Two classes of ouabain binding sites in ferret heart and two forms of Na+-K+-ATPase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ng, Y.C.; Akera, T.

1987-05-01

In partially purified Na+-K+-adenosinetriphosphatase (ATPase) obtained from ferret heart, ouabain produced a monophasic inhibition curve; however, the curve spanned over 5 logarithmic units, indicating the presence of more than one classes of enzyme. (/sup 3/H)ouabain binding studies revealed high-and low-affinity binding sites in approximately equal abundance, with apparent dissociation constants of 10 and 230 nM, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of phosphoenzyme formed from (gamma-/sup 32/P)ATP showed two distinct K+-sensitive bands of approximately 100,000 molecular weight. Phosphoenzyme formation from the high-molecular-weight alpha(+) form was selectively inhibited by N-ethylmaleimide. Ouabain caused a 50% inhibition of phosphorylation of the alpha(+) formmore » at 40 nM and the lower-molecular-weight alpha form at 300 nM. In papillary muscle preparations, 1-30 nM ouabain produced a modest positive inotropic effect that reached an apparent plateau at 30 nM. Further increases in ouabain concentrations, however, produced additional and prominent inotropic effects at 0.1-10 microM. These results indicate for the first time in cardiac muscle that the high- and low-affinity ouabain binding sites are associated with the alpha(+) and alpha forms of the Na+-K+-ATPase, respectively, and that binding of ouabain to either of these sites causes enzyme inhibition and the positive inotropic effect.« less

Acid-base and copper-binding properties of three organic matter fractions isolated from a forest floor soil solution

NASA Astrophysics Data System (ADS)

van Schaik, Joris W. J.; Kleja, Dan B.; Gustafsson, Jon Petter

2010-02-01

Vast amounts of knowledge about the proton- and metal-binding properties of dissolved organic matter (DOM) in natural waters have been obtained in studies on isolated humic and fulvic (hydrophobic) acids. Although macromolecular hydrophilic acids normally make up about one-third of DOM, their proton- and metal-binding properties are poorly known. Here, we investigated the acid-base and Cu-binding properties of the hydrophobic (fulvic) acid fraction and two hydrophilic fractions isolated from a soil solution. Proton titrations revealed a higher total charge for the hydrophilic acid fractions than for the hydrophobic acid fraction. The most hydrophilic fraction appeared to be dominated by weak acid sites, as evidenced by increased slope of the curve of surface charge versus pH at pH values above 6. The titration curves were poorly predicted by both Stockholm Humic Model (SHM) and NICA-Donnan model calculations using generic parameter values, but could be modelled accurately after optimisation of the proton-binding parameters (pH ⩽ 9). Cu-binding isotherms for the three fractions were determined at pH values of 4, 6 and 9. With the optimised proton-binding parameters, the SHM model predictions for Cu binding improved, whereas the NICA-Donnan predictions deteriorated. After optimisation of Cu-binding parameters, both models described the experimental data satisfactorily. Iron(III) and aluminium competed strongly with Cu for binding sites at both pH 4 and pH 6. The SHM model predicted this competition reasonably well, but the NICA-Donnan model underestimated the effects significantly at pH 6. Overall, the Cu-binding behaviour of the two hydrophilic acid fractions was very similar to that of the hydrophobic acid fraction, despite the differences observed in proton-binding characteristics. These results show that for modelling purposes, it is essential to include the hydrophilic acid fraction in the pool of 'active' humic substances.

Kinetic Analyses of Data from a Human Serum Albumin Assay Using the liSPR System.

PubMed

Henseleit, Anja; Pohl, Carolin; Kaltenbach, Hans-Michael; Hettwer, Karina; Simon, Kirsten; Uhlig, Steffen; Haustein, Natalie; Bley, Thomas; Boschke, Elke

2015-01-19

We used the interaction between human serum albumin (HSA) and a high-affinity antibody to evaluate binding affinity measurements by the bench-top liSPR system (capitalis technology GmbH). HSA was immobilized directly onto a carboxylated sensor layer, and the mechanism of interaction between the antibody and HSA was investigated. The bivalence and heterogeneity of the antibody caused a complex binding mechanism. Three different interaction models (1:1 binding, heterogeneous analyte, bivalent analyte) were compared, and the bivalent analyte model best fit the curves obtained from the assay. This model describes the interaction of a bivalent analyte with one or two ligands (A + L ↔ LA + L ↔ LLA). The apparent binding affinity for this model measured 37 pM for the first reaction step, and 20 pM for the second step.

Kinetic Analyses of Data from a Human Serum Albumin Assay Using the liSPR System

PubMed Central

Henseleit, Anja; Pohl, Carolin; Kaltenbach, Hans-Michael; Hettwer, Karina; Simon, Kirsten; Uhlig, Steffen; Haustein, Natalie; Bley, Thomas; Boschke, Elke

2015-01-01

We used the interaction between human serum albumin (HSA) and a high-affinity antibody to evaluate binding affinity measurements by the bench-top liSPR system (capitalis technology GmbH). HSA was immobilized directly onto a carboxylated sensor layer, and the mechanism of interaction between the antibody and HSA was investigated. The bivalence and heterogeneity of the antibody caused a complex binding mechanism. Three different interaction models (1:1 binding, heterogeneous analyte, bivalent analyte) were compared, and the bivalent analyte model best fit the curves obtained from the assay. This model describes the interaction of a bivalent analyte with one or two ligands (A + L ↔ LA + L ↔ LLA). The apparent binding affinity for this model measured 37 pM for the first reaction step, and 20 pM for the second step. PMID:25607476

Universal energy relations and metal/ceramic interfaces

NASA Technical Reports Server (NTRS)

Smith, John R.; Schlosser, Herbert; Ferrante, John

1990-01-01

Known general relationships between pertinent variables are applied to investigate metal-ceramic interfaces. The adhesive energy is determined. The electronic exchange-correlation energy is found to be the dominant attractive term in the total energy. Results for the adhesive energy are obtained for junctions of all combinations of the low index surfaces of Al,Na, Mg, and Zn. This leads to a variety of curves, all with a single minimum of separation and equilibrium binding energy. Scaling results for 10 contacts fall closely onto a single curve, a universal energy relation for adhesion. The scaled chemisorption curves fall accurately on the same universal form that was found for adhesion. For the case of cohesion, all-first principle results are scaled and again all scaled curves for a variety of metals fall accurately on the universal form for adhesion and chemisorption. An intimate relationship between the energetics of solids and molecules is inferred.

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

PubMed Central

Magnus, Carsten

2013-01-01

Antibodies binding to the surface of virions can lead to virus neutralisation. Different theories have been proposed to determine the number of antibodies that must bind to a virion for neutralisation. Early models are based on chemical binding kinetics. Applying these models lead to very low estimates of the number of antibodies needed for neutralisation. In contrast, according to the more conceptual approach of stoichiometries in virology a much higher number of antibodies is required for virus neutralisation by antibodies. Here, we combine chemical binding kinetics with (virological) stoichiometries to better explain virus neutralisation by antibody binding. This framework is in agreement with published data on the neutralisation of the human immunodeficiency virus. Knowing antibody reaction constants, our model allows us to estimate stoichiometrical parameters from kinetic neutralisation curves. In addition, we can identify important parameters that will make further analysis of kinetic neutralisation curves more valuable in the context of estimating stoichiometries. Our model gives a more subtle explanation of kinetic neutralisation curves in terms of single-hit and multi-hit kinetics. PMID:23468602

Ap4A and ADP-beta-S binding to P2 purinoceptors present on rat brain synaptic terminals.

PubMed Central

Pintor, J.; Díaz-Rey, M. A.; Miras-Portugal, M. T.

1993-01-01

1. Diadenosine tetraphosphate (Ap4A) a dinucleotide stored and released from rat brain synaptic terminals presents two types of affinity binding sites in synaptosomes. When [3H]-Ap4A was used for binding studies a Kd value of 0.10 +/- 0.014 nM and a Bmax value of 16.6 +/- 1.2 fmol mg-1 protein were obtained for the high affinity binding site from the Scatchard analysis. The second binding site, obtained by displacement studies, showed a Ki value of 0.57 +/- 0.09 microM. 2. Displacement of [3H]-Ap4A by non-labelled Ap4A and P2-purinoceptor ligands showed a displacement order of Ap4A > adenosine 5'-O-(2-thiodiphosphate) (ADP-beta-S) > 5'-adenylyl-imidodiphosphate (AMP-PNP) > alpha,beta-methylene adenosine 5'-triphosphate (alpha,beta-MeATP) in both sites revealed by the Ki values of 0.017 nM, 0.030 nM, 0.058 nM and 0.147 nM respectively for the high affinity binding site and values of 0.57 microM, 0.87 microM, 2.20 microM and 4.28 microM respectively for the second binding site. 3. Studies of the P2-purinoceptors present in synaptosomes were also performed with [35S]-ADP-beta-S. This radioligand showed two binding sites the first with Kd and Bmax values of 0.11 +/- 0.022 nM and 3.9 +/- 2.1 fmol mg-1 of protein respectively for the high affinity binding site obtained from the Scatchard plot. The second binding site showed a Ki of 0.018 +/- 0.0035 microM obtained from displacement curves. 4. Competition studies with diadenosine polyphosphates of [35S]-ADP-beta-S binding showed a displacement order of Ap4A > Ap5A > Ap6A in the high affinity binding site and Ki values of 0.023 nM, 0.081 nM and 5.72 nM respectively.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8485620

Early stages of clathrin aggregation at a membrane in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Giani, M.; den Otter, W. K.; Briels, W. J.

2017-04-01

The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions

PubMed Central

Greenfield, Norma J.

2009-01-01

Circular dichroism (CD) is an excellent spectroscopic technique for following the unfolding and folding of proteins as a function of temperature. One of its principal applications is to determine the effects of mutations and ligands on protein and polypeptide stability If the change in CD as a function of temperature is reversible, analysis of the data may be used to determined the van't Hoff enthalpy (ΔH) and entropy (ΔS) of unfolding, the midpoint of the unfolding transition (TM) and the free energy (ΔG) of unfolding. Binding constants of protein-protein and protein-ligand interactions may also be estimated from the unfolding curves. Analysis of CD spectra obtained as a function of temperature is also useful to determine whether a protein has unfolding intermediates. Measurement of the spectra of five folded proteins and their unfolding curves at a single wavelength takes approximately eight hours. PMID:17406506

Breakdown of the single-exchange approximation in third-order symmetry-adapted perturbation theory.

PubMed

Lao, Ka Un; Herbert, John M

2012-03-22

We report third-order symmetry-adapted perturbation theory (SAPT) calculations for several dimers whose intermolecular interactions are dominated by induction. We demonstrate that the single-exchange approximation (SEA) employed to derive the third-order exchange-induction correction (E(exch-ind)((30))) fails to quench the attractive nature of the third-order induction (E(ind)((30))), leading to one-dimensional potential curves that become attractive rather than repulsive at short intermolecular separations. A scaling equation for (E(exch-ind)((30))), based on an exact formula for the first-order exchange correction, is introduced to approximate exchange effects beyond the SEA, and qualitatively correct potential energy curves that include third-order induction are thereby obtained. For induction-dominated systems, our results indicate that a "hybrid" SAPT approach, in which a dimer Hartree-Fock calculation is performed in order to obtain a correction for higher-order induction, is necessary not only to obtain quantitative binding energies but also to obtain qualitatively correct potential energy surfaces. These results underscore the need to develop higher-order exchange-induction formulas that go beyond the SEA. © 2012 American Chemical Society

Electronic transport in methylated fragments of DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almeida, M. L. de; Oliveira, J. I. N.; Lima Neto, J. X.

2015-11-16

We investigate the electronic transport properties of methylated deoxyribonucleic-acid (DNA) strands, a biological system in which methyl groups are added to DNA (a major epigenetic modification in gene expression), sandwiched between two metallic platinum electrodes. Our theoretical simulations apply an effective Hamiltonian based on a tight-binding model to obtain current-voltage curves related to the non-methylated/methylated DNA strands. The results suggest potential applications in the development of novel biosensors for molecular diagnostics.

Electronic transport in methylated fragments of DNA

NASA Astrophysics Data System (ADS)

de Almeida, M. L.; Oliveira, J. I. N.; Lima Neto, J. X.; Gomes, C. E. M.; Fulco, U. L.; Albuquerque, E. L.; Freire, V. N.; Caetano, E. W. S.; de Moura, F. A. B. F.; Lyra, M. L.

2015-11-01

We investigate the electronic transport properties of methylated deoxyribonucleic-acid (DNA) strands, a biological system in which methyl groups are added to DNA (a major epigenetic modification in gene expression), sandwiched between two metallic platinum electrodes. Our theoretical simulations apply an effective Hamiltonian based on a tight-binding model to obtain current-voltage curves related to the non-methylated/methylated DNA strands. The results suggest potential applications in the development of novel biosensors for molecular diagnostics.

A quantitative analysis of the effects of 2,3-diphosphoglycerate, adenosine triphosphate and inositol hexaphosphate on the oxygen dissociation curve of human haemoglobin.

PubMed Central

Goodford, P J; St-Louis, J; Wootton, R

1978-01-01

1. Oxygen dissociation curves have been measured for human haemoglobin solutions with different concentrations of the allosteric effectors 2,3-diphosphoglycerate, adenosine triphosphate and inositol hexaphosphate. 2. Each effector produces a concentration dependent right shift of the oxygen dissociation curve, but a point is reached where the shift is maximal and increasing the effector concentration has no further effect. 3. Mathematical models based on the Monod, Wyman & Changeux (1965) treatment of allosteric proteins have been fitted to the data. For each compound the simple two-state model and its extension to take account of subunit inequivalence were shown to be inadequate, and a better fit was obtained by allowing the effector to lower the oxygen affinity of the deoxy conformational state as well as binding preferentially to this conformation. PMID:722582

Differences in the binding mechanism of RU486 and progesterone to the progesterone receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skafar, D.F.

1991-11-12

The binding mechanism of the antagonist RU486 to the progesterone receptor was compared with that of the agonists progesterone and R5020. Both progesterone and RU486 bound to the receptor with a Hill coefficient of 1.2, indicating the binding of each ligand is positive cooperative. However, when each ligand was used to compete with ({sup 3}H)progesterone for binding to the receptor at receptor concentrations near 8 nM, at which the receptor is likely a dimer, the competition curve for RU486 was significantly steeper than the curves for progesterone and R5020. This indicated that a difference in the binding mechanism of RU486more » and progesterone can be detected when both ligands are present. In contrast, at receptor concentrations near 1 nM, at which the receptor is likely a monomer, the competition curves for all three ligands were indistinguishable. These results indicate that RU486 and agonists have different binding mechanisms for the receptor and further suggest that this difference may be related to site-site interactions within the receptor.« less

Determination of the molecular complexation constant between alprostadil and alpha-cyclodextrin by conductometry: implications for a freeze-dried formulation.

PubMed

Sheehy, Philip M; Ramstad, Tore

2005-10-04

The binding constant between alprostadil (PGE1) and alpha-cyclodextrin (alpha-CD) was determined at four temperatures using conductance measurements. Alpha-cyclodextrin is an excipient material in Caverject dual chamber syringe (DCS) that was added to enhance stability. The binding constant was used to calculate the amount of PGE1 free upon reconstitution and injection, since only the free drug is clinically active. The conductivity measurement is based on a decrease in specific conductance as alprostadil is titrated with alpha-CD. The change in conductivity was plotted versus free ligand concentration (alpha-CD) to generate a binding curve. As the value of the binding constant proved to be dependent on substrate concentration, it is really a pseudo binding constant. A value of 742+/-60 M(-1) was obtained for a 0.5 mM solution of alprostadil at 27 degrees C and a value of 550+/-52 M(-1) at 37 degrees C. These results compare favorably to values previously obtained by NMR and capillary electrophoresis. Calculation of the fraction PGE1 free upon reconstitution and injection show it to approach the desired outcome of one. Hence, the amount of drug delivered by Caverject DCS is nominally equivalent to that delivered by Caverject S. Po., a predecessor product that contains no alpha-cyclodextrin.

Investigation of interactions of Comtan with human serum albumin by mathematically modeled voltammetric data: A study from bio-interaction to biosensing.

PubMed

Jalalvand, Ali R; Ghobadi, Sirous; Goicoechea, Hector C; Gu, Hui-Wen; Sanchooli, Esmael

2018-05-16

In this work, voltammetric data recorded at a glassy carbon electrode (GCE) were separately used to investigate the interactions of entacapone (Comtan, CAT) with human serum albumin (HSA). Then, an augmented data matrix was constructed by the combination of voltammetric and spectroscopic data and simultaneously analysed by multivariate curve resolution-alternating least squares (MCR-ALS) to obtain more information about CAT-HSA interactions. The absence of rotational ambiguities in results obtained by MCR-ALS was verified with the help of MCR-BANDS and we confirmed that the results were unambiguous and reliable. Binding of CAT to HSA was also modeled by molecular docking and the results were compatible with those of obtained by recording experimental data. Hard-modeling of combined voltammetric and spectroscopic data by EQUISPEC as an efficient chemometric algorithm helped us to compute binding constant of CAT-HSA complex specie which was in a good agreement with the binding constant value obtained by direct analysis of experimental data. For electrochemical sensing of serum albumin two amperometric measurements were performed to determine HSA in 2-27 nM and 27-70 nM with a limit of detection of 0.51 nM and a sensitivity of 1.84 μA nM -1 . Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular Docking for Prediction and Interpretation of Adverse Drug Reactions.

PubMed

Luo, Heng; Fokoue-Nkoutche, Achille; Singh, Nalini; Yang, Lun; Hu, Jianying; Zhang, Ping

2018-05-23

Adverse drug reactions (ADRs) present a major burden for patients and the healthcare industry. Various computational methods have been developed to predict ADRs for drug molecules. However, many of these methods require experimental or surveillance data and cannot be used when only structural information is available. We collected 1,231 small molecule drugs and 600 human proteins and utilized molecular docking to generate binding features among them. We developed machine learning models that use these docking features to make predictions for 1,533 ADRs. These models obtain an overall area under the receiver operating characteristic curve (AUROC) of 0.843 and an overall area under the precision-recall curve (AUPR) of 0.395, outperforming seven structural fingerprint-based prediction models. Using the method, we predicted skin striae for fluticasone propionate, dermatitis acneiform for mometasone, and decreased libido for irinotecan, as demonstrations. Furthermore, we analyzed the top binding proteins associated with some of the ADRs, which can help to understand and/or generate hypotheses for underlying mechanisms of ADRs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Gold Nanoparticle-Aptamer-Based LSPR Sensing of Ochratoxin A at a Widened Detection Range by Double Calibration Curve Method

NASA Astrophysics Data System (ADS)

Liu, Boshi; Huang, Renliang; Yu, Yanjun; Su, Rongxin; Qi, Wei; He, Zhimin

2018-04-01

Ochratoxin A (OTA) is a type of mycotoxin generated from the metabolism of Aspergillus and Penicillium, and is extremely toxic to humans, livestock, and poultry. However, traditional assays for the detection of OTA are expensive and complicated. Other than OTA aptamer, OTA itself at high concentration can also adsorb on the surface of gold nanoparticles (AuNPs), and further inhibit AuNPs salt aggregation. We herein report a new OTA assay by applying the localized surface plasmon resonance effect of AuNPs and their aggregates. The result obtained from only one single linear calibration curve is not reliable, and so we developed a “double calibration curve” method to address this issue and widen the OTA detection range. A number of other analytes were also examined, and the structural properties of analytes that bind with the AuNPs were further discussed. We found that various considerations must be taken into account in the detection of these analytes when applying AuNP aggregation-based methods due to their different binding strengths.

Homogeneous bioluminescence competitive binding assay for folate based on a coupled glucose-6-phosphate dehydrogenase--bacterial luciferase enzyme system.

PubMed

Huang, W; Feltus, A; Witkowski, A; Daunert, S

1996-05-01

A homogeneous bioluminescence competitive binding assay for folate was developed by using a coupled enzyme system of glucose-6-phosphate dehydrogenase (G6PDH) and bacterial luciferase. A highly substituted G6PDH-folate conjugate was prepared by employing an N-hydroxysuccinimide/carbodiimide method. Folate binding protein inhibits the activity of the conjugate. In the presence of folate, there is a competition between folate and the G6PDH-folate conjugate for the binding site of the folate binding protein, and the activity of the conjugate is recovered. Thus, the concentration of folate can be related to the activity of the G6PDH-folate conjugate, which is directly related to the bioluminescence produced by the coupled enzyme reaction. Using this assay, dose-response curves with a detection limit of 2.5 x 10(-8) M folate were obtained, which is an improvement of an order of magnitude with respect to an assay that monitors G6PDH activity spectrophotometrically. The assay was validated using vitamin tablets and a cell culture medium.

Radioligand binding characterization of the bradykinin B(2) receptor in the rabbit and pig ileal smooth muscle.

