T) values is interpreted from solvation of the dissociation components and their Gibbs energy of transfer from water to aqueous organic solutions. PMID:24720707

  7. Effects of alkyl chain length and solvents on thermodynamic dissociation constants of the ionic liquids with one carboxyl group in the alkyl chain of imidazolium cations.

    PubMed

    Chen, Yuehua; Wang, Huiyong; Wang, Jianji

    2014-05-01

    Thermodynamic dissociation constants of the Brønsted acidic ionic liquids (ILs) are important for their catalytic and separation applications. In this work, a series of imidazolium bromides with one carboxylic acid substitute group in their alkyl chain ([{(CH2)nCOOH}mim]Br, n = 1,3,5,7) have been synthesized, and their dissociation constants (pKa) at different ionic strengths have been determined in aqueous and aqueous organic solvents at 0.1 mole fraction (x) of ethanol, glycol, iso-propanol, and dimethyl sulfoxide by potentiometric titrations at 298.2 K. The standard thermodynamic dissociation constants (pKa(T)) of the ILs in these solvents were calculated from the extended Debye-Hückel equation. It was found that the pKa values increased with the increase of ionic strength of the media and of the addition of organic solvent in water. The pKa(T) values also increased with the increase of the alkyl chain length of cations of the ILs. In addition, the effect of solvent nature on pKa(T) values is interpreted from solvation of the dissociation components and their Gibbs energy of transfer from water to aqueous organic solutions.

  8. Boltzmann's constant: A laboratory experiment

    NASA Astrophysics Data System (ADS)

    Kruglak, Haym

    1989-03-01

    The mean-square displacement of a latex microsphere is determined from its projection on a TV monitor. The distribution of displacement is shown to be Gaussian. Boltzmann's constant, calculated from the pooled data of several observers, is in excellent agreement with the accepted value. The experiment is designed for one laboratory period in the advanced undergraduate laboratory.

  9. Ten Thousand Solar Constants Radiometer

    NASA Technical Reports Server (NTRS)

    Kendall, J. M., Sr.

    1985-01-01

    "Radiometer for Accurate (+ or - 1%) Measurement of Solar Irradiances Equal to 10,000 Solar Constants," gives additional information on radiometer described elsewhere. Self-calibrating, water-cooled, thermopile radiometer measures irradiance produced in solar image formed by parabolic reflector or by multiple-mirror solar installation.

  10. Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue.

    PubMed

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2015-12-10

    The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.

  11. Heat loss analysis of a 10 kA warm dielectric HTS DC cable

    NASA Astrophysics Data System (ADS)

    Dai, Shaotao; Xiao, Liye; Teng, Yuping; Song, Naihao; Gao, Zhiyuan; Zhu, Zhiqing; Liang, Xueming; Cao, Zhicheng; Zhang, Dong; Ma, Tao; Zhang, Hongen; Lin, Liangzhen

    2014-09-01

    A 10 kA/360 m warm-dielectric high-temperature superconducting direct current (DC) power cable system (10 kA cable), supported jointly the Chinese government and industrial enterprise, was developed and has been operating as a branch circuit to transmit power for a 320 kA aluminum electrolyzing production line for more than 10 months at an industrial plant in central China. Both the 10 kA cable and its supporting system of the cable system are introduced. The cryogenic system for the 10 kA cable adopts closed loop and the sub-cooled liquid nitrogen is forced to flow inside by a pump. The design of corrugated cryogenic envelope pipe is modularized and every independent module has two standardized joints, which makes it easy to integrate with the other pipes and the terminations. The heat loss sources and the structure including both the termination and the cryogenic envelope pipe of the 10 kA cable are discussed. The total heat loss of the 10 kA cable excluding the loss of cryogenic pipe for liquid nitrogen backward flowing is designed to be less than 1698 W at 10 kA, and the heat loss was compared and discussed with that of the aluminum bar. The field test and commissioning of the cable show that the 10 kA cable performs steadily and its heat loss is less than the expected value.

  12. The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

    PubMed

    Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

    2013-11-01

    We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens.

  13. Energy-dependent dissociation of ATP from high affinity catalytic sites of beef heart mitochondrial adenosine triphosphatase

    SciTech Connect

    Penefsky, H.S.

    1985-11-05

    Incubation of (gamma-TSP)ATP with a molar excess of the membrane-bound form of mitochondrial ATPase (F1) results in binding of the bulk of the radioactive nucleotide in high affinity catalytic sites (Ka = 10(12) M-1). Subsequent initiation of respiration by addition of succinate or NADH is accompanied by a profound decrease in the affinity for ATP. About one-third of the bound radioactive ATP appears to dissociate, that is, the (gamma-TSP)ATP becomes accessible to hexokinase. The NADH-stimulated dissociation of (gamma-TSP)ATP is energy-dependent since the stimulation is inhibited by uncouplers of oxidative phosphorylation and is prevented by respiratory chain inhibitors. The rate of the energy-dependent dissociation of ATP that occurs in the presence of NADH, ADP, and Pi is commensurate with the measured initial rate of ATP synthesis in NADH-supported oxidative phosphorylation catalyzed by the same submitochondrial particles. Thus, the rate of dissociation of ATP from the high affinity catalytic site of submitochondrial particles meets the criterion of kinetic competency under the conditions of oxidative phosphorylation. These experiments provide evidence in support of the argument that energy conserved during the oxidation of substrates by the respiratory chain can be utilized to reduce the very tight binding of product ATP in high affinity catalytic sites and to promote dissociation of the nucleotide.

  14. Proteolytic fragments of laminin promote excitotoxic neurodegeneration by up-regulation of the KA1 subunit of the kainate receptor.

    PubMed

    Chen, Zu-Lin; Yu, Huaxu; Yu, Wei-Ming; Pawlak, Robert; Strickland, Sidney

    2008-12-29

    Degradation of the extracellular matrix (ECM) protein laminin contributes to excitotoxic cell death in the hippocampus, but the mechanism of this effect is unknown. To study this process, we disrupted laminin gamma1 (lamgamma1) expression in the hippocampus. Lamgamma1 knockout (KO) and control mice had similar basal expression of kainate (KA) receptors, but the lamgamma1 KO mice were resistant to KA-induced neuronal death. After KA injection, KA1 subunit levels increased in control mice but were unchanged in lamgamma1 KO mice. KA1 levels in tissue plasminogen activator (tPA)-KO mice were also unchanged after KA, indicating that both tPA and laminin were necessary for KA1 up-regulation after KA injection. Infusion of plasmin-digested laminin-1 into the hippocampus of lamgamma1 or tPA KO mice restored KA1 up-regulation and KA-induced neuronal degeneration. Interfering with KA1 function with a specific anti-KA1 antibody protected against KA-induced neuronal death both in vitro and in vivo. These results demonstrate a novel pathway for neurodegeneration involving proteolysis of the ECM and KA1 KA receptor subunit up-regulation.

  15. Ka-Band, MEMS Switched Line Phase Shifters Implemented in Finite Ground Coplanar Waveguide

    NASA Technical Reports Server (NTRS)

    Scardelletti, Maximilian C.; Ponchak, George E.; Varaljay, Nicholas C.

    2005-01-01

    Ka-band MEMS switched line phase shifters implemented in finite ground coplanar waveguide are described in this paper. The phase shifters are constructed of single-pole double-throw (SPDT) switches with additional reference and phase offset transmission line lengths. The one- and two-bit phase shifters are fabricated on high resistivity (HR) silicon with a dielectric constant, Epsilon(sub T) = 11.7 and a substrate thickness, t = 500microns. The switching architectures integrated within the phase shifters consist of MEMS switches that are doubly anchored cantilever beam capacitive switches with additional high inductive sections (MEMS LC device). The SPDT switch is composed of a T-junction with a MEMS LC device at each output port. The one-bit phase shifter described in this paper has an insertion loss (IL) and return loss (RL) of 0.9 dB and 30 dB while the two-bit described has an IL and RL of 1.8 dB and 30 dB respectively. The one-bit phase shifter's designed offset phase is 22.5deg and actual measured phase shift is 21.8deg. The two-bit phase shifter's designed offset phase is 22.5deg, 45deg, and 67.5deg and the actual measured phase shifts are 21.4deg, 44.2deg, and 65.8deg, respectively.

  16. Axial mass fraction measurements in a 300kA dense plasma focus

    NASA Astrophysics Data System (ADS)

    Caballero Bendixsen, L. S.; Bott-Suzuki, S. C.; Cordaro, S. W.; Krishnan, M.; Chapman, S.; Coleman, P.; Chittenden, J.

    2016-09-01

    The dynamics and characteristics of the plasma sheath during the axial phase in a ˜300 kA, ˜2 kJ dense plasma focus using a static gas load of Ne at 1-4 Torr are reported. The sheath, which is driven axially at a constant velocity ˜105 m/s by the j × B force, is observed using optical imaging, to form an acute angle between the electrodes. This angle becomes more acute (more parallel to the axis) along the rundown. The average sheath thickness nearer the anode is 0.69 ± 0.02 mm and nearer the cathode is 0.95 ± 0.02 mm. The sheath total mass increases from 1 ± 0.02 μg to 6 ± 0.02 μg over the pressure range of 1-4 Torr. However, the mass fraction (defined as the sheath mass/total mass of cold gas between the electrodes) decreases from 7% to 5%. In addition, the steeper the plasma sheath, the more mass is lost from the sheath, which is consistent with radial and axial motion. Experimental results are compared to the Lee code when 100% of the current drives the axial and radial phase.

  17. A larger number of L chains (Tac) enhance the association rate of interleukin 2 to the high affinity site of the interleukin 2 receptor

    PubMed Central

    1988-01-01

    The IL-2-R is composed of at least two proteins, that is, a 55-kD protein (p55, the L chain, or Tac) and a 75-kD protein (p75, the H chain, or converter). The high affinity binding of IL-2 results in the formation of the ternary complex consisting of IL-2, and the L and H chains. To distinguish the affinity conversion model and the binary complex model we have carried out kinetic studies on the IL-2 binding to the high affinity IL-2-R on T lymphocytes expressing various numbers of L chains and a relatively constant number of H chains. We found that expression of a larger number of L chains accelerated the association of IL-2 to the high affinity receptor. The results are not compatible with the binary complex model that assumes a fixed number of high affinity sites determined by the numbers of a limiting chain. Instead, the results are consistent with the prediction of the affinity conversion model that assumes association of IL-2 to the L chain as the first step of the ternary complex formation and they indicate that the possible role of excess L chains is to accelerate the formation of the ternary complex. The reaction rate constants calculated from the affinity conversion model were reasonably constant. PMID:3263463

  18. The 1% concordance Hubble constant

    SciTech Connect

    Bennett, C. L.; Larson, D.; Weiland, J. L.; Hinshaw, G.

    2014-10-20

    The determination of the Hubble constant has been a central goal in observational astrophysics for nearly a hundred years. Extraordinary progress has occurred in recent years on two fronts: the cosmic distance ladder measurements at low redshift and cosmic microwave background (CMB) measurements at high redshift. The CMB is used to predict the current expansion rate through a best-fit cosmological model. Complementary progress has been made with baryon acoustic oscillation (BAO) measurements at relatively low redshifts. While BAO data do not independently determine a Hubble constant, they are important for constraints on possible solutions and checks on cosmic consistency. A precise determination of the Hubble constant is of great value, but it is more important to compare the high and low redshift measurements to test our cosmological model. Significant tension would suggest either uncertainties not accounted for in the experimental estimates or the discovery of new physics beyond the standard model of cosmology. In this paper we examine in detail the tension between the CMB, BAO, and cosmic distance ladder data sets. We find that these measurements are consistent within reasonable statistical expectations and we combine them to determine a best-fit Hubble constant of 69.6 ± 0.7 km s{sup –1} Mpc{sup –1}. This value is based upon WMAP9+SPT+ACT+6dFGS+BOSS/DR11+H {sub 0}/Riess; we explore alternate data combinations in the text. The combined data constrain the Hubble constant to 1%, with no compelling evidence for new physics.

  19. Variation of fundamental constants: theory

    NASA Astrophysics Data System (ADS)

    Flambaum, Victor

    2008-05-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. There are some hints for the variation of different fundamental constants in quasar absorption spectra and Big Bang nucleosynthesis data. A large number of publications (including atomic clocks) report limits on the variations. We want to study the variation of the main dimensionless parameters of the Standard Model: 1. Fine structure constant alpha (combination of speed of light, electron charge and Plank constant). 2. Ratio of the strong interaction scale (LambdaQCD) to a fundamental mass like electron mass or quark mass which are proportional to Higgs vacuum expectation value. The proton mass is propotional to LambdaQCD, therefore, the proton-to-electron mass ratio comes into this second category. We performed necessary atomic, nuclear and QCD calculations needed to study variation of the fundamental constants using the Big Bang Nucleosynthsis, quasar spectra, Oklo natural nuclear reactor and atomic clock data. The relative effects of the variation may be enhanced in transitions between narrow close levels in atoms, molecules and nuclei. If one will study an enhanced effect, the relative value of systematic effects (which are not enhanced) may be much smaller. Note also that the absolute magnitude of the variation effects in nuclei (e.g. in very narrow 7 eV transition in 229Th) may be 5 orders of magnitude larger than in atoms. A different possibility of enhancement comes from the inversion transitions in molecules where splitting between the levels is due to the quantum tunneling amplitude which has strong, exponential dependence on the electron to proton mass ratio. Our study of NH3 quasar spectra has already given the best limit on the variation of electron to proton mass ratio.

  20. Varying Fine-Structure Constant and the Cosmological Constant Problem

    NASA Astrophysics Data System (ADS)

    Fujii, Yasunori

    We start with a brief account of the latest analysis of the Oklo phenomenon providing the still most stringent constraint on time variability of the fine-structure constant α. Comparing this with the recent result from the measurement of distant QSO's appears to indicate a non-uniform time-dependence, which we argue to be related to another recent finding of the accelerating universe. This view is implemented in terms of the scalar-tensor theory, applied specifically to the small but nonzero cosmological constant. Our detailed calculation shows that these two phenomena can be understood in terms of a common origin, a particular behavior of the scalar field, dilaton. We also sketch how this theoretical approach makes it appropriate to revisit non-Newtonian gravity featuring small violation of Weak Equivalence Principle at medium distances.

  1. Determination of acid-base dissociation constants of amino- and guanidinopurine nucleotide analogs and related compounds by capillary zone electrophoresis.

    PubMed

    Solínová, Veronika; Kasicka, Václav; Koval, Dusan; Cesnek, Michal; Holý, Antonín

    2006-03-01

    CZE has been applied for determination of acid-base dissociation constants (pKa) of ionogenic groups of newly synthesized amino- and (amino)guanidinopurine nucleotide analogs, such as acyclic nucleoside phosphonate, acyclic nucleoside phosphonate diesters and other related compounds. These compounds bear characteristic pharmacophores contained in various important biologically active substances, such as cytostatics and antivirals. The pKa values of ionogenic groups of the above compounds were determined by nonlinear regression analysis of the experimentally measured pH dependence of their effective electrophoretic mobilities. The effective mobilities were measured by CZE performed in series of BGEs in a broad pH range (3.50-11.25), at constant ionic strength (25 mM) and temperature (25 degrees C). pKa values were determined for the protonated guanidinyl group in (amino)guanidino 9-alkylpurines and in (amino)guanidinopurine nucleotide analogs, such as acyclic nucleoside phosphonates and acyclic nucleoside phosphonate diesters, for phosphonic acid to the second dissociation degree (-2) in acyclic nucleoside phosphonates of amino and (amino)guanidino 9-alkylpurines, and for protonated nitrogen in position 1 (N1) of purine moiety in acyclic nucleoside phosphonates of amino 9-alkylpurines. Thermodynamic pKa of protonated guanidinyl group was estimated to be in the range of 7.75-10.32, pKa of phosphonic acid to the second dissociation degree achieved values of 6.64-7.46, and pKa of protonated nitrogen in position 1 of purine was in the range of 4.13-4.89, depending on the structure of the analyzed compounds.

  2. Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells

    PubMed Central

    Day, Christopher J.; Tran, Elizabeth N.; Semchenko, Evgeny A.; Tram, Greg; Hartley-Tassell, Lauren E.; Ng, Preston S. K.; King, Rebecca M.; Ulanovsky, Rachel; McAtamney, Sarah; Apicella, Michael A.; Tiralongo, Joe; Morona, Renato; Korolik, Victoria; Jennings, Michael P.

    2015-01-01

    Cells from all domains of life express glycan structures attached to lipids and proteins on their surface, called glycoconjugates. Cell-to-cell contact mediated by glycan:glycan interactions have been considered to be low-affinity interactions that precede high-affinity protein–glycan or protein–protein interactions. In several pathogenic bacteria, truncation of surface glycans, lipooligosaccharide (LOS), or lipopolysaccharide (LPS) have been reported to significantly reduce bacterial adherence to host cells. Here, we show that the saccharide component of LOS/LPS have direct, high-affinity interactions with host glycans. Glycan microarrays reveal that LOS/LPS of four distinct bacterial pathogens bind to numerous host glycan structures. Surface plasmon resonance was used to determine the affinity of these interactions and revealed 66 high-affinity host–glycan:bacterial–glycan pairs with equilibrium dissociation constants (KD) ranging between 100 nM and 50 µM. These glycan:glycan affinity values are similar to those reported for lectins or antibodies with glycans. Cell assays demonstrated that glycan:glycan interaction-mediated bacterial adherence could be competitively inhibited by either host cell or bacterial glycans. This is the first report to our knowledge of high affinity glycan:glycan interactions between bacterial pathogens and the host. The discovery of large numbers of glycan:glycan interactions between a diverse range of structures suggests that these interactions may be important in all biological systems. PMID:26676578

  3. Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells.

    PubMed

    Day, Christopher J; Tran, Elizabeth N; Semchenko, Evgeny A; Tram, Greg; Hartley-Tassell, Lauren E; Ng, Preston S K; King, Rebecca M; Ulanovsky, Rachel; McAtamney, Sarah; Apicella, Michael A; Tiralongo, Joe; Morona, Renato; Korolik, Victoria; Jennings, Michael P

    2015-12-29

    Cells from all domains of life express glycan structures attached to lipids and proteins on their surface, called glycoconjugates. Cell-to-cell contact mediated by glycan:glycan interactions have been considered to be low-affinity interactions that precede high-affinity protein-glycan or protein-protein interactions. In several pathogenic bacteria, truncation of surface glycans, lipooligosaccharide (LOS), or lipopolysaccharide (LPS) have been reported to significantly reduce bacterial adherence to host cells. Here, we show that the saccharide component of LOS/LPS have direct, high-affinity interactions with host glycans. Glycan microarrays reveal that LOS/LPS of four distinct bacterial pathogens bind to numerous host glycan structures. Surface plasmon resonance was used to determine the affinity of these interactions and revealed 66 high-affinity host-glycan:bacterial-glycan pairs with equilibrium dissociation constants (K(D)) ranging between 100 nM and 50 µM. These glycan:glycan affinity values are similar to those reported for lectins or antibodies with glycans. Cell assays demonstrated that glycan:glycan interaction-mediated bacterial adherence could be competitively inhibited by either host cell or bacterial glycans. This is the first report to our knowledge of high affinity glycan:glycan interactions between bacterial pathogens and the host. The discovery of large numbers of glycan:glycan interactions between a diverse range of structures suggests that these interactions may be important in all biological systems. PMID:26676578

  4. New Quasar Studies Keep Fundamental Physical Constant Constant

    NASA Astrophysics Data System (ADS)

    2004-03-01

    Very Large Telescope sets stringent limit on possible variation of the fine-structure constant over cosmological time Summary Detecting or constraining the possible time variations of fundamental physical constants is an important step toward a complete understanding of basic physics and hence the world in which we live. A step in which astrophysics proves most useful. Previous astronomical measurements of the fine structure constant - the dimensionless number that determines the strength of interactions between charged particles and electromagnetic fields - suggested that this particular constant is increasing very slightly with time. If confirmed, this would have very profound implications for our understanding of fundamental physics. New studies, conducted using the UVES spectrograph on Kueyen, one of the 8.2-m telescopes of ESO's Very Large Telescope array at Paranal (Chile), secured new data with unprecedented quality. These data, combined with a very careful analysis, have provided the strongest astronomical constraints to date on the possible variation of the fine structure constant. They show that, contrary to previous claims, no evidence exist for assuming a time variation of this fundamental constant. PR Photo 07/04: Relative Changes with Redshift of the Fine Structure Constant (VLT/UVES) A fine constant To explain the Universe and to represent it mathematically, scientists rely on so-called fundamental constants or fixed numbers. The fundamental laws of physics, as we presently understand them, depend on about 25 such constants. Well-known examples are the gravitational constant, which defines the strength of the force acting between two bodies, such as the Earth and the Moon, and the speed of light. One of these constants is the so-called "fine structure constant", alpha = 1/137.03599958, a combination of electrical charge of the electron, the Planck constant and the speed of light. The fine structure constant describes how electromagnetic forces hold

  5. Formation and stability of N-heterocyclic carbenes in water: the carbon acid pKa of imidazolium cations in aqueous solution.

    PubMed

    Amyes, Tina L; Diver, Steven T; Richard, John P; Rivas, Felix M; Toth, Krisztina

    2004-04-01

    We report second-order rate constants kDO (M-1 s-1) for exchange for deuterium of the C(2)-proton of a series of simple imidazolium cations to give the corresponding singlet imidazol-2-yl carbenes in D2O at 25 degrees C and I = 1.0 (KCl). Evidence is presented that the reverse protonation of imidazol-2-yl carbenes by solvent water is limited by solvent reorganization and occurs with a rate constant of kHOH = kreorg = 10(11) s-1. The data were used to calculate reliable carbon acid pK(a)s for ionization of imidazolium cations at C(2) to give the corresponding singlet imidazol-2-yl carbenes in water: pKa = 23.8 for the imidazolium cation, pKa = 23.0 for the 1,3-dimethylimidazolium cation, pKa = 21.6 for the 1,3-dimethylbenzimidazolium cation, and pKa = 21.2 for the 1,3-bis-((S)-1-phenylethyl)benzimidazolium cation. The data also provide the thermodynamic driving force for a 1,2-hydrogen shift at a singlet carbene: K12 = 5 x 10(16) for rearrangement of the parent imidazol-2-yl carbene to give neutral imidazole in water at 298 K, which corresponds to a favorable Gibbs free energy change of 23 kcal/mol. We present a simple rationale for the observed substituent effects on the thermodynamic stability of N-heterocyclic carbenes relative to a variety of neutral and cationic derivatives that emphasizes the importance of the choice of reference reaction when assessing the stability of N-heterocyclic carbenes.

  6. Determination of the acid dissociation constant of the biosurfactant monorhamnolipid in aqueous solution by potentiometric and spectroscopic methods.