PubMed

Meini, Stefania; Cucchi, Paola; Catalani, Claudio; Bellucci, Francesca; Santicioli, Paolo; Giuliani, Sandro; Maggi, Carlo Alberto

2010-06-10

Several species-related differences have been reported in kinin B(2) receptor pharmacology. The present study aimed to evaluate the affinity of the bradykinin B(2) receptor antagonist MEN16132 for the rabbit and pig B(2) receptor, and radioligand binding experiments using [(3)H]bradykinin and membranes of rabbit and pig ileum smooth muscle were conducted. The [(3)H]bradykinin binding was characterized by homologous displacement curves indicating K(d) values of 0.65 and 0.33nM in rabbit and pig, respectively. The B(2) receptor specificity of [(3)H]bradykinin binding was shown by the low affinity (>microM) displayed by agonists ([desArg(9)]bradykinin and Lys[desArg(9)]bradykinin) and antagonists [Leu(8),desArg(9)]bradykinin and Lys[Leu(8),desArg(9)]bradykinin) selective for the B(1) receptor. The affinity of MEN16132 and other antagonists was determined by inhibition curves (pK(i) values in the rabbit and pig assay, respectively): MEN16132 (10.4 and 10.3) and peptide compounds such as icatibant (10.1 and 9.9) and MEN11270 (10.3 and 10.1) displayed subnanomolar potency in both assays; the nonpeptide LF16-0687 (8.4 and 8.5) and FR173657 (8.2 and 9.1) exhibited a different affinity pattern, whereas WIN64338 displayed low affinity (5.7 and

Comparison of cation adsorption by isostructural rutile and cassiterite.

PubMed

Machesky, Michael; Wesolowski, David; Rosenqvist, Jörgen; Předota, Milan; Vlcek, Lukas; Ridley, Moira; Kohli, Vaibhav; Zhang, Zhan; Fenter, Paul; Cummings, Peter; Lvov, Serguei; Fedkin, Mark; Rodriguez-Santiago, Victor; Kubicki, James; Bandura, Andrei

2011-04-19

Macroscopic net proton charging curves for powdered rutile and cassiterite specimens with the (110) crystal face predominant, as a function of pH in RbCl and NaCl solutions, trace SrCl(2) in NaCl, and trace ZnCl(2) in NaCl and Na Triflate solutions, are compared to corresponding molecular-level information obtained from static DFT optimizations and classical MD simulations, as well as synchrotron X-ray methods. The similarities and differences in the macroscopic charging behavior of rutile and cassiterite largely reflect the cation binding modes observed at the molecular level. Cation adsorption is primarily inner-sphere on both isostructural (110) surfaces, despite predictions that outer-sphere binding should predominate on low bulk dielectric constant oxides such as cassiterite (ε(bulk) ≈ 11). Inner-sphere adsorption is also significant for Rb(+) and Na(+) on neutral surfaces, whereas Cl(-) binding is predominately outer-sphere. As negative surface charge increases, relatively more Rb(+), Na(+), and especially Sr(2+) are bound in highly desolvated tetradentate fashion on the rutile (110) surface, largely accounting for enhanced negative charge development relative to cassiterite. Charging curves in the presence of Zn(2+) are very steep but similar for both oxides, reflective of Zn(2+) hydrolysis (and accompanying proton release) during the adsorption process, and the similar binding modes for ZnOH(+) on both surfaces. These results suggest that differences in cation adsorption between high and low bulk dielectric constant oxides are more subtly related to the relative degree of cation desolvation accompanying inner-sphere binding (i.e., more tetradentate binding on rutile), rather than distinct inner- and outer-sphere adsorption modes. Cation desolvation may be favored at the rutile (110) surface in part because inner-sphere water molecules are bound further from and less tightly than on the cassiterite (110) surface. Hence, their removal upon inner-sphere cation binding is relatively more favorable. © 2011 American Chemical Society

Novel 18F-Labeled κ-Opioid Receptor Antagonist as PET Radiotracer: Synthesis and In Vivo Evaluation of 18F-LY2459989 in Nonhuman Primates.

PubMed

Li, Songye; Cai, Zhengxin; Zheng, Ming-Qiang; Holden, Daniel; Naganawa, Mika; Lin, Shu-Fei; Ropchan, Jim; Labaree, David; Kapinos, Michael; Lara-Jaime, Teresa; Navarro, Antonio; Huang, Yiyun

2018-01-01

The κ-opioid receptor (KOR) has been implicated in depression, addictions, and other central nervous system disorders and, thus, is an important target for drug development. We previously developed several 11 C-labeled PET radiotracers for KOR imaging in humans. Here we report the synthesis and evaluation of 18 F-LY2459989 as the first 18 F-labeled KOR antagonist radiotracer in nonhuman primates and its comparison with 11 C-LY2459989. Methods: The novel radioligand 18 F-LY2459989 was synthesized by 18 F displacement of a nitro group or an iodonium ylide. PET scans in rhesus monkeys were obtained on a small-animal scanner to assess the pharmacokinetic and in vivo binding properties of the ligand. Metabolite-corrected arterial activity curves were measured and used as input functions in the analysis of brain time-activity curves and the calculation of binding parameters. Results: With the iodonium ylide precursor, 18 F-LY2459989 was prepared at high radiochemical yield (36% ± 7% [mean ± SD]), radiochemical purity (>99%), and mean molar activity (1,175 GBq/μmol; n = 6). In monkeys, 18 F-LY2459989 was metabolized at a moderate rate, with a parent fraction of approximately 35% at 30 min after injection. Fast and reversible kinetics were observed, with a regional peak uptake time of less than 20 min. Pretreatment with the selective KOR antagonist LY2456302 (0.1 mg/kg) decreased the activity level in regions with high levels of binding to that in the cerebellum, thus demonstrating the binding specificity and selectivity of 18 F-LY2459989 in vivo. Regional time-activity curves were well fitted by the multilinear analysis 1 kinetic model to derive reliable estimates of regional distribution volumes. With the cerebellum as the reference region, regional binding potentials were calculated and ranked as follows: cingulate cortex > insula > caudate/putamen > frontal cortex > temporal cortex > thalamus, consistent with the reported KOR distribution in the monkey brain. Conclusion: The evaluation of 18 F-LY2459989 in nonhuman primates demonstrated many attractive imaging properties: fast tissue kinetics, specific and selective binding to the KOR, and high specific binding signals. A side-by-side comparison of 18 F-LY2459989 and 11 C-LY2459989 indicated similar kinetic and binding profiles for the 2 radiotracers. Taken together, the results indicated that 18 F-LY2459989 appears to be an excellent PET radiotracer for the imaging and quantification of the KOR in vivo. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Binding of KATP channel modulators in rat cardiac membranes

PubMed Central

Löffler-Walz, Cornelia; Quast, Ulrich

1998-01-01

The binding of [3H]-P1075, a potent opener of adenosine-5′-triphosphate-(ATP)-sensitive K+ channels, was studied in a crude heart membrane preparation of the rat, at 37°C.Binding required MgATP. In the presence of an ATP-regenerating system, MgATP supported [3H]-P1075 binding with an EC50 value of 100 μM and a Hill coefficient of 1.4.In saturation experiments [3H]-P1075 binding was homogeneous with a KD value of 6±1 nM and a binding capacity (Bmax) of 33±3 fmol mg−1 protein.Upon addition of an excess of unlabelled P1075, the [3H]-P1075-receptor complex dissociated in a mono-exponential manner with a dissociation rate constant of 0.13±0.01 min−1. If a bi-molecular association mechanism was assumed, the dependence of the association kinetics on label concentration gave an association rate constant of 0.030±0.003 nM−1 min−1. From the kinetic experiments the KD value was calculated as 4.7±0.6 nM.Openers of the ATP-sensitive K+ channel belonging to different structural classes inhibited specific [3H]-P1075 binding in a monophasic manner to completion; an exception was minoxidil sulphate where maximum inhibition was 68%. The potencies of the openers in this assay agree with published values obtained in rat cardiocytes and are on average 3.5 times lower than those determined in rat aorta.Sulphonylureas, such as glibenclamide and glibornuride and the sulphonylurea-related carboxylate, AZ-DF 265, inhibited [3H]-P1075 binding with biphasic inhibition curves. The high affinity component comprised about 60% of the curves with the IC50 value of glibenclamide being ≈amp;90 nM; affinities for the low affinity component were in the μM concentration range. The fluorescein derivative, phloxine B, showed a monophasic inhibition curve with an IC50 value of 6 μM, a maximum inhibition of 94% and a Hill coefficient of 1.5.It is concluded that binding studies with [3H]-P1075 are feasible in rat heart membranes in the presence of MgATP and of an ATP-regenerating system. The pharmacological profile of the [3H]-P1075 binding sites in the cardiac preparation, which probably contains sulphonylurea receptors (SURs) from cardiac myocytes (SUR2A) and vascular smooth muscle cells (SUR2B), differs from that expected for SUR2A and SUR2B. PMID:9579735

Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction.

PubMed

Eble, Johannes A

2018-02-15

The dissociation constant describes the interaction between two partners in the binding equilibrium and is a measure of their affinity. It is a crucial parameter to compare different ligands, e.g., competitive inhibitors, protein isoforms and mutants, for their binding strength to a binding partner. Dissociation constants are determined by plotting concentrations of bound versus free ligand as binding curves. In contrast, titration curves, in which a signal that is proportional to the concentration of bound ligand is plotted against the total concentration of added ligand, are much easier to record. The signal can be detected spectroscopically and by enzyme-linked immunosorbent assay (ELISA). This is exemplified in a protocol for a titration ELISA that measures the binding of the snake venom-derived rhodocetin to its immobilized target domain of α2β1 integrin. Titration ELISAs are versatile and widely used. Any pair of interacting proteins can be used as immobilized receptor and soluble ligand, provided that both proteins are pure, and their concentrations are known. The difficulty so far has been to determine the dissociation constant from a titration curve. In this study, a mathematical function underlying titration curves is introduced. Without any error-prone graphical estimation of a saturation yield, this algorithm allows processing of the raw data (signal intensities at different concentrations of added ligand) directly by mathematical evaluation via non-linear regression. Thus, several titration curves can be recorded simultaneously and transformed into a set of characteristic parameters, among them the dissociation constant and the concentration of binding-active receptor, and they can be evaluated statistically. When combined with this algorithm, titration ELISAs gain the advantage of directly presenting the dissociation constant. Therefore, they may be used more efficiently in the future.

Kinetic mechanism of Escherichia coli isocitrate dehydrogenase and its inhibition by glyoxylate and oxaloacetate.

PubMed Central

Nimmo, H G

1986-01-01

The inhibition of Escherichia coli isocitrate dehydrogenase by glyoxylate and oxaloacetate was examined. The shapes of the progress curves in the presence of the inhibitors depended on the order of addition of the assay components. When isocitrate dehydrogenase or NADP+ was added last, the rate slowly decreased until a new, inhibited, steady state was obtained. When isocitrate was added last, the initial rate was almost zero, but the rate increased slowly until the same steady-state value was obtained. Glyoxylate and oxaloacetate gave competitive inhibition against isocitrate and uncompetitive inhibition against NADP+. Product-inhibition studies showed that isocitrate dehydrogenase obeys a compulsory-order mechanism, with coenzyme binding first. Glyoxylate and oxaloacetate bind to and dissociate from isocitrate dehydrogenase slowly. These observations can account for the shapes of the progress curves observed in the presence of the inhibitors. Condensation of glyoxylate and oxaloacetate produced an extremely potent inhibitor of isocitrate dehydrogenase. Analysis of the reaction by h.p.l.c. showed that this correlated with the formation of oxalomalate. This compound decomposed spontaneously in assay mixtures, giving 4-hydroxy-2-oxoglutarate, which was a much less potent inhibitor of the enzyme. Oxalomalate inhibited isocitrate dehydrogenase competitively with respect to isocitrate and was a very poor substrate for the enzyme. The data suggest that the inhibition of isocitrate dehydrogenase by glyoxylate and oxaloacetate is not physiologically significant. PMID:3521584

Competition effects in cation binding to humic acid: Conditional affinity spectra for fixed total metal concentration conditions

NASA Astrophysics Data System (ADS)

David, Calin; Mongin, Sandrine; Rey-Castro, Carlos; Galceran, Josep; Companys, Encarnació; Garcés, José Luis; Salvador, José; Puy, Jaume; Cecilia, Joan; Lodeiro, Pablo; Mas, Francesc

2010-09-01

Information on the Pb and Cd binding to a purified Aldrich humic acid (HA) is obtained from the influence of different fixed total metal concentrations on the acid-base titrations of this ligand. NICA (Non-Ideal Competitive Adsorption) isotherm has been used for a global quantitative description of the binding, which has then been interpreted by plotting the Conditional Affinity Spectra of the H + binding at fixed total metal concentrations (CAScTM). This new physicochemical tool, here introduced, allows the interpretation of binding results in terms of distributions of proton binding energies. A large increase in the acidity of the phenolic sites as the total metal concentration increases, especially in presence of Pb, is revealed from the shift of the CAScTM towards lower affinities. The variance of the CAScTM distribution, which can be used as a direct measure of the heterogeneity, also shows a significant dependence on the total metal concentration. A discussion of the factors that influence the heterogeneity of the HA under the conditions of each experiment is provided, so that the smoothed pattern exhibited by the titration curves can be justified.

Universal binding energy relations in metallic adhesion

NASA Technical Reports Server (NTRS)

Ferrante, J.; Smith, J. R.; Rose, J. H.

1981-01-01

Scaling relations which map metallic adhesive binding energy onto a single universal binding energy curve are discussed in relation to adhesion, friction, and wear in metals. The scaling involved normalizing the energy to the maximum binding energy and normalizing distances by a suitable combination of Thomas-Fermi screening lengths. The universal curve was found to be accurately represented by E*(A*)= -(1+beta A) exp (-Beta A*) where E* is the normalized binding energy, A* is the normalized separation, and beta is the normalized decay constant. The calculated cohesive energies of potassium, barium, copper, molybdenum, and samarium were also found to scale by similar relations, suggesting that the universal relation may be more general than for the simple free electron metals.

Anomalous diffusion and dynamics of fluorescence recovery after photobleaching in the random-comb model

NASA Astrophysics Data System (ADS)

Yuste, S. B.; Abad, E.; Baumgaertner, A.

2016-07-01

We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ ,P (ℓ ) ˜ℓ-(1 +α ) (α >0 ). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems.

Conductance of single microRNAs chains related to the autism spectrum disorder

NASA Astrophysics Data System (ADS)

Oliveira, J. I. N.; Albuquerque, E. L.; Fulco, U. L.; Mauriz, P. W.; Sarmento, R. G.; Caetano, E. W. S.; Freire, V. N.

2014-09-01

The charge transport properties of single-stranded microRNAs (miRNAs) chains associated to autism disorder were investigated. The computations were performed within a tight-binding model, together with a transfer matrix technique, with ionization energies and hopping parameters obtained by quantum chemistry method. Current-voltage (I× V) curves of twelve miRNA chains related to the autism spectrum disorders were calculated and analysed. We have obtained both semiconductor and insulator behavior, and a relationship between the current intensity and the autism-related miRNA bases sequencies, suggesting that a kind of electronic biosensor can be developed to distinguish different profiles of autism disorders.

Electrochemical and spectroscopic study on the interaction between isoprenaline and DNA using multivariate curve resolution-alternating least squares.

PubMed

Ni, Yongnian; Wei, Min; Kokot, Serge

2011-11-01

Interaction of isoprenaline (ISO) with calf-thymus DNA was studied by spectroscopic and electrochemical methods. The behavior of ISO was investigated at a glassy carbon electrode (GCE) by cyclic voltammetry (CV) and differential pulse stripping voltammetry (DPSV); ISO was oxidized and an irreversible oxidation peak was observed. The binding constant K and the stoichiometric coefficient m of ISO with DNA were evaluated. Also, with the addition of DNA, hyperchromicity of the UV-vis absorption spectra of ISO was noted, while the fluorescence intensity decreased significantly. Multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics method was applied to resolve the combined spectroscopic data matrix, which was obtained by the UV-vis and fluorescence methods. Pure spectra of ISO, DNA and ISO-DNA complex, and their concentration profiles were then successfully obtained. The results indicated that the ISO molecule intercalated into the base-pairs of DNA, and the complex of ISO-DNA was formed. Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of geometry and scale for axial and radial flow membrane chromatography-Experimental study of bovin serum albumin adsorption.

PubMed

Teepakorn, Chalore; Fiaty, Koffi; Charcosset, Catherine

2015-07-17

During the last 10 years, membrane chromatography (MC) has been increasingly reported for biomolecule purification at both small and large scales. Although, several axial and radial flow MC devices are commercialized, the effect of the device dimensions on the adsorption performance has not been fully investigated. In this study, axial and radial flow anion ion-exchange MC devices were used for bovine serum albumin (BSA) adsorption. For both axial and radial flow, three devices at different scales were compared, two having similar diameter and two similar bed height. The pressure drop and the flow distribution using acetone as a non-binding solute were measured, as well as BSA breakthrough curves at different flow rates and BSA loading concentrations. For all devices, it was observed that the flow rate had no effect on the breakthrough curve, which confirms the advantage of MC to be used at high flow rates. In addition, the BSA binding capacity increased with increasing BSA concentration, which suggests that it could be preferable to work with concentrated solutions rather than with very dilute solutions, when using buffer at high phosphate concentration. For both axial and radial flow, the bed height had a negative impact on the binding capacity, as the lowest binding capacities per membrane volume were obtained with the devices having the highest bed height. Radial flow MC has potential at large-scale applications, as a short bed thickness can be combined with a large inlet surface area. Copyright © 2015 Elsevier B.V. All rights reserved.

Valerian extract and valerenic acid are partial agonists of the 5-HT5a receptor in vitro.

PubMed

Dietz, Birgit M; Mahady, Gail B; Pauli, Guido F; Farnsworth, Norman R

2005-08-18

Insomnia is the most frequently encountered sleep complaint worldwide. While many prescription drugs are used to treat insomnia, extracts of valerian (Valeriana officinalis L., Valerianaceae) are also used for the treatment of insomnia and restlessness. To determine novel mechanisms of action, radioligand binding studies were performed with valerian extracts (100% methanol, 50% methanol, dichloromethane [DCM], and petroleum ether [PE]) at the melatonin, glutamate, and GABA(A) receptors, and 8 serotonin receptor subtypes. Both DCM and PE extracts had strong binding affinity to the 5-HT(5a) receptor, but only weak binding affinity to the 5-HT(2b) and the serotonin transporter. Subsequent binding studies focused on the 5-HT(5a) receptor due to the distribution of this receptor in the suprachiasmatic nucleus of the brain, which is implicated in the sleep-wake cycle. The PE extract inhibited [(3)H]lysergic acid diethylamide (LSD) binding to the human 5-HT(5a) receptor (86% at 50 microg/ml) and the DCM extract inhibited LSD binding by 51%. Generation of an IC(50) curve for the PE extract produced a biphasic curve, thus GTP shift experiments were also performed. In the absence of GTP, the competition curve was biphasic (two affinity sites) with an IC(50) of 15.7 ng/ml for the high-affinity state and 27.7 microg/ml for the low-affinity state. The addition of GTP (100 microM) resulted in a right-hand shift of the binding curve with an IC(50) of 11.4 microg/ml. Valerenic acid, the active constituent of both extracts, had an IC(50) of 17.2 microM. These results indicate that valerian and valerenic acid are new partial agonists of the 5-HT(5a) receptor.

Valerian extract and valerenic acid are partial agonists of the 5-HT5a receptor in vitro

PubMed Central

Dietz, Birgit M.; Mahady, Gail B.; Pauli, Guido F.; Farnsworth, Norman R.

2018-01-01

Insomnia is the most frequently encountered sleep complaint worldwide. While many prescription drugs are used to treat insomnia, extracts of valerian (Valeriana officinalis L., Valerianaceae) are also used for the treatment of insomnia and restlessness. To determine novel mechanisms of action, radioligand binding studies were performed with valerian extracts (100% methanol, 50% methanol, dichloromethane [DCM], and petroleum ether [PE]) at the melatonin, glutamate, and GABAA receptors, and 8 serotonin receptor subtypes. Both DCM and PE extracts had strong binding affinity to the 5-HT5a receptor, but only weak binding affinity to the 5-HT2b and the serotonin transporter. Subsequent binding studies focused on the 5-HT5a receptor due to the distribution of this receptor in the suprachiasmatic nucleus of the brain, which is implicated in the sleep–wake cycle. The PE extract inhibited [3H]lysergic acid diethylamide (LSD) binding to the human 5-HT5a receptor (86% at 50 μg/ml) and the DCM extract inhibited LSD binding by 51%. Generation of an IC50 curve for the PE extract produced a biphasic curve, thus GTP shift experiments were also performed. In the absence of GTP, the competition curve was biphasic (two affinity sites) with an IC50 of 15.7 ng/ml for the high-affinity state and 27.7 μg/ml for the low-affinity state. The addition of GTP (100 AM) resulted in a right-hand shift of the binding curve with an IC50 of 11.4 μg/ml. Valerenic acid, the active constituent of both extracts, had an IC50 of 17.2 AM. These results indicate that valerian and valerenic acid are new partial agonists of the 5-HT5a receptor. PMID:15921820

Prediction of Nucleotide Binding Peptides Using Star Graph Topological Indices.

PubMed

Liu, Yong; Munteanu, Cristian R; Fernández Blanco, Enrique; Tan, Zhiliang; Santos Del Riego, Antonino; Pazos, Alejandro

2015-11-01

The nucleotide binding proteins are involved in many important cellular processes, such as transmission of genetic information or energy transfer and storage. Therefore, the screening of new peptides for this biological function is an important research topic. The current study proposes a mixed methodology to obtain the first classification model that is able to predict new nucleotide binding peptides, using only the amino acid sequence. Thus, the methodology uses a Star graph molecular descriptor of the peptide sequences and the Machine Learning technique for the best classifier. The best model represents a Random Forest classifier based on two features of the embedded and non-embedded graphs. The performance of the model is excellent, considering similar models in the field, with an Area Under the Receiver Operating Characteristic Curve (AUROC) value of 0.938 and true positive rate (TPR) of 0.886 (test subset). The prediction of new nucleotide binding peptides with this model could be useful for drug target studies in drug development. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.

PubMed

Wang, Lian; Pan, Danling; Hu, Xihao; Xiao, Jinyu; Gao, Yangyang; Zhang, Huifang; Zhang, Yan; Liu, Juan; Zhu, Shanfeng

2009-05-01

Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.

A hybrid deconvolution approach for estimation of in vivo non-displaceable binding for brain PET targets without a reference region

PubMed Central

Mann, J. John; Ogden, R. Todd

2017-01-01

Background and aim Estimation of a PET tracer’s non-displaceable distribution volume (VND) is required for quantification of specific binding to its target of interest. VND is generally assumed to be comparable brain-wide and is determined either from a reference region devoid of the target, often not available for many tracers and targets, or by imaging each subject before and after blocking the target with another molecule that has high affinity for the target, which is cumbersome and involves additional radiation exposure. Here we propose, and validate for the tracers [11C]DASB and [11C]CUMI-101, a new data-driven hybrid deconvolution approach (HYDECA) that determines VND at the individual level without requiring either a reference region or a blocking study. Methods HYDECA requires the tracer metabolite-corrected concentration curve in blood plasma and uses a singular value decomposition to estimate the impulse response function across several brain regions from measured time activity curves. HYDECA decomposes each region’s impulse response function into the sum of a parametric non-displaceable component, which is a function of VND, assumed common across regions, and a nonparametric specific component. These two components differentially contribute to each impulse response function. Different regions show different contributions of the two components, and HYDECA examines data across regions to find a suitable common VND. HYDECA implementation requires determination of two tuning parameters, and we propose two strategies for objectively selecting these parameters for a given tracer: using data from blocking studies, and realistic simulations of the tracer. Using available test-retest data, we compare HYDECA estimates of VND and binding potentials to those obtained based on VND estimated using a purported reference region. Results For [11C]DASB and [11C]CUMI-101, we find that regardless of the strategy used to optimize the tuning parameters, HYDECA provides considerably less biased estimates of VND than those obtained, as is commonly done, using a non-ideal reference region. HYDECA test-retest reproducibility is comparable to that obtained using a VND determined from a non-ideal reference region, when considering the binding potentials BPP and BPND. Conclusions HYDECA can provide subject-specific estimates of VND without requiring a blocking study for tracers and targets for which a valid reference region does not exist. PMID:28459878

Principles for designing proteins with cavities formed by curved β sheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marcos, Enrique; Basanta, Benjamin; Chidyausiku, Tamuka M.

Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheetmore » curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.« less

A model of high-affinity antibody binding to type III group B Streptococcus capsular polysaccharide.

PubMed

Wessels, M R; Muñoz, A; Kasper, D L

1987-12-01

We recently reported that the single repeating-unit pentasaccharide of type III group B Streptococcus (GBS) capsular polysaccharide is only weakly reactive with type III GBS antiserum. To further elucidate the relationship between antigen-chain length and antigenicity, tritiated oligosaccharides derived from type III capsular polysaccharide were used to generate detailed saturation binding curves with a fixed concentration of rabbit antiserum in a radioactive antigen-binding assay. A graded increase in affinity of antigen-antibody binding was seen as oligosaccharide size increased from 2.6 repeating units to 92 repeating units. These differences in affinity of antibody binding to oligosaccharides of different molecular size were confirmed by immunoprecipitation and competitive ELISA, two independent assays of antigen-antibody binding. Analysis of the saturation binding experiment indicated a difference of 300-fold in antibody-binding affinity for the largest versus the smallest tested oligosaccharides. Unexpectedly, the saturation binding values approached by the individual curves were inversely related to oligosaccharide chain length on a molar basis but equivalent on a weight basis. This observation is compatible with a model in which binding of an immunoglobulin molecule to an antigenic site on the polysaccharide facilitates subsequent binding of antibody to that antigen.

Plasma fatty acid-binding protein 4 (FABP4) as a novel biomarker to predict gestational diabetes mellitus.

PubMed

Ning, Hui; Tao, Hong; Weng, Zhanping; Zhao, Xingbo

2016-12-01

Fatty acid-binding protein 4 (FABP4) is mainly expressed in adipocytes and macrophages and is demonstrated to be elevated in diabetes patients. The aim of this study was to evaluate the possible role of FABP4 in the diagnosis of GDM and to investigate the relationship between FABP4 and overweight, insulin resistance and inflammatory marker TNF-α. A total of 46 women with GDM and 55 age-matched pregnant women without GDM (non-GDM) were eligible for the study. Demographic and biochemical parameters and fasting venous blood samples of two groups were collected from all cases. Serum concentrations of FABP4 were determined using enzyme-linked immunosorbent assay (ELISA). The predictive value of Serum FABP4 level was evaluated using receiver operating characteristic curve (ROC curve) analysis. We found that the serum FABP4 levels were significantly higher in GDM compared to the non-GDM group. The area under the ROC curve assay yielded a satisfactory result of 0.94 (95 % confidence interval 0.90-0.98; p < 0.001). The best compromise between 86.96 % specificity and 89.09 % sensitivity was obtained with a cutoff value of 1.96 ng/mL for GDM diagnosis. Moreover, a significant positive correlation was observed between FABP4 and overweight, insulin resistance and TNF-α in pregnant women with GDM. These results suggest that serum FABP4 may potentially serve as a novel biomarker for the prediction of GDM.

Is nuclear matter a quantum crystal?

NASA Technical Reports Server (NTRS)

Canuto, V.; Chitre, S. M.

1973-01-01

A possible alternative to the ordinary gas-like computation for nuclear matter is investigated under the assumption that the nucleons are arranged in a lattice. BCC, FCC and HCP structures are investigated. Only HCP shows a minimum in the energy vs. density curve with a modest binding energy of -1.5 MeV. The very low density limit is investigated and sensible results are obtained only if the tensor force decreases with the density. A study of the elastic properties indicates that the previous structures are mechanically unstable against shearing stresses.

Biomolecular Interaction Analysis Using an Optical Surface Plasmon Resonance Biosensor: The Marquardt Algorithm vs Newton Iteration Algorithm

PubMed Central

Hu, Jiandong; Ma, Liuzheng; Wang, Shun; Yang, Jianming; Chang, Keke; Hu, Xinran; Sun, Xiaohui; Chen, Ruipeng; Jiang, Min; Zhu, Juanhua; Zhao, Yuanyuan

2015-01-01

Kinetic analysis of biomolecular interactions are powerfully used to quantify the binding kinetic constants for the determination of a complex formed or dissociated within a given time span. Surface plasmon resonance biosensors provide an essential approach in the analysis of the biomolecular interactions including the interaction process of antigen-antibody and receptors-ligand. The binding affinity of the antibody to the antigen (or the receptor to the ligand) reflects the biological activities of the control antibodies (or receptors) and the corresponding immune signal responses in the pathologic process. Moreover, both the association rate and dissociation rate of the receptor to ligand are the substantial parameters for the study of signal transmission between cells. A number of experimental data may lead to complicated real-time curves that do not fit well to the kinetic model. This paper presented an analysis approach of biomolecular interactions established by utilizing the Marquardt algorithm. This algorithm was intensively considered to implement in the homemade bioanalyzer to perform the nonlinear curve-fitting of the association and disassociation process of the receptor to ligand. Compared with the results from the Newton iteration algorithm, it shows that the Marquardt algorithm does not only reduce the dependence of the initial value to avoid the divergence but also can greatly reduce the iterative regression times. The association and dissociation rate constants, ka, kd and the affinity parameters for the biomolecular interaction, KA, KD, were experimentally obtained 6.969×105 mL·g-1·s-1, 0.00073 s-1, 9.5466×108 mL·g-1 and 1.0475×10-9 g·mL-1, respectively from the injection of the HBsAg solution with the concentration of 16ng·mL-1. The kinetic constants were evaluated distinctly by using the obtained data from the curve-fitting results. PMID:26147997

The correlation between ouabain binding and potassium pump inhibition in human and sheep erythrocytes.

PubMed Central

Joiner, C H; Lauf, P K

1978-01-01

1. [3H]Ouabain binding to human and sheep red blood cells was shown to be specific for receptors associated with Na/K transport. Virtually all tritium binding was abolished by dilution with unlabelled drug. Saturation levels of binding were independent of glycoside concentration and were identical to those associated with 100% inhibition of K pumping. 2. [3H]Ouabain binding and 42K influx were measured simultaneously in order to correlate the degree of K pump inhibition with the amount of glycoside bound. Results by this method agreed exactly with those obtained by pre-exposing cells to drug, followed by washing and then measuring K influx. 3. Plots of [3H]oubain binding vs. K pump inhibition were rectilinear for human and low K (LK) sheep red cells, indicating one glycoside receptor per K pump site and functional homogeneity of pump sites. High K (HK) sheep red cells exhibited curved plots of binding versus inhibition, which were best explained in terms of one receptor per pump, but a heterogeneous population of pump sites. 4. External K reduced the rate of glycoside binding, but did not alter the relationship between binding and inhibition. 5. The number of K pump sites was estimated as 450--500 per human cell and 30--50 per LK sheep cell. HK sheep cells had 90--130 sites per cell, of which eighty to ninety were functionally dominant. The number of K pump sites on LK sheep cells was not changed by anti-L, although the maximum velocity of pump turnover was increased. PMID:722573

Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching

PubMed Central

Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W.; Knoch, Tobias A.; Waldeck, Waldemar; Langowski, Jörg

2003-01-01

Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of ∼13 s. PMID:12719264

Analyzing intracellular binding and diffusion with continuous fluorescence photobleaching.

PubMed

Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W; Knoch, Tobias A; Waldeck, Waldemar; Langowski, Jörg

2003-05-01

Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of approximately 13 s.

Influence of binding pH and protein solubility on the dynamic binding capacity in hydrophobic interaction chromatography.

PubMed

Baumann, Pascal; Baumgartner, Kai; Hubbuch, Jürgen

2015-05-29

Hydrophobic interaction chromatography (HIC) is one of the most frequently used purification methods in biopharmaceutical industry. A major drawback of HIC, however, is the rather low dynamic binding capacity (DBC) obtained when compared to e.g. ion exchange chromatography (IEX). The typical purification procedure for HIC includes binding at neutral pH, independently of the proteins nature and isoelectric point. Most approaches to process intensification are based on resin and salt screenings. In this paper a combination of protein solubility data and varying binding pH leads to a clear enhancement of dynamic binding capacity. This is shown for three proteins of acidic, neutral, and alkaline isoelectric points. High-throughput solubility screenings as well as miniaturized and parallelized breakthrough curves on Media Scout RoboColumns (Atoll, Germany) were conducted at pH 3-10 on a fully automated robotic workstation. The screening results show a correlation between the DBC and the operational pH, the protein's isoelectric point and the overall solubility. Also, an inverse relationship of DBC in HIC and the binding kinetics was observed. By changing the operational pH, the DBC could be increased up to 30% compared to the standard purification procedure performed at neutral pH. As structural changes of the protein are reported during HIC processes, the applied samples and the elution fractions were proven not to be irreversibly unfolded. Copyright © 2015 Elsevier B.V. All rights reserved.

Fluorescence correlation spectroscopy study of the complexation of DNA hybrids, IgG antibody, and a chimeric protein of IgG-binding ZZ domains fused with a carbohydrate binding module.

PubMed

Rosa, A M M; Prazeres, D M F; Paulo, P M R

2017-06-28

Fluorescence correlation spectroscopy (FCS) was used to characterize the molecular interactions between the four components of a DNA recognition system. A fluorescent DNA probe was used to assess: (i) the hybridization with a complementary biotin-labeled target, (ii) the complexation of the resulting hybrid and an anti-biotin antibody, and (iii) the binding of the latter complex to a ZZ-CBM fusion protein that combines small synthetic IgG Fc-binding Z domains with a carbohydrate binding module (CBM). These binding interactions were monitored by exposing the fluorescent DNA probe to different amounts and combinations of the other molecules in solution. Through the analysis of FCS autocorrelation curves, an association constant (K a ) of 2.9 × 10 7 M -1 was estimated for DNA·DNA hybridization, and the presence of (non-) complementary target DNA in solution could be discriminated. The specific capture of biotinylated DNA hybrids by anti-biotin IgG was verified, with an apparent K a of 2.5 × 10 6 M -1 . The increment in the diffusion time measured when the DNA·DNA:antibody complexes were in contact with the ZZ-CBM fusion protein suggested that the binding occurs at a stoichiometric ratio of DNA/antibody complex to fusion larger than 1 : 1. The FCS-derived information obtained is useful to gain insight into molecular interactions involved in diagnostic assays.

Identification and quantification of human kidney atrial natriuretic peptide receptors.

PubMed

Kahana, L; Yechiely, H; Mecz, Y; Lurie, A

1995-04-01

The present study determined 125I-label atrial natriuretic peptide (ANP) binding sites in human kidney glomerular and papillary membranes. The membranes were prepared from non-malignant renal tissue obtained at nephrectomy of patients with renal carcinoma. To evaluate the proportion of ANP receptor classes ANP-R1 (ANPR-A, -B) versus ANP-R2 (ANPR-C), competitive binding studies were performed using [125I]-ANP in the presence of increasing concentrations of ANP or an internally ring-deleted analog, des(Gln116, Ser117, Gly118, Leu119, Gly120)ANP(102-121), called C-ANP, which binds selectively to ANPR-C receptors. Analysis of the competitive binding curve with ANP in glomerular membranes suggested the presence of one group of high-affinity receptors with dissociation constant Kd = 26 +/- 12 pmol/l and density Bmax = 101 +/- 47 nmol/kg protein. A decrease of 10-30% in Bmax with no change in Kd was obtained in the presence of excess (10(-6) mol/l) C-ANP, suggesting the existence of a small amount of a second class of receptors, the ANPR-C class. The densities of ANPR-A, -B versus ANPR-C receptors in human glomeruli, calculated from competitive inhibition experiments, were 75 +/- 42 and 22 +/- 16 nmol/kg protein (N = 8). Autoradiography of the sodium dodecyl sulfate polyacrylamide gel electrophoresis under reducing conditions showed two bands: a highly labeled 130kD band and a weakly labeled 66 kD band, both displaced by ANP. Only the 66-kD band was displaced by the C-ANP analog. Human papilla membrane, as shown by competition binding studies and SDS gel electrophoresis, presented only one class of receptors with Kd = 40 +/- 23 pmol/l (mean +/- SD, N = 3) and Bmax = 17 +/- 6.3 nmol/kg protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Different components of /sup 3/H-imipramine binding in rat brain membranes: relation to serotonin uptake sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gobbi, M.; Taddei, C.; Mennini, T.

1988-01-01

In the present paper, the authors confirm and extend previous studies showing heterogeneous /sup 3/H-imipramine (/sup 3/H-IMI) binding sites. Inhibition curves of various drugs (serotonin, imipramine, desmethyl-imipramine, d-fenfluramine, d-norfenfluramine and indalpine, a potent serotonin uptake inhibitor) obtained using 2 nM /sup 3/H-IMI and in presence of 120 mM NaCl, confirmed the presence of at least three /sup 3/H-IMI binding sites: two of these were serotonin-insensitive while the third one was selectively inhibited by serotonin and indalpine with nanomolar affinities. Moreover this last component was found to be selectively modulated by chronic imipramine treatment thus suggesting a close relation to serontoninmore » uptake mechanism. These data indicate that the use of a more selective inhibitors of the serotonin-sensitive component (like indalpine or serotonin itself) to define non specific /sup 3/H-IMI, may be of help in understanding its relation with serotonin uptake system. 22 references, 2 figures, 2 tables.« less

Interaction of berberine with human platelet. alpha. sub 2 adrenoceptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hui, Ka Kit; Yu, Jun Liang; Chan, Wai Fong A.

1991-01-01

Berberine was found to inhibit competitively the specific binding of ({sup 3}H)-yohimbine. The displacement curve was parallel to those of clonidine, epinephrine, norepinephrine, with the rank order of potency (IC{sub 50}) being clonidine {gt} epinephrine {gt} norepinephrine (14.5 {mu}M) = berberine. Increasing concentrations of berberine from 0.1 {mu}M to 10 {mu}M inhibited ({sup 3}H)-yohimbine binding, shifting the saturation binding curve to the right without decreasing the maximum binding capacity. In platelet cyclic AMP accumulation experiments, berberine at concentrations of 0.1 {mu}M to 0.1 mM inhibited the cAMP accumulation induced by 10 {mu}M prostaglandin E{sub 1} in a dose dependent manner,more » acting as an {alpha}{sub 2} adrenoceptor agonist. In the presence of L-epinephrine, berberine blocked the inhibitory effect of L-epinephrine behaving as an {alpha}{sub 2} adrenoceptor antagonist.« less

Chemometrics-assisted investigation of interactions of Tasmar with human serum albumin at a glassy carbon disk: Application to electrochemical biosensing of electro-inactive serum albumin.

PubMed

Mohammadi, Ghobad; Faramarzi, Elahe; Mahmoudi, Majid; Ghobadi, Sirous; Ghiasvand, Ali Reza; Goicoechea, Hector C; Jalalvand, Ali R

2018-07-15

In this work, voltammetric data recorded by a glassy carbon electrode (GCE) was used to investigate the interactions of tolcapone (Tasmar, TAS) with human serum albumin (HSA) at the electrode surface. The recorded voltammetric data was also combined with spectroscopic data to construct an augmented data matrix which was analysed by multivariate curve resolution-alternating least squares (MCR-ALS) as an efficient chemometric tool to obtain more information about TAS-HSA interactions. The results of MCR-ALS confirmed formation of one complex species (HSA-TAS 2 ) and application of MCR-BANDS to the results of MCR-ALS confirmed the absence of rotational ambiguities and existing unambiguous and reliable results. Binding of TAS to HSA was also modeled by molecular docking and the results showed that the TAS was bound to sub-domain IIA of HSA which were compatible with the ones obtained by recording experimental data. Hard-modeling of combined voltammetric and spectroscopic data by EQUISPEC helped us to compute binding constant of HSA-TAS 2 complex species which was compatible with the binding constant value obtained by direct analysis of experimental data. Finally, a new electroanalytical method was developed based on TAS-HSA interactions for determination of HSA in two ranges of 0-541 nM and 541-1200 nM with a limit of detection of 0.04 nM and a sensitivity of 0.02 μA nM -1 . Copyright © 2018 Elsevier B.V. All rights reserved.

Assessment of the nickel-albumin binding assay for diagnosis of acute coronary syndrome.

PubMed

da Silva, Sandra Huber; Pereira, Renata da Silva; Hausen, Bruna dos Santos; Signor, Cristiane; Gomes, Patrícia; de Campos, Marli Matiko Anraku; Moresco, Rafael Noal

2011-03-01

Myocardial ischemia may alter the metal binding capacity of circulating serum albumin. Thus, the aim of this study was to describe an automated method to measure ischemia-induced alterations in the binding capacity of serum albumin for exogenous nickel, and to evaluate the diagnostic characteristics of this assay for the assessment of acute coronary syndrome (ACS) in patients presenting to the emergency room (ER) with acute chest pain. We assessed the concentrations of cardiac troponin I (cTnI), serum albumin, ischemia-modified albumin (IMA) measured by the cobalt-albumin binding assay (CABA), and by an automated nickel-albumin binding assay (NABA) in the following groups: ACS (n=63) and non-ischemic chest pain (NICP, n=26). Biochemical markers were determined in blood samples obtained from patients within 3 h of ER admission. cTnI, CABA and NABA concentrations were higher in ACS group in comparison to the NICP group. A significant correlation between NABA and CABA was observed (r=0.5387, p<0.001). Areas under the curve for CABA and NABA were 0.7289 and 0.7582, respectively. Both CABA and NABA have the ability to discriminate patients with ACS. However, NABA has a slightly higher ability to discriminate ACS compared with CABA. Patients with ACS have reduced nickel binding to human serum albumin, and NABA may have an important role as an early marker of myocardial ischemia, particularly in patients presenting to the ER with acute chest pain.

Pseudo-magnetic fields of strongly-curved graphene nanobubbles

NASA Astrophysics Data System (ADS)

Liu, Li-Chi

2018-04-01

We use the π-orbital axis vector (POAV) analysis to deal with large curvature effect of graphene in the tight-binding model. To test the validities of pseudo-magnetic fields (PMFs) derived from the tight-binding model and the model with Dirac equation coupled to a curved surface, we propose two types of spatially constant-field topographies for strongly-curved graphene nanobubbles, which correspond to these two models, respectively. It is shown from the latter model that the PMF induced by any spherical graphene nanobubble is always equivalent to the magnetic field caused by one magnetic monopole charge distributed on a complete spherical surface with the same radius. Such a PMF might be attributed to the isometry breaking of a graphene layer attached conformably to a spherical substrate with adhesion.