    PubMed

    Lebrón-Paler, Ariel; Pemberton, Jeanne E; Becker, Bridget A; Otto, William H; Larive, Cynthia K; Maier, Raina M

    2006-11-15

    The acid dissociation constant in water for a monorhamnolipid mixture extracted from Pseudomonas aeruginosa ATCC 9027 has been determined using potentiometry and two spectroscopic approaches at concentrations below and above the critical micelle concentration (cmc). Potentiometric titrations resulted in pKa values ranging from 4.28 +/- 0.16 to 5.50 +/- 0.06 depending on concentration. 1H NMR spectrochemical titrations at concentrations below the cmc revealed a pKa value of 4.39 +/- 0.06. ATR-FT-IR spectrochemical titrations on solutions well above the cmc gave a pKa value of 4.84 +/- 0.05. The value of 4.28 for the free rhamnolipid molecule for concentrations below the cmc differs markedly from that reported previously. However, the pKa of 5.50 for surface-adsorbed and solution aggregates correlates closely to that previously reported. Differences in these pKa values are rationalized in terms of the pH- and concentration-dependent aggregation behavior of rhamnolipids in aqueous solution.

  7. Determination of acid dissociation constant of 20 coumarin derivatives by capillary electrophoresis using the amine capillary and two different methodologies.

    PubMed

    Nowak, Paweł Mateusz; Woźniakiewicz, Michał; Piwowarska, Monika; Kościelniak, Paweł

    2016-05-13

    In this work capillary electrophoresis has been used to determine acid dissociation constant of 20 structurally diverse coumarin derivatives. For a majority of compounds pKa value has been determined for the first time. The obtained values vary between 4.16-9.10pH unit, pointing to the interesting structure-acidity relationships. The amine permanently coated capillary has been applied for that purpose, because it has turned out to be more effective in pKa determination than the bare silica and other coated capillaries, ensuring good precision and shorter migration times. A traditional methodology relying on measurements in a broad pH range and fitting of a sigmoidal function has been compared to an alternative simplified approach, reported for the first time, where only two electrophoretic mobility values suffice for pKa estimation. The first value corresponds to the partially ionized form and it is measured experimentally, while the second one to the totally ionized form - it is measured experimentally (two-values method) or estimated directly from molecular mass (one-value method). We show that despite a limited measurements number, the alternative approach may be consistent with the traditional methodology, yielding the relatively low pKa deviation. Its reliability has also been confirmed by the analytical predictions, comprising resolution, migration order, migration times and peaks overlapping. Therefore, combination of the amine capillary with the simplified calculation method is an attractive tool for fast and reliable pKa estimation.

  8. Dating North European mammoths (Mammuthus primigenius Blum.): a nearly continuous record from 53 ka to 11 ka

    NASA Astrophysics Data System (ADS)

    Ukkonen, P.; Aaris-Sørensen, K.; Arppe, L.; Clark, P. U.; Daugnora, L.; Lister, A.; Lõugas, L.; Seppä, H. A.; Stuart, A. J.; Wojtal, P.; Zupins, I.

    2010-05-01

    nearly continuously from 53 ka to 11 ka, completely disappearing from the area only during the Last Glacial Maximum (LGM). From the northern parts of the study area, mammoths disappeared ca. 27 ka ago. In the south they survived until the LGM, and occupied the area again during deglaciation. Mammoths survived in the eastern part of the study area until the end of Younger Dryas. References Weninger, B., Jöris, O., 2008. A 14C age calibration curve for the last 60 ka: the Greenland-Hulu U/Th timescale and its impact on understanding the Middle to Upper Paleolithic transition in Western Eurasia. Journal of Human Evolution 55,772-781. Weninger, B., Jöris, O., Danzeglocke, U., 2008. CalPal-2007. Cologne Radiocarbon Calibration & Palaeoclimate Research Package. http://www.calpal.de/ [2008-09-18].

  9. Increasing Diversity in STEM through Ka Hikina O Ka Lā Summer Bridge Program for Native Hawaiian Students

    NASA Astrophysics Data System (ADS)

    Coopersmith, A.; Cie, D. K.; Calder, S.; Naho`olewa, D.; Rai, B.

    2014-12-01

    The Advanced Technology Solar Telescope (ATST) Mitigation Initiative and the Kahikina O Ka Lā Program are NSF-funded projects at the University of Hawai`i Maui College. These projects offer instruction and activities intended to increase diversity in STEM careers. Ke Alahaka, the 2014 summer bridge program, was offered to Native Hawaiian high-school students who indicated an interest in STEM areas. Content workshops were offered in Marine Science, Physics, Biotechnology, and Computer Science and Engineering as well as a Hawaiian Studies course designed to provide a cultural context for the STEM instruction. Focus groups and other program assessments indicate that 50% of the students attending the workshops intend to pursue a STEM major during their undergraduate studies.

  10. Ka mauli o ka 'oina a he mauli kanaka: an ethnographic study from an Hawaiian sense of place.

    PubMed

    Oneha, M F

    2001-09-01

    Ka Mauli O Ka 'Aina A He Mauli Kanaka: The Life of the Land is the Life of the People. A sense of place has been directly linked to spiritual well being for all indigenous peoples. Yet, there is minimal evidence that demonstrates understanding and awareness of indigenous health issues from this perspective. Health, or the lack of it, appears to be related to place or the loss of it. Issues of Hawaiian health are inseparable from issues of land, water, and atmosphere. The purpose of this research study was to explore the experience of a sense of place and its relationship to health as perceived and experienced by Hawaiian participants living in Wai'anae, Hawai'i. Thirteen adult men and women, ranging in age from 36 to 80 years, participated in this ethnographic study. Two interviews conducted with each participant addressed the research question, "What is the experience of the relationship between a sense of place and health for Hawaiians?" Participants were also asked to photograph how they experienced this relationship. The qualitative data analysis computer software, Atlas.ti, was used to assist in data analysis. The findings suggest that the relationship between sense of place and health embodies four categories: (1) relationship to akua (god, spirit), (2) relationship to natural elements, (3) relationship to self and others, and (4) belonging to a particular place. Three major traditional Hawaiian concepts, which defined how the relationship between sense of place and health are experienced, were pono, mana, and kuleana. The relationship between these concepts revealed five cultural themes. Health for Hawaiians: I. is having a spiritual connection to their ancestral place; II. relates to the past, present, and future; III. is experienced with intention and understanding; IV. means an openness to the flow and use of energy; and V. is experienced as a pu'uhonua or safe place. These themes suggest implications for Hawaiian health education, practice, and further

  11. New insights on water level variability for Lake Turkana for the past 15 ka and at 150 ka from relict beaches

    NASA Astrophysics Data System (ADS)

    Forman, S. L.; Wright, D.

    2015-12-01

    Relict beaches adjacent to Lake Turkana provide a record of water level variability for the Late Quaternary. This study focused on deciphering the geomorphology, sedimentology, stratigraphy and 14C chronology of strand plain sequences in the Kalokol and Lothagam areas. Nine >30 m oscillations in water level were documented between ca. 15 and 4 ka. The earliest oscillation between ca. 14.5 and 13 ka is not well constrained with water level to at least 70 m above the present surface and subsequently fell to at least 50 m. Lake level increased to ~ 90 m between ca. 11.2 and 10.4 ka, post Younger Dryas cooling. Water level fell by >30 m by 10.2 ka, with another potential rise at ca. 8.5 ka to >70 m above current level. Lake level regressed by > 40 m at 8.2 ka coincident with cooling in the equatorial Eastern Atlantic Ocean. Two major >70 m lake level oscillations centered at 6.6 and 5.2 ka may reflect enhanced convection with warmer sea surface temperatures in the Western Indian Ocean. The end of the African Humid Period occurred from ca. 8.0 to 4.5 ka and was characterized by variable lake level (± > 40 m), rather than one monotonic fall in water level. This lake level variability reflects a complex response to variations in the extent and intensity of the East and West African Monsoons near geographic and topographic limits within the catchment of Lake Turkana. Also, for this closed lake basin excess and deficits in water input are amplified with a cascading lake effect in the East Rift Valley and through the Chew Bahir Basin. The final regression from a high stand of > 90 m began at. 5.2 ka and water level was below 20 m by 4.5 ka; and for the remainder of the Holocene. This sustained low stand is associated with weakening of the West African Monsoon, a shift of the mean position of Congo Air Boundary west of the Lake Turkana catchment and with meter-scale variability in lake level linked to Walker circulation across the Indian Ocean. A surprising observation is

  12. Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations

    PubMed Central

    Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P.; E., Bertrand García-Moreno; Jensen, Kristine Steen; Toleikis, Zigmantas; Teilum, Kaare; Nielsen, Jens Erik

    2015-01-01

    Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatics calculations are essential for this purpose, but their use have been limited by a long-standing discussion on which value to use for the dielectric constants (εeff and εp) required in Coulombic models and Poisson-Boltzmann models. The currently used values for εeff and εp are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for εeff and εp by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in fourteen proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (εeff) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (εp) rangedsfrom 2-5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders, and how different it is from the εp of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of εp = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pKa values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable εp common to most folded proteins. PMID:24124752

  13. Photometric method for determination of acidity constants through integral spectra analysis.

    PubMed

    Zevatskiy, Yuriy Eduardovich; Ruzanov, Daniil Olegovich; Samoylov, Denis Vladimirovich

    2015-04-15

    An express method for determination of acidity constants of organic acids, based on the analysis of the integral transmittance vs. pH dependence is developed. The integral value is registered as a photocurrent of photometric device simultaneously with potentiometric titration. The proposed method allows to obtain pKa using only simple and low-cost instrumentation. The optical part of the experimental setup has been optimized through the exclusion of the monochromator device. Thus it only takes 10-15 min to obtain one pKa value with the absolute error of less than 0.15 pH units. Application limitations and reliability of the method have been tested for a series of organic acids of various nature.

  14. Photometric method for determination of acidity constants through integral spectra analysis

    NASA Astrophysics Data System (ADS)

    Zevatskiy, Yuriy Eduardovich; Ruzanov, Daniil Olegovich; Samoylov, Denis Vladimirovich

    2015-04-01

    An express method for determination of acidity constants of organic acids, based on the analysis of the integral transmittance vs. pH dependence is developed. The integral value is registered as a photocurrent of photometric device simultaneously with potentiometric titration. The proposed method allows to obtain pKa using only simple and low-cost instrumentation. The optical part of the experimental setup has been optimized through the exclusion of the monochromator device. Thus it only takes 10-15 min to obtain one pKa value with the absolute error of less than 0.15 pH units. Application limitations and reliability of the method have been tested for a series of organic acids of various nature.

  15. Structure-Affinity Properties of a High-Affinity Ligand of FKBP12 Studied by Molecular Simulations of a Binding Intermediate

    PubMed Central

    Olivieri, Lilian; Gardebien, Fabrice

    2014-01-01

    With a view to explaining the structure-affinity properties of the ligands of the protein FKBP12, we characterized a binding intermediate state between this protein and a high-affinity ligand. Indeed, the nature and extent of the intermolecular contacts developed in such a species may play a role on its stability and, hence, on the overall association rate. To find the binding intermediate, a molecular simulation protocol was used to unbind the ligand by gradually decreasing the biasing forces introduced. The intermediate was subsequently refined with 17 independent stochastic boundary molecular dynamics simulations that provide a consistent picture of the intermediate state. In this state, the core region of the ligand remains stable, notably because of the two anchoring oxygen atoms that correspond to recurrent motifs found in all FKBP12 ligand core structures. Besides, the non-core regions participate in numerous transient intermolecular and intramolecular contacts. The dynamic aspect of most of the contacts seems important both for the ligand to retain at least a part of its configurational entropy and for avoiding a trapped state along the binding pathway. Since the transient and anchoring contacts contribute to increasing the stability of the intermediate, as a corollary, the dissociation rate constant of this intermediate should be decreased, resulting in an increase of the affinity constant . The present results support our previous conclusions and provide a coherent rationale for explaining the prevalence in high-affinity ligands of (i) the two oxygen atoms found in carbonyl or sulfonyl groups of dissimilar core structures and of (ii) symmetric or pseudo-symmetric mobile groups of atoms found as non-core moieties. Another interesting aspect of the intermediate is the distortion of the flexible 80 s loop of the protein, mainly in its tip region, that promotes the accessibility to the bound state. PMID:25502559

  16. Three pion nucleon coupling constants

    NASA Astrophysics Data System (ADS)

    Ruiz Arriola, E.; Amaro, J. E.; Navarro Pérez, R.

    2016-08-01

    There exist four pion nucleon coupling constants, fπ0pp, - fπ0nn, fπ+pn/2 and fπ-np/2 which coincide when up and down quark masses are identical and the electron charge is zero. While there is no reason why the pion-nucleon-nucleon coupling constants should be identical in the real world, one expects that the small differences might be pinned down from a sufficiently large number of independent and mutually consistent data. Our discussion provides a rationale for our recent determination fp2 = 0.0759(4),f 02 = 0.079(1),f c2 = 0.0763(6), based on a partial wave analysis of the 3σ self-consistent nucleon-nucleon Granada-2013 database comprising 6713 published data in the period 1950-2013.

  17. Quaternions as astrometric plate constants

    NASA Technical Reports Server (NTRS)

    Jefferys, William H.

    1987-01-01

    A new method for solving problems in relative astrometry is proposed. In it, the relationship between the measured quantities and the components of the position vector of a star is modeled using quaternions, in effect replacing the plate constants of a standard four-plate-constant solution with the four components of a quaternion. The method allows a direct solution for the position vectors of the stars, and hence for the equatorial coordinates. Distortions, magnitude, and color effects are readily incorporated into the formalism, and the method is directly applicable to overlapping-plate problems. The advantages of the method include the simplicity of the resulting equations, their freedom from singularities, and the fact that trigonometric functions and tangential point transformations are not needed to model the plate material. A global solution over the entire sky is possible.

  18. Three pion nucleon coupling constants

    NASA Astrophysics Data System (ADS)

    Ruiz Arriola, E.; Amaro, J. E.; Navarro Pérez, R.

    2016-08-01

    There exist four pion nucleon coupling constants, fπ0pp, ‑ fπ0nn, fπ+pn/2 and fπ‑np/2 which coincide when up and down quark masses are identical and the electron charge is zero. While there is no reason why the pion-nucleon-nucleon coupling constants should be identical in the real world, one expects that the small differences might be pinned down from a sufficiently large number of independent and mutually consistent data. Our discussion provides a rationale for our recent determination fp2 = 0.0759(4),f 02 = 0.079(1),f c2 = 0.0763(6), based on a partial wave analysis of the 3σ self-consistent nucleon-nucleon Granada-2013 database comprising 6713 published data in the period 1950-2013.

  19. Time-Varying Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Olive, Keith

    2003-04-01

    Recent data from quasar absorption systems can be interpreted as arising from a time variation in the fine-structure constant. However, there are numerous cosmological, astro-physical, and terrestrial bounds on any such variation. These includes bounds from Big Bang Nucleosynthesis (from the ^4He abundance), the Oklo reactor (from the resonant neutron capture cross-section of Sm), and from meteoretic lifetimes of heavy radioactive isotopes. The bounds on the variation of the fine-structure constant are significantly strengthened in models where all gauge and Yukawa couplings vary in a dependent manner, as would be expected in unified theories. Models which are consistent with all data are severly challenged when Equivalence Principle constraints are imposed.

  20. Substituent effects and pH profiles for stability constants of arylboronic acid diol esters.

    PubMed

    Martínez-Aguirre, Mayte A; Villamil-Ramos, Raul; Guerrero-Alvarez, Jorge A; Yatsimirsky, Anatoly K

    2013-05-17

    Stability constants of boronic acid diol esters in aqueous solution have been determined potentiometrically for a series of meta-, para-substituted phenylboronic acids and diols of variable acidity. The constants β(11-1) for reactions between neutral forms of reactants producing the anionic ester plus proton follow the Hammett equation with ρ depending on pKa of diol and varying from 2.0 for glucose to 1.29 for 4-nitrocatechol. Observed stability constants (K(obs)) measured by UV-vis and fluorometric titrations at variable pH for esters of 4,5-dihydroxy-1,3-benzenedisulfonate (Tiron) generally agree with those expected on the basis of β(11-1) values, but the direct fitting of K(obs) vs pH profiles gives shifted pKa values both for boronic acids and diol as a result of significant interdependence of fitting parameters. The subsituent effects on absorption and fluorescence spectra of Tiron arylboronate esters are characterized. The K(obs) for Tiron determined by (11)B NMR titrations are approximately 1 order of magnitude smaller than those determined by UV-vis titrations under identical conditions. A general equation, which makes possible an estimate of β(11-1) for any pair of boronic acid and diol from their pKa values, is proposed on the basis of established Brönsted-type correlation of Hammett parameters for β(11-1) with acidity of diols. The equation allows one to calculate stability constants expected only on basis of acid-base properties of the components, thus permitting more strict evaluation of contributions of additional factors such as steric or charge effects to the ester stability.

  1. A method for computing association rate constants of atomistically represented proteins under macromolecular crowding

    NASA Astrophysics Data System (ADS)

    Qin, Sanbo; Cai, Lu; Zhou, Huan-Xiang

    2012-12-01

    In cellular environments, two protein molecules on their way to form a specific complex encounter many bystander macromolecules. The latter molecules, or crowders, affect both the energetics of the interaction between the test molecules and the dynamics of their relative motion. In earlier work (Zhou and Szabo 1991 J. Chem. Phys. 95 5948-52), it has been shown that, in modeling the association kinetics of the test molecules, the presence of crowders can be accounted for by their energetic and dynamic effects. The recent development of the transient-complex theory for protein association in dilute solutions makes it possible to easily incorporate the energetic and dynamic effects of crowders. The transient complex refers to a late on-pathway intermediate, in which the two protein molecules have near-native relative separation and orientation, but have yet to form the many short-range specific interactions of the native complex. The transient-complex theory predicts the association rate constant as ka = ka0exp( - ΔG*el/kBT), where ka0 is the ‘basal’ rate constant for reaching the transient complex by unbiased diffusion, and the Boltzmann factors captures the influence of long-range electrostatic interactions between the protein molecules. Crowders slow down the diffusion, therefore reducing the basal rate constant (to kac0), and induce an effective interaction energy ΔGc. We show that the latter interaction energy for atomistic proteins in the presence of spherical crowders is ‘long’-ranged, allowing the association rate constant under crowding to be computed as kac = kac0exp[ - (ΔG*el + ΔG*c)/kBT]. Applications demonstrate that this computational method allows for realistic modeling of protein association kinetics under crowding.

  2. Modal affinities of endplate acetylcholine receptors caused by loop C mutations

    PubMed Central

    Vij, Ridhima; Purohit, Prasad

    2015-01-01

    The time course of the endplate current is determined by the rate and equilibrium constants for acetylcholine receptor (AChR) activation. We measured these constants in single-channel currents from AChRs with mutations at the neurotransmitter-binding sites, in loop C. The main findings are: (a) Almost all perturbations of loop C generate heterogeneity in the channel open probability (“modes”). (b) Modes are generated by different affinities for ACh that can be either higher or lower than in the wild-type receptors. (c) The modes are stable, in so far as each receptor maintains its affinity for at least several minutes. (d) Different agonists show different degrees of modal activity. With the loop C mutation αP197A, there are four modes with ACh but only two with partial agonists. (e) The affinity variations arise exclusively from the αδ-binding site. (f) Substituting four γ-subunit residues into the δ subunit (three in loop E and one in the β5–β5′ linker) reduces modal activity. (g) At each neurotransmitter-binding site, affinity is determined by a core of five aromatic residues. Modes are eliminated by an alanine mutation at δW57 but not at the other aromatics. (h) Modes are eliminated by a phenylalanine substitution at all core aromatics except αY93. The results suggest that, at the αδ agonist site, loop C and the complementary subunit surface can each adopt alternative conformations and interact with each other to influence the position of δW57 with respect to the aromatic core and, hence, affinity. PMID:26503719

  3. Highly Efficient Amplifier for Ka-Band Communications

    NASA Technical Reports Server (NTRS)

    1996-01-01

    An amplifier developed under a Small Business Innovation Research (SBIR) contract will have applications for both satellite and terrestrial communications. This power amplifier uses an innovative series bias arrangement of active devices to achieve over 40-percent efficiency at Ka-band frequencies with an output power of 0.66 W. The amplifier is fabricated on a 2.0- by 3.8-square millimeter chip through the use of Monolithic Microwave Integrated Circuit (MMIC) technology, and it uses state-of-the-art, Pseudomorphic High-Electron-Mobility Transistor (PHEMT) devices. Although the performance of the MMIC chip depends on these high-performance devices, the real innovations here are a unique series bias scheme, which results in a high-voltage chip supply, and careful design of the on-chip planar output stage combiner. This design concept has ramifications beyond the chip itself because it opens up the possibility of operation directly from a satellite power bus (usually 28 V) without a dc-dc converter. This will dramatically increase the overall system efficiency. Conventional microwave power amplifier designs utilize many devices all connected in parallel from the bias supply. This results in a low-bias voltage, typically 5 V, and a high bias current. With this configuration, substantial I(sup 2) R losses (current squared times resistance) may arise in the system bias-distribution network. By placing the devices in a series bias configuration, the total current is reduced, leading to reduced distribution losses. Careful design of the on-chip planar output stage power combiner is also important in minimizing losses. Using these concepts, a two-stage amplifier was designed for operation at 33 GHz and fabricated in a standard MMIC foundry process with 0.20-m PHEMT devices. Using a 20-V bias supply, the amplifier achieved efficiencies of over 40 percent with an output power of 0.66 W and a 16-dB gain over a 2-GHz bandwidth centered at 33 GHz. With a 28-V bias, a power

  4. Determination of the pKa of ionizable enzyme groups by nonlinear regression using a second degree equation.

    PubMed

    O'Reilly, S; Riveros, M C

    1994-01-01

    A second degree equation fitted by nonlinear regression for the analysis of the pH effect on enzyme activity is proposed for diprotic enzyme systems. This method allows the calculation of two molecular dissociation constants (KE1 and KE2 for the free enzyme, KES1 and KES2 for the ES complex) and the pH independent parameters (Vmax and Vmax/Km). The method is validated by bibliographic (alpha-chymotrypsin) and experimental data (almond beta-D-glucosidase). No significant differences were found between present data and those previously reported in the literature using similar experimental conditions. This method works using comparatively few [H+] concentration values within a narrow pH range, preferentially around the optimum, being adequate for diprotic systems with close pKa values. PMID:8728828

  5. Determination of the pKa of ionizable enzyme groups by nonlinear regression using a second degree equation.

    PubMed

    O'Reilly, S; Riveros, M C

    1994-01-01

    A second degree equation fitted by nonlinear regression for the analysis of the pH effect on enzyme activity is proposed for diprotic enzyme systems. This method allows the calculation of two molecular dissociation constants (KE1 and KE2 for the free enzyme, KES1 and KES2 for the ES complex) and the pH independent parameters (Vmax and Vmax/Km). The method is validated by bibliographic (alpha-chymotrypsin) and experimental data (almond beta-D-glucosidase). No significant differences were found between present data and those previously reported in the literature using similar experimental conditions. This method works using comparatively few [H+] concentration values within a narrow pH range, preferentially around the optimum, being adequate for diprotic systems with close pKa values.