1H and 31P nuclear magnetic resonance investigation of the interaction between 2,3-diphosphoglycerate and human normal adult hemoglobin.

PubMed

Russu, I M; Wu, S S; Bupp, K A; Ho, N T; Ho, C

1990-04-17

High-resolution 1H and 31P nuclear magnetic resonance spectroscopy has been used to investigate the binding of 2,3-diphosphoglycerate to human normal adult hemoglobin and the molecular interactions involved in the allosteric effect of the 2,3-diphosphoglycerate molecule on hemoglobin. Individual hydrogen ion NMR titration curves have been obtained for 22-26 histidyl residues of hemoglobin and for each phosphate group of 2,3-diphosphoglycerate with hemoglobin in both the deoxy and carbonmonoxy forms. The results indicate that 2,3-diphosphoglycerate binds to deoxyhemoglobin at the central cavity between the two beta chains and the binding involves the beta 2-histidyl residues. Moreover, the results suggest that the binding site of 2,3-diphosphoglycerate to carbonmonoxyhemoglobin contains the same (or at least some of the same) amino acid residues responsible for binding in the deoxy form. As a result of the specific interactions with 2,3-diphosphoglycerate, the beta 2-histidyl residues make a significant contribution to the alkaline Bohr effect under these experimental conditions (up to 0.5 proton/Hb tetramer). 2,3-Diphosphoglycerate also affects the individual hydrogen ion equilibria of several histidyl residues located away from the binding site on the surface of the hemoglobin molecule, and, possibly, in the heme pockets. These results give the first experimental demonstration that long-range electrostatic and/or conformational effects of the binding could play an important role in the allosteric effect of 2,3-diphosphoglycerate on hemoglobin.(ABSTRACT TRUNCATED AT 250 WORDS)

Toxicokinetics, including saturable protein binding, of 4-chloro-2-methyl phenoxyacetic acid (MCPA) in patients with acute poisoning

PubMed Central

Roberts, Darren M.; Dawson, Andrew H.; Senarathna, Lalith; Mohamed, Fahim; Cheng, Ron; Eaglesham, Geoffrey; Buckley, Nick A.

2011-01-01

Human data on protein binding and dose-dependent changes in toxicokinetics for MCPA are very limited. 128 blood samples were obtained in 49 patients with acute MCPA poisoning and total and unbound concentrations of MCPA were determined. The Scatchard plot was biphasic suggesting protein binding to two sites. The free MCPA concentration increased when the total concentration exceeded 239 mg/L (95% confidence interval 198–274 mg/L). Nonlinear regression using a two-site binding hyperbola model estimated saturation of the high affinity binding site at 115 mg/L (95%CI 0–304). Further analyses using global fitting of serial data and adjusting for the concentration of albumin predicted similar concentrations for saturable binding (184 mg/L and 167 mg/L, respectively) without narrowing the 95%CI. In 25 patients, the plasma concentration–time curves for both bound and unbound MCPA were approximately log-linear which may suggest first order elimination, although sampling was infrequent so zero order elimination cannot be excluded. Using a cut-off concentration of 200 mg/L, the half-life of MCPA at higher concentrations was 25.5 h (95%CI 15.0–83.0 h; n = 16 patients) compared to 16.8 h (95%CI 13.6–22.2 h; n = 10 patients) at lower concentrations. MCPA is subject to saturable protein binding but the influence on half-life appears marginal. PMID:21256202

Gravitropism in higher plant shoots. VI. Changing sensitivity to auxin in gravistimulated soybean hypocotyls

NASA Technical Reports Server (NTRS)

Rorabaugh, P. A.; Salisbury, F. B.

1989-01-01

Although the Cholodny-Went model of auxin redistribution has been used to explain the transduction phase of gravitropism for over 60 years, problems are apparent, especially with dicot stems. An alternative to an auxin gradient is a physiological gradient in which lower tissues of a horizontal stem become more sensitive than upper tissues to auxin already present. Changes in tissue sensitivity to auxin were tested by immersing marked Glycine max Merrill (soybean) hypocotyl sections in buffered auxin solutions (0, 10(-8) to 10(-2) molar indoleacetic acid) and observing bending and growth of upper and lower surfaces. The two surfaces of horizontal hypocotyl sections responded differently to the same applied auxin stimulus; hypocotyls bent up (lower half grew more) in buffer alone or in low auxin levels, but bent down (upper half grew more) in high auxin. Dose-response curves were evaluated with Michaelis-Menten kinetics, with auxin-receptor binding analogous to enzyme-substrate binding. Vmax for the lower half was usually greater than that for the upper half, which could indicate more binding sites in the lower half. Km of the upper half was always greater than that of the lower half (unmeasurably low), which could indicate that upper-half binding sites had a much lower affinity for auxin than lower-half sites. Dose-response curves were also obtained for sections scrubbed' (cuticle abraded) on top or bottom before immersion in auxin, and gravitropic memory' experiments of L. Brauner and A. Hagar (1958 Planta 51: 115-147) were duplicated. [1-14C]Indoleacetic acid penetration was equal into the two halves, and endogenous plus exogenously supplied (not radiolabeled) free auxin in the two halves (by gas chromatography-selected ion monitoring-mass spectrometry) was also equal. Thus, differential growth occurred without free auxin redistribution, contrary to Cholodny-Went but in agreement with a sensitivity model.

Malathion-induced inhibition of human plasma cholinesterase studied by the fluorescence spectroscopy method

NASA Astrophysics Data System (ADS)

Pavelkić, V. M.; Krinulović, K. S.; Savić, J. Z.; Ilić, M. A.

2008-05-01

The in vitro effect of technical grade malathion was assessed via the kinetic parameters of human plasma butyrylcholinesterase (BChE) using N-methylindoxyl acetate as a substrate for BChE. An inhibitor kinetics study demonstrated the existence of a biphasic inhibition curve, indicating high-and low-affinity binding sites of malathion. The IC 50 values as calculated from the experimental inhibition curves were 1.33 × 10-9 and 1.48 × 10-5 M for the high-and low-affinity binding sites, respectively; Hill’s analysis gave 1.29 × 10-9 and 1.38 × 10-6 M. The Cornish-Bowden plots and their secondary plots indicated that the nature of inhibition was of mixed type with the predominant competitive character of both affinity binding sites.

O(2)-dependent K(+) fluxes in trout red blood cells: the nature of O(2) sensing revealed by the O(2) affinity, cooperativity and pH dependence of transport.

PubMed

Berenbrink, M; Völkel, S; Heisler, N; Nikinmaa, M

2000-07-01

The effects of pH and O(2) tension on the isotonic ouabain-resistant K(+) (Rb+) flux pathway and on haemoglobin O2 binding were studied in trout red blood cells (RBCs) in order to test for a direct effect of haemoglobin O(2) saturation on K(+) transport across the RBC membrane. At pH values corresponding to in vivo control arterial plasma pH and higher, elevation of the O(2) partial pressure (PO(2)) from 7.8 to 157 mmHg increased unidirectional K(+) influx across the RBC membrane several-fold. At lower extracellular pH values, stimulation of K(+) influx by O(2) was depressed, exhibiting an apparent pK(a) (pK'(a)) for the process of 8.0. Under similar conditions the pK'(a) for acid-induced deoxygenation of haemoglobin (Hb) was 7.3. When trout RBCs were exposed to PO(2) values between 0 and 747 mmHg, O(2) equilibrium curves typical of Hb O(2) saturation were also obtained for K(+) influx and efflux. However, at pH 7.9, the PO(2) for half-maximal K(+) efflux and K(+) influx (P50) was about 8- to 12-fold higher than the P(50) for Hb-O(2) binding. While K(+) influx and efflux stimulation by O(2) was essentially non-cooperative, Hb-O(2) equilibrium curves were distinctly sigmoidal (Hill parameters close to 1 and 3, respectively). O(2)-stimulated K(+) influx and efflux were strongly pH dependent. When the definition of the Bohr factor for respiratory pigments (Phi = delta logP50 x delta pH(-1)) was extended to the effect of pH on O(2)-dependent K(+) influx and efflux, extracellular Bohr factors (Phi(o) of -2.00 and -2.06 were obtained, values much higher than that for Hb (Phi(o) = -0.49). The results of this study are consistent with an O(2) sensing mechanism differing markedly in affinity and cooperativity of O(2) binding, as well as in pH sensitivity, from bulk Hb.

Demonstration of four immunoassay formats using the array biosensor

NASA Technical Reports Server (NTRS)

Sapsford, Kim E.; Charles, Paul T.; Patterson, Charles H Jr; Ligler, Frances S.

2002-01-01

The ability of a fluorescence-based array biosensor to measure and quantify the binding of an antigen to an immobilized antibody has been demonstrated using the four different immunoassay formats: direct, competitive, displacement, and sandwich. A patterned array of antibodies specific for 2,4,6-trinitrotoluene (TNT) immobilized onto the surface of a planar waveguide and used to measure signals from different antigen concentrations simultaneously. For direct, competitive, and displacement assays, which are one-step assays, measurements were obtained in real time. Dose-response curves were calculated for all four assay formats, demonstrating the array biosensor's ability to quantify the amount of antigen present in solution.

Orbital-Dependent-Functionals within Density Functional Theory: Methodology and Applications

NASA Astrophysics Data System (ADS)

Makmal, Adi

I have designed and implemented a new numerical scheme for solving Kohn-Sham (KS) equations for diatomic systems, together with a full solution of the OEP equation. The equations are solved on a real-space prolate spheroidal coordinate grid, such that all the system's electrons are taken into account. The OEP equation is solved via the S-iteration scheme. This newly developed software package is called DARSEC (DiAtomic Real-Space Electronic structure Calculations). It involves no approximation except for the one inherent in the XC functional. Thus it is especially suitable for examining new functionals of any kind, and ODFs in particular. It is also an ideal tool for assessing the validity of commonly used approximations, for the same reasons. One case for which this uniqueness of DARSEC was exploited in this thesis is the examination of the validity of the pseudopotential approximation for KS gaps that are calculated with EXX OEP (xOEP). Before this study, use of the pseudopotential approximation in such calculations was called into question. I have shown that KS gaps obtained with pseudopotentials that have been constructed in a manner consistent with the exact-exchange functional agree with the all-electron results (i.e. without the pseudopotential approximation), for the cases studied. This confirmed the reliability of the pseudopotential approximation for ODFs such as EXX. Explicit density-dependent XC functionals traditionally fail to obtain atomization-energy as well as charge-dissociation curves that are, at least qualitatively, correct for diatomic systems. On the other hand, Hartree-Fock (HF) theory encounters no such problem. Hence, an additional goal of this research was to study the performances of the EXX functional (being the DFT counterpart of HF) in describing binding energies and charge dissociations for stretched diatomic molecules. Moreover, I wanted to investigate the special features of the resulting single and local EXX KS potential, as opposed to the non-local orbital specific HF potentials. I asked the following questions: Is it at all possible to obtain correct binding energy curves and charge dissociation curves with the local exact-exchange KS potential? What are the main features of such a local KS potential? And how are they related to the spatial shapes of the KS orbitals? To answer these questions, I calculated the electronic structures of highly stretched H2, HF and LiF molecules with EXX, using the Krieger, Li, and Iafrate (KLI) scheme. All calculations were done with DARSEC, whose coordinate system is highly suitable for calculating such stretched diatomic molecules. By examining several electronic configurations in a systematic manner, low energy ones were identified, and qualitatively correct binding-energy curves were obtained. For the LiF molecule a qualitatively correct charge separation curve was also achieved. Once the local EXX KLI potential was obtained for highly stretched diatomic systems, I could study its properties. Specifically, I have identified and demonstrated the following features: (a) The location and size of a constant shift in the potential and its relation to orbital spatial shapes; (b) The dependence of the shift's position on the inter-atomic separation length; (c) The existence of multiple constant shifts of the same kind; (d) The relation between the eigenvalues of the highly stretched diatomic system and the corresponding eigenvalues of the separated atoms - and how this relation is correlated with the asymptotic shift of the local potential. Understanding this unique combination of features sheds light on the mechanism with which the EXX potential enforces the correct charge dissociation. Last, a study on a novel ODF was initiated. The new ODF, suggested by Stephan Kummel, has a local function that mixes a fraction of EXX with a complementary fraction of exchange of the homogenous electronic gas (LDA), where a different fraction is assigned for each point in space. To derive the corresponding potential, the functional derivative of the new energy expression with respect to the KS orbitals was analytically derived. The new energy and potential expressions were implemented into DARSEC, and preliminary examinations were carried out. (Abstract shortened by UMI.)

Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals.

PubMed Central

Bruno, S.; Bettati, S.; Manfredini, M.; Mozzarelli, A.; Bolognesi, M.; Deriu, D.; Rosano, C.; Tsuneshige, A.; Yonetani, T.; Henry, E. R.

2000-01-01

Oxygen binding by hemoglobin fixed in the T state either by crystallization or by encapsulation in silica gels is apparently noncooperative. However, cooperativity might be masked by different oxygen affinities of alpha and beta subunits. Metal hybrid hemoglobins, where the noniron metal does not bind oxygen, provide the opportunity to determine the oxygen affinities of alpha and beta hemes separately. Previous studies have characterized the oxygen binding by alpha(Ni2+)2beta(Fe2+)2 crystals. Here, we have determined the three-dimensional (3D) structure and oxygen binding of alpha(Fe2+)2beta(Ni2+)2 crystals grown from polyethylene glycol solutions. Polarized absorption spectra were recorded at different oxygen pressures with light polarized parallel either to the b or c crystal axis by single crystal microspectrophotometry. The oxygen pressures at 50% saturation (p50s) are 95 +/- 3 and 87 +/- 4 Torr along the b and c crystal axes, respectively, and the corresponding Hill coefficients are 0.96 +/- 0.06 and 0.90 +/- 0.03. Analysis of the binding curves, taking into account the different projections of the alpha hemes along the optical directions, indicates that the oxygen affinity of alpha1 hemes is 1.3-fold lower than alpha2 hemes. Inspection of the 3D structure suggests that this inequivalence may arise from packing interactions of the Hb tetramer within the monoclinic crystal lattice. A similar inequivalence was found for the beta subunits of alpha(Ni2+)2beta(Fe2+)2 crystals. The average oxygen affinity of the alpha subunits (p50 = 91 Torr) is about 1.2-fold higher than the beta subunits (p50 = 110 Torr). In the absence of cooperativity, this heterogeneity yields an oxygen binding curve of Hb A with a Hill coefficient of 0.999. Since the binding curves of Hb A crystals exhibit a Hill coefficient very close to unity, these findings indicate that oxygen binding by T-state hemoglobin is noncooperative, in keeping with the Monod, Wyman, and Changeux model. PMID:10794410

Characterization of the [125I]-neurokinin A binding site in the circular muscle of human colon

PubMed Central

Warner, Fiona J; Comis, Alfio; Miller, Robert C; Burcher, Elizabeth

1999-01-01

Neurokinin A (NKA) is a potent contractile agonist of human colon circular muscle. These responses are mediated predominantly through tachykinin NK2 receptors. In the present study, the NK2 receptor radioligand [125I]-NKA has been used to characterize binding sites in this tissue, using tachykinin agonists and antagonists. 125INKA labelled a single, high affinity binding site. Specific binding (95% of total binding) of [125I]-NKA was saturable (KD 0.47±0.05 nM), of high capacity (Bmax 2.1±0.1 fmol mg−1 wet weight tissue) and reversible (kinetically derived KD 0.36±0.07 nM). The rank order of agonists competing for the [125I]-NKA binding site was neuropeptide γ (NPγ)≥NKA≥[Lys5,MeLeu9,Nle10]NKA (4–10) (NK2 agonist)>>substance P (SP)>neurokinin B (NKB)≥[Pro9]SP (NK1 agonist)>>senktide (NK3 agonist), indicating binding to an NK2 site. The nonpeptide selective NK2 antagonist SR48968 showed higher affinity for the [125I]-NKA site than selective peptide NK2 antagonists. The rank order of potency for NK2 antagonists was SR48968≥MEN11420>GR94800≥MEN10627>MEN10376≥R396. The NK1 antagonist SR140333 was a weak competitor. The competition curve for SP could be resolved into two sites. When experiments were repeated in the presence of SR140333 (0.1 μM), the curve for SP became monophasic and showed a significant shift to the right, whereas curves to NKA and NKB were unaffected. In conclusion, binding of the radioligand [125I]-NKA to membranes from circular muscle is predominantly to the NK2 receptor. There may be a small component of binding to the NK1 receptor. The NK2 receptor mediates circular muscle contraction, whereas the role of the NK1 receptor in circular muscle is unclear. PMID:10455255

3H[2-(2-benzofuranyl)-2-imidazoline] (BFI) binding in human platelets: modulation by tranylcypromine.

PubMed

Wiest, S A; Steinberg, M I

1999-08-01

2-(2-Benzofuranyl)-2-imidazoline (BFI) is a highly selective ligand for imidazoline-type 2 (I2) binding sites that are known to be associated with monoamine oxidase (MAO). Recently we demonstrated a potentiation of 3H-BFI binding in human but not in rat brain by the nonselective MAO inhibitor tranylcypromine. In the present studies, we evaluated the effect of tranylcypromine on the binding of 3H-BFI to human platelet inner membranes. Membranes were incubated with 3H-BFI at 22 degrees C in 50 mM Tris, 1.5 mM EDTA, pH 7.5. Saturation experiments with 3H-BFI (0.5-80 nM) were analyzed using non-linear curve fitting. Addition of tranylcypromine (0.1 mM) increased the number of 3H-BFI binding sites (Bmax=0.35+/-0.06 vs. 1.87+/-0.15 pmol/mg protein for vehicle and tranylcypromine, respectively) and increased 3H-BFI affinity slightly (KD =16.0+/-4.1 vs. 6.5+/-0.3 nM for vehicle and tranylcypromine, respectively). In competitive binding experiments using the less selective I2 ligand, 3H-idazoxan, tranylcypromine only weakly inhibited binding. Preincubation of platelet membranes with tranylcypromine (1 nM-10 microM) enhanced the Bmax of 3H-BFI binding in a concentration-dependent manner peaking at 1 microM (13 x control) and returning to near baseline at 100 microM. 3H-BFI binding was displaced monophasically (in order of decreasing potency) by BFI > or = 2-(4,5-dihydroimidazol-2-yl)quinoline (BU224) > or = cirazoline >idazoxan >(1,4-benzodioxan-2-methoxy-2-yl)-2-imidazoline (RX821002)= moxonidine. Amiloride, clorgyline, guanabenz and clonidine displayed biphasic curves with nanomolar high affinity components. Tranylcypromine altered the competition curves for all ligands (except BFI) by increasing the affinities for clonidine and RX821002 and decreasing affinities for BU224, cirazoline, guanabenz, idazoxan, clorgyline, moxonidine, and amiloride. Thus, in human platelets tranylcypromine exposes a high capacity 3H-BFI binding site distinct from previously described I2 sites that retains high affintiy for BFI but not other I2 ligands. Our results suggest that 3H-BFI and 3H-idazoxan may not be considered as interchangeable probes for the I2 binding site.

Comparison of a Resonant Mirror Biosensor (IAsys) and a Quartz Crystal Microbalance (QCM) for the Study on Interaction between Paeoniae Radix 801 and Endothelin-1.

PubMed

Huang, Jiadong; Lin, Qing; Yu, Jinghua; Ge, Shenguang; Li, Jing; Yu, Min; Zhao, Zixia; Wang, Xinsheng; Zhang, Xiuming; He, Xiaorui; Yuan, Liang; Yin, Huijun; Osa, Tetsuo; Chen, Keji; Chen, Qiang

2008-12-15

A resonant mirror biosensor, IAsys, and a quartz crystal microbalance (QCM) are known independently as surface sensitive analytical devices capable of label-free and in situ bioassays. In this study, an IAsys and a QCM are employed for a new study on the action mechanism of Paeoniae Radix 801 (P. radix 801) by detecting the specific interaction between P. radix 801 and endothelin-1 (ET-1). In the experiments, ET-1 was immobilized on the surfaces of the IAsys cuvette and the QCM substrate by surface modification techniques, and then P. radix 801 solution was contacted to the cuvette and the substrate, separately. Then, the binding and interaction process between P. radix 801 and ET-1 was monitored by IAsys and QCM, respectively. The experimental results showed that P. radix 801 binds ET-1 specifically. The IAsys and QCM response curves to the ET-1 immobilization and P. radix 801 binding are similar in reaction process, but different in binding profiles, reflecting different resonation principles. Although both IAsys and QCM could detect the interaction of P. radix 801 and ET-1 with high reproducibility and reliability through optimization of the ET-1 coating, the reproducibility and reliability obtained by IAsys are better than those obtained by QCM, since the QCM frequency is more sensitive to temperature fluctuations, atmospheric changes and mechanical disturbances. However, IAsys and QCM are generally potent and reliable tools to study the interaction of P. radix 801 and ET-1, and can conclusively be applied to the action mechanism of P. radix 801.