  6. Smooth big bounce from affine quantization

    NASA Astrophysics Data System (ADS)

    Bergeron, Hervé; Dapor, Andrea; Gazeau, Jean Pierre; Małkiewicz, Przemysław

    2014-04-01

    We examine the possibility of dealing with gravitational singularities on a quantum level through the use of coherent state or wavelet quantization instead of canonical quantization. We consider the Robertson-Walker metric coupled to a perfect fluid. It is the simplest model of a gravitational collapse, and the results obtained here may serve as a useful starting point for more complex investigations in the future. We follow a quantization procedure based on affine coherent states or wavelets built from the unitary irreducible representation of the affine group of the real line with positive dilation. The main issue of our approach is the appearance of a quantum centrifugal potential allowing for regularization of the singularity, essential self-adjointness of the Hamiltonian, and unambiguous quantum dynamical evolution.

  7. Affinity Chromatography in Nonionic Detergent Solutions

    NASA Astrophysics Data System (ADS)

    Robinson, Jack B.; Strottmann, James M.; Wick, Donald G.; Stellwagen, Earle

    1980-10-01

    Anionic dye affinity chromatography is commonly unproductive in the presence of nonionic detergents used to extract particulate proteins. Using lactate dehydrogenase as a model protein, Cibacron blue F3GA as a model dye, and Triton X-100 as a model detergent, we find that the dye is encapsulated in nonionic detergent micelles, rendering the dye incapable of ligation with the enzyme. However, the dye can be liberated from the micelles without altering the nonionic detergent concentration by addition of an anionic detergent, such as deoxycholate or sodium dodecyl sulfate, forming mixed anionic/nonionic micelles that displace the anionic dye. Encapsulation of the anionic detergents prevents their activity as protein denaturants. These observations have been successfully translated to the dye affinity chromatography of a detergent extract of brain particulate cyclic nucleotide phosphodiesterase.

  8. Artificial Affinity Proteins as Ligands of Immunoglobulins

    PubMed Central

    Mouratou, Barbara; Béhar, Ghislaine; Pecorari, Frédéric

    2015-01-01

    A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized. PMID:25647098

  9. Ka Hana `Imi Na`auao: A Science Curriculum Project

    NASA Astrophysics Data System (ADS)

    Napeahi, K.; Roberts, K. D.; Galloway, L. M.; Stodden, R. A.; Akuna, J.; Bruno, B.

    2005-12-01

    In antiquity, the first people to step foot on what are now known as the Hawaiian islands skillfully traversed the Pacific Ocean using celestial navigation and learned observations of scientific phenomena. Long before the Western world ventured beyond the horizon, Hawaiians had invented the chronometer, built aqueduct systems (awai) that continue to amaze modern engineers, and had preventive health systems as well as a comprehensive knowledge of medicinal plants (including antivirals) which only now are working their way through trials for use in modern pharmacopia. Yet, today, Native Hawaiians are severely underrepresented in science-related fields, reflecting (in part) a failure of the Western educational system to nurture the potential of these resourceful students, particularly the many "at-risk" students who are presently over-represented in special education. A curriculum which draws from and incorporates traditional Hawaiian values and knowledge is needed to reinforce links to the inquiry process which nurtured creative thinking during the renaissance of Polynesian history. The primary goal of the Ka Hana `Imi Na`auao Project (translation: `science` or `work in which you seek enlightenment, knowledge or wisdom`) is to increase the number of Native Hawaiian adults in science-related postsecondary education and employment fields. Working closely with Native Hawaiian cultural experts and our high school partners, we will develop and implement a culturally responsive 11th and 12th grade high school science curriculum, infused with math, literacy and technology readiness skills. Software and assistive technology will be used to adapt instruction to individual learners` reading levels, specific disabilities and learning styles. To ease the transition from secondary to post-secondary education, selected grade 12 students will participate in planned project activities that link high school experiences with college science-related programs of study. Ka Hana `Imi Na

  10. Did the 8.2 ka event affect southern Africa?

    NASA Astrophysics Data System (ADS)

    Shaw, Paul

    2014-05-01

    Palaeoenvironmental reconstruction of southern Africa over the past 4 decades has focused largely on the last glacial cycle, and, more recently, events during to Holocene, interpreted largely at the millennial scale. Little attention has been given to sub-millenial drivers and impacts, other than the Little Ice Age (HolmgreN et al 2001). The 8.2ka event has been recognized in Europe for over half a century from peat cores and dendrochronology. A Bond Event caused by disruption of the Gulf Stream by melting Laurentian ice, it lasted around 100 years and resulted in a fall in temperature in northern Europe of up to 6o C. Recently published high-resolution speleothem records have indicated significant short-term change over a much wider area than previously thought, including the Caribbean, eastern Brazil, Spain, Oman and China. A recent paper on Trinidad (Boyd et al, in press) emphasizes a period of prolonged drought in the southern Caribbean due to a southerly emplacement of the ITCZ. The question then arises whether this shift affected the southern hemisphere, and if so, what would be the likely impacts and evidence. A study of late Quaternary lake levels in Lake Chilwa, Malawi (Thomas et al 2009) noted a correspondence between high lake stands and Heinrich events, whilst modeling of Atlantic freshwater influx using the HadCM3 GCM indicates negative precipitation anomalies in the Caribbean and west Africa, with a significant positive anomaly in the interior of southern Africa, possibly linked to enhanced monsoonal activity in the Indian Ocean. These patterns in southern and western Africa have been suggested around 8.2 ka in a review of early Holocene data (Burrough & Thomas 2013), but the chronological resolution is not sufficient to conclude the observation. The only speleothem record for this period, T8 in Cold Air Cave, Makapansgat Valley (Holmgren et al 2003) shows an anomaly, but with temporal resolution at a 50 yr sampling interval, this again is speculative

  11. X/X/Ka-band prime focus feed antenna for the Mars Observer beacon spacecraft

    NASA Technical Reports Server (NTRS)

    Stanton, P.; Reilly, H.; Esquivel, M.

    1988-01-01

    The results of an X/X/Ka-band feed design concept demonstration are presented. The purpose is to show the feasibility of adding a Ka-band beacon to the Mars Observer spacecraft. Scale model radiation patterns were made and analyzed.

  12. School Ka Sabaq: Literacy in a Girls' Primary School in Rural Pakistan.

    ERIC Educational Resources Information Center

    Farah, Iffat

    Literacy learning practices in the context of a girls' school in Pakistan are described as part of a larger study. "School ka sabaq" or "school lesson" is recognized as involving reading and writing activities as well as behavior particular to the institution of the school. The goals of school ka sabaq, which are to pass exams and acquire…

  13. Permeability of self-affine rough fractures

    PubMed

    Drazer; Koplik

    2000-12-01

    The permeability of two-dimensional fractures with self-affine fractal roughness is studied via analytic arguments and numerical simulations. The limit where the roughness amplitude is small compared with average fracture aperture is analyzed by a perturbation method, while in the opposite case of narrow aperture, we use heuristic arguments based on lubrication theory. Numerical simulations, using the lattice Boltzmann method, are used to examine the complete range of aperture sizes, and confirm the analytic arguments. PMID:11138092

  14. The gall bladder cholecystokinin receptor exists in two guanine nucleotide-binding protein-regulated affinity states

    SciTech Connect

    Molero, X.; Miller, L.J. )

    1991-02-01

    To study proximal events in cholecystokinin (CCK) action on bovine gall bladder smooth muscle, we used the hormone analogue D-Tyr-Gly-((N1e28,31)CCK-26-32)-phenethyl ester (OPE), which has unique biological properties. This fully efficacious agonist differs from native CCK by not expressing supramaximal inhibition of cell shortening, yet it clearly interacts with the same receptor molecule. This was demonstrated in binding and affinity labeling studies, where both peptides label the same Mr 70,000-85,000 protein and both fully compete for binding of the other ligand. Further, its relatively high affinity for the low affinity CCK receptor permits the clear demonstration of two affinity states of a CCK receptor on a membrane preparation and makes possible evaluation of the molecular basis of these affinity states and their regulation. Analysis of homologous and heterologous binding curves performed with both CCK and OPE peptides and radioligands demonstrated the presence of two affinity states, with CCK being able to distinguish them (Kd1 = 0.48 +/- 0.04 nM and Kd2 = 56.5 +/- 7.4 nM) and OPE recognizing them equally (Kd1 = 0.94 +/- 0.31 nM and Kd2 = 0.96 +/- 0.23 nM). In the presence of nonhydrolyzable GTP analogues, there was a shift in distribution of receptors toward the low affinity state, with the total number of receptors and their absolute affinities for each peptide remaining constant. Thus, the gall bladder CCK receptor is a single molecule capable of assuming two interconvertible affinity states, regulated by a guanine nucleotide-binding protein. Two full agonists are capable of interacting with this molecule to yield different biological responses via different molecular events.

  15. On constructing purely affine theories with matter

    NASA Astrophysics Data System (ADS)

    Cervantes-Cota, Jorge L.; Liebscher, D.-E.

    2016-08-01

    We explore ways to obtain the very existence of a space-time metric from an action principle that does not refer to it a priori. Although there are reasons to believe that only a non-local theory can viably achieve this goal, we investigate here local theories that start with Schrödinger's purely affine theory (Schrödinger in Space-time structure. Cambridge UP, Cambridge, 1950), where he gave reasons to set the metric proportional to the Ricci curvature aposteriori. When we leave the context of unified field theory, and we couple the non-gravitational matter using some weak equivalence principle, we can show that the propagation of shock waves does not define a lightcone when the purely affine theory is local and avoids the explicit use of the Ricci tensor in realizing the weak equivalence principle. When the Ricci tensor is substituted for the metric, the equations seem to have only a very limited set of solutions. This backs the conviction that viable purely affine theories have to be non-local.

  16. Overview of affinity biosensors in food analysis.

    PubMed

    Patel, Pradip D

    2006-01-01

    The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field.

  17. Overview of affinity biosensors in food analysis.

    PubMed

    Patel, Pradip D

    2006-01-01

    The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field. PMID:16792079

  18. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture. PMID:26584922

  19. Trematode hemoglobins show exceptionally high oxygen affinity.

    PubMed

    Kiger, L; Rashid, A K; Griffon, N; Haque, M; Moens, L; Gibson, Q H; Poyart, C; Marden, M C

    1998-08-01

    Ligand binding studies were made with hemoglobin (Hb) isolated from trematode species Gastrothylax crumenifer (Gc), Paramphistomum epiclitum (Pe), Explanatum explanatum (Ee), parasitic worms of water buffalo Bubalus bubalis, and Isoparorchis hypselobagri (Ih) parasitic in the catfish Wallago attu. The kinetics of oxygen and carbon monoxide binding show very fast association rates. Whereas oxygen can be displaced on a millisecond time scale from human Hb at 25 degrees C, the dissociation of oxygen from trematode Hb may require a few seconds to over 20 s (for Hb Pe). Carbon monoxide dissociation is faster, however, than for other monomeric hemoglobins or myoglobins. Trematode hemoglobins also show a reduced rate of autoxidation; the oxy form is not readily oxidized by potassium ferricyanide, indicating that only the deoxy form reacts rapidly with this oxidizing agent. Unlike most vertebrate Hbs, the trematodes have a tyrosine residue at position E7 instead of the usual distal histidine. As for Hb Ascaris, which also displays a high oxygen affinity, the trematodes have a tyrosine in position B10; two H-bonds to the oxygen molecule are thought to be responsible for the very high oxygen affinity. The trematode hemoglobins display a combination of high association rates and very low dissociation rates, resulting in some of the highest oxygen affinities ever observed.

  20. High speed transfer switch with 50 kA and 50 kV

    SciTech Connect

    Reass, W.A.; Kasik, R.J.; Wilds, W.A.

    1989-01-01

    This paper gives the mechanical design and electrical parameters of a pneumatically operated transfer switch. This design is used to switch 3-second 50-kA current pulses, and is easily capable of 75 kA operation (2 {times} 10{sup 10} I{sup 2}t); with water-cooled versions capable of 20 kA continuously. Although the switch is not specifically designed to make or break 50 kA, it is provided with auxiliary Elkonite arcing contacts have proven their value in protecting the main electrodes even under repetitive (50 kA) fault conditions. Included in this presentation will be the results of extensive life testing and associated criteria. 6 figs., 1 tab.

  1. X-/Ka-band dichroic plate design and grating lobe study

    NASA Technical Reports Server (NTRS)

    Chen, J. C.

    1991-01-01

    An X-/Ka-band dichroic plate is needed for simultaneously receiving X-band and Ka-band in the DSS-13 Beam Waveguide Antenna. The plate is transparent to the allocated Ka-band downlink (31.8-32.3 GHz) and the frequency band for the Mars Observer Ka-band Beacon Link Experiment (KABLE) (33.6-33.8 GHz), while at the same time reflecting the X-band downlink (8.4-8.5 GHz). The design is made using a computer program for dichroic plates with rectangular holes. The theoretical performance of the X-/Ka-band dichroic plate is presented. A study of the grating lobe problem is also included in this article.

  2. The intrinsic pKa values for phosphatidylserine and phosphatidylethanolamine in phosphatidylcholine host bilayers.

    PubMed Central

    Tsui, F C; Ojcius, D M; Hubbell, W L

    1986-01-01

    Potentiometric titrations and surface potential measurements have been used to determine the intrinsic pKa values of both the carboxyl and amino groups of phosphatidylserine (PS) in mixed vesicles of PS and phosphatidylcholine (PC), and also of the amino group of phosphatidylethanolamine (PE) in mixed PE-PC vesicles. The pKa of the carboxyl group of PS in liposomes with different PS/PC lipid ratios measured by the two different methods is 3.6 +/- 0.1, and the pKa of its amino group is 9.8 +/- 0.1. The pKa of the amino group of PE in PE-PC vesicles, determined solely by surface potential measurements, is 9.6 +/- 0.1. These pKa values are independent of the aqueous phase ionic strength and of the effect of the liposome's surface potential due to the presence of these partially charged lipids. PMID:3955180

  3. Binding affinities of CRBPI and CRBPII for 9-cis-retinoids

    PubMed Central

    Kane, Maureen A.; Bright, Frank V.; Napoli, Joseph L.

    2014-01-01

    Background Cellular retinol binding-protein I (CRBPI) and cellular retinol binding-protein II (CRBPII) serve as intracellular retinoid chaperones that bind retinol and retinal with high affinity and facilitate substrate delivery to select enzymes that catalyze retinoic acid (RA) and retinyl ester biosynthesis. Recently, 9-cis-RA has been identified in vivo in the pancreas, where it contributes to regulating glucose-stimulated insulin secretion. In vitro, 9-cis-RA activates RXR (retinoid×receptors), which serve as therapeutic targets for treating cancer and metabolic diseases. Binding affinities and structure–function relationships have been well characterized for CRBPI and CRBPII with all-trans-retinoids, but not for 9-cis-retinoids. This study extended current knowledge by establishing binding affinities for CRBPI and CRBPII with 9-cis-retinoids. Methods We have determined apparent dissociation constants, Kd′, through monitoring binding of 9-cis-retinol, 9-cis-retinal, and 9-cis-RA with CRBPI and CRBPII by fluorescence spectroscopy, and analyzing the data with non-linear regression. We compared these data to the data we obtained for all-trans- and 13-cis-retinoids under identical conditions. Results CRBPI and CRBPII, respectively, bind 9-cis-retinol ( Kd′, 11 nM and 68 nM) and 9-cis-retinal ( Kd′, 8 nM and 5 nM) with high affinity. No significant 9-cis-RA binding was observed with CRBPI or CRBPII. Conclusions CRBPI and CRBPII bind 9-cis-retinol and 9-cis-retinal with high affinities, albeit with affinities somewhat lower than for all-trans-retinol and all-trans-retinal. General significance These data provide further insight into structure–binding relationships of cellular retinol binding-proteins and are consistent with a model of 9-cis-RA biosynthesis that involves chaperoned delivery of 9-cis-retinoids to enzymes that recognize retinoid binding-proteins. PMID:21382444

  4. Absolute paleointensity from Hawaiian lavas younger than 35 ka

    USGS Publications Warehouse

    Valet, J.-P.; Tric, E.; Herrero-Bervera, E.; Meynadier, L.; Lockwood, J.P.

    1998-01-01

    Paleointensity studies have been conducted in air and in argon atmosphere on nine lava flows with radiocarbon ages distributed between 3.3 and 28.2 ka from the Mauna Loa volcano in the big island of Hawaii. Determinations of paleointensity obtained at eight sites depict the same overall pattern as the previous results for the same period in Hawaii, although the overall average field intensity appears to be lower. Since the present results were determined at higher temperatures than in the previous studies, this discrepancy raises questions regarding the selection of low versus high-temperature segments that are usually made for absolute paleointensity. The virtual dipole moments are similar to those displayed by the worldwide data set obtained from dated lava flows. When averaged within finite time intervals, the worldwide values match nicely the variations of the Sint-200 synthetic record of relative paleointensity and confirm the overall decrease of the dipole field intensity during most of this period. The convergence between the existing records at Hawaii and the rest of the world does not favour the presence of persistent strong non-dipole components beneath Hawaii for this period.

  5. Rain Fade Compensation for Ka-Band Communications Satellites

    NASA Technical Reports Server (NTRS)

    Mitchell, W. Carl; Nguyen, Lan; Dissanayake, Asoka; Markey, Brian; Le, Anh

    1997-01-01

    This report provides a review and evaluation of rain fade measurement and compensation techniques for Ka-band satellite systems. This report includes a description of and cost estimates for performing three rain fade measurement and compensation experiments. The first experiment deals with rain fade measurement techniques while the second one covers the rain fade compensation techniques. The third experiment addresses a feedback flow control technique for the ABR service (for ATM-based traffic). The following conclusions were observed in this report; a sufficient system signal margin should be allocated for all carriers in a network, that is a fixed clear-sky margin should be typically in the range of 4-5 dB and should be more like 15 dB in the up link for moderate and heavy rain zones; to obtain a higher system margin it is desirable to combine the uplink power control technique with the technique that implements the source information rate and FEC code rate changes resulting in a 4-5 dB increase in the dynamic part of the system margin. The experiments would assess the feasibility of the fade measurements and compensation techniques, and ABR feedback control technique.

  6. Ka-Band Transponder for Deep-Space Radio Science

    NASA Technical Reports Server (NTRS)

    Dennis, Matthew S.; Mysoor, Narayan R.; Folkner, William M.; Mendoza, Ricardo; Venkatesan, Jaikrishna

    2008-01-01

    A one-page document describes a Ka-band transponder being developed for use in deep-space radio science. The transponder receives in the Deep Space Network (DSN) uplink frequency band of 34.2 to 34.7 GHz, transmits in the 31.8- to 32.3 GHz DSN downlink band, and performs regenerative ranging on a DSN standard 4-MHz ranging tone subcarrier phase-modulated onto the uplink carrier signal. A primary consideration in this development is reduction in size, relative to other such transponders. The transponder design is all-analog, chosen to minimize not only the size but also the number of parts and the design time and, thus, the cost. The receiver features two stages of frequency down-conversion. The receiver locks onto the uplink carrier signal. The exciter signal for the transmitter is derived from the same source as that used to generate the first-stage local-oscillator signal. The ranging-tone subcarrier is down-converted along with the carrier to the second intermediate frequency, where the 4-MHz tone is demodulated from the composite signal and fed into a ranging-tone-tracking loop, which regenerates the tone. The regenerated tone is linearly phase-modulated onto the downlink carrier.

  7. A dual frequency microstrip antenna for Ka band

    NASA Technical Reports Server (NTRS)

    Lee, R. Q.; Baddour, M. F.

    1985-01-01

    For fixed satellite communication systems at Ka band with downlink at 17.7 to 20.2 GHz and uplink at 27.5 to 30.0 GHz, the focused optics and the unfocused optics configurations with monolithic phased array feeds have often been used to provide multiple fixed and multiple scanning spot beam coverages. It appears that a dual frequency microstrip antenna capable of transmitting and receiving simultaneously is highly desirable as an array feed element. This paper describes some early efforts on the development and experimental testing of a dual frequency annular microstrip antenna. The antenna has potential application for use in conjunction with a monolithic microwave integrated circuit device as an active radiating element in a phased array of phased array feeds. The antenna is designed to resonate at TM sub 12 and TM sub 13 modes and tuned with a circumferential microstrip ring to vary the frequency ratio. Radiation characteristics at both the high and low frequencies are examined. Experimental results including radiating patterns and swept frequency measurements are presented.

  8. Experimental approaches for measuring pKa's in RNA and DNA.

    PubMed

    Thaplyal, Pallavi; Bevilacqua, Philip C

    2014-01-01

    RNA and DNA carry out diverse functions in biology including catalysis, splicing, gene regulation, and storage of genetic information. Interest has grown in understanding how nucleic acids perform such sophisticated functions given their limited molecular repertoire. RNA can fold into diverse shapes that often perturb pKa values and allow it to ionize appreciably under biological conditions, thereby extending its molecular diversity. The goal of this chapter is to enable experimental measurement of pKa's in RNA and DNA. A number of experimental methods for measuring pKa values in RNA and DNA have been developed over the last 10 years, including RNA cleavage kinetics; UV-, fluorescence-, and NMR-detected pH titrations; and Raman crystallography. We begin with general considerations for choosing a pKa assay and then describe experimental conditions, advantages, and disadvantages for these assays. Potential pitfalls in measuring a pKa are provided including the presence of apparent pKa's due to a kinetic pKa or coupled acid- and alkali-promoted RNA unfolding, as well as degradation of RNA, precipitation of metal hydroxides and poor baselines. Use of multiple data fitting procedures and the study of appropriate mutants are described as ways to avoid some of these pitfalls. Application of these experimental methods to RNA and DNA will increase the number of available nucleic acid pKa values in the literature, which should deepen insight into biology and provide benchmarks for pKa calculations. Future directions for measuring pKa's in nucleic acids are discussed.

  9. Measurement of State-Specific Association Constants in Allosteric Sensors through Molecular Stapling and NMR.

    PubMed

    Moleschi, Kody J; Akimoto, Madoka; Melacini, Giuseppe

    2015-08-26

    Allostery is a ubiquitous mechanism to control biological function and arises from the coupling of inhibitory and binding equilibria. The extent of coupling reflects the inactive vs active state selectivity of the allosteric effector. Hence, dissecting allosteric determinants requires quantification of state-specific association constants. However, observed association constants are typically population-averages, reporting on overall affinities but not on allosteric coupling. Here we propose a general method to measure state-specific association constants in allosteric sensors based on three key elements, i.e., state-selective molecular stapling through disulfide bridges, competition binding saturation transfer experiments and chemical shift correlation analyses to gauge state populations. The proposed approach was applied to the prototypical cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA-RIα), for which the structures of the inactive and active states are available, as needed to design the state-selective disulfide bridges. Surprisingly, the PKA-RIα state-specific association constants are comparable to those of a structurally homologous domain with ∼10(3)-fold lower cAMP-affinity, suggesting that the affinity difference arises primarily from changes in the position of the dynamic apo inhibitory equilibrium.