Fluorescence resonance energy-transfer affects the determination of the affinity between ligand and proteins obtained by fluorescence quenching method

NASA Astrophysics Data System (ADS)

Xiao, Jianbo; Wei, Xinlin; Wang, Yuanfeng; Liu, Chunxi

2009-11-01

The interaction between esculin and serum albumins was investigated to illustrate that the fluorescence resonance energy-transfer (FRET) affects the determination of the binding constants obtained by fluorescence quenching method. The binding constants ( Ka) obtained by the double-logarithm curve for esculin-BSA and esculin-HSA were 1.02 × 10 7 and 2.07 × 10 4 L/mol, respectively. These results from synchronous fluorescence showed that the Tyr and Trp residues of HSA were affected more deeply than those in BSA. The excitation profile of esculin showed that in the presence of BSA and HSA, the S 0 → S 1 transition of esculin ( λexmax≈340 nm) appears, which is similar to the λemmax of BSA and HSA. The critical distance ( R0) between BSA and esculin is higher than that of HSA, which showed that the affinity of esculin and HSA should be higher than that of BSA. After centrifugation, the concentrations of esculin bound to albumins were determined by means of the fluorescence of esculin. It was found that much more esculin was bound to HSA than to BSA. However, the bound models for BSA and HSA are almost the same. The concentration of esculin bound to serum albumin at first decreased with the addition of esculin and then increased. From above results, it can be concluded that the affinity of esculin and HSA should be higher than that of esculin and BSA. This example showed that in the presence of FRET, the binding constants between ligands and proteins based on fluorescence quenching might be deviated.

Fluorescence resonance energy-transfer affects the determination of the affinity between ligand and proteins obtained by fluorescence quenching method.

PubMed

Xiao, Jianbo; Wei, Xinlin; Wang, Yuanfeng; Liu, Chunxi

2009-11-01

The interaction between esculin and serum albumins was investigated to illustrate that the fluorescence resonance energy-transfer (FRET) affects the determination of the binding constants obtained by fluorescence quenching method. The binding constants (K(a)) obtained by the double-logarithm curve for esculin-BSA and esculin-HSA were 1.02x10(7) and 2.07x10(4)L/mol, respectively. These results from synchronous fluorescence showed that the Tyr and Trp residues of HSA were affected more deeply than those in BSA. The excitation profile of esculin showed that in the presence of BSA and HSA, the S(0)-->S(1) transition of esculin (lambda(ex)(max) approximately 340nm) appears, which is similar to the lambda(em)(max) of BSA and HSA. The critical distance (R(0)) between BSA and esculin is higher than that of HSA, which showed that the affinity of esculin and HSA should be higher than that of BSA. After centrifugation, the concentrations of esculin bound to albumins were determined by means of the fluorescence of esculin. It was found that much more esculin was bound to HSA than to BSA. However, the bound models for BSA and HSA are almost the same. The concentration of esculin bound to serum albumin at first decreased with the addition of esculin and then increased. From above results, it can be concluded that the affinity of esculin and HSA should be higher than that of esculin and BSA. This example showed that in the presence of FRET, the binding constants between ligands and proteins based on fluorescence quenching might be deviated.

Sensitive albuminuria analysis using dye-binding based test strips.

PubMed

Delanghe, Joris R; Himpe, Jonas; De Cock, Naomi; Delanghe, Sigurd; De Herde, Kevin; Stove, Veronique; Speeckaert, Marijn M

2017-08-01

Populations at increased risk for chronic kidney disease should be screened for albuminuria. Possibilities of advanced urine strip readers based on complementary metal oxide semiconductor (CMOS) sensor technology were investigated for obtaining quantitative albuminuria results. Reflectance data of test strips (Sysmex UFC 3500 reader+CMOS) were compared with albuminuria (BNII) and with proteinuria (Cobas 8000). Urinary creatinine was assayed using a Jaffe-based creatinine assay (Cobas 8000). Calibration curve was made between 11.5 and 121.5mg/L with detection limit of 5.5mg/L. Within-run CV values of reflectance data were 0.21% (UC-Control L; 10mg/L) and 0.37% (UC-Control H; >150mg/L) for albumin, and 0.71%/3.97% for creatinine. Between-run CV values were 0.24%/0.42% for albumin and 0.93%/5.13% for creatinine. A strong correlation (r=0.92) was obtained between albuminuria (BNII) and protein strip reflectance data. Creatinine reflectance data correlated well with Jaffe-based urinary creatinine data (r=0.90). Albumin:creatinine ratio obtained by test strip and by wet chemistry showed a good correlation (r=0.59). Carbamylated, glycated and partially hydrolyzed isoforms of albumin could be detected by test strip. Dye-binding based albumin test strip assay in combination with a CMOS based reader would potentially allow quantitative analysis of albuminuria and determination of albumin:creatinine ratio. Copyright © 2017 Elsevier B.V. All rights reserved.

Binding properties of food colorant allura red with human serum albumin in vitro.

PubMed

Wang, Langhong; Zhang, Guowen; Wang, Yaping

2014-05-01

Allura red (AR) is a widely used colorant in food industry, but may have a potential security risk. In this study, the properties of interaction between AR and human serum albumin (HSA) in vitro were determined by fluorescence, UV-Vis absorption and circular dichroism (CD) spectroscopy combining with multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics and molecular modeling approaches. An expanded UV-Vis data matrix was resolved by MCR-ALS method, and the concentration profiles and pure spectra for the three reaction components (AR, HSA, and AR-HSA complex) of the system were then successfully obtained to evaluate the progress interaction of AR with HSA. The calculated thermodynamic parameters indicated that hydrogen binding and hydrophobic interactions played major roles in the binding process, and the interaction induced a decrease in the protein surface hydrophobicity. The competitive experiments revealed that AR mainly located in Sudlow's site I of HSA, and this result was further supported by molecular modeling studies. Analysis of CD spectra found that the addition of AR induced the conformational changes of HSA. This study have provided new insight into the mechanism of interaction between AR and HSA.

Kinetic modeling of benzodiazepine receptor binding with PET and high specific activity [(11)C]Iomazenil in healthy human subjects.

PubMed

Bremner, J D; Horti, A; Staib, L H; Zea-Ponce, Y; Soufer, R; Charney, D S; Baldwin, R

2000-01-01

Quantitation of the PET benzodiazepine receptor antagonist, [(11)C]Iomazenil, using low specific activity radioligand was recently described. The purpose of this study was to quantitate benzodiazepine receptor binding in human subjects using PET and high specific activity [(11)C]Iomazenil. Six healthy human subjects underwent PET imaging following a bolus injection of high specific activity (>100 Ci/mmol) [(11)C]iomazenil. Arterial samples were collected at multiple time points after injection for measurement of unmetabolized total and nonprotein-bound parent compound in plasma. Time activity curves of radioligand concentration in brain and plasma were analyzed using two and three compartment model. Kinetic rate constants of transfer of radioligand between plasma, nonspecifically bound brain tissue, and specifically bound brain tissue compartments were fitted to the model. Values for fitted kinetic rate constants were used in the calculation of measures of benzodiazepine receptor binding, including binding potential (the ratio of receptor density to affinity), and product of BP and the fraction of free nonprotein-bound parent compound (V(3)'). Use of the three compartment model improved the goodness of fit in comparison to the two compartment model. Values for kinetic rate constants and measures of benzodiazepine receptor binding, including BP and V(3)', were similar to results obtained with the SPECT radioligand [(123)I]iomazenil, and a prior report with low specific activity [(11)C]Iomazenil. Kinetic modeling using the three compartment model with PET and high specific activity [(11)C]Iomazenil provides a reliable measure of benzodiazepine receptor binding. Synapse 35:68-77, 2000. Published 2000 Wiley-Liss, Inc.

Effects of flow changes on radiotracer binding: Simultaneous measurement of neuroreceptor binding and cerebral blood flow modulation.

PubMed

Sander, Christin Y; Mandeville, Joseph B; Wey, Hsiao-Ying; Catana, Ciprian; Hooker, Jacob M; Rosen, Bruce R

2017-01-01

The potential effects of changes in blood flow on the delivery and washout of radiotracers has been an ongoing question in PET bolus injection studies. This study provides practical insight into this topic by experimentally measuring cerebral blood flow (CBF) and neuroreceptor binding using simultaneous PET/MRI. Hypercapnic challenges (7% CO 2 ) were administered to non-human primates in order to induce controlled increases in CBF, measured with pseudo-continuous arterial spin labeling. Simultaneously, dopamine D 2 /D 3 receptor binding of [ 11 C]raclopride or [ 18 F]fallypride was monitored with dynamic PET. Experiments showed that neither time activity curves nor quantification of binding through binding potentials ( BP ND ) were measurably affected by CBF increases, which were larger than two-fold. Simulations of experimental procedures showed that even large changes in CBF should have little effect on the time activity curves of radiotracers, given a set of realistic assumptions. The proposed method can be applied to experimentally assess the flow sensitivity of other radiotracers. Results demonstrate that CBF changes, which often occur due to behavioral tasks or pharmacological challenges, do not affect PET [ 11 C]raclopride or [ 18 F]fallypride binding studies and their quantification. The results from this study suggest flow effects may have limited impact on many PET neuroreceptor tracers with similar properties.

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

Despite irreversible binding, PET tracer [11C]-SA5845 is suitable for imaging of drug competition at sigma receptors-the cases of ketamine and haloperidol.

PubMed

Kortekaas, Rudie; Maguire, R Paul; van Waarde, Aren; Leenders, Klaus L; Elsinga, Philip H

2008-07-01

Many psychotropic compounds bind to sigma receptors and several new sigma ligands are in development for psychiatric indications such as anxiety, attention deficit hyperactivity disorder, depression and psychosis. Of special interest for drug development are tomographic methods that can quantify the binding of promising sigma ligands in a regional manner. Here we present the development of such a method and the first evaluation of sigma ligand [11C]-SA5845 in a primate. Extensive pharmacokinetic modeling was done on tissue curves and a heart lumen curve. The effects of pretreatment and challenge with haloperidol were studied as well as those of pretreatment with +/- -ketamine. The tracer had a plasma half-life of 77+/-1.7min and was rapidly taken up by all brain areas. The binding pattern was consistent with binding to sigma receptors and compartment modeling showed there was considerable specific binding that was irreversible. We therefore calculated the net influx rate, Ki, with the Gjedde-Patlak linearization, as a measure of free receptors. As expected, Ki was very sensitive to the presence of competing ligands - -ketamine and/or haloperidol. Summarizing, the tracer is well suited for visualizing sigma receptors in the brain and moreover, the presented method is able to quantify, on a regional basis, specific binding of unlabeled ligands to sigma receptors.

‘Partial’ competition of heterobivalent ligand binding may be mistaken for allosteric interactions: a comparison of different target interaction models

PubMed Central

Vauquelin, Georges; Hall, David; Charlton, Steven J

2015-01-01

Background and Purpose Non-competitive drugs that confer allosteric modulation of orthosteric ligand binding are of increasing interest as therapeutic agents. Sought-after advantages include a ceiling level to drug effect and greater receptor-subtype selectivity. It is thus important to determine the mode of interaction of newly identified receptor ligands early in the drug discovery process and binding studies with labelled orthosteric ligands constitute a traditional approach for this. According to the general allosteric ternary complex model, allosteric ligands that exhibit negative cooperativity may generate distinctive ‘competition’ curves: they will not reach baseline levels and their nadir will increase in par with the orthosteric ligand concentration. This behaviour is often considered a key hallmark of allosteric interactions. Experimental Approach The present study is based on differential equation-based simulations. Key Results The differential equation-based simulations revealed that the same ‘competition binding’ pattern was also obtained when a monovalent ligand binds to one of the target sites of a heterobivalent ligand, even if this process is exempt of allosteric interactions. This pattern was not strictly reciprocal when the binding of each of the ligands was recorded. The prominence of this phenomenon may vary from one heterobivalent ligand to another and we suggest that this phenomenon may take place with ligands that have been proposed to bind according to ‘two-domain’ and ‘charnière’ models. Conclusions and Implications The present findings indicate a familiar experimental situation where bivalency may give rise to observations that could inadvertently be interpreted as allosteric binding. Yet, both mechanisms could be differentiated based on alternative experiments and structural considerations. PMID:25537684

3- and 4-O-sulfoconjugated and methylated dopamine: highly reduced binding affinity to dopamine D2 receptors in rat striatal membranes.

PubMed

Werle, E; Lenz, T; Strobel, G; Weicker, H

1988-07-01

The binding properties of 3- and 4-O-sulfo-conjugated dopamine (DA-3-O-S, DA-4-O-S) as well as 3-O-methylated dopamine (MT) to rat striatal dopamine D2 receptors were investigated. 3H-spiperone was used as a radioligand in the binding studies. In saturation binding experiments (+)butaclamol, which has been reported to bind to dopaminergic D2 and serotoninergic 5HT2 receptors, was used in conjunction with ketanserin and sulpiride, which preferentially label 5HT2 and D2 receptors, respectively, in order to discriminate between 3H-spiperone binding to D2 and to 5HT2 receptors. Under our particular membrane preparation and assay conditions, 3H-spiperone binds to D2 and 5HT2 receptors with a maximal binding capacity (Bmax) of 340 fmol/mg protein in proportions of about 75%:25% with similar dissociation constants KD (35 pmol/l; 43 pmol/l). This result was verified by the biphasic competition curve of ketanserin, which revealed about 20% high (KD = 24 nmol/l) and 80% low (KD = 420 nmol/l) affinity binding sites corresponding to 5HT2 and D2 receptors, respectively. Therefore, all further competition experiments at a tracer concentration of 50 pmol/l were performed in the presence of 0.1 mumol/l ketanserin to mask the 5HT2 receptors. DA competition curves were best fitted assuming two binding sites, with high (KH = 0.12 mumol/l) and low (KL = 18 mumol/l) affinity, present in a ratio of 3:1. The high affinity binding sites were interconvertible by 100 mumol/l guanyl-5-yl imidodiphosphate [Gpp(NH)p], resulting in a homogenous affinity state of DA receptors (KD = 2.8 mumol/l).2+ off

The Parallel Episodic Processing (PEP) model 2.0: A single computational model of stimulus-response binding, contingency learning, power curves, and mixing costs.

PubMed

Schmidt, James R; De Houwer, Jan; Rothermund, Klaus

2016-12-01

The current paper presents an extension of the Parallel Episodic Processing model. The model is developed for simulating behaviour in performance (i.e., speeded response time) tasks and learns to anticipate both how and when to respond based on retrieval of memories of previous trials. With one fixed parameter set, the model is shown to successfully simulate a wide range of different findings. These include: practice curves in the Stroop paradigm, contingency learning effects, learning acquisition curves, stimulus-response binding effects, mixing costs, and various findings from the attentional control domain. The results demonstrate several important points. First, the same retrieval mechanism parsimoniously explains stimulus-response binding, contingency learning, and practice effects. Second, as performance improves with practice, any effects will shrink with it. Third, a model of simple learning processes is sufficient to explain phenomena that are typically (but perhaps incorrectly) interpreted in terms of higher-order control processes. More generally, we argue that computational models with a fixed parameter set and wider breadth should be preferred over those that are restricted to a narrow set of phenomena. Copyright © 2016 Elsevier Inc. All rights reserved.

Spectroscopic studies on the interaction of sodium benzoate, a food preservative, with calf thymus DNA.

PubMed

Zhang, Guowen; Ma, Yadi

2013-11-01

The interaction between sodium benzoate (SB) and calf thymus DNA in simulated physiological buffer (pH 7.4) using acridine orange (AO) dye as a fluorescence probe, was investigated by UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopy along with DNA melting studies and viscosity measurements. An expanded UV-Vis spectral data matrix was resolved by multivariate curve resolution-alternating least squares (MCR-ALS) approach. The equilibrium concentration profiles and the pure spectra for SB, DNA and DNA-SB complex from the high overlapping composite response were simultaneously obtained. The results indicated that SB could bind to DNA, and hydrophobic interactions and hydrogen bonds played a vital role in the binding process. Moreover, SB was able to quench the fluorescence of DNA-AO complex through a static procedure. The quenching observed was indicative of an intercalative mode of interaction between SB and DNA, which was supported by melting studies, viscosity measurements and CD analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Graphene- and aptamer-based electrochemical biosensor

NASA Astrophysics Data System (ADS)

Xu, Ke; Meshik, Xenia; Nichols, Barbara M.; Zakar, Eugene; Dutta, Mitra; Stroscio, Michael A.

2014-05-01

This study investigated the effectiveness of a graphene- and aptamer-based field-effect-transistor-like (FET-like) sensor in detecting lead and potassium ions. The sensor consists of a graphene-covered Si/SiO2 wafer with thrombin binding aptamer (TBA) attached to the graphene layer and terminated by a methylene blue (MB) molecule. K+ and Pb2+ both bind to TBA and cause a conformational change, which results in MB moving closer to the graphene surface and donating an electron. Thus, the abundance of K+ and Pb2+ can be determined by monitoring the current across the source and drain channel. Device transfer curves were obtained with ambipolar field effect observed. Current readings were taken for K+ concentrations of 100 μM to 50 mM and Pb2+ concentrations of 10 μM to 10 mM. As expected, I d decreased as ion concentration increased. In addition, there was a negative shift in V Dirac in response to increased ion concentration.

Traction curves for the decohesion of covalent crystals

NASA Astrophysics Data System (ADS)

Enrique, Raúl A.; Van der Ven, Anton

2017-01-01

We study, by first principles, the energy versus separation curves for the cleavage of a family of covalent crystals with the diamond and zincblende structure. We find that there is universality in the curves for different materials which is chemistry independent but specific to the geometry of the particular cleavage plane. Since these curves do not strictly follow the universal binding energy relationship (UBER), we present a derivation of an extension to this relationship that includes non-linear force terms. This extended form of UBER allows for a flexible and practical mathematical description of decohesion curves that can be applied to the quantification of cohesive zone models.

Quantifying protein-protein interactions in high throughput using protein domain microarrays.

PubMed

Kaushansky, Alexis; Allen, John E; Gordus, Andrew; Stiffler, Michael A; Karp, Ethan S; Chang, Bryan H; MacBeath, Gavin

2010-04-01

Protein microarrays provide an efficient way to identify and quantify protein-protein interactions in high throughput. One drawback of this technique is that proteins show a broad range of physicochemical properties and are often difficult to produce recombinantly. To circumvent these problems, we have focused on families of protein interaction domains. Here we provide protocols for constructing microarrays of protein interaction domains in individual wells of 96-well microtiter plates, and for quantifying domain-peptide interactions in high throughput using fluorescently labeled synthetic peptides. As specific examples, we will describe the construction of microarrays of virtually every human Src homology 2 (SH2) and phosphotyrosine binding (PTB) domain, as well as microarrays of mouse PDZ domains, all produced recombinantly in Escherichia coli. For domains that mediate high-affinity interactions, such as SH2 and PTB domains, equilibrium dissociation constants (K(D)s) for their peptide ligands can be measured directly on arrays by obtaining saturation binding curves. For weaker binding domains, such as PDZ domains, arrays are best used to identify candidate interactions, which are then retested and quantified by fluorescence polarization. Overall, protein domain microarrays provide the ability to rapidly identify and quantify protein-ligand interactions with minimal sample consumption. Because entire domain families can be interrogated simultaneously, they provide a powerful way to assess binding selectivity on a proteome-wide scale and provide an unbiased perspective on the connectivity of protein-protein interaction networks.

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.

PubMed

Nielsen, Morten; Lundegaard, Claus; Worning, Peder; Hvid, Christina Sylvester; Lamberth, Kasper; Buus, Søren; Brunak, Søren; Lund, Ole

2004-06-12

Prediction of which peptides will bind a specific major histocompatibility complex (MHC) constitutes an important step in identifying potential T-cell epitopes suitable as vaccine candidates. MHC class II binding peptides have a broad length distribution complicating such predictions. Thus, identifying the correct alignment is a crucial part of identifying the core of an MHC class II binding motif. In this context, we wish to describe a novel Gibbs motif sampler method ideally suited for recognizing such weak sequence motifs. The method is based on the Gibbs sampling method, and it incorporates novel features optimized for the task of recognizing the binding motif of MHC classes I and II. The method locates the binding motif in a set of sequences and characterizes the motif in terms of a weight-matrix. Subsequently, the weight-matrix can be applied to identifying effectively potential MHC binding peptides and to guiding the process of rational vaccine design. We apply the motif sampler method to the complex problem of MHC class II binding. The input to the method is amino acid peptide sequences extracted from the public databases of SYFPEITHI and MHCPEP and known to bind to the MHC class II complex HLA-DR4(B1*0401). Prior identification of information-rich (anchor) positions in the binding motif is shown to improve the predictive performance of the Gibbs sampler. Similarly, a consensus solution obtained from an ensemble average over suboptimal solutions is shown to outperform the use of a single optimal solution. In a large-scale benchmark calculation, the performance is quantified using relative operating characteristics curve (ROC) plots and we make a detailed comparison of the performance with that of both the TEPITOPE method and a weight-matrix derived using the conventional alignment algorithm of ClustalW. The calculation demonstrates that the predictive performance of the Gibbs sampler is higher than that of ClustalW and in most cases also higher than that of the TEPITOPE method.