  10. Millikan's measurement of Planck's constant

    NASA Astrophysics Data System (ADS)

    Franklin, Allan

    2013-12-01

    Robert Millikan is famous for measuring the charge of the electron. His result was better than any previous measurement and his method established that there was a fundamental unit of charge, or charge quantization. He is less well-known for his measurement of Planck's constant, although, as discussed below, he is often mistakenly given credit for providing significant evidence in support of Einstein's photon theory of light.1 His Nobel Prize citation was "for his work on the elementary electric charge of electricity and the photoelectric effect," an indication of the significance of his work on the photoelectric effect.

  11. Chandra Independently Determines Hubble Constant

    NASA Astrophysics Data System (ADS)

    2006-08-01

    A critically important number that specifies the expansion rate of the Universe, the so-called Hubble constant, has been independently determined using NASA's Chandra X-ray Observatory. This new value matches recent measurements using other methods and extends their validity to greater distances, thus allowing astronomers to probe earlier epochs in the evolution of the Universe. "The reason this result is so significant is that we need the Hubble constant to tell us the size of the Universe, its age, and how much matter it contains," said Max Bonamente from the University of Alabama in Huntsville and NASA's Marshall Space Flight Center (MSFC) in Huntsville, Ala., lead author on the paper describing the results. "Astronomers absolutely need to trust this number because we use it for countless calculations." Illustration of Sunyaev-Zeldovich Effect Illustration of Sunyaev-Zeldovich Effect The Hubble constant is calculated by measuring the speed at which objects are moving away from us and dividing by their distance. Most of the previous attempts to determine the Hubble constant have involved using a multi-step, or distance ladder, approach in which the distance to nearby galaxies is used as the basis for determining greater distances. The most common approach has been to use a well-studied type of pulsating star known as a Cepheid variable, in conjunction with more distant supernovae to trace distances across the Universe. Scientists using this method and observations from the Hubble Space Telescope were able to measure the Hubble constant to within 10%. However, only independent checks would give them the confidence they desired, considering that much of our understanding of the Universe hangs in the balance. Chandra X-ray Image of MACS J1149.5+223 Chandra X-ray Image of MACS J1149.5+223 By combining X-ray data from Chandra with radio observations of galaxy clusters, the team determined the distances to 38 galaxy clusters ranging from 1.4 billion to 9.3 billion

  12. Henry's law constants of polyols

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Müller, J.-F.

    2014-05-01

    Henry's law constants (HLC) are derived for several polyols bearing between 2 and 6 hydroxyl groups, based on literature data for water activity, vapour pressure and/or solubility. Depending on the case, infinite dilution activity coefficients (IDACs), solid state pressures or activity coefficient ratios are obtained as intermediary results. For most compounds, these are the first values reported, while others compare favourably with literature data in most cases. Using these values and those from a previous work (Compernolle and Müller, 2014), an assessment is made on the partitioning of polyols, diacids and hydroxy acids to droplet and aqueous aerosol.

  13. Studies on recombinant single chain Jacalin lectin reveal reduced affinity for saccharides despite normal folding like native Jacalin.

    PubMed

    Sahasrabuddhe, Anagh A; Gaikwad, Sushama M; Krishnasastry, M V; Khan, M Islam

    2004-12-01

    Sugar binding studies, inactivation, unfolding, and refolding of native Jacalin (nJacalin) from Artocarpus integrifolia and recombinant single-chain Jacalin (rJacalin) expressed in Escherichia coli were studied by intrinsic fluorescence and thermal and chemical denaturation approaches. Interestingly, rJacalin does not undergo any proteolytic processing in an E. coli environment. It has 100fold less affinity for methyl-alpha-galactose (Ka: 2.48 x 10(2)) in comparison to nJacalin (Ka: 1.58 x 10(4)), and it also binds Thomsen-Friedenreich (TF) disaccharide (Galbeta1-3GalNAc) with less affinity. Overall sugar binding characteristics of rJacalin are qualitatively similar to that of nJacalin (Galaffinity.

  14. The rise and fall of Lake Bonneville between 45 and 10.5 ka

    USGS Publications Warehouse

    Benson, L.V.; Lund, S.P.; Smoot, J.P.; Rhode, D.E.; Spencer, R.J.; Verosub, K.L.; Louderback, L.A.; Johnson, C.A.; Rye, R.O.; Negrini, R.M.

    2011-01-01

    A sediment core taken from the western edge of the Bonneville Basin has provided high-resolution proxy records of relative lake-size change for the period 45.1-10.5 calendar ka (hereafter ka). Age control was provided by a paleomagnetic secular variation (PSV)-based age model for Blue Lake core BL04-4. Continuous records of ??18O and total inorganic carbon (TIC) generally match an earlier lake-level envelope based on outcrops and geomorphic features, but with differences in the timing of some hydrologic events/states. The Stansbury Oscillation was found to consist of two oscillations centered on 25 and 24 ka. Lake Bonneville appears to have reached its geomorphic highstand and began spilling at 18.5 ka. The fall from the highstand to the Provo level occurred at 17.0 ka and the lake intermittently overflowed at the Provo level until 15.2 ka, at which time the lake fell again, bottoming out at ~14.7 ka. The lake also fell briefly below the Provo level at ~15.9 ka. Carbonate and ??18O data indicate that between 14.7 and 13.1 ka the lake slowly rose to the Gilbert shoreline and remained at about that elevation until 11.6 ka, when it fell again. Chemical and sedimentological data indicate that a marsh formed in the Blue Lake area at 10.5 ka.Relatively dry periods in the BL04-4 records are associated with Heinrich events H1-H4, suggesting that either the warming that closely followed a Heinrich event increased the evaporation rate in the Bonneville Basin and (or) that the core of the polar jet stream (PJS) shifted north of the Bonneville Basin in response to massive losses of ice from the Laurentide Ice Sheet (LIS) during the Heinrich event. The second Stansbury Oscillation occurred during Heinrich event H2, and the Gilbert wet event occurred during the Younger Dryas cold interval. Several relatively wet events in BL04-4 occur during Dansgaard-Oeschger (DO) warm events.The growth of the Bear River glacier between 32 and 17 ka paralleled changes in the values of proxy

  15. Binding affinities and thermodynamics of noncovalent functionalization of carbon nanotubes with surfactants.

    PubMed

    Oh, Hyunkyu; Sim, Jinsook; Ju, Sang-Yong

    2013-09-01

    Binding affinity and thermodynamic understanding between a surfactant and carbon nanotube is essential to develop various carbon nanotube applications. Flavin mononucleotide-wrapped carbon nanotubes showing a large redshift in optical signature were utilized to determine the binding affinity and related thermodynamic parameters of 12 different nanotube chiralities upon exchange with other surfactants. Determined from the midpoint of sigmoidal transition, the equilibrium constant (K), which is inversely proportional to the binding affinity of the initial surfactant-carbon nanotube, provided quantitative binding strengths of surfactants as SDBS > SC ≈ FMN > SDS, irrespective of electronic types of SWNTs. Binding affinity of metallic tubes is weaker than that of semiconducting tubes. The complex K patterns from semiconducting tubes show preference to certain SWNT chiralities and surfactant-specific cooperativity according to nanotube chirality. Controlling temperature was effective to modulate K values by 30% and enables us to probe thermodynamic parameters. Equally signed enthalpy and entropy changes produce Gibbs energy changes with a magnitude of a few kJ/mol. A greater negative Gibbs energy upon exchange of surfactant produces an enhanced nanotube photoluminescence, implying the importance of understanding thermodynamics for designing nanotube separation and supramolecular assembly of surfactant.

  16. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

    PubMed Central

    Schoukroun-Barnes, Lauren R.; White, Ryan J.

    2015-01-01

    The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes. PMID:25835184

  17. Chemiluminescently labeled aptamers as the affinity probe for interaction analysis by capillary electrophoresis.

    PubMed

    Li, Hong-Yi; Deng, Qin-Pei; Zhang, De-Wen; Zhou, Ying-Lin; Zhang, Xin-Xiang

    2010-07-01

    Aptamers are nucleic acid oligonucleotides, which can recognize targets with high affinity and specificity. Fluorescently labeled aptamers have been used as affinity probes in CE for interaction analysis. In this study, a method of labeling aptamers chemiluminescently with isoluminol isothiocyanate (ILITC) through covalent bonds was proposed and realized. The ILITC-labeled aptamers were characterized by HPLC-MS and purified by HPLC. After desalination, the ILITC-labeled aptamers were employed as the affinity probe for interaction analysis in CE coupled with chemiluminescence detection (CE-CL) by interface of end column reaction mode, the apparatus of which was home-designed and setup. CE-CL experiment conditions, including buffer pH, concentrations of horseradish peroxidase and H(2)O(2), were optimized first. The system of thrombin and its 29-mer aptamer was chosen as the model. Binding parameters, namely the dissociation constant (K(d)) and the binding site number (n), were calculated. The K(d) obtained was 124.0+/-6.9 nM in agreement with the reported values. Thus, interaction analysis method based on chemiluminescently labeled aptamers as the affinity probe in CE-CL has been established. This method can be widely applied due to the ease and universality of the labeling method, simplicity of CE-CL apparatus and combination with aptamers for a wide range of targets.

  18. The low-affinity complex of cytochrome c and its peroxidase

    PubMed Central

    Van de Water, Karen; Sterckx, Yann G. J.; Volkov, Alexander N.

    2015-01-01

    The complex of yeast cytochrome c peroxidase and cytochrome c is a paradigm of the biological electron transfer (ET). Building on seven decades of research, two different models have been proposed to explain its functional redox activity. One postulates that the intermolecular ET occurs only in the dominant, high-affinity protein–protein orientation, while the other posits formation of an additional, low-affinity complex, which is much more active than the dominant one. Unlike the high-affinity interaction—extensively studied by X-ray crystallography and NMR spectroscopy—until now the binding of cytochrome c to the low-affinity site has not been observed directly, but inferred mainly from kinetics experiments. Here we report the structure of this elusive, weak protein complex and show that it consists of a dominant, inactive bound species and an ensemble of minor, ET-competent protein–protein orientations, which summarily account for the experimentally determined value of the ET rate constant. PMID:25944250

  19. Stability constant estimator user`s guide

    SciTech Connect

    Hay, B.P.; Castleton, K.J.; Rustad, J.R.

    1996-12-01

    The purpose of the Stability Constant Estimator (SCE) program is to estimate aqueous stability constants for 1:1 complexes of metal ions with ligands by using trends in existing stability constant data. Such estimates are useful to fill gaps in existing thermodynamic databases and to corroborate the accuracy of reported stability constant values.

  20. Quantification of the Effects of Ionic Strength, Viscosity, and Hydrophobicity on Protein–Ligand Binding Affinity

    PubMed Central

    2014-01-01

    In order to quantify the interactions between molecules of biological interest, the determination of the dissociation constant (Kd) is essential. Estimation of the binding affinity in this way is routinely performed in “favorable” conditions for macromolecules. Crucial data for ligand–protein binding elucidation is mainly derived from techniques (e.g., macromolecular crystallography) that require the addition of high concentration of salts and/or other additives. In this study we have evaluated the effect of temperature, ionic strength, viscosity, and hydrophobicity on the Kd of three previously characterized protein–ligand systems, based on variation in their binding sites, in order to provide insight into how these often overlooked unconventional circumstances impact binding affinity. Our conclusions are as follows: (1) increasing solvent viscosity in general is detrimental to ligand binding, (2) moderate increases in temperature have marginal effects on the dissociation constant, and (3) the degree of hydrophobicity of the ligand and the binding site determines the extent of the influence of cosolvents and salt concentration on ligand binding affinity. PMID:25147617

  1. Multi-wavelength spectrophotometric determination of the protolytic constants of tetracycline hydrochloride in some nonaqueous-water mixed solvents: A solvatochromism study

    NASA Astrophysics Data System (ADS)

    Ghasemi, Jahan B.; Jalalvand, Ali R.

    2011-01-01

    Annihilation of the contribution of one chemical component from the original data matrix is a general method in rank annihilation factor analysis (RAFA). However, RAFA is not applicable for studying the protonation equilibria of multiprotic acids but in this study two-rank annihilation factor analysis (TRAFA) was used as an efficient chemometrics algorithm for determination of the protolytic constants (p Ka) of tetracycline hydrochloride (TCHC) in some nonaqueous-water mixed solvents such as acetonitrile (AN)-water and methanol (MeOH)-water from the spectral pH-absorbance data. The spectral data was obtained from spectrophotometric acid-base titrations of different solutions of TCHC at (25.0 ± 0.10) °C and an ionic strength of 0.10 M. In TRAFA algorithm the p Ka values were obtained with relationship between residual standard deviation (R.S.D.) and hypothetical p Ka values. In the case of TCHC, the spectra were divided in two consecutive subdivisions according to their pH range having two p Ka and TRAFA was run twice. The validity of the obtained p Ka values was checked with well-known chemometrics algorithms such as DATAN, EQUSPEC, SPECFIT/32 and SQUAD. The effects of changing solvent composition on the protolytic constants were explained by linear solvation energy relationships (LSER) utilizing solvatochromic parameters.

  2. Importin {beta}-type nuclear transport receptors have distinct binding affinities for Ran-GTP

    SciTech Connect

    Hahn, Silvia; Schlenstedt, Gabriel

    2011-03-18

    Highlights: {yields} Determination of binding properties of nuclear transport receptor/Ran-GTP complexes. {yields} Biosensor measurements provide constants for dissociation, on-rates, and off-rates. {yields} The affinity of receptors for Ran-GTP is widely divergent. {yields} Dissociation constants differ for three orders of magnitude. {yields} The cellular concentration of yeast Ran is not limiting. -- Abstract: Cargos destined to enter or leave the cell nucleus are typically transported by receptors of the importin {beta} family to pass the nuclear pore complex. The yeast Saccharomyces cerevisiae comprises 14 members of this protein family, which can be divided in importins and exportins. The Ran GTPase regulates the association and dissociation of receptors and cargos as well as the transport direction through the nuclear pore. All receptors bind to Ran exclusively in its GTP-bound state and this event is restricted to the nuclear compartment. We determined the Ran-GTP binding properties of all yeast transport receptors by biosensor measurements and observed that the affinity of importins for Ran-GTP differs significantly. The dissociation constants range from 230 pM to 270 nM, which is mostly based on a variability of the off-rate constants. The divergent affinity of importins for Ran-GTP suggests the existence of a novel mode of nucleocytoplasmic transport regulation. Furthermore, the cellular concentration of {beta}-receptors and of other Ran-binding proteins was determined. We found that the number of {beta}-receptors altogether about equals the amounts of yeast Ran, but Ran-GTP is not limiting in the nucleus. The implications of our results for nucleocytoplasmic transport mechanisms are discussed.

  3. Analysis of Fade Detection and Compensation Experimental Results in a Ka-Band Satellite System. Degree awarded by Akron Univ., May 2000

    NASA Technical Reports Server (NTRS)

    Johnson, Sandra

    2001-01-01

    The frequency bands being used for new satellite communication systems are constantly increasing to accommodate the requirements for additional capacity. At these higher frequencies, propagation impairments that did not significantly affect the signal at lower frequencies begin to have considerable impact. In Ka-band, the next logical commercial frequency band to be used for satellite communication, attenuation of the signal due to rain is a primary concern. An experimental satellite built by NASA, the Advanced Communication Technology Satellite (ACTS), launched in September 1993, is the first US communication satellite operating in the Ka-band. In addition to higher carrier frequencies, a number of other new technologies, including onboard baseband processing, multiple beam antennas, and rain fade detection and compensation techniques, were designed into the ACTS. Verification experiments have been conducted since the launch to characterize the new technologies. The focus of this thesis is to describe and validate the method used by the ACTS Very Small Aperture Terminal (VSAT) ground stations in detecting the presence of fade in the communication signal and to adaptively compensate for it by the addition of burst rate reduction and forward error correction. Measured data obtained from the ACTS program is used to validate the compensation technique. In this thesis, models in MATLAB are developed to statistically characterize the increased availability achieved by the compensation techniques in terms of the bit error rate time enhancement factor. Several improvements to the ACTS technique are discussed and possible implementations for future Ka-band systems are also presented.

  4. Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.

    PubMed

    Broeker, Nina K; Gohlke, Ulrich; Müller, Jürgen J; Uetrecht, Charlotte; Heinemann, Udo; Seckler, Robert; Barbirz, Stefanie

    2013-01-01

    Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold.

  5. Henry's law constants of some environmentally important aldehydes

    SciTech Connect

    Betterton, E.A.; Hoffmann, M.R.

    1988-12-01

    The Henry's law constants of seven aldehydes have been determined as a function of temperature by bubble-column and by head-space techniques. The compounds were chosen for their potential importance in the polluted troposphere and to allow structure-reactivity patterns to be investigated. The results (at 25/degree/C) are as follows (in units of M atm/sup /minus/1/): chloral, 3.44 /times/ 10/sup 5/; glyoxal, greater than or equal to3 /times/ 10/sup 5/; methylglyoxal, 3.71 /times/ 10/sup 3/; formaldehyde, 2.97 /times/ 10/sup 3/; benzaldehyde, 3.74 /times/ 10/sup 1/; hydroxyacetaldehyde, 4.14 /times/ 10/sup 4/; acetaldehyde, 1.14 /times/ 10/sup 1/. A plot of Taft's parameter, ..sigma..sigma*, vs log H* (the apparent Henry's law constant) gives a straight line with a slope of 1.72. H* for formaldehyde is anomalously high, as expected, but the extremely high value for hydroxyacetaldehyde was unexpected and may indicate that ..cap alpha..-hydroxy-substituted aldehydes could have an usually high affinity for the aqueous phase. The intrinsic Henry's law constants, H, corrected for hydration, do not show a clear structure-reactivity pattern for this series of aldehydes.

  6. Cyclone Xaver seen by SARAL/AltiKa

    NASA Astrophysics Data System (ADS)

    Scharroo, Remko; Fenoglio, Luciana; Annunziato, Alessandro

    2014-05-01

    During the first week of December 2013, Cyclone Xaver pounded the coasts and the North Sea. On 6 December, all along the Wadden Sea, the barrier islands along the north of the Netherlands and the northwest of Germany experienced record storm surges. We show a comparison of the storm surge measured by the radar altimeter AltiKa on-board the SARAL satellite and various types of in-situ data and models. Two tide gauges along the German North Sea coast, one in the southern harbour of the island of Helgoland and one on an offshore lighthouse Alte Weser, confirmed that the storm drove sea level to about three meters above the normal tide level. Loading effects during the storm are also detected by the GPS measurements at several tide gauge stations. The altimeter in the mean time shows that the storm surge was noticeable as far as 400 km from the coast. The altimeter measured wind speeds of 20 m/s nearly monotonically throughout the North Sea. An offshore anemometer near the island of Borkum corroborated this value. A buoy near the FINO1 offshore platform measured wave heights of 8 m, matching quite well the measurements from the altimeter, ranging from 6 m near the German coast to 12 m further out into the North Sea. Furthermore we compare the altimeter-derived and in-situ sea level, wave height and wind speed products with outputs from the Operation Circulation and Forecast model of the Bundesamt für Seeschifffahrt und Hydrographie (BSH) and with a global storm surge forecast and inundation model of the Joint Research Centre (JRC) of the European Commission. The Operational circulation model of BSH (BSHcmod) and its component, the surge model (BSHsmod), perform daily predictions for the next 72 hours based on the meteorological model of the Deutsche Wetterdienst (DWD). The JRC Storm Surge Calculation System is a new development that has been established at the JRC in the framework of the Global Disasters Alerts and Coordination System (GDACS). The system uses

  7. Studying NASA's Transition to Ka-Band Communications for Low Earth Orbit

    NASA Technical Reports Server (NTRS)

    Chelmins, David; Reinhart, Richard; Mortensen, Dale; Welch, Bryan; Downey, Joseph; Evans, Mike

    2014-01-01

    As the S-band spectrum becomes crowded, future space missions will need to consider moving command and telemetry services to Ka-band. NASAs Space Communications and Navigation (SCaN) Testbed provides a software-defined radio (SDR) platform that is capable of supporting investigation of this service transition. The testbed contains two S-band SDRs and one Ka-band SDR. Over the past year, SCaN Testbed has demonstrated Ka-band communications capabilities with NASAs Tracking and Data Relay Satellite System (TDRSS) using both open- and closed-loop antenna tracking profiles. A number of technical areas need to be addressed for successful transition to Ka-band. The smaller antenna beamwidth at Ka-band increases the criticality of antenna pointing, necessitating closed loop tracking algorithms and new techniques for received power estimation. Additionally, the antenna pointing routines require enhanced knowledge of spacecraft position and attitude for initial acquisition, versus an S-band antenna. Ka-band provides a number of technical advantages for bulk data transfer. Unlike at S-band, a larger bandwidth may be available for space missions, allowing increased data rates. The potential for high rate data transfer can also be extended for direct-to-ground links through use of variable or adaptive coding and modulation. Specific examples of Ka-band research from SCaN Testbeds first year of operation will be cited, such as communications link performance with TDRSS, and the effects of truss flexure on antenna pointing.

  8. Standard Observing Bands: Is Now the Time to Replace S/X with X/Ka?

    NASA Astrophysics Data System (ADS)

    Jacobs, Christopher S.; Lanyi, G. E.; Naudet, C. J.

    2004-06-01

    In this paper we will argue that the VLBI community should be developing a road map to transition from S/X to simultaneous X and Ka-band (32 GHz) observations. There are both negative and positive reasons for planning such a transition. On the negative side, we will outline concerns that S-band observations may be headed toward obsolescence. On the positive side, we will refer to evidence that X/Ka has potential for providing a more stable reference frame than S/X. We will propose timetables for a transition to X/Ka observing starting from the current status of X/Ka and plans that are now taking shape. First X/Ka fringes were obtained in 2001 with the Deep Space Network. Future plans will be discussed including a proposed X/Ka-band upgrade to the VLBA. Lastly, we will consider the need for a period of overlap between S/X and X/Ka so that the long and rich history of astrometric and geodetic VLBI is not compromised.

  9. Standard Observing Bands: Is Now the Time to Replace S/X with X/Ka?

    NASA Technical Reports Server (NTRS)

    Jacobs, C. S.; Lanyi, G. E.; Naudet, C. J.

    2004-01-01

    In this paper we will argue that the VLBI community should be developing a road map to transition from S/X to simultaneous X and Ka-band (32 GHz) observations. There are both negative and positive reasons for planning such a transition. On the negative side, we will outline concerns that S-band observations may be headed toward obsolescence. On the positive side, we will refer to evidence that X/Ka has potential for providing a more stable reference frame than S/X. We will propose timetables for a transition to X/Ka observing starting from the current status of X/Ka and plans that are now taking shape. First X/Ka fringes were obtained in 2001 with the Deep Space Network. Future plans will be discussed including a proposed X/Ka-band upgrade to the VLBA. Lastly, we will consider the need for a period of overlap between S/X and X/Ka so that the long and rich history of astrometric and geodetic VLBI is not compromised.

  10. Studying NASA's Transition to Ka-Band Communications for Low Earth Orbit

    NASA Technical Reports Server (NTRS)

    Chelmins, David T.; Reinhart, Richard C.; Mortensen, Dale; Welch, Bryan; Downey, Joseph; Evans, Michael

    2014-01-01

    As the S-band spectrum becomes crowded, future space missions will need to consider moving command and telemetry services to Ka-band. NASA's Space Communications and Navigation (SCaN) Testbed provides a software-defined radio (SDR) platform that is capable of supporting investigation of this service transition. The testbed contains two S-band SDRs and one Ka-band SDR. Over the past year, SCaN Testbed has demonstrated Ka-band communications capabilities with NASAs Tracking and Data Relay Satellite System (TDRSS) using both open- and closed-loop antenna tracking profiles. A number of technical areas need to be addressed for successful transition to Ka-band. The smaller antenna beamwidth at Ka-band increases the criticality of antenna pointing, necessitating closed loop tracking algorithms and new techniques for received power estimation. Additionally, the antenna pointing routines require enhanced knowledge of spacecraft position and attitude for initial acquisition, versus an S-band antenna. Ka-band provides a number of technical advantages for bulk data transfer. Unlike at S-band, a larger bandwidth may be available for space missions, allowing increased data rates. The potential for high rate data transfer can also be extended for direct-to-ground links through use of variable or adaptive coding and modulation. Specific examples of Ka-band research from SCaN Testbeds first year of operation will be cited, such as communications link performance with TDRSS, and the effects of truss flexure on antenna pointing.

  11. Coeval ages of Australasian, Central American and Western Canadian tektites reveal multiple impacts 790 ka ago

    NASA Astrophysics Data System (ADS)

    Schwarz, Winfried H.; Trieloff, Mario; Bollinger, Klemens; Gantert, Niklas; Fernandes, Vera A.; Meyer, Hans-Peter; Povenmire, Hal; Jessberger, Elmar K.; Guglielmino, Massimo; Koeberl, Christian

    2016-04-01

    High resolution 40Ar-39Ar step heating dating of australites and indochinites, representing a large area of the Australasian strewn field, and more recently discovered tektite-like glasses from Central America (Belize) and Western Canada, were carried out. Precise plateau ages were obtained in all cases, yielding indistinguishable ages of 789 ± 9 ka for four australites, 783 ± 5 ka for four indochinites, 783 ± 17 ka for one Western Canadian and 769 ± 16 ka for one Belize impact glass. Concerning major elements and REEs, australites and the Western Canadian impact glass are indistinguishable. If the Western Canadian sample was transported by impact ejection and belongs to the Australasian strewn field, this implies extremely far ballistic transport of 9000 km distance, assuming a source crater in southern Asia. The distinct major element and REE composition of the Belize impact glass suggests formation in another separate impact event. We conclude that the Australasian/Western Canadian impact glasses formed 785 ± 7 ka ago in a single event and Belize impact glass in a separate event 769 ± 16 ka ago. The two impact events forming these two strewn fields occurred remarkably closely related in time, i.e., separated by <30 ka.

  12. KA-SB: from data integration to large scale reasoning

    PubMed Central

    Roldán-García, María del Mar; Navas-Delgado, Ismael; Kerzazi, Amine; Chniber, Othmane; Molina-Castro, Joaquín; Aldana-Montes, José F

    2009-01-01

    Background The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. Methods KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning). Results In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts. Conclusion These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool , which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases. PMID:19796402

  13. Resilient FTS3 service at GridKa

    NASA Astrophysics Data System (ADS)

    Hartmann, T.; Bubeliene, J.; Hoeft, B.; Obholz, L.; Petzold, A.; Wisniewski, K.

    2015-12-01

    The FTS (File Transfer Service) service provides a transfer job scheduler to distribute and replicate vast amounts of data over the heterogeneous WLCG infrastructures. Compared to the channel model of the previous versions, the most recent version of FTS simplifies and improves the flexibility of the service while reducing the load to the service components. The improvements allow to handle a higher number of transfers with a single FTS3 setup. Covering now continent-wide transfers compared to the previous version, whose installations handled only transfers within specific clouds, a resilient system becomes even more necessary with the increased number of depending users. Having set up a FTS3 services at the German T1 site GridKa at KIT in Karlsruhe, we present our experiences on the preparations for a high-availability FTS3 service. Trying to avoid single points of failure, we rely on a database cluster as fault tolerant data back-end and the FTS3 service deployed on an own cluster setup to provide a resilient infrastructure for the users. With the database cluster providing a basic resilience for the data back-end, we ensure on the FTS3 service level a consistent and reliable database access through a proxy solution. On each FTS3 node a HAproxy instance is monitoring the integrity of each database node and distributes database queries over the whole cluster for load balancing during normal operations; in case of a broken database node, the proxy excludes it transparently to the local FTS3 service. The FTS3 service itself consists of a main and a backup instance, which takes over the identity of the main instance, i.e., IP, in case of an error using a CTDB (Cluster Trivial Database) infrastructure offering clients a consistent service.

  14. A 75 ka Stalagmite Paleoclimate Record from Northern Venezuela

    NASA Astrophysics Data System (ADS)

    Retrum, J. B.; Gonzalez, L. A.; Edwards, R.; Tincher, S. M.; Cheng, H.; Urbani, F.

    2011-12-01

    A stalagmite collected from Cueva Zarraga in the northern Venezuelan Andes was analyzed to determine local paleoclimatic history and help examine climate change in the Caribbean. Ages were determined by U/Th disequilibrium and the stalagmite shows a nearly complete record for ~ 75 ka. Two significant periods of non-deposition have been identified. The first period ranges between the Last Glacial Maximum at 19,820 ± 149 cal yr BP and a brief resumption of stalagmite growth at 15,409 ± 747 cal yr BP, likely representing the Bølling-Allerød interstadial. After the brief period of deposition, growth does not resume unil the Holocene at 10,408 ± 78 cal yr BP. Carbon and oxygen isotopes show a major depletion shift from the last glacial period to the Holocene, suggesting warmer and wetter conditions during the Holocene. The oxygen isotope depletion shift is also seen in the Cariaco Basin foraminifera record off the northern coast of Venezuela. While tempting to attribute δ13C depletion to decrease of the C4 plant contribution, there is no evidence that the area experience major vegetation changes. We attribute the δ13C depletion to enhanced recycling of soil CO2 resulting from canopy effects. Today, Cueva Zarraga is at the northern extent of the Inter-Tropical Convergence Zone (ITCZ). The cooler and drier conditions of the last glacial period suggest a southern displacement of the ITCZ. The close proximity of Cueva Zarraga to Cariaco Basin may allow for a high resolution tropical terrestrial and oceanic climatic response comparison.

  15. Latest European coelacanth shows Gondwanan affinities.

    PubMed

    Cavin, Lionel; Forey, Peter L; Buffetaut, Eric; Tong, Haiyan

    2005-06-22

    The last European fossil occurrence of a coelacanth is from the Mid-Cretaceous of the English Chalk (Turonian, 90 million years ago). Here, we report the discovery of a coelacanth from Late Cretaceous non-marine rocks in southern France. It consists of a left angular bone showing structures that imply close phylogenetic affinities with some extinct Mawsoniidae. The closest relatives are otherwise known from Cretaceous continental deposits of southern continents and suggest that the dispersal of freshwater organisms from Africa to Europe occurred in the Late Cretaceous.

  16. On the structure of self-affine convex bodies

    SciTech Connect

    Voynov, A S

    2013-08-31

    We study the structure of convex bodies in R{sup d} that can be represented as a union of their affine images with no common interior points. Such bodies are called self-affine. Vallet's conjecture on the structure of self-affine bodies was proved for d = 2 by Richter in 2011. In the present paper we disprove the conjecture for all d≥3 and derive a detailed description of self-affine bodies in R{sup 3}. Also we consider the relation between properties of self-affine bodies and functional equations with a contraction of an argument. Bibliography: 10 titles.

  17. Measuring an antibody affinity distribution molecule by molecule.

    PubMed

    Temirov, Jamshid P; Bradbury, Andrew R M; Werner, James H

    2008-11-15

    Single molecule fluorescence microscopy was used to observe the binding and unbinding of hapten decorated quantum dots to individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  18. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  19. Metal-affinity separations: A new dimension in protein processing

    SciTech Connect

    Arnold, F.H. )

    1991-02-01

    Rapid growth in the preparative and high-resolution analytical applications of metal-affinity chromatography demonstrate the appeal of metal recognition as a basis for protein separations. Stable, inexpensive chelated metals effectively mimic biospecific interactions, providing selective ligands for protein binding. This article reviews recent progress in understanding the mechanisms of metal-protein recognition that underlie metal-affinity separations. Also discussed are schemes for integrating metal-affinity purifications into the expression and bioprocessing of recombinant proteins. Promising future developments include new metal-affinity processes for analytical and preparative-scale separations and a range of techniques for enhancing the selectivity of metal-affinity separations.

  20. Asympotics with positive cosmological constant

    NASA Astrophysics Data System (ADS)

    Bonga, Beatrice; Ashtekar, Abhay; Kesavan, Aruna

    2014-03-01

    Since observations to date imply that our universe has a positive cosmological constant, one needs an extension of the theory of isolated systems and gravitational radiation in full general relativity from the asymptotically flat to asymptotically de Sitter space-times. In current definitions, one mimics the boundary conditions used in asymptotically AdS context to conclude that the asymptotic symmetry group is the de Sitter group. However, these conditions severely restricts radiation and in fact rules out non-zero flux of energy, momentum and angular momentum carried by gravitational waves. Therefore, these formulations of asymptotically de Sitter space-times are uninteresting beyond non-radiative spacetimes. The situation is compared and contrasted with conserved charges and fluxes at null infinity in asymptotically flat space-times.

  1. Henry's law constants of polyols

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Müller, J.-F.

    2014-12-01

    Henry's law constants (HLC) are derived for several polyols bearing between 2 and 6 hydroxyl groups, based on literature data for water activity, vapour pressure and/or solubility. While deriving HLC and depending on the case, also infinite dilution activity coefficients (IDACs), solid state vapour pressures or activity coefficient ratios are obtained as intermediate results. An error analysis on the intermediate quantities and the obtained HLC is included. For most compounds, these are the first values reported, while others compare favourably with literature data in most cases. Using these values and those from a previous work (Compernolle and Müller, 2014), an assessment is made on the partitioning of polyols, diacids and hydroxy acids to droplet and aqueous aerosol.

  2. Philicities, Fugalities, and Equilibrium Constants.

    PubMed

    Mayr, Herbert; Ofial, Armin R

    2016-05-17

    The mechanistic model of Organic Chemistry is based on relationships between rate and equilibrium constants. Thus, strong bases are generally considered to be good nucleophiles and poor nucleofuges. Exceptions to this rule have long been known, and the ability of iodide ions to catalyze nucleophilic substitutions, because they are good nucleophiles as well as good nucleofuges, is just a prominent example for exceptions from the general rule. In a reaction series, the Leffler-Hammond parameter α = δΔG(⧧)/δΔG° describes the fraction of the change in the Gibbs energy of reaction, which is reflected in the change of the Gibbs energy of activation. It has long been considered as a measure for the position of the transition state; thus, an α value close to 0 was associated with an early transition state, while an α value close to 1 was considered to be indicative of a late transition state. Bordwell's observation in 1969 that substituent variation in phenylnitromethanes has a larger effect on the rates of deprotonation than on the corresponding equilibrium constants (nitroalkane anomaly) triggered the breakdown of this interpretation. In the past, most systematic investigations of the relationships between rates and equilibria of organic reactions have dealt with proton transfer reactions, because only for few other reaction series complementary kinetic and thermodynamic data have been available. In this Account we report on a more general investigation of the relationships between Lewis basicities, nucleophilicities, and nucleofugalities as well as between Lewis acidities, electrophilicities, and electrofugalities. Definitions of these terms are summarized, and it is suggested to replace the hybrid terms "kinetic basicity" and "kinetic acidity" by "protophilicity" and "protofugality", respectively; in this way, the terms "acidity" and "basicity" are exclusively assigned to thermodynamic properties, while "philicity" and "fugality" refer to kinetics

  3. Avoiding degenerate coframes in an affine gauge approach to quantum gravity

    SciTech Connect

    Mielke, E.W.; McCrea, J.D.; Ne`eman, Y.; Hehl, F.W.

    1993-04-01

    This report discusses the following concepts on quantum gravity: The affine gauge approach; affine gauge transformations versus active differomorphisms; affine gauge approach to quantum gravity with topology change.

  4. High Affinity Macrocycle Threading by a Near-Infrared Croconaine Dye with Flanking Polymer Chains

    PubMed Central

    Liu, Wenqi; Peck, Evan M.; Smith, Bradley D.

    2016-01-01

    Croconaine dyes have narrow and intense absorption bands at ~800 nm, very weak fluorescence, and high photostabilities, which combine to make them very attractive chromophores for absorption-based imaging or laser heating technologies. The physical supramolecular properties of croconaine dyes have rarely been investigated, especially in water. This study focuses on a molecular threading process that encapsulates a croconaine dye inside a tetralactam macrocycle in organic or aqueous solvent. Macrocycle association and rate constant data are reported for a series of croconaine structures with different substituents attached to the ends of the dye. The association constants were highest in water (Ka ~109 M−1), and the threading rate constants (kon) increased in the solvent order H2O > MeOH > CHCl3. Systematic variation of croconaine substituents located just outside the croconaine/macrocycle complexation interface hardly changed Ka but had a strong influence on kon. A croconaine dye with N-propyl groups at each end of the structure exhibited a desirable mixture of macrocycle threading properties; that is, there was rapid and quantitative croconaine/macrocycle complexation at relatively high concentrations in water, and no dissociation of the pre-assembled complex when it was diluted into a solution of fetal bovine serum, even after laser induced photothermal heating of the solution. The combination of favorable near-infrared absorption properties and tunable mechanical stability makes threaded croconaine/macrocycle complexes very attractive as molecular probes or as supramolecular composites for various applications in absorption-based imaging or photothermal therapy. PMID:26807599

  5. A Ka-band (32 GHz) beacon link experiment (KABLE) with Mars Observer

    NASA Technical Reports Server (NTRS)

    Riley, A. L.; Hansen, D. M.; Mileant, A.; Hartop, R. W.

    1987-01-01

    A proposal for a Ka-Band (32 GHz) Link Experiment (KABLE) with the Mars Observer mission was submitted to NASA. The experiment will rely on the fourth harmonic of the spacecraft X-band transmitter to generate a 33.6 GHz signal. The experiment will rely also on the Deep Space Network (DSN) receiving station equipped to simultaneously receive X- and Ka-band signals. The experiment will accurately measure the spacecraft-to-Earth telecommunication link performance at Ka-band and X-band (8.4 GHz).

  6. The Palaeoclimate of Wadi Shati, Libyan Sahara: the last 130 ka

    NASA Astrophysics Data System (ADS)

    Drake, Nick A.; Lem, Rachel E.; Armitage, Simon J.; White, Kevin H.; El-Hawat, Ahmed; Salem, Mustafa J.; Hounslow, Mark; Franke, Jan

    2014-05-01

    The Fezzan region of Libya forms a large closed basin that contains a wealth of ancient palaeolake and riverine sediments indicative of past humidity in the central Sahara. We have used remote sensing, DEM analysis and Ultra Ground Penetrating Radar to map these features and have dated them using OSL and radiocarbon methods. Results suggest humid conditions during both MIS 5 and the Holocene with larger lakes and more extensive river systems being present during MIS 5 suggestive of greater humidity at this time. A 4m core was collected from Holocene sediments of the largest lake found in the region (1200 km2 during MIS5 and 660 km2 during the Holocene). Core sediments were dated using OSL and analysed using XRF, Ion Chromatography, Laser Granulometry and chemical extractions for ostracods, diatoms, pollen and phytoliths. The base of the core is dominated by clays deposited in a perennial lake environment from 7.75 ka to 6.6 ka. Gypsum deposition started at about 6.5 ka indicating a more arid environment. Four clay layers are found amongst the gypsum from 6.3 to 6.25 ka, 6.2 to 6.1, 6.0 to 5.8 and 5.7-5.6 ka suggests that aridification was not a sudden event, but consisted of a series of arid/humid oscillations before the lake finally desiccated just before 5 ka. No pollen, diatoms or ostracods are preserved in the sediments but phytoliths were present. Both tree and grass phytoliths were found in lower parts of the core, suggesting a wooded savannah environment from 7.75 to about 7 ka. Trees decline and grass increases up the core, signifying an increasingly arid environment. By the time the first gypsum bed is deposited at about 6.5 ka trees have disappeared and grass dominates. These results do not support the hypothesis of a sudden aridification of the Sahara at 4.9 ka and instead suggest that in the Fezzan region a gradual aridification had started by 7.75 ka and that the climate oscillated during the lake desiccation that started at 6.5 ka and was complete by

  7. A Novel Ku-Band/Ka-Band and Ka-Band/E-Band Multimode Waveguide Couplers for Power Measurement of Traveling-Wave Tube Amplifier Harmonic Frequencies

    NASA Technical Reports Server (NTRS)

    Wintucky, Edwin G.; Simons, Rainee N.

    2015-01-01

    This paper presents the design, fabrication and test results for a novel waveguide multimode directional coupler (MDC). The coupler, fabricated from two dissimilar frequency band waveguides, is capable of isolating power at the second harmonic frequency from the fundamental power at the output port of a traveling-wave tube (TWT) amplifier. Test results from proof-of-concept demonstrations are presented for a Ku-band/Ka-band MDC and a Ka-band/E-band MDC. In addition to power measurements at harmonic frequencies, a potential application of the MDC is in the design of a satellite borne beacon source for atmospheric propagation studies at millimeter-wave (mm-wave) frequencies (Ka-band and E-band).

  8. Probing the affinity of polyanions for acidic fibroblast growth factor by unfolding kinetics.

    PubMed

    Mach, H; Middaugh, C R

    1994-02-15

    The relationship between ligand-protein affinity and the extent of protein stabilization induced by such interactions has been investigated using the binding of polyanions to acidic fibroblast growth factor (aFGF) as a model system. It was found that the experimentally observed unfolding rate constant of aFGF consists of two components: one equal to the unfolding rate constant of the aFGF-ligand complex and the other the product of the unfolding rate constant of free aFGF, the aFGF-ligand dissociation constant (Kd), and the reciprocal of the molar ligand concentration. This reflects the presence of two possible unfolding pathways: at high ligand excess dissociation is suppressed and slow unfolding of the aFGF-ligand complex itself prevails. When lower concentrations of ligand allows equilibrium-driven appearance of free aFGF, a more rapid unfolding of dissociated protein predominates. Existence of a steady state of dissociated aFGF undergoing unfolding was demonstrated by computer simulation of the elementary events, using experimentally determined rate constants. The potential applications of such simulations are outlined. An equation allowing estimation of dissociation constants from equilibrium denaturation curves obtained in the presence of a varying amount of ligand is also proposed. In addition, determination of initial unfolding rates in the presence of excess protein permits the the stoichiometry of the interaction to be determined.

  9. Determination of thermodynamic values of acidic dissociation constants and complexation constants of profens and their utilization for optimization of separation conditions by Simul 5 Complex.

    PubMed

    Riesová, Martina; Svobodová, Jana; Ušelová, Kateřina; Tošner, Zdeněk; Zusková, Iva; Gaš, Bohuslav

    2014-10-17

    In this paper we determine acid dissociation constants, limiting ionic mobilities, complexation constants with β-cyclodextrin or heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin, and mobilities of resulting complexes of profens, using capillary zone electrophoresis and affinity capillary electrophoresis. Complexation parameters are determined for both neutral and fully charged forms of profens and further corrected for actual ionic strength and variable viscosity in order to obtain thermodynamic values of complexation constants. The accuracy of obtained complexation parameters is verified by multidimensional nonlinear regression of affinity capillary electrophoretic data, which provides the acid dissociation and complexation parameters within one set of measurements, and by NMR technique. A good agreement among all discussed methods was obtained. Determined complexation parameters were used as input parameters for simulations of electrophoretic separation of profens by Simul 5 Complex. An excellent agreement of experimental and simulated results was achieved in terms of positions, shapes, and amplitudes of analyte peaks, confirming the applicability of Simul 5 Complex to complex systems, and accuracy of obtained physical-chemical constants. Simultaneously, we were able to demonstrate the influence of electromigration dispersion on the separation efficiency, which is not possible using the common theoretical approaches, and predict the electromigration order reversals of profen peaks. We have shown that determined acid dissociation and complexation parameters in combination with tool Simul 5 Complex software can be used for optimization of separation conditions in capillary electrophoresis.

  10. Practical strategies for the evaluation of high-affinity protein/nucleic acid interactions.

    PubMed

    Altschuler, Sarah E; Lewis, Karen A; Wuttke, Deborah S

    2013-01-01

    The quantitative evaluation of binding interactions between proteins and nucleic acids is highly sensitive to a variety of experimental conditions. Optimization of these conditions is critical for obtaining high quality, reproducible data, particularly in the context of very high affinity interactions. Here, we discuss the practical considerations involved in optimizing the apparent binding constant of an interaction as measured by two common quantitative assays, electrophoretic mobility shift assay and double-filter binding when measuring extremely tight protein/nucleic acid interactions with sub-nanomolar binding affinities. We include specific examples from two telomere end-binding protein systems, Schizo -saccharomyces pombe Pot1 and Saccharomyces cerevisiae Cdc13, to demonstrate potential experimental pitfalls and some useful strategies for optimization.

  11. Practical strategies for the evaluation of high-affinity protein/nucleic acid interactions

    PubMed Central

    Altschuler, Sarah E.; Lewis, Karen A.; Wuttke, Deborah S.

    2014-01-01

    The quantitative evaluation of binding interactions between proteins and nucleic acids is highly sensitive to a variety of experimental conditions. Optimization of these conditions is critical for obtaining high quality, reproducible data, particularly in the context of very high affinity interactions. Here, we discuss the practical considerations involved in optimizing the apparent binding constant of an interaction as measured by two common quantitative assays, electrophoretic mobility shift assay and double-filter binding when measuring extremely tight protein/nucleic acid interactions with sub-nanomolar binding affinities. We include specific examples from two telomere end-binding protein systems, Schizo -saccharomyces pombe Pot1 and Saccharomyces cerevisiae Cdc13, to demonstrate potential experimental pitfalls and some useful strategies for optimization. PMID:25197549

  12. Relationship of nonreturn rates of dairy bulls to binding affinity of heparin to sperm

    SciTech Connect

    Marks, J.L.; Ax, R.L.