Negative cooperativity in binding of muscarinic receptor agonists and GDP as a measure of agonist efficacy

PubMed Central

Jakubík, J; Janíčková, H; El-Fakahany, EE; Doležal, V

2011-01-01

BACKGROUND AND PURPOSE Conventional determination of agonist efficacy at G-protein coupled receptors is measured by stimulation of guanosine-5′-γ−thiotriphosphate (GTPγS) binding. We analysed the role of guanosine diphosphate (GDP) in the process of activation of the M2 muscarinic acetylcholine receptor and provide evidence that negative cooperativity between agonist and GDP binding is an alternative measure of agonist efficacy. EXPERIMENTAL APPROACH Filtration and scintillation proximity assays measured equilibrium binding as well as binding kinetics of [35S]GTPγS and [3H]GDP to a mixture of G-proteins as well as individual classes of G-proteins upon binding of structurally different agonists to the M2 muscarinic acetylcholine receptor. KEY RESULTS Agonists displayed biphasic competition curves with the antagonist [3H]-N-methylscopolamine. GTPγS (1 µM) changed the competition curves to monophasic with low affinity and 50 µM GDP produced a similar effect. Depletion of membrane-bound GDP increased the proportion of agonist high-affinity sites. Carbachol accelerated the dissociation of [3H]GDP from membranes. The inverse agonist N-methylscopolamine slowed GDP dissociation and GTPγS binding without changing affinity for GDP. Carbachol affected both GDP association with and dissociation from Gi/o G-proteins but only its dissociation from Gs/olf G-proteins. CONCLUSIONS AND IMPLICATIONS These findings suggest the existence of a low-affinity agonist-receptor conformation complexed with GDP-liganded G-protein. Also the negative cooperativity between GDP and agonist binding at the receptor/G-protein complex determines agonist efficacy. GDP binding reveals differences in action of agonists versus inverse agonists as well as differences in activation of Gi/o versus Gs/olf G-proteins that are not identified by conventional GTPγS binding. PMID:20958290

Negative cooperativity in binding of muscarinic receptor agonists and GDP as a measure of agonist efficacy.

PubMed

Jakubík, J; Janíčková, H; El-Fakahany, E E; Doležal, V

2011-03-01

Conventional determination of agonist efficacy at G-protein coupled receptors is measured by stimulation of guanosine-5'-γ-thiotriphosphate (GTPγS) binding. We analysed the role of guanosine diphosphate (GDP) in the process of activation of the M₂ muscarinic acetylcholine receptor and provide evidence that negative cooperativity between agonist and GDP binding is an alternative measure of agonist efficacy. Filtration and scintillation proximity assays measured equilibrium binding as well as binding kinetics of [³⁵S]GTPγS and [³H]GDP to a mixture of G-proteins as well as individual classes of G-proteins upon binding of structurally different agonists to the M₂ muscarinic acetylcholine receptor. Agonists displayed biphasic competition curves with the antagonist [³H]-N-methylscopolamine. GTPγS (1 µM) changed the competition curves to monophasic with low affinity and 50 µM GDP produced a similar effect. Depletion of membrane-bound GDP increased the proportion of agonist high-affinity sites. Carbachol accelerated the dissociation of [³H]GDP from membranes. The inverse agonist N-methylscopolamine slowed GDP dissociation and GTPγS binding without changing affinity for GDP. Carbachol affected both GDP association with and dissociation from G(i/o) G-proteins but only its dissociation from G(s/olf) G-proteins. These findings suggest the existence of a low-affinity agonist-receptor conformation complexed with GDP-liganded G-protein. Also the negative cooperativity between GDP and agonist binding at the receptor/G-protein complex determines agonist efficacy. GDP binding reveals differences in action of agonists versus inverse agonists as well as differences in activation of G(i/o) versus G(s/olf) G-proteins that are not identified by conventional GTPγS binding. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

7 CFR 42.142 - Curve for obtaining Operating Characteristic (OC) curve information for skip lot sampling and...

Code of Federal Regulations, 2010 CFR

2010-01-01

... the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... CONDITION OF FOOD CONTAINERS Miscellaneous § 42.142 Curve for obtaining Operating Characteristic (OC) curve...

Using the MWC model to describe heterotropic interactions in hemoglobin

PubMed Central

Rapp, Olga

2017-01-01

Hemoglobin is a classical model allosteric protein. Research on hemoglobin parallels the development of key cooperativity and allostery concepts, such as the ‘all-or-none’ Hill formalism, the stepwise Adair binding formulation and the concerted Monod-Wymann-Changuex (MWC) allosteric model. While it is clear that the MWC model adequately describes the cooperative binding of oxygen to hemoglobin, rationalizing the effects of H+, CO2 or organophosphate ligands on hemoglobin-oxygen saturation using the same model remains controversial. According to the MWC model, allosteric ligands exert their effect on protein function by modulating the quaternary conformational transition of the protein. However, data fitting analysis of hemoglobin oxygen saturation curves in the presence or absence of inhibitory ligands persistently revealed effects on both relative oxygen affinity (c) and conformational changes (L), elementary MWC parameters. The recent realization that data fitting analysis using the traditional MWC model equation may not provide reliable estimates for L and c thus calls for a re-examination of previous data using alternative fitting strategies. In the current manuscript, we present two simple strategies for obtaining reliable estimates for MWC mechanistic parameters of hemoglobin steady-state saturation curves in cases of both evolutionary and physiological variations. Our results suggest that the simple MWC model provides a reasonable description that can also account for heterotropic interactions in hemoglobin. The results, moreover, offer a general roadmap for successful data fitting analysis using the MWC model. PMID:28793329

MODELING OF METAL BINDING ON HUMIC SUBSTANCES USING THE NIST DATABASE: AN A PRIORI FUNCTIONAL GROUP APPROACH

EPA Science Inventory

Various modeling approaches have been developed for metal binding on humic substances. However, most of these models are still curve-fitting exercises-- the resulting set of parameters such as affinity constants (or the distribution of them) is found to depend on pH, ionic stren...

Quantitative determination of testosterone levels with biolayer interferometry.

PubMed

Zhang, Hao; Li, Wei; Luo, Hong; Xiong, Guangming; Yu, Yuanhua

2017-10-01

Natural and synthetic steroid hormones are widely spread in the environment and are considered as pollutants due to their endocrine activities, even at low concentrations, which are harmful to human health. To detect steroid hormones in the environment, a novel biosensor system was developed based on the principle of biolayer interferometry. Detection is based on changes in the interference pattern of white light reflected from the surface of an optical fiber with bound biomolecules. Monitoring interactions between molecules does not require radioactive, enzymatic, or fluorescent labels. Here, 2 double-stranded DNA fragments of operator 1 (OP1) and OP2 containing 10-bp palindromic sequences in chromosomal Comamonas testosteroni DNA (ATCC11996) were surface-immobilized to streptavidin sensors. Interference changes were detected when repressor protein RepA bound the DNA sequences. DNA-protein interactions were characterized and kinetic parameters were obtained. The dissociation constants between the OP1 and OP2 DNA sequences and RepA were 9.865 × 10 -9  M and 2.750 × 10 -8  M, respectively. The reactions showed high specifically and affinity. Because binding of the 10-bp palindromic sequence and RepA was affected by RepA-testosterone binding, the steroid could be quantitatively determined rapidly using the biosensor system. The mechanism of the binding assay was as follows. RepA could bind both OP1 and testosterone. RepA binding to testosterone changed the protein conformation, which influenced the binding between RepA and OP1. The percentage of the signal detected negative correlation with the testosterone concentration. A standard curve was obtained, and the correlation coefficient value was approximately 0.97. We could quantitatively determine testosterone levels between 2.13 and 136.63 ng/ml. Each sample could be quantitatively detected in 17 min. These results suggested that the specific interaction between double-stranded OP1 DNA and the RepA protein could be used to rapidly and quantitatively determine environmental testosterone levels by the biolayer interferometry technique. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of 16-iodohexadecanoic acid (IHDA) and 15-p-iodophenylpentadecanoic acid (IPPA) metabolism and kinetics in the isolated rat heart.

PubMed

DeGrado, T R; Holden, J E; Ng, C K; Raffel, D M; Gatley, S J

1988-01-01

Time courses of radioactivity (residue curves) were obtained following bolus injection into working rat hearts of two 125I-labeled long chain fatty acids: 16-iodohexadecanoic acid (IHDA) and 15-p-iodophenylpentadecanoic acid (IPPA). Residue curves were analyzed in terms of a rapid vascular washout component, an early tissue clearance component, and a very slow late component. For IHDA and IPPA in control hearts, early myocardial clearance kinetics were rate limited by the diffusion of catabolites. Sensitivity of the kinetics to impaired fatty acid oxidation was examination by pretreatment of animals with 2[5(4-chlorophenyl)pentyl]oxirane-2-carboxylate (POCA). Decreased fatty acid oxidation was indicated in IHDA and IPPA residue curves by a decrease in the relative size of the early clearance component. Analysis of radiolabeled species in coronary effluent and heart homogenates showed that back diffusion of IPPA was slower than that of IHDA; this discrepancy was most apparent in POCA hearts. In vitro binding assays suggested higher tissue:albumin relative affinity for IPPA than for IHDA. Thus, IPPA early clearance kinetics were more closely related to the clearance of labeled catabolite(s) and were therefore more sensitive to the oxidation rate of long chain fatty acids.

Study of the binding way between saxitoxin and its aptamer and a fluorescent aptasensor for detection of saxitoxin.

PubMed

Cheng, Sheng; Zheng, Bin; Yao, Dongbao; Kuai, Shenglong; Tian, Jingjing; Liang, Haojun; Ding, Yunsheng

2018-06-11

Aptamers could be used to construct simple and effective biosensor because the conformational switch of aptamer upon target binding is easy to be transferred to optical or electrochemical signals. Nevertheless, we found that the binding between saxitoxin (STX) and aptamer (M-30f) is not accompanied with conformational switch. Here, the circular dichroism spectra, fluorophore and quencher labeled aptamer, and crystal violet-based assays were used to identify the binding way between STX and aptamer. The results show that the conformation of aptamer is stabilized in PBS buffer (10 mM phosphate buffer, 2.7 mM KCl, 137 mM NaCl, pH 7.4) and this conformation may provide an exactly suitable cave for STX binding. Through the analysis of UV-melting curves and circular dichroism-melting curves, it is found that different concentrations of STX produce different unfolding extents of the aptamer under high temperature. Then, a simple temperature-assisted "turn-on" fluorescent aptasensor was developed to detect STX and the application in real sample detection demonstrates its feasibility. The proposed method provides not only an alternative for STX detection but also a strategy for simple aptasensor design using aptamers that do not switch conformation upon targets binding. Copyright © 2018 Elsevier B.V. All rights reserved.

Great interactions: How binding incorrect partners can teach us about protein recognition and function.

PubMed

Vamparys, Lydie; Laurent, Benoist; Carbone, Alessandra; Sacquin-Mora, Sophie

2016-10-01

Protein-protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known to interact can be a useful tool for the prediction of likely binding patches on a protein surface. From the analysis of the protein interfaces generated by a massive cross-docking experiment using the 168 proteins of the Docking Benchmark 2.0, where all possible protein pairs, and not only experimental ones, have been docked together, we show that it is also possible to predict a protein's binding residues without having any prior knowledge regarding its potential interaction partners. Evaluating the performance of cross-docking predictions using the area under the specificity-sensitivity ROC curve (AUC) leads to an AUC value of 0.77 for the complete benchmark (compared to the 0.5 AUC value obtained for random predictions). Furthermore, a new clustering analysis performed on the binding patches that are scattered on the protein surface show that their distribution and growth will depend on the protein's functional group. Finally, in several cases, the binding-site predictions resulting from the cross-docking simulations will lead to the identification of an alternate interface, which corresponds to the interaction with a biomolecular partner that is not included in the original benchmark. Proteins 2016; 84:1408-1421. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

An interspecies comparison of mercury inhibition on muscarinic acetylcholine receptor binding in the cerebral cortex and cerebellum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basu, Niladri; Department of Natural Resource Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, H9X 3V9; Stamler, Christopher J.

2005-05-15

Mercury (Hg) is a ubiquitous pollutant that can disrupt neurochemical signaling pathways in mammals. It is well documented that inorganic Hg (HgCl{sub 2}) and methyl Hg (MeHg) can inhibit the binding of radioligands to the muscarinic acetylcholine (mACh) receptor in rat brains. However, little is known concerning this relationship in specific anatomical regions of the brain or in other species, including humans. The purpose of this study was to explore the inhibitory effects of HgCl{sub 2} and MeHg on [{sup 3}H]-quinuclidinyl benzilate ([{sup 3}H]-QNB) binding to the mACh receptor in the cerebellum and cerebral cortex regions from human, rat, mouse,more » mink, and river otter brain tissues. Saturation binding curves were obtained from each sample to calculate receptor density (B {sub max}) and ligand affinity (K {sub d}). Subsequently, samples were exposed to HgCl{sub 2} or MeHg to derive IC50 values and inhibition constants (K {sub i}). Results demonstrate that HgCl{sub 2} is a more potent inhibitor of mACh receptor binding than MeHg, and the receptors in the cerebellum are more sensitive to Hg-mediated mACh receptor inhibition than those in the cerebral cortex. Species sensitivities, irrespective of Hg type and brain region, can be ranked from most to least sensitive: river otter > rat > mink > mouse > humans. In summary, our data demonstrate that Hg can inhibit the binding [{sup 3}H]-QNB to the mACh receptor in a range of mammalian species. This comparative study provides data on interspecies differences and a framework for interpreting results from human, murine, and wildlife studies.« less

Comparative effectiveness of Calabadion and sugammadex to reverse non-depolarizing neuromuscular blocking agents

PubMed Central

Haerter, Friederike; Simons, Jeroen Cedric Peter; Foerster, Urs; Duarte, Ingrid Moreno; Diaz-Gil, Daniel; Ganapati, Shweta; Eikermann-Haerter, Katharina; Ayata, Cenk; Zhang, Ben; Blobner, Manfred; Isaacs, Lyle; Eikermann, Matthias

2015-01-01

Background We evaluated the comparative effectiveness of calabadion 2 to reverse non-depolarizing neuromuscular blocking agents (NMBAs) by binding and inactivation. Methods The dose-response relationship of drugs to reverse vecuronium, rocuronium, and cisatracurium-induced neuromuscular block (NMB) was evaluated in vitro (competition binding assays and urine analysis), ex vivo (n=34; phrenic nerve hemidiaphragm preparation) and in vivo (n=108; quadriceps femoris muscle of the rat). Cumulative dose-response curves of calabadions, neostigmine, or sugammadex were created ex vivo at steady-state deep NMB. In living rats, we studied the dose-response relationship of the test drugs to reverse deep block under physiological conditions and we measured the amount of calabadion 2 excreted in the urine. Results In vitro experiments showed that calabadion 2 binds rocuronium with 89 times the affinity of sugammadex (Ka = 3.4 × 109 M−1 and Ka = 3.8 × 107 M−1). Urine analysis (proton nuclear magnetic resonance), competition binding assays and ex vivo study results obtained in the absence of metabolic deactivation are in accordance with an 1:1 binding ratio of sugammadex and calabadion 2 toward rocuronium. In living rats, calabadion 2 dose-dependently and rapidly reversed all NMBAs tested. The molar potency of calabadion 2 to reverse vecuronium and rocuronium was higher compared to sugammadex. Calabadion 2 was eliminated renally, and did not affect blood pressure or heart rate. Conclusion Calabadion 2 reverses NMB-induced by benzylisoquinolines and steroidal NMBAs in rats more effectively, i.e. faster, than sugammadex. Calabadion 2 is eliminated in the urine and well tolerated in rats. PMID:26418697

Biochemical Study of Anti-Inflammatory Proteins vCCI and vMIP-II

DTIC Science & Technology

2014-07-17

protein ), where we showed that vCCI is able to bind so many different chemokines due to its general negatively charged surface , allowing it to bind...sample of these competition curves. Our conclusion from the data in Table 1 and Figure 1 is that the negatively charged surface of vCCI allows it to...Similar to our mutagenesis results, the overall data indicate that vCCI uses a negatively charged surface to bind positive charges on the chemokine

First-row diatomics: Calculation of the geometry and energetics using self-consistent gradient-functional approximations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kutzler, F.W.; Painter, G.S.

1992-02-15

A fully self-consistent series of nonlocal (gradient) density-functional calculations has been carried out using the augmented-Gaussian-orbital method to determine the magnitude of gradient corrections to the potential-energy curves of the first-row diatomics, Li{sub 2} through F{sub 2}. Both the Langreth-Mehl-Hu and the Perdew-Wang gradient-density functionals were used in calculations of the binding energy, bond length, and vibrational frequency for each dimer. Comparison with results obtained in the local-spin-density approximation (LSDA) using the Vosko-Wilk-Nusair functional, and with experiment, reveals that bond lengths and vibrational frequencies are rather insensitive to details of the gradient functionals, including self-consistency effects, but the gradient correctionsmore » reduce the overbinding commonly observed in the LSDA calculations of first-row diatomics (with the exception of Li{sub 2}, the gradient-functional binding-energy error is only 50--12 % of the LSDA error). The improved binding energies result from a large differential energy lowering, which occurs in open-shell atoms relative to the diatomics. The stabilization of the atom arises from the use of nonspherical charge and spin densities in the gradient-functional calculations. This stabilization is negligibly small in LSDA calculations performed with nonspherical densities.« less

Spectroscopic and electrochemical studies of the interaction between oleuropein, the major bio-phenol in olives, and salmon sperm DNA

NASA Astrophysics Data System (ADS)

Mohamadi, Maryam; Afzali, Daryoush; Esmaeili-Mahani, Saeed; Mostafavi, Ali; Torkzadeh-Mahani, Masoud

2015-09-01

Interaction of oleuropein, the major bio-phenol in olive leaf and fruit, with salmon sperm double-stranded DNA was investigated by employing electronic absorption titrations, fluorescence quenching spectroscopy, competitive fluorescence spectroscopy, thermal denaturation and voltammetric studies. Titration of oleuropein with the DNA caused a hypochromism accompanied with a red shift indicating an intercalative mode of interaction. Binding constant of 1.4 × 104 M-1 was obtained for this interaction. From the curves of fluorescence titration of oleuropein with the DNA, binding constant and binding sites were calculated to be 8.61 × 103 M-1 and 1.05, respectively. Competitive studies with ethidium bromide (a well-known DNA intercalator) showed that the bio-phenol could take the place of ethidium bromide in the DNA intercalation sites. The interaction of oleuropein with DNA was also studied electrochemically. In the presence of the DNA, the anodic and cathodic peak currents of oleuropein decreased accompanied with increases in peak-to-peak potential separation and formal potential, indicating the intercalation of oleuropein into the DNA double helix. Moreover, melting temperature of the DNA was found to increase in the presence of oleuropein, indicating the stabilization of the DNA double helix due to an intercalative interaction.

Sensitive and fast detection of fructose in complex media via symmetry breaking and signal amplification using surface-enhanced Raman spectroscopy.

PubMed

Sun, Fang; Bai, Tao; Zhang, Lei; Ella-Menye, Jean-Rene; Liu, Sijun; Nowinski, Ann K; Jiang, Shaoyi; Yu, Qiuming

2014-03-04

A new strategy is proposed to sensitively and rapidly detect analytes with weak Raman signals in complex media using surface-enhanced Raman spectroscopy (SERS) via detecting the SERS signal changes of the immobilized probe molecules on SERS-active substrates upon binding of the analytes. In this work, 4-mercaptophenylboronic acid (4-MPBA) was selected as the probe molecule which was immobilized on the gold surface of a quasi-three-dimensional plasmonic nanostructure array (Q3D-PNA) SERS substrate to detect fructose. The molecule of 4-MPBA possesses three key functions: molecule recognition and reversible binding of the analyte via the boronic acid group, amplification of SERS signals by the phenyl group and thus shielding of the background noise of complex media, and immobilization on the surface of SERS-active substrates via the thiol group. Most importantly, the symmetry breaking of the 4-MPBA molecule upon fructose binding leads to the change of area ratio between totally symmetric 8a ring mode and nontotally symmetric 8b ring mode, which enables the detection. The detection curves were obtained in phosphate-buffered saline (PBS) and in undiluted artificial urine at clinically relevant concentrations, and the limit of detection of 0.05 mM was achieved.

Number of independent parameters in the potentiometric titration of humic substances.

PubMed

Lenoir, Thomas; Manceau, Alain

2010-03-16

With the advent of high-precision automatic titrators operating in pH stat mode, measuring the mass balance of protons in solid-solution mixtures against the pH of natural and synthetic polyelectrolytes is now routine. However, titration curves of complex molecules typically lack obvious inflection points, which complicates their analysis despite the high-precision measurements. The calculation of site densities and median proton affinity constants (pK) from such data can lead to considerable covariance between fit parameters. Knowing the number of independent parameters that can be freely varied during the least-squares minimization of a model fit to titration data is necessary to improve the model's applicability. This number was calculated for natural organic matter by applying principal component analysis (PCA) to a reference data set of 47 independent titration curves from fulvic and humic acids measured at I = 0.1 M. The complete data set was reconstructed statistically from pH 3.5 to 9.8 with only six parameters, compared to seven or eight generally adjusted with common semi-empirical speciation models for organic matter, and explains correlations that occur with the higher number of parameters. Existing proton-binding models are not necessarily overparametrized, but instead titration data lack the sensitivity needed to quantify the full set of binding properties of humic materials. Model-independent conditional pK values can be obtained directly from the derivative of titration data, and this approach is the most conservative. The apparent proton-binding constants of the 23 fulvic acids (FA) and 24 humic acids (HA) derived from a high-quality polynomial parametrization of the data set are pK(H,COOH)(FA) = 4.18 +/- 0.21, pK(H,Ph-OH)(FA) = 9.29 +/- 0.33, pK(H,COOH)(HA) = 4.49 +/- 0.18, and pK(H,Ph-OH)(HA) = 9.29 +/- 0.38. Their values at other ionic strengths are more reliably calculated with the empirical Davies equation than any existing model fit.