    1985-08-01

    The binding of the glycosaminoglycan (3H) heparin to bull spermatozoa was compared with nonreturn rates of dairy bulls. Semen samples from five bulls above and five below an average 71% nonreturn rate were used. Samples consisted of first and second ejaculates on a single day collected 1 d/wk for up to 5 consecutive wk. Saturation binding assays using (TH) heparin were performed to quantitate the binding characteristics of each sample. Scatchard plot analyses indicated a significant difference in the binding affinity for (TH) heparin between bulls of high and low fertility. Dissociation constants were 69.0 and 119.3 pmol for bulls of high and low fertility, respectively. In contrast, the number of binding sites for (TH) heparin did not differ significantly among bulls. Differences in binding affinity of (TH) heparin to bull sperm might be used to predict relative fertility of dairy bulls.

  13. Structure-based Design of Peptides with High Affinity and Specificity to HER2 Positive Tumors

    PubMed Central

    Geng, Lingling; Wang, Zihua; Yang, Xiaoliang; Li, Dan; Lian, Wenxi; Xiang, Zhichu; Wang, Weizhi; Bu, Xiangli; Lai, Wenjia; Hu, Zhiyuan; Fang, Qiaojun

    2015-01-01

    To identify peptides with high affinity and specificity against human epidermal growth factor receptor 2 (HER2), a series of peptides were designed based on the structure of HER2 and its Z(HER2:342) affibody. By using a combination protocol of molecular dynamics modeling, MM/GBSA binding free energy calculations, and binding free energy decomposition analysis, two novel peptides with 27 residues, pep27 and pep27-24M, were successfully obtained. Immunocytochemistry and flow cytometry analysis verified that both peptides can specifically bind to the extracellular domain of HER2 protein at cellular level. The Surface Plasmon Resonance imaging (SPRi) analysis showed that dissociation constants (KD) of these two peptides were around 300 nmol/L. Furthermore, fluorescence imaging of peptides against nude mice xenografted with SKBR3 cells indicated that both peptides have strong affinity and high specificity to HER2 positive tumors. PMID:26284145

  14. Preorganized Peptide Scaffolds as Mimics of Phosphorylated Proteins Binding Sites with a High Affinity for Uranyl.

    PubMed

    Starck, Matthieu; Sisommay, Nathalie; Laporte, Fanny A; Oros, Stéphane; Lebrun, Colette; Delangle, Pascale

    2015-12-01

    Cyclic peptides with two phosphoserines and two glutamic acids were developed to mimic high-affinity binding sites for uranyl found in proteins such as osteopontin, which is believed to be a privileged target of this ion in vivo. These peptides adopt a β-sheet structure that allows the coordination of the latter amino acid side chains in the equatorial plane of the dioxo uranyl cation. Complementary spectroscopic and analytical methods revealed that these cyclic peptides are efficient uranyl chelating peptides with a large contribution from the phosphorylated residues. The conditional affinity constants were measured by following fluorescence tryptophan quenching and are larger than 10(10) at physiological pH. These compounds are therefore promising models for understanding uranyl chelation by proteins, which is relevant to this actinide ion toxicity. PMID:26583259

  15. Phosphatidylserine Reversibly Binds Cu2+ with Extremely High Affinity

    PubMed Central

    Monson, Christopher F.; Cong, Xiao; Robison, Aaron; Pace, Hudson P.; Liu, Chunming; Poyton, Matthew F.; Cremer, Paul S.

    2012-01-01

    Phosphatidylserine (PS) embedded within supported lipid bilayers (SLBs) was found to bind Cu2+ from solution with extraordinarily high affinity. In fact, the equilibrium dissociation constant was in the femtomolar range. The resulting complex formed in a 1:2 Cu2+ to PS ratio and quenches a broad spectrum of lipid-bound fluorophores in a reversible and pH-dependent fashion. At acidic pH values, the fluorophores were almost completely unquenched, while at basic pH values significant quenching (85–90%) was observed. The pH at which the transition occurred was dependent on the PS concentration and ranged from approximately pH 5 to 8. The quenching kinetics was slow at low Cu2+ concentrations and basic values pH (up to several hours), while the unquenching reaction was orders of magnitude more rapid upon lowering the pH. This was consistent with diffusion limited complex formation at basic pH, but rapid dissociation under acidic conditions. The tight binding of Cu2+ to PS may have physiological consequences under certain circumstances. PMID:22548290

  16. Limited proteolysis for assaying ligand binding affinities of nuclear receptors.

    PubMed

    Benkoussa, M; Nominé, B; Mouchon, A; Lefebvre, B; Bernardon, J M; Formstecher, P; Lefebvre, P

    1997-01-01

    The binding of natural or synthetic ligands to nuclear receptors is the triggering event leading to gene transcription activation or repression. Ligand binding to the ligand binding domain of these receptors induces conformational changes that are evidenced by an increased resistance of this domain to proteases. In vitro labeled receptors were incubated with various synthetic or natural agonists or antagonists and submitted to trypsin digestion. Proteolysis products were separated by SDS-PAGE and quantified. The amount of trypsin-resistant fragments was proportional to receptor occupancy by the ligand, and allowed the determination of dissociation constants (kDa). Using the wild-type or mutated human retinoic acid receptor alpha as a model, kDa values determined by classical competition binding assays using tritiated ligands are in agreement with those measured by the proteolytic assay. This method was successfully extended to human retinoic X receptor alpha, glucocorticoid receptor, and progesterone receptor, thus providing a basis for a new, faster assay to determine simultaneously the affinity and conformation of receptors when bound to a given ligand.

  17. Glass transition of two-dimensional 80-20 Kob-Andersen model at constant pressure

    NASA Astrophysics Data System (ADS)

    Li, D.; Xu, H.; Wittmer, J. P.

    2016-02-01

    We reconsider numerically the two-dimensional version of the Kob-Andersen model (KA2d) with a fraction of 80% of large spheres. A constant moderate pressure is imposed while the temperature T is systematically quenched from the liquid limit through the glass transition at {{T}\\text{g}}≈ 0.3 down to very low temperatures. Monodisperse Lennard-Jones (mdLJ) bead systems, forming a crystal phase at low temperatures, are used to highlight several features of the KA2d model. As can be seen, e.g. from the elastic shear modulus G(T), determined using the stress-fluctuation formalism, our KA2d model is a good glass-former. A continuous cusp-singularity, G(T)\\propto {{≤ft(1-T/{{T}\\text{g}}\\right)}α} with α ≈ 0.6 , is observed in qualitative agreement with other recent numerical and theoretical work, however in striking conflict with the additive jump discontinuity predicted by mode-coupling theory.

  18. Fatigue damage prognosis using affine arithmetic

    NASA Astrophysics Data System (ADS)

    Gbaguidi, Audrey; Kim, Daewon

    2014-02-01

    Among the essential steps to be taken in structural health monitoring systems, damage prognosis would be the field that is least investigated due to the complexity of the uncertainties. This paper presents the possibility of using Affine Arithmetic for uncertainty propagation of crack damage in damage prognosis. The structures examined are thin rectangular plates made of titanium alloys with central mode I cracks and a composite plate with an internal delamination caused by mixed mode I and II fracture modes, under a harmonic uniaxial loading condition. The model-based method for crack growth rates are considered using the Paris Erdogan law model for the isotropic plates and the delamination growth law model proposed by Kardomateas for the composite plate. The parameters for both models are randomly taken and their uncertainties are considered as defined by an interval instead of a probability distribution. A Monte Carlo method is also applied to check whether Affine Arithmetic (AA) leads to tight bounds on the lifetime of the structure.

  19. Exploring Fluorous Affinity by Liquid Chromatography.

    PubMed

    Catani, Martina; Guzzinati, Roberta; Marchetti, Nicola; Pasti, Luisa; Cavazzini, Alberto

    2015-07-01

    Terms such as "fluorous affinity" and "fluorophilicity" have been used to describe the unique partition and sorption properties often exhibited by highly fluorinated organic compounds, that is molecules rich in sp(3) carbon-fluorine bonds. In this work, we made use of a highly fluorinated stationary phase and a series of benzene derivatives to study the effect of one single perfluorinated carbon on the chromatographic behavior and adsorption properties of molecules. For this purpose, the adsorption equilibria of α,α,α-trifluorotoluene, toluene, and other alkylbenzenes have been studied by means of nonlinear chromatography in a variety of acetonitrile/water eluents. Our results reveal that one single perfluorinated carbon is already enough to induce a drastic change in the adsorption properties of molecules on the perfluorinated stationary phase. In particular, it has been found that adsorption is monolayer if the perfluoroalkyl carbon is present but that, when this unit is missing, molecules arrange as multilayer stack structures. These findings can contribute to the understanding of molecular mechanisms of fluorous affinity. PMID:26047527

  20. Quantification of hydrophobic interaction affinity of colloids

    NASA Astrophysics Data System (ADS)

    Saini, G.; Nasholm, N.; Wood, B. D.

    2009-12-01

    Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.

  1. Climate and hillslope degradation vary in concert; 85 ka to present, eastern Sierra Nevada, CA, USA

    NASA Astrophysics Data System (ADS)

    Madoff, Risa D.; Putkonen, Jaakko

    2016-08-01

    Degradation in the landscape results when the interactions of climate, substrate, and biota dislodge and transport sediment that is mantling landforms. Rates of degradation through time control landform stability and resiliency. Therefore, records of past degradation rates can be used to inform us on how a given landscape responded to significant changes in past climates. For example, climate has varied at many temporal scales, and some of the largest recent shifts enabled the glacial advances and retreats in time scales of 20-100 ka. Therefore, it is reasonable to expect that the rate of landscape degradation has also varied at similar time scales. However, the general hillslope diffusion equation that is commonly used to model cross-profiles of hillslopes on time scales of thousands to tens of thousands of years typically relies on a constant and optimized rate parameter to generate a model cross-profile approximating the current observed landform cross-profile. Using a time-varying diffusivity parameter, we generated three separate degradation scenarios for the Mono Basin moraine in the eastern Sierra Nevada, CA, USA, in order to assess the potential impact of varying past climates on sediment transport. We used published paleoclimate records in the study area and modern rates of surface degradation from climates that correspond broadly to those paleoclimates. The results indicate that, in this case, the climate driven and, therefore, time-dependent degradation model produces a good fit between the modeled and observed landform profiles. Results showed that, when the surface elevations of the reference case (constant optimized diffusivity) were compared through time to the surface elevations of the time-dependent model, the differences were relatively small. The largest deviation was found to occur during the Last Glacial Maximum (LGM). We found that for investigations into the geological effects of climate change in glacial and polar regions, the use of time

  2. Nucleic acid binding affinity of fd gene 5 protein in the cooperative binding mode.

    PubMed

    Bobst, A M; Ireland, J C; Bobst, E V

    1984-02-25

    A sensitive ESR method which allows a direct quantitative determination of nucleic acid binding affinities of proteins under physiologically relevant conditions has been applied to the gene 5 protein of bacteriophage fd. This was achieved with two spin-labeled nucleic acids, (ldT, dT)n and (lA,A)n, which served as macro-molecular spin probes in ESR competition experiments. With the two different macromolecular spin probes, it was possible to determine the relative apparent affinity constants, Kapp, over a large affinity domain. In 20 mM Tris X HCl (pH 8.1), 1 mM sodium EDTA, 0.1 mM dithiothreitol, 10% (w/v) glycerol, 0.05% Triton, and 125 mM NaCl, the following affinity relationship was observed: K(dT)napp = 10(3) KfdDNAapp = 2 X 10(4) K(A)napp = 6.6 X 10(4) KrRNAapp = 1.5 X 10(5) KR17RNAapp. Increasing the [NaCl] from 125 to 200 mM caused considerably less tight binding of gene 5 protein to (lA,A)n, and a typical cooperative binding isotherm was observed, whereas at the lower [NaCl] used for the competition experiments, the binding was essentially stoichiometric. A computer fit of the experimental titration data at 200 mM NaCl gave an intrinsic binding constant, Kint, of 1300 M-1 and a cooperativity factor, omega, of 60 (Kint omega = Kapp) for (lA,A)n.

  3. Is There a Cosmological Constant?

    NASA Technical Reports Server (NTRS)

    Kochanek, Christopher; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    The grant contributed to the publication of 18 refereed papers and 5 conference proceedings. The primary uses of the funding have been for page charges, travel for invited talks related to the grant research, and the support of a graduate student, Charles Keeton. The refereed papers address four of the primary goals of the proposal: (1) the statistics of radio lenses as a probe of the cosmological model (#1), (2) the role of spiral galaxies as lenses (#3), (3) the effects of dust on statistics of lenses (#7, #8), and (4) the role of groups and clusters as lenses (#2, #6, #10, #13, #15, #16). Four papers (#4, #5, #11, #12) address general issues of lens models, calibrations, and the relationship between lens galaxies and nearby galaxies. One considered cosmological effects in lensing X-ray sources (#9), and two addressed issues related to the overall power spectrum and theories of gravity (#17, #18). Our theoretical studies combined with the explosion in the number of lenses and the quality of the data obtained for them is greatly increasing our ability to characterize and understand the lens population. We can now firmly conclude both from our study of the statistics of radio lenses and our survey of extinctions in individual lenses that the statistics of optically selected quasars were significantly affected by extinction. However, the limits on the cosmological constant remain at lambda < 0.65 at a 2-sigma confidence level, which is in mild conflict with the results of the Type la supernova surveys. We continue to find that neither spiral galaxies nor groups and clusters contribute significantly to the production of gravitational lenses. The lack of group and cluster lenses is strong evidence for the role of baryonic cooling in increasing the efficiency of galaxies as lenses compared to groups and clusters of higher mass but lower central density. Unfortunately for the ultimate objective of the proposal, improved constraints on the cosmological constant, the next

  4. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

    PubMed

    Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter

    2016-08-26

    Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach. PMID:27498895

  5. Arginine-82 regulates the pKa of the group responsible for the light-driven proton release in bacteriorhodopsin.

    PubMed Central

    Govindjee, R; Misra, S; Balashov, S P; Ebrey, T G; Crouch, R K; Menick, D R

    1996-01-01

    In wild-type bacteriorhodopsin light-induced proton release occurs before uptake at neutral pH. In contrast, in mutants in which R82 is replaced by a neutral residue (as in R82A and R82Q), only a small fraction of the protons is released before proton uptake at neutral pH; the major fraction is released after uptake. In R82Q the relative amounts of the two types of proton release, "early" (preceding proton uptake) and "late" (following proton uptake), are pH dependent. The main conclusions are that 1) R82 is not the normal light-driven proton release group; early proton release can be observed in the R82Q mutant at higher pH values, suggesting that the proton release group has not been eliminated. 2) R82 affects the pKa of the proton release group both in the unphotolyzed state of the pigment and during the photocycle. In the wild type (in 150 mM salt) the pKa of this group decreases from approximately 9.5 in the unphotolyzed pigment to approximately 5.8 in the M intermediate, leading to early proton release at neutral pH. In the R82 mutants the respective values of pKa of the proton release group in the unphotolyzed pigment and in M are approximately 8 and 7.5 in R82Q (in 1 M salt) and approximately 8 and 6.5 in R82K (in 150 mM KCl). Thus in R82Q the pKa of the proton release group does not decrease enough in the photocycle to allow early proton release from this group at neutral pH. 3) Early proton release in R82Q can be detected as a photocurrent signal that is kinetically distinct from those photocurrents that are due to proton movements from the Schiff base to D85 during M formation and from D96 to the Schiff base during the M-->N transition. 4) In R82Q, at neutral pH, proton uptake from the medium occurs during the formation of O. The proton is released during the O-->bacteriorhodopsin transition, probably from D85 because the normal proton release group cannot deprotonate at this pH. 5) The time constant of early proton release is increased from 85

  6. Negative homotropic cooperativity and affinity heterogeneity: preparation of yeast glyceraldehyde-3-phosphate dehydrogenase with maximal affinity homogeneity.

    PubMed Central

    Gennis, L S

    1976-01-01

    A three-step procedure including affinity chromatography on NAD+-azobenzamidopropyl-Sepharose has been designed for the purification of yeast glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12] with maximized specific activity and maximized homogeneity with respect to affinity for the coenzyme, NAD+.Binding isotherms allow the analysis of cooperativity patterns that disclose both the average ligand affinity in the system and the distribution of ligands among the sites, only for systems with complete affinity homogeneity. The presence of affinity heterogeneity, resulting from multiple oligomeric species differing only in their affinity for coenzyme, gives rise to isotherms which falsely manifest apparent negative cooperativity. A method for distinguishing negative homotropic cooperativity from affinity heterogeneity is suggested. PMID:186779

  7. Characteristics of the interaction of calcium with casein submicelles as determined by analytical affinity chromatography

    SciTech Connect

    Jang, H.D.; Swaisgood, H.E. )

    1990-12-01

    Interaction of calcium with casein submicelles was investigated in CaCl2 and calcium phosphate buffers and with synthetic milk salt solutions using the technique of analytical affinity chromatography. Micelles that had been prepared by size exclusion chromatography with glycerolpropyl controlled-pore glass from fresh raw skim milk that had never been cooled, were dialyzed at room temperature against calcium-free imidazole buffer, pH 6.7. Resulting submicelles were covalently immobilized on succinamidopropyl controlled-pore glass (300-nm pore size). Using 45Ca to monitor the elution retardation, the affinity of free Ca2+ and calcium salt species was determined at temperatures of 20 to 40 degrees C and pH 6.0 to 7.5. Increasing the pH in this range or increasing the temperature strengthened the binding of calcium to submicelles, similar to previous observations with individual caseins. However, the enthalpy change obtained from the temperature dependence was considerably greater than that reported for alpha s1- and beta-caseins. Furthermore, the elution profiles for 45Ca in milk salt solutions were decidedly different from those in CaCl2 or calcium phosphate buffers and the affinities were also greater. For example, at pH 6.7 and 30 degrees C the average dissociation constant for the submicelle-calcium complex is 0.074 mM for CaCl2 and calcium phosphate buffers, vs 0.016 mM for the milk salt solution. The asymmetric frontal boundaries and higher average affinities observed with milk salts may be due to binding of calcium salts with greater affinity in addition to the binding of free Ca2+ in these solutions.

  8. Advances in Ka-Band Communication System for CubeSats and SmallSats

    NASA Technical Reports Server (NTRS)

    Kegege, Obadiah; Wong, Yen F.; Altunc, Serhat

    2016-01-01

    A study was performed that evaluated the feasibility of Ka-band communication system to provide CubeSat/SmallSat high rate science data downlink with ground antennas ranging from the small portable 1.2m/2.4m to apertures 5.4M, 7.3M, 11M, and 18M, for Low Earth Orbit (LEO) to Lunar CubeSat missions. This study included link analysis to determine the data rate requirement, based on the current TRL of Ka-band flight hardware and ground support infrastructure. Recent advances in Ka-band transceivers and antennas, options of portable ground stations, and various coverage distances were included in the analysis. The link/coverage analysis results show that Cubesat/Smallsat missions communication requirements including frequencies and data rates can be met by utilizing Near Earth Network (NEN) Ka-band support with 2 W and high gain (>6 dBi) antennas.

  9. Design and Validation of High Date Rate Ka-Band Software Defined Radio for Small Satellite

    NASA Technical Reports Server (NTRS)

    Xia, Tian

    2016-01-01

    The Design and Validation of High Date Rate Ka- Band Software Defined Radio for Small Satellite project will develop a novel Ka-band software defined radio (SDR) that is capable of establishing high data rate inter-satellite links with a throughput of 500 megabits per second (Mb/s) and providing millimeter ranging precision. The system will be designed to operate with high performance and reliability that is robust against various interference effects and network anomalies. The Ka-band radio resulting from this work will improve upon state of the art Ka-band radios in terms of dimensional size, mass and power dissipation, which limit their use in small satellites.

  10. Design of Input Coupler and Output Window for Ka-Band Gyro-TWT

    NASA Astrophysics Data System (ADS)

    Alaria, M. K.; Singh, Khushbu; Choyal, Y.; Sinha, A. K.

    2013-10-01

    The design of input coupler with loaded interaction structure for Ka-band gyro traveling wave tube (gyro-TWT) has been carried out using Ansoft HFSS to operate in the TE11 mode. The return loss (S11) and transmission loss (S21) of the Ka-band gyro-TWT input coupler have been found -27.3 and -0.05 dB respectively. The design of output window for Ka-band gyro-TWT has been carried out using CST microwave studio. In this paper thermal analysis of the input coupler for Ka-band gyro-TWT has also been carried out using ANSYS software. In the simulation results, the temperature on the ceramic disc of window does not exceed 80 °C and found in safe limit. The optimized design of input and output window for gyro-TWT allows low heat loads in the ceramic and consequently low temperature increase.

  11. Ka-Band Atmospheric Noise Temperature Measurements Using a 34-Meter Beam-Waveguide Antenna

    NASA Technical Reports Server (NTRS)

    Morabito, D.; Clauss, B.; Speranza, M.

    1997-01-01

    (viewgraphs) NASA's Deep space missions have used 960 MHz, 2.3 GHz, and 8.4 GHz for spacecraft communication downlinks. Ka-band (32 GHz) is being considered as a downlink frequency for future flight projects.

  12. Development of a sensitive method for selection of affinity ligand for trypsin using quartz crystal microbalance sensor.

    PubMed

    Bayramoglu, Gulay; Yakup Arica, M

    2012-03-01

    In this work, a new methodology is developed for selection of affinity ligands towards the enzyme "trypsin" using quartz crystals microbalance (QCM) technique. To achieve this goal, the surface amination of gold plated QCM crystals was achieved in 13.56 MHz plasma polymerization system by using ethylenediamine. Three different ligands (i.e., 4-aminobenzamidine, 4-aminobenzoic acid, and phenylalanine) were immobilized on the aminated QCM crystals surface via glutaraldehyde coupling. All three ligand immobilized QCM crystals were characterized and compared under different experimental conditions. It was observed that the benzamidine ligand showed higher affinity to trypsin with a dissociation constant on the order of 1.76 × 10(-9) M, which is within the range of 10(-4)-10(-8) M for affinity ligands. Thus, its selectivity was suitable for purification of trypsin from biological fluids. PMID:21853329

  13. Complementary DNA display selection of high-affinity peptides binding the vacuolating toxin (VacA) of Helicobacter pylori.

    PubMed

    Hayakawa, Yumiko; Matsuno, Mitsuhiro; Tanaka, Makoto; Wada, Akihiro; Kitamura, Koichiro; Takei, Osamu; Sasaki, Ryuzo; Mizukami, Tamio; Hasegawa, Makoto

    2015-09-01

    Artificial peptides designed for molecular recognition of a bacterial toxin have been developed. Vacuolating cytotoxin A protein (VacA) is a major virulence factor of Helicobacter pylori, a gram-negative microaerophilic bacterium inhabiting the upper gastrointestinal tract, particularly the stomach. This study attempted to identify specific peptide sequences with high affinity for VacA using systematic directed evolution in vitro, a cDNA display method. A surface plasmon resonance-based biosensor and fluorescence correlation spectroscopy to examine binding of peptides with VacA identified a peptide (GRVNQRL) with high affinity. Cyclization of the peptide by attaching cysteine residues to both termini improved its binding affinity to VacA, with a dissociation constant (Kd ) of 58 nm. This study describes a new strategy for the development of artificial functional peptides, which are promising materials in biochemical analyses and medical applications.