Binding characteristics of levetiracetam to synaptic vesicle protein 2A (SV2A) in human brain and in CHO cells expressing the human recombinant protein.

PubMed

Gillard, Michel; Chatelain, Pierre; Fuks, Bruno

2006-04-24

A specific binding site for the antiepileptic drug levetiracetam (2S-(oxo-1-pyrrolidinyl)butanamide, Keppra) in rat brain, referred to as the levetiracetam binding site, was discovered several years ago. More recently, this binding site has been identified as the synaptic vesicle protein 2A (SV2A), a protein present in synaptic vesicles [Lynch, B., Lambeng, N., Nocka, K., Kensel-Hammes, P., Bajjalieh, S.M., Matagne, A., Fuks, B., 2004. The synaptic vesicle protein SV2A is the binding site for the antiepileptic drug levetiracetam. Proc. Natl. Acad. Sci. USA, 101, 9861-9866.]. In this study, we characterized the binding properties of levetiracetam in post-mortem human brain and compared them to human SV2A expressed in Chinese hamster ovary (CHO) cells. The results showed that the binding properties of levetiracetam and [3H]ucb 30889, an analogue that was previously characterized as a suitable ligand for levetiracetam binding site/SV2A in rat brain [Gillard, M., Fuks, B., Michel, P., Vertongen, P., Massingham, R. Chatelain, P., 2003. Binding characteristics of [3H]ucb 30889 to levetiracetam binding sites in rat brain. Eur. J. Pharmacol. 478, 1-9.], are almost identical in human brain samples (cerebral cortex, hippocampus and cerebellum) and in CHO cell membranes expressing the human SV2A protein. Moreover, the results are also similar to those previously obtained in rat brain. [3H]ucb 30889 binding in human brain and to SV2A was saturable and reversible. At 4 degrees C, its binding kinetics were best fitted assuming a two-phase model in all tissues. The half-times of association for the fast component ranged between 1 to 2 min and represent 30% to 36% of the sites whereas the half-times for the slow component ranged from 20 to 29 min. In dissociation experiments, the half-times were from 2 to 4 min for the fast component (33% to 49% of the sites) and 20 to 41 min for the slow component. Saturation binding curves led to Kd values for [3H]ucb 30889 of 53+/-7, 55+/-9, 70+/-11 and 75+/-33 nM in human cerebral cortex, hippocampus, cerebellum and CHO cells expressing SV2A respectively. Bmax values around 3-4 pmol/mg protein were calculated in all brain regions. Some of the saturation curves displayed curvilinear Scatchard plots indicating the presence of high and low affinity binding sites. When this was the case, Kd values from 25 to 30 nM for the high affinity sites (24% to 34% of total sites) and from 200 to 275 nM for the low affinity sites were calculated. This was observed in all brain regions and in CHO cell membranes expressing the SV2A protein. It cannot be explained by putative binding of [3H]ucb 30889 to SV2B or C isoforms but may reflect different patterns of SV2A glycosylation or the formation of SV2A oligomers. Competition experiments were performed to determine the affinities for SV2A of a variety of compounds including levetiracetam, some of its analogues and other molecules known to interact with levetiracetam binding sites in rat brain such as bemegride, pentylenetetrazol and chlordiazepoxide. We found an excellent correlation between the affinities of these compounds measured in human brain, rat brain and CHO cells expressing human SV2A. In conclusion, we report for the first time that the binding characteristics of native levetiracetam binding sites/SV2A in human brain and rat brain share very similar properties with human recombinant SV2A expressed in CHO cells.

Safe uses of Hill's model: an exact comparison with the Adair-Klotz model

PubMed Central

2011-01-01

Background The Hill function and the related Hill model are used frequently to study processes in the living cell. There are very few studies investigating the situations in which the model can be safely used. For example, it has been shown, at the mean field level, that the dose response curve obtained from a Hill model agrees well with the dose response curves obtained from a more complicated Adair-Klotz model, provided that the parameters of the Adair-Klotz model describe strongly cooperative binding. However, it has not been established whether such findings can be extended to other properties and non-mean field (stochastic) versions of the same, or other, models. Results In this work a rather generic quantitative framework for approaching such a problem is suggested. The main idea is to focus on comparing the particle number distribution functions for Hill's and Adair-Klotz's models instead of investigating a particular property (e.g. the dose response curve). The approach is valid for any model that can be mathematically related to the Hill model. The Adair-Klotz model is used to illustrate the technique. One main and two auxiliary similarity measures were introduced to compare the distributions in a quantitative way. Both time dependent and the equilibrium properties of the similarity measures were studied. Conclusions A strongly cooperative Adair-Klotz model can be replaced by a suitable Hill model in such a way that any property computed from the two models, even the one describing stochastic features, is approximately the same. The quantitative analysis showed that boundaries of the regions in the parameter space where the models behave in the same way exhibit a rather rich structure. PMID:21521501

The prognostic performance of the complement system in septic patients in emergency department: a cohort study.

PubMed

Zhao, Xin; Chen, Yun-Xia; Li, Chun-Sheng

2015-01-01

To investigate the prognostic performance of complement components in septic patients, complement 3, membrane attack complex (MAC) and mannose-binding lectin were measured and compared among adult patients with sepsis, severe sepsis and septic shock, as well as between in-hospital nonsurvivors and survivors. The prognostic value of complement components was compared with mortality in emergency department sepsis (MEDS) score. Median complement 3, MAC and mannose-binding lectin increased directly with the sepsis, severe sepsis and septic shock groups, and were significantly higher in nonsurvivors than in survivors. MEDS and MAC independently predicted in-hospital mortality. The prognostic performance of MAC was superior to MEDS as analyzed by receiver operating characteristic curve and area under the curve.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Minfei; Li, Yue; Wyborny, Shane

ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCDmore » mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.« less

Evaluation of quantification methods for real-time PCR minor groove binding hybridization probe assays.

PubMed

Durtschi, Jacob D; Stevenson, Jeffery; Hymas, Weston; Voelkerding, Karl V

2007-02-01

Real-time PCR data analysis for quantification has been the subject of many studies aimed at the identification of new and improved quantification methods. Several analysis methods have been proposed as superior alternatives to the common variations of the threshold crossing method. Notably, sigmoidal and exponential curve fit methods have been proposed. However, these studies have primarily analyzed real-time PCR with intercalating dyes such as SYBR Green. Clinical real-time PCR assays, in contrast, often employ fluorescent probes whose real-time amplification fluorescence curves differ from those of intercalating dyes. In the current study, we compared four analysis methods related to recent literature: two versions of the threshold crossing method, a second derivative maximum method, and a sigmoidal curve fit method. These methods were applied to a clinically relevant real-time human herpes virus type 6 (HHV6) PCR assay that used a minor groove binding (MGB) Eclipse hybridization probe as well as an Epstein-Barr virus (EBV) PCR assay that used an MGB Pleiades hybridization probe. We found that the crossing threshold method yielded more precise results when analyzing the HHV6 assay, which was characterized by lower signal/noise and less developed amplification curve plateaus. In contrast, the EBV assay, characterized by greater signal/noise and amplification curves with plateau regions similar to those observed with intercalating dyes, gave results with statistically similar precision by all four analysis methods.

Synthesis, spectroscopic, biological activity and thermal characterization of ceftazidime with transition metals

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; Ali, Alaa E.; Elasala, Gehan S.; Kolkaila, Sherif A.

2018-03-01

Synthesis, physicochemical characterization and thermal analysis of ceftazidime complexes with transition metals (Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II)) were discussed. It's obtained that ceftazidime act as bidentate ligand. From magnetic measurement and spectral data, octahedral structures were proposed for all complexes except for cobalt, nickel and mercury had tetrahedral structural. Hyper chemistry program confirmed binding sites of ceftazidime. Ceftazidime complexes show higher activity than ceftazidime for some strains. From TG and DTA curves the thermal decomposition mechanisms of ceftazidime and their metal complexes were suggested. The thermal decomposition of the complexes ended with the formation of metal oxides as a final product except in case of Hg complex.

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 of biomolecular interaction by using Newton Iteration Method and Least Squares Method. First, the pseudo first order kinetic model of biomolecular interaction was established. Then the data of molecular interaction of HBsAg and HBsAb was obtained by bioanalyzer. Finally, we used the optical SPR bioanalyzer software which was written by ourselves to make nonlinear fit about the association and dissociation curves. The correlation coefficient R-squared is 0.99229 and 0.99593, respectively. Furthermore, the kinetic parameters and affinity constants were evaluated using the obtained data from the fitting results.

Diffraction catastrophes and semiclassical quantum mechanics for Veselago lensing in graphene

NASA Astrophysics Data System (ADS)

Reijnders, K. J. A.; Katsnelson, M. I.

2017-07-01

We study the effect of trigonal warping on the focusing of electrons by n-p junctions in graphene. We find that perfect focusing, which was predicted for massless Dirac fermions, is only preserved for one specific lattice orientation. In the general case, trigonal warping leads to the formation of cusp caustics, with a different position of the focus for graphene's two valleys. We develop a semiclassical theory to compute these positions and find very good agreement with tight-binding simulations. Considering the transmission as a function of potential strength, we find that trigonal warping splits the single Dirac peak into two distinct peaks, leading to valley polarization. We obtain the transmission curves from tight-binding simulations and find that they are in very good agreement with the results of a billiard model that incorporates trigonal warping. Furthermore, the positions of the transmission maxima and the scaling of the peak width are accurately predicted by our semiclassical theory. Our semiclassical analysis can easily be carried over to other Dirac materials, which generally have different Fermi surface distortions.

Systematic Interpolation Method Predicts Antibody Monomer-Dimer Separation by Gradient Elution Chromatography at High Protein Loads.

PubMed

Creasy, Arch; Reck, Jason; Pabst, Timothy; Hunter, Alan; Barker, Gregory; Carta, Giorgio

2018-05-29

A previously developed empirical interpolation (EI) method is extended to predict highly overloaded multicomponent elution behavior on a cation exchange (CEX) column based on batch isotherm data. Instead of a fully mechanistic model, the EI method employs an empirically modified multicomponent Langmuir equation to correlate two-component adsorption isotherm data at different salt concentrations. Piecewise cubic interpolating polynomials are then used to predict competitive binding at intermediate salt concentrations. The approach is tested for the separation of monoclonal antibody monomer and dimer mixtures by gradient elution on the cation exchange resin Nuvia HR-S. Adsorption isotherms are obtained over a range of salt concentrations with varying monomer and dimer concentrations. Coupled with a lumped kinetic model, the interpolated isotherms predict the column behavior for highly overloaded conditions. Predictions based on the EI method showed good agreement with experimental elution curves for protein loads up to 40 mg/mL column or about 50% of the column binding capacity. The approach can be extended to other chromatographic modalities and to more than two components. This article is protected by copyright. All rights reserved.

Time-Temperature Superposition to Determine the Stress-Rupture of Aramid Fibres

NASA Astrophysics Data System (ADS)

Alwis, K. G. N. C.; Burgoyne, C. J.

2006-07-01

Conventional creep testing takes a long time to obtain stress-rupture data for aramid fibres at the low stress levels likely to be used in practical applications. However, the rate of creep of aramid can be accelerated by a thermally activated process to obtain the failure of fibres within a few hours. It is possible to obtain creep curves at different temperature levels which can be shifted along the time axis to generate a single curve know as a master curve, from which stress-rupture data can be obtained. This technique is known as the time-temperature superposition principle and will be applied to Kevlar 49 yarns. Important questions relating to the techniques needed to obtain smooth master curves will be discussed, as will the validity the resulting curves and the corresponding stress-rupture lifetime.

( sup 3 H)-DOB(4-bromo-2,5-dimethoxyphenylisopropylamine) and ( sup 3 H) ketanserin label two affinity states of the cloned human 5-hydroxytryptamine2 receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branchek, T.; Adham, N.; Macchi, M.

1990-11-01

The binding properties of the 5-hydroxytryptamine2 (5-HT2) receptor have been the subject of much interest and debate in recent years. The hallucinogenic amphetamine derivative 4-bromo-2,5-dimethoxyphenylisopropylamine (DOB) has been shown to bind to a small number of binding sites with properties very similar to (3H)ketanserin-labeled 5-HT2 receptors, but with much higher agonist affinities. Some researchers have interpreted this as evidence for the existence of a new subtype of 5-HT2 receptor (termed 5-HT2A), whereas others have interpreted these data as indicative of agonist high affinity and agonist low affinity states for the 5-HT2 receptor. In this investigation, a cDNA clone encoding themore » serotonin 5-HT2 receptor was transiently transfected into monkey kidney Cos-7 cells and stably transfected into mouse fibroblast L-M(TK-) cells. In both systems, expression of this single serotonin receptor cDNA led to the appearance of both (3H)DOB and (3H)ketanserin binding sites with properties that matched their binding characteristics in mammalian brain homogenates. Addition of guanosine 5'-(beta, gamma-imido) triphosphate (Gpp(NH)p) to this system caused a rightward shift and steepening of agonist competition curves for (3H) ketanserin binding, converting a two-site binding curve to a single low affinity binding state. Gpp(NH)p addition also caused a 50% decrease in the number of high affinity (3H)DOB binding sites, with no change in the dissociation constant of the remaining high affinity states. These data on a single human 5-HT2 receptor cDNA expressed in two different transfection host cells indicate that (3H)DOB and (3H)ketanserin binding reside on the same gene product, apparently interacting with agonist and antagonist conformations of a single human 5-HT2 receptor protein.« less

Fibronectin forms the most extensible biological fibers displaying switchable force-exposed cryptic binding sites.

PubMed

Klotzsch, Enrico; Smith, Michael L; Kubow, Kristopher E; Muntwyler, Simon; Little, William C; Beyeler, Felix; Gourdon, Delphine; Nelson, Bradley J; Vogel, Viola

2009-10-27

Rather than maximizing toughness, as needed for silk and muscle titin fibers to withstand external impact, the much softer extracellular matrix fibers made from fibronectin (Fn) can be stretched by cell generated forces and display extraordinary extensibility. We show that Fn fibers can be extended more than 8-fold (>700% strain) before 50% of the fibers break. The Young's modulus of single fibers, given by the highly nonlinear slope of the stress-strain curve, changes orders of magnitude, up to MPa. Although many other materials plastically deform before they rupture, evidence is provided that the reversible breakage of force-bearing backbone hydrogen bonds enables the large strain. When tension is released, the nano-sized Fn domains first contract in the crowded environment of fibers within seconds into random coil conformations (molten globule states), before the force-bearing hydrogen bond networks that stabilize the domain's secondary structures are reestablished within minutes (double exponential). The exposure of cryptic binding sites on Fn type III modules increases steeply upon stretching. Thus fiber extension steadily up-regulates fiber rigidity and cryptic epitope exposure, both of which are known to differentially alter cell behavior. Finally, since stress-strain relationships cannot directly be measured in native extracellular matrix (ECM), the stress-strain curves were correlated with stretch-induced alterations of intramolecular fluorescence resonance energy transfer (FRET) obtained from trace amounts of Fn probes (mechanical strain sensors) that can be incorporated into native ECM. Physiological implications of the extraordinary extensibility of Fn fibers and contraction kinetics are discussed.

Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing.

PubMed

Kowalsky, Caitlin A; Whitehead, Timothy A

2016-12-01

The comprehensive sequence determinants of binding affinity for type I cohesin toward dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2970 and 2778 single point mutants of C. thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with the three independent experimental methods. This reconstruction results in a narrow dynamic range of -0.8-0.5 kcal/mol. The computational software packages FoldX and Rosetta were used to predict mutations that disrupt binding by more than 0.4 kcal/mol. The area under the curve of receiver operator curves was 0.82 for FoldX and 0.77 for Rosetta, showing reasonable agreements between predictions and experimental results. Destabilizing mutations to core and rim positions were predicted with higher accuracy than support positions. This benchmark dataset may be useful for developing new computational prediction tools for the prediction of the mutational effect on binding affinities for protein-protein interactions. Experimental considerations to improve precision and range of the reconstruction method are discussed. Proteins 2016; 84:1914-1928. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Analysis of metastasis associated signal regulatory network in colorectal cancer.

PubMed

Qi, Lu; Ding, Yanqing

2018-06-18

Metastasis is a key factor that affects the survival and prognosis of colorectal cancer patients. To elucidate molecular mechanism associated with the metastasis of colorectal cancer, genes related to the metastasis time of colorectal cancer were screened. Then, a network was constructed with this genes. Data was obtained from colorectal cancer expression profile. Molecular mechanism elucidated the time of tumor metastasis and the expression of genes related to colorectal cancer. We found that metastasis-promoting and metastasis-inhibiting networks included protein hubs of high connectivity. These protein hubs were components of organelles. Some ribosomal proteins promoted the metastasis of colorectal cancer. In some components of organelles, such as proteasomes, mitochondrial ribosome, ATP synthase, and splicing factors, the metastasis of colorectal cancer was inhibited by some sections of these organelles. After performing survival analysis of proteins in organelles, joint survival curve of proteins was constructed in ribosomal network. This joint survival curve showed metastasis was promoted in patients with colorectal cancer (P = 0.0022939). Joint survival curve of proteins was plotted against proteasomes (P = 7 e-07), mitochondrial ribosome (P = 0.0001157), ATP synthase (P = 0.0001936), and splicing factors (P = 1.35e-05). These curves indicate that metastasis of colorectal cancer can be inhibited. After analyzing proteins that bind with organelle components, we also found that some proteins were associated with the time of colorectal cancer metastasis. Hence, different cellular components play different roles in the metastasis of colorectal cancer. Copyright © 2018 Elsevier Inc. All rights reserved.

Automated data processing and radioassays.

PubMed

Samols, E; Barrows, G H

1978-04-01

Radioassays include (1) radioimmunoassays, (2) competitive protein-binding assays based on competition for limited antibody or specific binding protein, (3) immunoradiometric assay, based on competition for excess labeled antibody, and (4) radioreceptor assays. Most mathematical models describing the relationship between labeled ligand binding and unlabeled ligand concentration have been based on the law of mass action or the isotope dilution principle. These models provide useful data reduction programs, but are theoretically unfactory because competitive radioassay usually is not based on classical dilution principles, labeled and unlabeled ligand do not have to be identical, antibodies (or receptors) are frequently heterogenous, equilibrium usually is not reached, and there is probably steric and cooperative influence on binding. An alternative, more flexible mathematical model based on the probability or binding collisions being restricted by the surface area of reactive divalent sites on antibody and on univalent antigen has been derived. Application of these models to automated data reduction allows standard curves to be fitted by a mathematical expression, and unknown values are calculated from binding data. The vitrues and pitfalls are presented of point-to-point data reduction, linear transformations, and curvilinear fitting approaches. A third-order polynomial using the square root of concentration closely approximates the mathematical model based on probability, and in our experience this method provides the most acceptable results with all varieties of radioassays. With this curvilinear system, linear point connection should be used between the zero standard and the beginning of significant dose response, and also towards saturation. The importance is stressed of limiting the range of reported automated assay results to that portion of the standard curve that delivers optimal sensitivity. Published methods for automated data reduction of Scatchard plots for radioreceptor assay are limited by calculation of a single mean K value. The quality of the input data is generally the limiting factor in achieving good precision with automated as it is with manual data reduction. The major advantages of computerized curve fitting include: (1) handling large amounts of data rapidly and without computational error; (2) providing useful quality-control data; (3) indicating within-batch variance of the test results; (4) providing ongoing quality-control charts and between assay variance.

Fluorometric titration approach for calibration of quantity of binding site of purified monoclonal antibody recognizing epitope/hapten nonfluorescent at 340 nm.

PubMed

Yang, Xiaolan; Hu, Xiaolei; Xu, Bangtian; Wang, Xin; Qin, Jialin; He, Chenxiong; Xie, Yanling; Li, Yuanli; Liu, Lin; Liao, Fei

2014-06-17

A fluorometric titration approach was proposed for the calibration of the quantity of monoclonal antibody (mcAb) via the quench of fluorescence of tryptophan residues. It applied to purified mcAbs recognizing tryptophan-deficient epitopes, haptens nonfluorescent at 340 nm under the excitation at 280 nm, or fluorescent haptens bearing excitation valleys nearby 280 nm and excitation peaks nearby 340 nm to serve as Förster-resonance-energy-transfer (FRET) acceptors of tryptophan. Titration probes were epitopes/haptens themselves or conjugates of nonfluorescent haptens or tryptophan-deficient epitopes with FRET acceptors of tryptophan. Under the excitation at 280 nm, titration curves were recorded as fluorescence specific for the FRET acceptors or for mcAbs at 340 nm. To quantify the binding site of a mcAb, a universal model considering both static and dynamic quench by either type of probes was proposed for fitting to the titration curve. This was easy for fitting to fluorescence specific for the FRET acceptors but encountered nonconvergence for fitting to fluorescence of mcAbs at 340 nm. As a solution, (a) the maximum of the absolute values of first-order derivatives of a titration curve as fluorescence at 340 nm was estimated from the best-fit model for a probe level of zero, and (b) molar quantity of the binding site of the mcAb was estimated via consecutive fitting to the same titration curve by utilizing such a maximum as an approximate of the slope for linear response of fluorescence at 340 nm to quantities of the mcAb. This fluorometric titration approach was proved effective with one mcAb for six-histidine and another for penicillin G.