  14. Structure of a High-Affinity

    SciTech Connect

    Saphire, E.O.; Montero, M.; Menendez, A.; Houten, N.E.van; Irving, M.B.; Pantophlet, R.; Swick, M.B.; Parren, P.W.H.I.; Burton, D.R.; Scott, J.K.; Wilson, I.A.; /Scripps Res. Inst. /Simon Fraser U. /British Columbia U.

    2007-07-13

    The human antibody b12 recognizes a discontinuous epitope on gp120 and is one of the rare monoclonal antibodies that neutralize a broad range of primary human immunodeficiency virus type 1 (HIV-1) isolates. We previously reported the isolation of B2.1, a dimeric peptide that binds with high specificity to b12 and competes with gp120 for b12 antibody binding. Here, we show that the affinity of B2.1 was improved 60-fold over its synthetic-peptide counterpart by fusing it to the N terminus of a soluble protein. This affinity, which is within an order of magnitude of that of gp120, probably more closely reflects the affinity of the phage-borne peptide. The crystal structure of a complex between Fab of b12 and B2.1 was determined at 1.8 Angstrom resolution. The structural data allowed the differentiation of residues that form critical contacts with b12 from those required for maintenance of the antigenic structure of the peptide, and revealed that three contiguous residues mediate B2.1's critical contacts with b12. This single region of critical contact between the B2.1 peptide and the b12 paratope is unlikely to mimic the discontinuous key binding residues involved in the full b12 epitope for gp120, as previously identified by alanine scanning substitutions on the gp120 surface. These structural observations are supported by experiments that demonstrate that B2.1 is an ineffective immunogenic mimic of the b12 epitope on gp120. Indeed, an extensive series of immunizations with B2.1 in various forms failed to produce gp120 cross-reactive sera. The functional and structural data presented here, however, suggest that the mechanism by which b12 recognizes the two antigens is very different. Here, we present the first crystal structure of peptide bound to an antibody that was originally raised against a discontinuous protein epitope. Our results highlight the challenge of producing immunogens that mimic discontinuous protein epitopes, and the necessity of combining

  15. Experiments for Ka-band mobile applications: The ACTS mobile terminal

    NASA Technical Reports Server (NTRS)

    Estabrook, Polly; Dessouky, Khaled; Jedrey, Thomas

    1990-01-01

    To explore the potential of Ka-band to support mobile satellite services, the Jet Propulsion Laboratory (JPL) has initiated the design and development of a Ka-band land-mobile terminal to be used with the Advanced Communications Technology Satellite (ACTS). The planned experimental setup with ACTS is described. Brief functional descriptions of the mobile and fixed terminals are provided. The inputs required from the propagation community to support the design activities and the planned experiments are also discussed.

  16. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins.

    PubMed

    Awoonor-Williams, Ernest; Rowley, Christopher N

    2016-09-13

    Methods for the calculation of the pKa ionizable amino acids are valuable tools for understanding pH-dependent properties of proteins. Cysteine is unique among the amino acids because of the chemical reactivity of its thiol group (S-H), which plays an instrumental role in several biochemical and regulatory functions. The acidity of noncatalytic cysteine residues is a factor in their susceptibility to chemical modification. Despite the plethora of existing pKa computing methods, no definitive protocol exists for accurately calculating the pKa's of cysteine residues in proteins. A cysteine pKa test set was developed, which is comprised of 18 cysteine residues in 12 proteins where the pKa's have been determined experimentally and an experimental structure is available. The pKa's of these residues were calculated using three methods that use an implicit solvent model (H++, MCCE, and PROPKA) and an all-atom replica-exchange thermodynamic integration approach with the CHARMM36 and AMBER ff99SB-ILDNP force fields. The models that use implicit solvation methods were generally unreliable in predicting cysteine residue pKa's, with RMSDs between 3.41 and 4.72 pKa units. On average, the explicit solvent methods performed better than the implicit solvent methods. RMSD values of 2.40 and 3.20 were obtained for simulations with the CHARMM36 and AMBER ff99SB-ILDNP force fields, respectively. Further development of these methods is necessary because the performance of the best method is similar to that of the null-model (RMSD = 2.74) and these differences in RMSD are of limited statistical significance given the small size of our test set. PMID:27541839

  17. NASA's Evolution to Ka-Band Space Communications for Near-Earth Spacecraft

    NASA Technical Reports Server (NTRS)

    McCarthy, Kevin; Stocklin, Frank; Geldzahler, Barry; Friedman, Daniel; Celeste, Peter

    2010-01-01

    This slide presentation reviews the exploration of NASA using a Ka-band system for spacecraft communications in Near-Earth orbits. The reasons for changing to Ka-band are the higher data rates, and the current (X-band spectrum) is becoming crowded. This will require some modification to the current ground station antennas systems. The results of a Request for Information (RFI) are discussed, and the recommended solution is reviewed.

  18. Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3

    SciTech Connect

    Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Teshima, Hazuki; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ivanova, N; Pagani, Ioanna; Vannier, Pauline; Oger, Phil; Bartlett, Douglas; Noll, Kenneth M; Woyke, Tanja; Jebbar, Mohamed

    2012-01-01

    Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

  19. An abrupt and prominent climatic reversal at 9.2 ka in the northeastern North America

    NASA Astrophysics Data System (ADS)

    Hou, J.; Huang, Y.; Shuman, B. N.; Oswald, W.; Foster, D. R.

    2008-12-01

    Continental climate during the early Holocene (from 10 to 7 ka) is characterized by multiple abrupt climatic reversals such as the well-known 8.2 ka event that has been observed worldwide and attributed to the terminal collapse of the Laurentide Ice Sheet (LIS) in the North American continent. However, many episodes of meltwater releases occurred prior to the final collapse of LIS, their impact on the continental climate is much less understood. We present in this paper decadal-scale hydrogen isotopic records of aquatic and terrestrial plant biomarkers from Blood Pond, Massachusetts during the early Holocene. Our isotopic records infer a cooling of 3~4 degree between 9.3 and 9.1 ka against the millennial scale climate background, mainly induced by changes in precipitation seasonality. In comparison, the 8.2 ka event displays smaller amplitude of temperature cooling of 1~2 degree at our southern New England site. We interpret our observed climatic reversal at ~ 9.2 ka as representing increased proportion of winter precipitation in conjunction with a drier and cooler summer, triggered by slowdown in thermohaline circulation as a result of freshwater release from the proglacial lakes. We attribute the difference in climate response at 8.2 ka and 9.2 ka events to the configuration of LIS, with 9.2 ka LIS having a much stronger blocking effect on the moisture from the Gulf of Mexico during the summer. Our data suggest that the seasonality of the precipitation at the southern New England was highly sensitive to meltwater releases, especially prior to the final collapse of the LIS.

  20. A View from the Cocoon--Space Categorization in the Korean Verb [na-ka-ta].

    ERIC Educational Resources Information Center

    Kim, Alan Hyun-Oak

    1996-01-01

    Analysis of the Korean verb "na-ka-ta" ("to get out, exit") focuses on why an expression such as "kyengkicang-ey na-ka-ta" ("someone goes out/in to the sports arena") is acceptable only in the context that the person's entering the arena is for the purpose of a contest, while it becomes semantically anomalous if intended to express the situation…

  1. Capacitive Cells for Dielectric Constant Measurement

    ERIC Educational Resources Information Center

    Aguilar, Horacio Munguía; Maldonado, Rigoberto Franco

    2015-01-01

    A simple capacitive cell for dielectric constant measurement in liquids is presented. As an illustrative application, the cell is used for measuring the degradation of overheated edible oil through the evaluation of their dielectric constant.

  2. High voltage compliance constant current ballast

    NASA Technical Reports Server (NTRS)

    Rosenthal, L. A.

    1976-01-01

    A ballast circuit employing a constant current diode and a vacuum tube that can provide a constant current over a voltage range of 1000 volts. The simple circuit can prove useful in studying voltage breakdown characteristics.

  3. Temporal variation of coupling constants and nucleosynthesis

    NASA Astrophysics Data System (ADS)

    Oberhummer, H.; Csótó, A.; Fairbairn, M.; Schlattl, H.; Sharma, M. M.

    2003-05-01

    We investigate the triple-alpha process and the Oklo phenomenon to obtain constraints on possible cosmological time variations of fundamental constants. Specifically we study cosmological temporal constraints for the fine structure constant and nucleon and meson masses.

  4. High-resolution sea surface reconstructions off Cape Hatteras over the last 10 ka

    NASA Astrophysics Data System (ADS)

    CléRoux, Caroline; Debret, Maxime; Cortijo, Elsa; Duplessy, Jean-Claude; Dewilde, Fabien; Reijmer, John; Massei, Nicolas

    2012-03-01

    This study presents high-resolution foraminiferal-based sea surface temperature, sea surface salinity and upper water column stratification reconstructions off Cape Hatteras, a region sensitive to atmospheric and thermohaline circulation changes associated with the Gulf Stream. We focus on the last 10,000 years (10 ka) to study the surface hydrology changes under our current climate conditions and discuss the centennial to millennial time scale variability. We observed opposite evolutions between the conditions off Cape Hatteras and those south of Iceland, known today for the North Atlantic Oscillation pattern. We interpret the temperature and salinity changes in both regions as co-variation of activities of the subtropical and subpolar gyres. Around 8.3 ka and 5.2-3.5 ka, positive salinity anomalies are reconstructed off Cape Hatteras. We demonstrate, for the 5.2-3.5 ka period, that the salinity increase was caused by the cessation of the low salinity surface flow coming from the north. A northward displacement of the Gulf Stream, blocking the southbound low-salinity flow, concomitant to a reduced Meridional Overturning Circulation is the most likely scenario. Finally, wavelet transform analysis revealed a 1000-year period pacing the δ18O signal over the early Holocene. This 1000-year frequency band is significantly coherent with the 1000-year frequency band of Total Solar Irradiance (TSI) between 9.5 ka and 7 ka and both signals are in phase over the rest of the studied period.

  5. Pre-Flight Testing and Performance of a Ka-Band Software Defined Radio

    NASA Technical Reports Server (NTRS)

    Downey, Joseph A.; Reinhart, Richard C.; Kacpura, Thomas

    2012-01-01

    National Aeronautics and Space Administration (NASA) has developed a space-qualified, reprogrammable, Ka-band Software Defined Radio (SDR) to be utilized as part of an on-orbit, reconfigurable testbed. The testbed will operate on the truss of the International Space Station beginning in late 2012. Three unique SDRs comprise the testbed, and each radio is compliant to the Space Telecommunications Radio System (STRS) Architecture Standard. The testbed provides NASA, industry, other Government agencies, and academic partners the opportunity to develop communications, navigation, and networking applications in the laboratory and space environment, while at the same time advancing SDR technology, reducing risk, and enabling future mission capability. Designed and built by Harris Corporation, the Ka-band SDR is NASA's first space-qualified Ka-band SDR transceiver. The Harris SDR will also mark the first NASA user of the Ka-band capabilities of the Tracking Data and Relay Satellite System (TDRSS) for on-orbit operations. This paper describes the testbed's Ka-band System, including the SDR, travelling wave tube amplifier (TWTA), and antenna system. The reconfigurable aspects of the system enabled by SDR technology are discussed and the Ka-band system performance is presented as measured during extensive pre-flight testing.

  6. pKa determination by ¹H NMR spectroscopy - an old methodology revisited.

    PubMed

    Bezençon, Jacqueline; Wittwer, Matthias B; Cutting, Brian; Smieško, Martin; Wagner, Bjoern; Kansy, Manfred; Ernst, Beat

    2014-05-01

    pKa values of acids and protonated bases have an essential impact on organic synthesis, medicinal chemistry, and material and food sciences. In drug discovery and development, they are of utmost importance for the prediction of pharmacokinetic and pharmacodynamic properties. To date, various methods for the determination of pKa values are available, including UV-spectroscopic, potentiometric, and capillary electrophoretic techniques. An additional option is provided by nuclear magnetic resonance (NMR) spectroscopy. The underlying principle is the alteration of chemical shifts of NMR-active nuclei (e.g., (13)C and (1)H) depending on the protonation state of adjacent acidic or basic sites. When these chemical shifts are plotted against the pH, the inflection point of the resulting sigmoidal curve defines the pKa value. Although pKa determinations by (1)H NMR spectroscopy are reported for numerous cases, the potential of this approach is not yet fully evaluated. We therefore revisited this method with a diverse set of test compounds covering a broad range of pKa values (pKa 0.9-13.8) and made a comparison with four commonly used approaches. The methodology revealed excellent correlations (R(2)=0.99 and 0.97) with electropotentiometric and UV spectroscopic methods. Moreover, the comparison with in silico results (Epik and Marvin) also showed high correlations (R(2)=0.92 and 0.94), further confirming the reliability and utility of this approach. PMID:24462329

  7. Earth as diode: monsoon source of the orbital ~100 ka climate cycle

    NASA Astrophysics Data System (ADS)

    Anderson, R. Y.

    2010-08-01

    A potential source for Earth's enigmatic ~100 ka climate cycle, which is found in many ancient geological records at low latitudes and also in the pacing of glaciation during the late Pleistocene, is traced to a climatic rectifying process inherent in the monsoon. Seasonal information needed to identify the rectifying mechanism is preserved within varves of a continuous, 200 ka recording of annual maximum surface temperature (Tmax) from the equator of Western Pangea. Specific seasonal reactions recorded in varves show how the monsoon reacted to seasonal differences in insolation at equinox to produce a 11.7 ka semi-precession cycle in Tmax. At solstice, anti-phasing of insolation in the Northern and Southern Hemispheres, intensified and focused by a highly asymmetric Pangea relative to the equator, produced a strong equatorial maritime monsoon that performed a nonlinear rectifying function similar to that of a simple rectifying diode. Expressed in the resulting varve series are substantial cycles in Tmax of 100 ka, 23.4 ka, and 11.7 ka. Importantly, any external or internal forcing of the tropical (monsoon) climate system at higher-than-orbital frequencies (e.g. solar, ENSO) should also be amplified at Milankovitch frequencies by the monsoon.

  8. Design research on the conductor of 10 kA class HTS DC power cable

    NASA Astrophysics Data System (ADS)

    Zhang, Dong; Dai, Shaotao; Zhang, Fengyuan; Huang, Tianbin; Wang, Yinshun; Lin, Yubao; Teng, Yuping; Zhang, Guomin; Xiao, Liye; Lin, Liangzhen

    2012-12-01

    High temperature superconducting (HTS) DC power cable shows a wide application prospect in the field of power transmission for its nearly lossless and rather high capacity. A 360 m/10 kA HTS DC power cable system, which connects the rectifier output of a substation with the bus bar of an electrolytic aluminium cell, will be put into operation at Henan Zhongfu Industrial Co., Ltd. As one of the items in this project, a 5 m/10 kA HTS DC power cable was developed, which is used to investigate the conductor design, fabrication, current-carrying capacity and stability of the 360 m/10 kA HTS power cable. The HTS DC power cable core consists of five conductor layers wound with spliced Bi-2223 wires with the length of 600 m. The cable core has five layers and 23 conductors in each layer with the outer diameter of 45.42 mm. The superconducting power cable is fabricated and tested. The critical current is about 14.3 kA at 77 K. The superconducting power cable is charged to 10 kA with rate of 10 A/s and operates at steady-state for 30 min. In this paper, the 10 kA HTS DC power cable design, fabrication and test are presented. The experimental research of the performance of spliced superconducting wire and charging, steady-state operating performance of the cable was carried out.

  9. Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)

    PubMed Central

    2011-01-01

    Background The cotton boll weevil (Anthonomus grandis) is a serious insect-pest in the Americas, particularly in Brazil. The use of chemical or biological insect control is not effective against the cotton boll weevil because of its endophytic life style. Therefore, the use of biotechnological tools to produce insect-resistant transgenic plants represents an important strategy to reduce the damage to cotton plants caused by the boll weevil. The present study focuses on the identification of novel molecules that show improved toxicity against the cotton boll weevil. In vitro directed molecular evolution through DNA shuffling and phage display screening was applied to enhance the insecticidal activity of variants of the Cry8Ka1 protein of Bacillus thuringiensis. Results Bioassays carried out with A. grandis larvae revealed that the LC50 of the screened mutant Cry8Ka5 toxin was 3.15-fold higher than the wild-type Cry8Ka1 toxin. Homology modelling of Cry8Ka1 and the Cry8Ka5 mutant suggested that both proteins retained the typical three-domain Cry family structure. The mutated residues were located mostly in loops and appeared unlikely to interfere with molecular stability. Conclusions The improved toxicity of the Cry8Ka5 mutant obtained in this study will allow the generation of a transgenic cotton event with improved potential to control A. grandis. PMID:21906288

  10. The GridKa Tier-1 Computing Center within the ALICE Grid Framework

    NASA Astrophysics Data System (ADS)

    Park, WooJin J.; Christopher, Jung; Heiss, Andreas; Petzold, Andreas; Schwarz, Kilian

    2014-06-01

    The GridKa computing center, hosted by Steinbuch Centre for Computing at the Karlsruhe Institute for Technology (KIT) in Germany, is serving as the largest Tier-1 center used by the ALICE collaboration at the LHC. In 2013, GridKa provides 30k HEPSPEC06, 2.7 PB of disk space, and 5.25 PB of tape storage to ALICE. The 10Gbit/s network connections from GridKa to CERN, several Tier-1 centers and the general purpose network are used by ALICE intensively. In 2012 a total amount of ~1 PB was transferred to and from GridKa. As Grid framework, AliEn (ALICE Environment) is being used to access the resources, and various monitoring tools including the MonALISA (MONitoring Agent using a Large Integrated Services Architecture) are always running to alert in case of any problem. GridKa on-call engineers provide 24/7 support to guarantee minimal loss of availability of computing and storage resources in case of hardware or software problems. We introduce the GridKa Tier-1 center from the viewpoint of ALICE services.

  11. A Ka-Band Celestial Reference Frame with Applications to Deep Space Navigation

    NASA Technical Reports Server (NTRS)

    Jacobs, Christopher S.; Clark, J. Eric; Garcia-Miro, Cristina; Horiuchi, Shinji; Sotuela, Ioana

    2011-01-01

    The Ka-band radio spectrum is now being used for a wide variety of applications. This paper highlights the use of Ka-band as a frequency for precise deep space navigation based on a set of reference beacons provided by extragalactic quasars which emit broadband noise at Ka-band. This quasar-based celestial reference frame is constructed using X/Ka-band (8.4/32 GHz) from fifty-five 24-hour sessions with the Deep Space Network antennas in California, Australia, and Spain. We report on observations which have detected 464 sources covering the full 24 hours of Right Ascension and declinations down to -45 deg. Comparison of this X/Ka-band frame to the international standard S/X-band (2.3/8.4 GHz) ICRF2 shows wRMS agreement of approximately 200 micro-arcsec in alpha cos(delta) and approximately 300 micro-arcsec in delta. There is evidence for systematic errors at the 100 micro-arcsec level. Known errors include limited SNR, lack of instrumental phase calibration, tropospheric refraction mis-modeling, and limited southern geometry. The motivation for extending the celestial reference frame to frequencies above 8 GHz is to access more compact source morphology for improved frame stability and to support spacecraft navigation for Ka-band based NASA missions.

  12. Progress in the prediction of pKa values in proteins

    SciTech Connect

    Alexov, Emil; Mehler, Ernest L.; Baker, Nathan A.; Baptista, Antonio; Huang, Yong; Milletti, Francesca; Nielsen, Jens E.; Farrell, Damien; Carstensen, Tommy; Olsson, Mats H.; Shen, Jana K.; Warwicker, Jim; Williams, Sarah; Word, J Michael

    2011-12-15

    The pKa-cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pKa values and protein electrostatics in general. The first round of the pKa -cooperative, which challenged computational labs to carry out blind predictions against pKas experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6-10, 2009). This paper serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. Here we briefly outline existing approaches for pKa calculations, emphasizing methods that were used by the participants in calculating the blind pKa values in the first round of the cooperative. We then point out some of the difficulties encountered by the participating groups in making their blind predictions, and finally try to provide some insights for future developments aimed at improving the accuracy of pKa calculations.

  13. Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides.

    PubMed

    Sastre, S; Casasnovas, R; Muñoz, F; Frau, J

    2016-04-28

    Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods. PMID:27052591

  14. Effectively nonlocal metric-affine gravity

    NASA Astrophysics Data System (ADS)

    Golovnev, Alexey; Koivisto, Tomi; Sandstad, Marit

    2016-03-01

    In metric-affine theories of gravity such as the C-theories, the spacetime connection is associated to a metric that is nontrivially related to the physical metric. In this article, such theories are rewritten in terms of a single metric, and it is shown that they can be recast as effectively nonlocal gravity. With some assumptions, known ghost-free theories with nonsingular and cosmologically interesting properties may be recovered. Relations between different formulations are analyzed at both perturbative and nonperturbative levels, taking carefully into account subtleties with boundary conditions in the presence of integral operators in the action, and equivalences between theories related by nonlocal redefinitions of the fields are verified at the level of equations of motion. This suggests a possible geometrical interpretation of nonlocal gravity as an emergent property of non-Riemannian spacetime structure.

  15. Affinity chromatography with an immobilized RNA enzyme.

    PubMed Central

    Vioque, A; Altman, S

    1986-01-01

    M1 RNA, the catalytic subunit of Escherichia coli RNase P, has been covalently linked at its 3' terminus to agarose beads. Unlike M1 RNA, which is active in solution in the absence of the protein component (C5) of RNase P, the RNA linked to the beads is active only in the presence of C5 protein. Affinity chromatography of crude extracts of E. coli on a column prepared from the beads to which the RNA has been crosslinked results in the purification of C5 protein in a single step. The protein has been purified in this manner from cells that contain a plasmid, pINIIIR20, which includes the gene that codes for C5 protein. A 6-fold amplification of the expression of C5 protein is found in these cells after induction as compared to cells that do not harbor the plasmid. Images PMID:3526344

  16. Wetting on rough self-affine surfaces

    NASA Astrophysics Data System (ADS)

    Palasantzas, George

    1995-05-01

    In this paper, we present a general investigation of the effective potential for complete wetting on self-affine rough surfaces. The roughness effect is investigated by means of the height-height correlation model in Fourier space ~(1+aξ2q2)-1-H. The parameters H and ξ are, respectively, the roughness exponent and the substrate in-plane correlation length. It is observed that the effect of H on the free interface profile is significant for ξ>ξ) regime is characterized by a power-law scaling ~Y-2.

  17. High-affinity neuropeptide Y receptor antagonists.

    PubMed Central

    Daniels, A J; Matthews, J E; Slepetis, R J; Jansen, M; Viveros, O H; Tadepalli, A; Harrington, W; Heyer, D; Landavazo, A; Leban, J J

    1995-01-01

    Neuropeptide Y (NPY) is one of the most abundant peptide transmitters in the mammalian brain. In the periphery it is costored and coreleased with norepinephrine from sympathetic nerve terminals. However, the physiological functions of this peptide remain unclear because of the absence of specific high-affinity receptor antagonists. Three potent NPY receptor antagonists were synthesized and tested for their biological activity in in vitro, ex vivo, and in vivo functional assays. We describe here the effects of these antagonists inhibiting specific radiolabeled NPY binding at Y1 and Y2 receptors and antagonizing the effects of NPY in human erythroleukemia cell intracellular calcium mobilization perfusion pressure in the isolated rat kidney, and mean arterial blood pressure in anesthetized rats. PMID:7568074

  18. Evaluation system of negative electron affinity photocathode

    NASA Astrophysics Data System (ADS)

    Fu, Rongguo; Chang, Benkang; Qian, Yunsheng; Wang, Guihua; Zong, Zhiyuan

    2001-10-01

    This article first describes the background of the research and manufacture of evaluation system of Negative Electron Affinity photocathode. This article designs a set of super high vacuum system for activating NEA photocathode on the base of activation theory, the process of design and debugging is given. The system is composed of three parts: super high vacuum system for GaAs material activation, multi-meter testing system, surface analysis system. The system is used for on-line evaluation of activating of NEA photocathode. The technical parameters and structure of the evaluation system of NEA photocathode are given in the paper. The system is finished and experiments are made. At last the picture of the system is given.

  19. AMPHOTERIC BEHAVIOR OF COMPLEX SYSTEMS : IV. NOTE ON THE ISOELECTRIC POINT AND IONIZATION CONSTANTS OF SULFANILIC ACID.

    PubMed

    Stearn, A E

    1927-01-20

    From the solubility minimum the value of the basic ionization constant of sulfanilic acid is shown to lie probably between the values 1.7 x 10(-15) and 3.2 x 10(-15). From solubility measurements the value of this same constant is shown to lie probably between 2.0 and 2.2 x 10(-15), and the isoelectric point of sulfanilic acid is thus at a cH of 0.056 or a pH of 1.25. From conductivity ratios the acid ionization constant of sulfanilic acid is shown to be 7.05 x 10(-4) at room temperature (21 degrees C.). Calculations are made, from data published in preceding papers, of the ionization constants of glycine, K(a) being 2.3 x 10(-10), and K(b) being 2.2 x 10(-12).

  20. Dye affinity cryogels for plasmid DNA purification.

    PubMed

    Çimen, Duygu; Yılmaz, Fatma; Perçin, Işık; Türkmen, Deniz; Denizli, Adil

    2015-11-01

    The aim of this study is to prepare megaporous dye-affinity cryogel discs for the purification of plasmid DNA (pDNA) from bacterial lysate. Poly(hydroxyethyl methacrylate) [PHEMA] cryogel discs were produced by free radical polymerization initiated by N,N,N',N'-tetramethylene diamine (TEMED) and ammonium persulfate (APS) redox pair in an ice bath. Cibacron Blue F3GA was used as an affinity ligand (loading amount: 68.9μmol/g polymer). The amount of pDNA adsorbed onto the PHEMA-Cibacron Blue F3GA cryogel discs first increased and then reached a plateau value (i.e., 32.5mg/g cryogel) at 3.0mg/mL pDNA concentration. Compared with the PHEMA cryogel (0.11mg/g cryogel), the pDNA adsorption capacity of the PHEMA-Cibacron Blue F3GA cryogel (32.4mg/g polymer) was improved significantly due to the Cibacron Blue 3GA immobilization onto the polymeric matrix. pDNA adsorption amount decreased from 11.7mg/g to 1.1mg/g with the increasing of NaCl concentration. The maximum pDNA adsorption was achieved at 4°C. The overall recovery of pDNA was calculated as 90%. The PHEMA-Cibacron Blue F3GA cryogel discs could be used five times without decreasing the pDNA adsorption capacity significantly. The results show that the PHEMA-Cibacron Blue F3GA cryogel discs promise high selectivity for pDNA. PMID:26249596

  1. High Affinity Binding of Indium and Ruthenium Ions by Gastrins.

    PubMed

    Baldwin, Graham S; George, Graham N; Pushie, M Jake

    2015-01-01

    The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS) spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd) of 3.3 x 10-7 and 1.1 x 10-6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10-15 and 1.7 x 10-7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10-13 and 1.2 x 10-5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0-3.3 Å, the Ru complex clearly demonstrated a short range Ru-Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy.

  2. High Affinity Binding of Indium and Ruthenium Ions by Gastrins

    PubMed Central

    Baldwin, Graham S.; George, Graham N.; Pushie, M. Jake

    2015-01-01

    The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS) spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd) of 3.3 x 10−7 and 1.1 x 10−6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10−15 and 1.7 x 10−7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10−13 and 1.2 x 10−5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0–3.3 Å, the Ru complex clearly demonstrated a short range Ru—Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy. PMID:26457677

  3. Characterizing low affinity epibatidine binding to α4β2 nicotinic acetylcholine receptors with ligand depletion and nonspecific binding

    PubMed Central

    2011-01-01

    Background Along with high affinity binding of epibatidine (Kd1≈10 pM) to α4β2 nicotinic acetylcholine receptor (nAChR), low affinity binding of epibatidine (Kd2≈1-10 nM) to an independent binding site has been reported. Studying this low affinity binding is important because it might contribute understanding about the structure and synthesis of α4β2 nAChR. The binding behavior of epibatidine and α4β2 AChR raises a question about interpreting binding data from two independent sites with ligand depletion and nonspecific binding, both of which can affect equilibrium binding of [3H]epibatidine and α4β2 nAChR. If modeled incorrectly, ligand depletion and nonspecific binding lead to inaccurate estimates of binding constants. Fitting total equilibrium binding as a function of total ligand accurately characterizes a single site with ligand depletion and nonspecific binding. The goal of this study was to determine whether this approach is sufficient with two independent high and low affinity sites. Results Computer simulations of binding revealed complexities beyond fitting total binding for characterizing the second, low affinity site of α4β2 nAChR. First, distinguishing low-affinity specific binding from nonspecific binding was a potential problem with saturation data. Varying the maximum concentration of [3H]epibatidine, simultaneously fitting independently measured nonspecific binding, and varying α4β2 nAChR concentration were effective remedies. Second, ligand depletion helped identify the low affinity site when nonspecific binding was significant in saturation or competition data, contrary to a common belief that ligand depletion always is detrimental. Third, measuring nonspecific binding without α4β2 nAChR distinguished better between nonspecific binding and low-affinity specific binding under some circumstances of competitive binding than did presuming nonspecific binding to be residual [3H]epibatidine binding after adding a large concentration of

  4. Boronate Affinity-Molecularly Imprinted Biocompatible Probe: An Alternative for Specific Glucose Monitoring.

    PubMed

    Chen, Guosheng; Qiu, Junlang; Fang, Xu'an; Xu, Jianqiao; Cai, Siying; Chen, Qing; Liu, Yan; Zhu, Fang; Ouyang, Gangfeng

    2016-08-19

    A biocompatible probe for specific glucose recognition is based on photoinitiated boronate affinity-molecular imprinted polymers (BA-MIPs). The unique pre-self-assembly between glucose and boronic acids creates glucose-specific memory cavities in the BA-MIPs coating. As a result, the binding constant toward glucose was enhanced by three orders of magnitude. The BA-MIPs probe was applied to glucose determination in serum and urine and implanted into plant tissues for low-destructive and long-term in vivo continuous glucose monitoring. PMID:27411946

  5. Purification of glycolytic enzymes by using affinity-elution chromatography.

    PubMed Central

    Scopes, R K

    1977-01-01

    1. A systematic procedure for the purification of enzymes by affinity-elution chromatography is described. Enzymes are adsorbed on a cation-exchanger, and eluted with ligands specific for the enzyme concerned. 2. All of the glycolytic and some related enzymes present in rabbit muscle can be purified by the affinity-elution technique. The pH range for adsorption and elution of each enzyme was found, and the effects of minor variations of conditions are described. 3. A description of experimental conditions suitable for affinity elution of each enzyme is given, together with special features relevant to each individual enzyme. 4. Theoretical considerations of affinity elution chromatography are discussed, including its limitations, advantages and disadvantages compared with affinity-adsorption chromatography. Possible developments are suggested to cover enzymes which because of their adsorption characteristics are not at present amenable to affinity-elution procedures. PMID:192194

  6. Antibody-based affinity cryo-EM grid.

    PubMed

    Yu, Guimei; Li, Kunpeng; Jiang, Wen

    2016-05-01

    The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states.

  7. Prediction of Neutral Salt Elution Profiles for Affinity Chromatography

    NASA Astrophysics Data System (ADS)

    Robinson, Jack B.; Strottmann, James M.; Stellwagen, Earle

    1981-04-01

    Neutral salts exhibit very marked differences as eluants of proteins from affinity columns. We observe: (i) that the relative potencies of neutral salts as eluants are independent of the protein or the affinity ligand in the systems studied, (ii) that the absolute salt concentration necessary to elute any given protein bound to the affinity matrix is proportional to the algebraic sum of a set of elution coefficients defined herein for the separate ions present in the solution, and (iii) that the proportionality between elution potency and elution coefficient is a function of the affinity of the protein for the immobilized ligand. Given the concentration of one neutral salt required for elution of a protein of interest from an affinity column, the elution capability of any neutral salt at any temperature can be quantitatively predicted for that protein. Accordingly, application and elution protocols for affinity chromatography can be designed to optimize the yield and fold purification of proteins.

  8. Coupling Isotachophoresis with Affinity Chromatography for Rapid and Selective Purification with High Column Utilization, Part 1: Theory

    PubMed Central

    2015-01-01

    We present a novel technique that couples isotachophoresis (ITP) with affinity chromatography (AC) to achieve rapid, selective purification with high column utilization. ITP simultaneously preconcentrates an analyte and purifies it, based on differences in mobility of sample components, excluding species that may foul or compete with the target at the affinity substrate. ITP preconcentration accelerates the affinity reaction, reducing assay time, improving column utilization, and allowing for capture of targets with higher dissociation constants. Furthermore, ITP-AC separates the target and contaminants into nondiffusing zones, thus achieving high resolution in a short distance and time. We present an analytical model for spatiotemporal dynamics of ITP-AC. We identify and explore the effect of key process parameters, including target distribution width and height, ITP zone velocity, forward and reverse reaction constants, and probe concentration on necessary affinity region length, assay time, and capture efficiency. Our analytical approach shows collapse of these variables to three nondimensional parameters. The analysis yields simple analytical relations for capture length and capture time in relevant ITP-AC regimes, and it demonstrates how ITP greatly reduces assay time and improves column utilization. In the second part of this two-part series, we will present experimental validation of our model and demonstrate ITP-AC separation of the target from 10,000-fold more-abundant contaminants. PMID:24937679

  9. [Cell-ELA-based determination of binding affinity of DNA aptamer against U87-EGFRvIII cell].

    PubMed

    Tan, Yan; Liang, Huiyu; Wu, Xidong; Gao, Yubo; Zhang, Xingmei

    2013-05-01

    A15, a DNA aptamer with binding specificity for U87 glioma cells stably overexpressing the epidermal growth factor receptor variant III (U87-EGFRvIII), was generated by cell systematic evolution of ligands by exponential enrichment (cell-SELEX) using a random nucleotide library. Subsequently, we established a cell enzyme-linked assay (cell-ELA) to detect the affinity of A15 compared to an EGFR antibody. We used A15 as a detection probe and cultured U87-EGFRvIII cells as targets. Our data indicate that the equilibrium dissociation constants (K(d)) for A15 were below 100 nmol/L and had similar affinity compared to an EGFR antibody for U87-EGFRvIII. We demonstrated that the cell-ELA was a useful method to determine the equilibrium dissociation constants (K(d)) of aptamers generated by cell-SELEX.

  10. Sperm in poor quality semen from bulls during heat stress have a lower affinity for binding hydrogen-3 heparin

    SciTech Connect

    Ax, R.L.; Gilbert, G.R.; Shook, G.E.

    1987-01-01

    Binding assays with (/sup 3/H) heparin were performed using spermatozoa collected prior to, during, and following summer heat stress to dairy bulls. Ejaculates collected in August 1983 after a period of ambient temperatures exceeding 29.4/sup 0/C exhibited a high frequency of abnormal sperm, and motility was reduced in some samples. Sperm in samples collected during heat stress possessed dissociation constants for binding (/sup 3/H) heparin ranging from 134.5 to 163.2 nmol. In contrast, sperm in semen collected prior to and after heat stress had significantly lower dissociation constants (higher affinity) for (/sup 3/H)heparin, 12.9 to 56.4 nmol. The number of binding sites for (/sup 3/H) heparin on sperm did not change among collection periods. It was concluded that the binding affinity for (/sup 3/H) heparin may reflect membrane integrity of bull sperm.

  11. Evidence for upper Great Lakes waters in the Erie Basin until 10. 5 ka

    SciTech Connect

    Tinkler, K.J. . Dept. of Geology) Lewis, C.F.M. ); Anderson, T.W. ); Cameron, G.D.M.

    1992-01-01

    Modern recession at Niagara Falls suggests that Erie basin flow alone produces a narrower gorge with recession reduced by an order of magnitude. Gorge interpretations relate dimensions to stages of Great Lakes evolution. A published date of 9.8 ka, for upper river shells at Whirlpool State Park favors an interpretation implying 3.5 kilometers of gorge were cut in the period 12.5 ka to 10.5 ka at a rate of 1.75 m/a, a value consistent with the pre-twentieth century rate of 1.37--1.52 m/a. Erie basin discharge alone would be insufficient to excavate the length of gorge seen. Stratigraphic studies of offshore sediments in lake Erie north-east of Long Point based on seismic profiles and core samples show evidence of lake level change. Following decline of the post-Whittlesey (< 13 ka) southwestward-draining proglacial lakes in the Erie basin and the establishment of Lake Iroquois at about 12.5 ka water levels fell to a control on the Niagara Peninsula. Glacial meltwater continued to pass through the Erie basin until 10.5 ka. Negative shifts in delta O-18 suggest increased meltwater flow through the Erie basin and increased lake level between 11 ka and 10.5 ka. An erosional unconformity, lag sediments, and a distinct former shoreface suggest that lake level subsequently fell in the Long Point area of eastern Lake Erie to about 30m below present by about 10.5 ka when meltwater runoff from the upper Great Lakes by-passed Erie basin. Both the lake cores and the gorge recession are consistent with a computational model of flow out to the Erie basin. According to the model great Lakes outflow, augmented by inflow from Lake Agassiz between 11 to 10.5 ka, would yield shorelines at the height attributed to Lake Tonawanda (180--182m), the immediate source of the Niagara River.

  12. Conformational and oligomeric effects on the cysteine pKa of typaredoxin peroxidase

    PubMed Central

    Yuan, Ye; Knaggs, Michael H.; Poole, Leslie B.; Fetrow, Jacquelyn S.; Salsbury, Freddie R.

    2010-01-01

    Typical 2-Cys peroxiredoxins (Prxs) are peroxidases which regulate cell signaling pathways, apoptosis, and differentiation. These enzymes are obligate homodimers, and can form decamers in solution. During catalysis, Prxs exhibit cysteine-dependent reactivity which requires the deprotonation of the peroxidatic cysteine (Cp) supported by a lowered pKa in the initial step. We present the results of molecular dynamics simulations combined with pKa calculations on the monomeric, dimeric and decameric forms of one typical 2-Cys Prx, the tryparedoxin peroxidase from Trypanosoma cruzi (PDB id, 1uul). The calculations indicate that Cp (C52) pKa values are highly affected by oligomeric state; an unshifted Cp pKa (~ 8.3, comparable to the pKa of isolated cysteine) is calculated for the monomer. In the dimers, starting with essentially identical structures, the Cps evolve dynamically asymmetric pKas during the simulations; one subunit’s Cp pKa is shifted downward at a time, while the other is unshifted. However, when averaged over time, or multiple simulations, the two subunits within a dimer exhibit the same Cp, showing no preference for a lowered pKa in either subunit. Two conserved pathways that communicate the asymmetric pKas between Cps of different subunits can be identified. In the decamer, all the Cp pKas are shifted downward, with slight asymmetry in the dimers which form the decamers. Structural analyses implicate oligomerization effects as responsible for these oligomeric state-dependent Cp pKa shifts. The intra-dimer and the inter-dimer subunit contacts in the decamer restrict the conformations of the side chains of several residues (T49, T54 and E55) calculated to be key in shifting the Cp pKa. In addition, the backbone fluctuations of a few residues (M46, D47 and F48) result in a different electrostatic environment for the Cp in dimers relative to the monomers. These side chain and backbone interactions which contribute to pKa modulation indicate the importance

  13. Comparing the Titrations of Mixed-Acid Solutions Using Dropwise and Constant-Flow Techniques

    NASA Astrophysics Data System (ADS)

    Charlesworth, Paul; Seguin, Matthew J.; Chesney, David J.

    2003-11-01

    A mixed-acid solution containing hydrochloric and phosphoric acids was used to determine the error associated with performing a real-time titration. The results were compared against those obtained by performing the titration in a more traditional dropwise addition of titrant near the equivalence points. It was found that the real-time techniques resulted in significantly decreased analysis times while maintaining a low experimental error. The constant-flow techniques were implemented into two different levels of chemistry. It was found that students could successfully utilize the modified experiments. Problems associated with the techniques, major sources of error, and their solutions are discussed. In both cases, the use of the constant-flow setup has increased student recollection of key concepts, such as pKa determination, proper indicator choice, and recognizing the shape of specific titration curves by increasing student interest in the experiment.

  14. The Effect of Past Climate Change on Regolith Erosion Rates for the Past 100 ka in the Eastern Sierra Nevada

    NASA Astrophysics Data System (ADS)

    Madoff, R. D.; Putkonen, J.

    2014-12-01

    Global climate change over the last 100 ka is known to have resulted in glacial fluctuations in the eastern Sierra Nevada evidenced today by moraines. The effect of past climate on regolith erosion rates is quantified by modeling hillslope diffusion and evolution of a profile cross-section of Mono Basin moraine in the eastern Sierra Nevada. The degradation in the model is described by the linear transport law, q = -κ(dz/dx), where the diffusivity coefficient, κ, is a parameter to account for factors affecting regolith transport rate (q) unrelated to slope (dz/dx), such as climate and substrate. Three scenarios were modeled with respective κ values. In the first, κ is held constant through the age of the landform and optimized to reproduce the current moraine cross-section. In the second, κ varies with time based on the documented variation in the paleoclimate and related degradation rate. In the third, κ is held constant and defined by present-day degradation values measured in the region. In all the scenarios the moraine initial slopes are at the angle of repose. Comparisons of the first (constant κ) and second (variable κ) scenarios show that the former can generate erosion rates that overestimate crest elevation by 30% during the first quarter of the landform age and underestimate it by 20% during the latter three-quarters. However, the third (current κ) scenario underestimates the degradation up to 58% of the current profile. This indicates that the past erosion rates were higher than what is observed today. Increased regolith erosion rates in the past were driven by climates colder and wetter than the present.

  15. Affinity chromatography for purification of two urokinases from human urine.

    PubMed

    Takahashi, R; Akiba, K; Koike, M; Noguchi, T; Ezure, Y

    2000-05-26

    A new affinity chromatography (hydrophobic-mediated affinity chromatography), which was characterized by the matrix having both affinity site to urokinase and hydrophobic site, was established for the purification of urokinase from human urine. The hydrophobic affinity matrix (tentatively named PAS in the text) was prepared by immobilizing 6-aminocaproic acid on Sepharose CL-6B, followed by a coupling p-aminobenzamidine to a part of the hydrophobic site on the matrix. The PAS matrix was applied to the purification of urokinase from human urine, and high- and low-molecular weight pure urokinases were efficiently obtained in high yield by the present method. PMID:10892585

  16. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    DOE PAGES

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0more » to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

  17. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    SciTech Connect

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.

  18. Fundamental Constants and Tests with Simple Atoms

    NASA Astrophysics Data System (ADS)

    Tan, Joseph

    2015-05-01

    Precise measurements with simple atoms provide stringent tests of physical laws, improving the accuracy of fundamental constants--a set of which will be selected to fully define the proposed New International System of Units. This talk focuses on the atomic constants (namely, the Rydberg constant, the fine-structure constant, and the proton charge radius), discussing the impact of the proton radius obtained from the Lamb-shift measurements in muonic hydrogen. Significant discrepancies persist despite years of careful examination: the slightly smaller proton radius obtained from muonic hydrogen requires the Rydberg constant and the fine-structure constant to have values that disagree significantly with the CODATA recommendations. After giving a general overview, I will discuss our effort to produce one-electron ions in Rydberg states, to enable a different test of theory and measurement of the Rydberg constant.

  19. Experimental determination of Henry's law constants of trifluoroacetic acid at 278-298 K

    NASA Astrophysics Data System (ADS)

    Kutsuna, Shuzo; Hori, Hisao

    Equilibrium partial pressures of trifluoroacetic acid ( P C(O)OH) over aqueous trifluoroacetic acid test solutions were determined at 278.15, 288.15, and 298.15 K. The concentration of undissociated trifluoroacetic acid ( C C(O)OH) in each test solution was determined by means of attenuated total reflection IR spectroscopy and window factor analysis. From the linear relationship between P C(O)OH and C C(O)OH, the Henry's law constant of trifluoroacetic acid ( KH) at 298.15 K was determined to be 5800±700 mol dm -3 atm -1 and KH at temperature T in K was determined to be KH=5780 exp[-4120×(1/298.15-1/ T)] in mol dm -3 atm -1. The KH value at 298.15 K was 0.65 times the reported value [Bowden, D.J., Clegg, S.L., Brimblecombe, P., 1996. The Henry's law constant of trifluoroacetic acid and its partitioning into liquid water in the atmosphere. Chemosphere 32, 405-420] for p Ka=0.47 and it was equal to that for p Ka=0.2.

  20. Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-12-01

    Predictions of protein-protein binders and binding affinities have traditionally focused on features pertaining to the native complexes. In developing a computational method for predicting protein-protein association rate constants, we introduced the concept of transient complex after mapping the interaction energy surface. The transient complex is located at the outer boundary of the bound-state energy well, having near-native separation and relative orientation between the subunits but not yet formed most of the short-range native interactions. We found that the width of the binding funnel and the electrostatic interaction energy of the transient complex are among the features predictive of binders and binding affinities. These ideas were very promising for the five affinity-related targets (T43-45, 55, and 56) of CAPRI rounds 20-27. For T43, we ranked the single crystallographic complex as number 1 and were one of only two groups that clearly identified that complex as a true binder; for T44, we ranked the only design with measurable binding affinity as number 4. For the nine docking targets, continuing on our success in previous CAPRI rounds, we produced 10 medium-quality models for T47 and acceptable models for T48 and T49. We conclude that the interaction energy landscape and the transient complex in particular will complement existing features in leading to better prediction of binding affinities.