Great interactions: How binding incorrect partners can teach us about protein recognition and function

PubMed Central

Vamparys, Lydie; Laurent, Benoist; Carbone, Alessandra

2016-01-01

ABSTRACT Protein–protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known to interact can be a useful tool for the prediction of likely binding patches on a protein surface. From the analysis of the protein interfaces generated by a massive cross‐docking experiment using the 168 proteins of the Docking Benchmark 2.0, where all possible protein pairs, and not only experimental ones, have been docked together, we show that it is also possible to predict a protein's binding residues without having any prior knowledge regarding its potential interaction partners. Evaluating the performance of cross‐docking predictions using the area under the specificity‐sensitivity ROC curve (AUC) leads to an AUC value of 0.77 for the complete benchmark (compared to the 0.5 AUC value obtained for random predictions). Furthermore, a new clustering analysis performed on the binding patches that are scattered on the protein surface show that their distribution and growth will depend on the protein's functional group. Finally, in several cases, the binding‐site predictions resulting from the cross‐docking simulations will lead to the identification of an alternate interface, which corresponds to the interaction with a biomolecular partner that is not included in the original benchmark. Proteins 2016; 84:1408–1421. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:27287388

Thermodynamics of Interaction between Some Cellulose Ethers and SDS by Titration Microcalorimetry.

PubMed

Singh; Nilsson

1999-05-01

The interaction between certain nonionic cellulose ethers (ethyl hydroxyethyl cellulose and hydroxypropyl methyl cellulose) and sodium dodecyl sulphate (SDS) has been investigated using isothermal titration microcalorimetry at temperatures between 25-50 degrees C. The observed heat flow curves have been interpreted in terms of a plausible mechanism of the interaction of the substituent groups with SDS monomers and clusters. The data have been related to changes occuring in the system at the macro- and microscopic levels with the addition of surfactants and with temperature. The process consists predominantly of polymer-surfactant interactions initially and surfactant-surfactant interactions at the later stages. A phenomenological model of the cooperative interaction (adsorption) process has been derived, and earlier published equilibrium binding data have been used to recover binding constants and Gibbs energy changes for this process. The adsorption enthalpies and entropies have been recovered along with the heat capacity change. The enthalpic cost of confining the nonpolar regions of the polymers in surfactant clusters is high, but the entropy gain from release of hydration shell water molecules as well as increased freedom of movement of these nonpolar regions in the clusters gives the process a strong entropic driving force. The process is entropy-driven initially and converts to being both enthalpy and entropy-driven at high SDS concentrations. An enthalpy-entropy compensation behavior is seen. Strongly negative heat capacity changes have been obtained resulting from the transfer of nonpolar groups from aqueous into nonpolar environments, as well as a reduction of conformational domains that the chains can populate. Changes in these two components cause the heat capacity change to become less negative at the higher binding levels. The system can be classified as exhibiting nonclassical hydrophobic binding at the later stages of binding. Copyright 1999 Academic Press.

Bonding in the first-row diatomic molecules within the local spin-density approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Painter, G.S.; Averill, F.W.

1982-08-15

The Hohenberg-Kohn-Sham density-functional equations in the local spin-density approximation (LSDA) have been solved with essentially no loss of accuracy for dimers of the first row of the Periodic Table with the use of a fully-self-consistent spin-polarized Gaussian-orbital approach. Spectroscopic constants (binding energies, equilibrium separations, and ground-state vibrational frequencies) have been derived from the calculated potential-energy curves. Intercomparison of results obtained using the exchange-correlation functionals of Slater (scaled exchange or X..cap alpha..), Gunnarsson and Lundqvist (GL), and Vosko, Wilk, and Nusair (VWN) permits assessment of the relative merits of each and serves to identify general shortcomings in the LSDA. Basic trendsmore » are similar for each functional, but the treatment of the spin dependence of the exchange-correlation energy in the GL and VWN functionals yields a variation of the binding energy across the series which is more systematic than that in the X..cap alpha.. approximation. Agreement between the present results and those of Dunlap, Connolly, and Sabin in the X..cap alpha.., approximation confirms the accuracy of the variational charge-density-fit procedure used in the latter work. The refinements in correlation treatment within the VWN functional are reflected in improvements in binding energies which are only slight for most dimers in the series. This behavior is attributed to the error remaining in the exchange channel within the LSDA and demonstrates the necessity for self-interaction corrections for more accurate binding-energy determinations. Within the current LSDA, absolute accuracies of the VWN functional for the first-row dimers are within 2.3 eV for binding energies, 0.07 a.u. for bond lengths, and approx.200 cm/sup -1/ for vibrational frequencies.« less

The prognostic and risk-stratified value of heart-type fatty acid-binding protein in septic patients in the emergency department.

PubMed

Chen, Yun-Xia; Li, Chun-Sheng

2014-08-01

To evaluate the prognostic and risk-stratified ability of heart-type fatty acid-binding protein (H-FABP) in septic patients in the emergency department (ED). From August to November 2012, 295 consecutive septic patients were enrolled. Circulating H-FABP was measured. The predictive value of H-FABP for 28-day mortality, organ dysfunction on ED arrival, and requirement for mechanical ventilation or a vasopressor within 6 hours after ED arrival was assessed by the receiver operating characteristic curve and logistic regression and was compared with Acute Physiology and Chronic Health Evaluation (APACHE) II score, Mortality in Emergency Department Sepsis (MEDS) score, and Sequential Organ Failure Assessment score. The 28-day mortality, APACHE II, MEDS, and Sequential Organ Failure Assessment scores were much higher in H-FABP-positive patients. The incidence of organ dysfunction at ED arrival and requirement for mechanical ventilation or a vasopressor within 6 hours after ED arrival was higher in H-FABP-positive patients. Heart-type fatty acid-binding protein was an independent predictor of 28-day mortality and organ dysfunction. The area under the receiver operating characteristic curve for H-FABP predicting 28-day mortality and organ dysfunction was 0.784 and 0.755, respectively. Combination of H-FABP and MEDS improved the performance of MEDS in predicting organ dysfunction, and the difference of AUC was statistically significant (P<.05). The combinations of H-FABP and MEDS or H-FABP and APACHE II also improved the prognostic value of MEDS and APACHE II, but the areas under the curve were not statistically different. Heart-type fatty acid-binding protein was helpful for prognosis and risk stratification of septic patients in the ED. Copyright © 2014 Elsevier Inc. All rights reserved.

Multi-Step Fibrinogen Binding to the Integrin αIIbβ3 Detected Using Force Spectroscopy

PubMed Central

Litvinov, Rustem I.; Bennett, Joel S.; Weisel, John W.; Shuman, Henry

2005-01-01

The regulated ability of integrin αIIbβ3 to bind fibrinogen plays a crucial role in platelet aggregation and hemostasis. We have developed a model system based on laser tweezers, enabling us to measure specific rupture forces needed to separate single receptor-ligand complexes. First of all, we performed a thorough and statistically representative analysis of nonspecific protein-protein binding versus specific αIIbβ3-fibrinogen interactions in combination with experimental evidence for single-molecule measurements. The rupture force distribution of purified αIIbβ3 and fibrinogen, covalently attached to underlying surfaces, ranged from ∼20 to 150 pN. This distribution could be fit with a sum of an exponential curve for weak to moderate (20–60 pN) forces, and a Gaussian curve for strong (>60 pN) rupture forces that peaked at 80–90 pN. The interactions corresponding to these rupture force regimes differed in their susceptibility to αIIbβ3 antagonists or Mn2+, an αIIbβ3 activator. Varying the surface density of fibrinogen changed the total binding probability linearly >3.5-fold but did not affect the shape of the rupture force distribution, indicating that the measurements represent single-molecule binding. The yield strength of αIIbβ3-fibrinogen interactions was independent of the loading rate (160–16,000 pN/s), whereas their binding probability markedly correlated with the duration of contact. The aggregate of data provides evidence for complex multi-step binding/unbinding pathways of αIIbβ3 and fibrinogen revealed at the single-molecule level. PMID:16040750

Hydrology beyond closing the water balance: energy conservative scaling of gradient flux relations

NASA Astrophysics Data System (ADS)

Zehe, Erwin; Loritz, Ralf; Jackisch, Conrad

2017-04-01

The value of physically-based models has been doubted since their idea was introduced by Freeze and Harlan. Physically-based models like typically rely on the Darcy-Richards concept for soil water dynamics, the Penman-Monteith equation for soil-vegetation-atmosphere exchange processes and hydraulic approaches for overland and stream flow. Each of these concepts is subject to limitations arising from our imperfect understanding of the related processes and is afflicted by the restricted transferability of process descriptions from idealized laboratory conditions to heterogeneous natural systems. Particularly the non-linearity of soil water characteristics in concert with the baffling heterogeneity subsurface properties is usually seen as the dead end for a meaningful application of physically based models outside of well observed research catchments and, more importantly, for an upscaling of point scale flux - gradient relation-ships. This study provides evidence that an energy conservative scaling of topographic gradients and soil water retention curves allows derivation of useful effective catchment scale topography and retention curve from distributed data, which allow successful simulations of the catchment water balance in two distinctly different landscapes. The starting point of our approach is that subsurface water fluxes are driven by differences in potential energy and chemical/capillary binding energy. The relief of a single hillslope controls the potential energy gradients driving downslope flows of free water, while catchment scale variability in hillslope relief is associated with differences in driving potential energy. It is more important to note that the soil water retention curve characterises the density of capillary binding energy of soil water (usually named soil water potential) at a given soil water content. Spatially variable soil water characteristics hence reflect fluctuations in capillary binding energy of soil water at a given soil water content among different sites. Essentially we propose that a meaning full effective representation of the driving topographic gradient needs to represent the mean distribution of geo-potential energy in a catchment, which leads us to the hypsometric integral. Similarly, we postulate that effective soil water characteristics should characterise the average relation between soil water content and capillary binding energy of soil water. For a given set of soil water retention curve derived from a set of undisturbed soil samples this can be achieved by grouping the observation points of all soil samples, averaging the soil water content at a given matric potential/binding energy density and fitting a parametric relation. We demonstrate that a single hillslope with the proposed effective topography and soil water retention curve is sufficient to simulate the water balance and runoff formation of two distinctly different catchments in the Attert experimental watershed.

Binding of Pentachloroiridite to Plasma Polymerized Vinylpyridine Films and Electrocatalytic Oxidation of Ascorbic Acid

DTIC Science & Technology

1981-12-21

anion. Voltametry in 1 M HC1 and in 1 M HC]O 4 is indis- tinguishable from that in Figure 2 except for a minor (10-20 mv.) potential shift in E rf...slope of Figure 9 agrees within a factor of 1.4 with that calculated from the irreversible potential sweep relation (36) using the known diffusion...Curve B. All in 1 M HSO4 2 ,4* Figure 9. Relationship of potential sweep rate and peak current for Curve B of Figure 6. Figure 10. Curve A: oxidation

Experimental, computational and chemometrics studies of BSA-vitamin B6 interaction by UV-Vis, FT-IR, fluorescence spectroscopy, molecular dynamics simulation and hard-soft modeling methods.

PubMed

Manouchehri, Firouzeh; Izadmanesh, Yahya; Aghaee, Elham; Ghasemi, Jahan B

2016-10-01

The interaction of pyridoxine (Vitamin B6) with bovine serum albumin (BSA) is investigated under pseudo-physiological conditions by UV-Vis, fluorescence and FTIR spectroscopy. The intrinsic fluorescence of BSA was quenched by VB6, which was rationalized in terms of the static quenching mechanism. According to fluorescence quenching calculations, the bimolecular quenching constant (kq), dynamic quenching (KSV) and static quenching (KLB) at 310K were obtained. The efficiency of energy transfer and the distance between the donor (BSA) and the acceptor (VB6) were calculated by Foster's non-radiative energy transfer theory and were equal to 41.1% and 2.11nm. The collected UV-Vis and fluorescence spectra were combined into a row-and column-wise augmented matrix and resolved by multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS helped to estimate the stoichiometry of interactions, concentration profiles and pure spectra for three species (BSA, VB6 and VB6-BSA complex) existed in the interaction procedure. Based on the MCR-ALS results, using mass balance equations, a model was developed and binding constant of complex was calculated using non-linear least squares curve fitting. FT-IR spectra showed that the conformation of proteins was altered in presence of VB6. Finally, the combined docking and molecular dynamics (MD) simulations were used to estimate the binding affinity of VB6 to BSA. Five-nanosecond MD simulations were performed on bovine serum albumin (BSA) to study the conformational features of its ligand binding site. From MD results, eleven BSA snapshots were extracted, at every 0.5ns, to explore the binding affinity (GOLD score) of VB6 using a docking procedure. MD simulations indicated that there is a considerable flexibility in the structure of protein that affected ligand recognition. Structural analyses and docking simulations indicated that VB6 binds to site I and GOLD score values depend on the conformations of both BSA and ligand. Molecular modeling results showed that VB6-BSA complex formed not only on the basis of electrostatic forces, but also on the basis of π-π staking and hydrogen bond. There was an excellent agreement between the experimental and computational results. The results presented in this paper, will offer a reference for detailed and systematic studies on the biological effects and action mechanism of small molecules with proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

Nanofiber Ion-Exchange Membranes for the Rapid Uptake and Recovery of Heavy Metals from Water

PubMed Central

Chitpong, Nithinart; Husson, Scott M.

2016-01-01

An evaluation of the performance of polyelectrolyte-modified nanofiber membranes was undertaken to determine their efficacy in the rapid uptake and recovery of heavy metals from impaired waters. The membranes were prepared by grafting poly(acrylic acid) (PAA) and poly(itaconic acid) (PIA) to cellulose nanofiber mats. Performance measurements quantified the dynamic ion-exchange capacity for cadmium (Cd), productivity, and recovery of Cd(II) from the membranes by regeneration. The dynamic binding capacities of Cd(II) on both types of nanofiber membrane were independent of the linear flow velocity, with a residence time of as low as 2 s. Analysis of breakthrough curves indicated that the mass flow rate increased rapidly at constant applied pressure after membranes approached equilibrium load capacity for Cd(II), apparently due to a collapse of the polymer chains on the membrane surface, leading to an increased porosity. This mechanism is supported by hydrodynamic radius (Rh) measurements for PAA and PIA obtained from dynamic light scattering, which show that Rh values decrease upon Cd(II) binding. Volumetric productivity was high for the nanofiber membranes, and reached 0.55 mg Cd/g/min. The use of ethylenediaminetetraacetic acid as regeneration reagent was effective in fully recovering Cd(II) from the membranes. Ion-exchange capacities were constant over five cycles of binding-regeneration. PMID:27999394

Nanofiber Ion-Exchange Membranes for the Rapid Uptake and Recovery of Heavy Metals from Water.

PubMed

Chitpong, Nithinart; Husson, Scott M

2016-12-20

An evaluation of the performance of polyelectrolyte-modified nanofiber membranes was undertaken to determine their efficacy in the rapid uptake and recovery of heavy metals from impaired waters. The membranes were prepared by grafting poly(acrylic acid) (PAA) and poly(itaconic acid) (PIA) to cellulose nanofiber mats. Performance measurements quantified the dynamic ion-exchange capacity for cadmium (Cd), productivity, and recovery of Cd(II) from the membranes by regeneration. The dynamic binding capacities of Cd(II) on both types of nanofiber membrane were independent of the linear flow velocity, with a residence time of as low as 2 s. Analysis of breakthrough curves indicated that the mass flow rate increased rapidly at constant applied pressure after membranes approached equilibrium load capacity for Cd(II), apparently due to a collapse of the polymer chains on the membrane surface, leading to an increased porosity. This mechanism is supported by hydrodynamic radius (R h ) measurements for PAA and PIA obtained from dynamic light scattering, which show that R h values decrease upon Cd(II) binding. Volumetric productivity was high for the nanofiber membranes, and reached 0.55 mg Cd/g/min. The use of ethylenediaminetetraacetic acid as regeneration reagent was effective in fully recovering Cd(II) from the membranes. Ion-exchange capacities were constant over five cycles of binding-regeneration.

A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.

PubMed

Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao

2016-10-17

In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.

(+/-)-cis-2-methylspiro[1,3-oxathiolane-5,3'-quinuclidine] hydrochloride, hemihydrate (SNI-2011, cevimeline hydrochloride) induces saliva and tear secretions in rats and mice: the role of muscarinic acetylcholine receptors.

PubMed

Iga, Y; Arisawa, H; Ogane, N; Saito, Y; Tomizuka, T; Nakagawa-Yagi, Y; Masunaga, H; Yasuda, H; Miyata, N

1998-11-01

We investigated effects of (+/-)-cis-2-methylspiro[1,3-oxathiolane-5,3'-quinuclidine] hydrochloride, hemihydrate (SNI-2011, cevimeline hydrochloride), a rigid analogue of acetylcholine, on saliva and tear secretions in rats and mice to evaluate its therapeutical efficacy for xerostomia and xerophthalmia in patients with Sjogren's syndrome and X-ray exposure in the head and neck. Intraduodenal administrations of SNI-2011 increased saliva secretion in a dose-dependent manner at doses ranging from 3 to 30 mg/kg in normal rats and mice, two strains of autoimmune disease mice and X-irradiated saliva secretion defective rats. The salivation elicited by SNI-2011 was completely inhibited by atropine. A similar atropine-sensitive response was observed in tear secretion. In rat submandibular/sublingual gland membranes, [3H]quinuclidinyl benzilate (QNB) binding was saturable, and Scatchard plot analysis revealed a single population of binding sites with a Kd of 22 pM and a maximal binding capacity of 60 fmol/mg protein. The competitive inhibition curve of the [3H]QNB binding by SNI-2011 was obtained, and its dissociation constant value calculated from IC50 was 1-2 microM. These results suggest that SNI-2011 increases saliva and tear secretions through a direct stimulation to muscarinic receptors in salivary and lacrimal glands, and they suggest that SNI-2011 should be beneficial to patients with Sjögren's syndrome and X-ray exposure in the head and neck.

A Physiologically Based Pharmacokinetic Model to Predict the Pharmacokinetics of Highly Protein-Bound Drugs and Impact of Errors in Plasma Protein Binding

PubMed Central

Ye, Min; Nagar, Swati; Korzekwa, Ken

2015-01-01

Predicting the pharmacokinetics of highly protein-bound drugs is difficult. Also, since historical plasma protein binding data was often collected using unbuffered plasma, the resulting inaccurate binding data could contribute to incorrect predictions. This study uses a generic physiologically based pharmacokinetic (PBPK) model to predict human plasma concentration-time profiles for 22 highly protein-bound drugs. Tissue distribution was estimated from in vitro drug lipophilicity data, plasma protein binding, and blood: plasma ratio. Clearance was predicted with a well-stirred liver model. Underestimated hepatic clearance for acidic and neutral compounds was corrected by an empirical scaling factor. Predicted values (pharmacokinetic parameters, plasma concentration-time profile) were compared with observed data to evaluate model accuracy. Of the 22 drugs, less than a 2-fold error was obtained for terminal elimination half-life (t1/2, 100% of drugs), peak plasma concentration (Cmax, 100%), area under the plasma concentration-time curve (AUC0–t, 95.4%), clearance (CLh, 95.4%), mean retention time (MRT, 95.4%), and steady state volume (Vss, 90.9%). The impact of fup errors on CLh and Vss prediction was evaluated. Errors in fup resulted in proportional errors in clearance prediction for low-clearance compounds, and in Vss prediction for high-volume neutral drugs. For high-volume basic drugs, errors in fup did not propagate to errors in Vss prediction. This is due to the cancellation of errors in the calculations for tissue partitioning of basic drugs. Overall, plasma profiles were well simulated with the present PBPK model. PMID:26531057

Cysteine optical sensing with an up-conversion host and two chemosensors derived from rhodamine: Construction, characterization and performance

NASA Astrophysics Data System (ADS)

Lin, Chen; Zhigang, Fang

2017-03-01

This paper focused on two rhodamine chemosensors for cysteine optical sensing. To minimize their photobleaching caused by excitation light, up-conversion NaYF4:Yb3 +/Er3 + nanocrystals were prepared and used as excitation host. Photophysical measurement on this host and the two chemosensors suggested that chemosensor absorption matched well with host emission. An efficient energy transfer between them was discussed and confirmed by their spectral analysis and emission lifetime comparison. Job's plot suggested that our chemosensors followed a simple recognition mechanism towards cysteine with binding stoichiometry of 1:1. Both chemosensors showed emission "off-on" effect triggered by cysteine and good photostability. Linear working curves with maximum sensitivity of 2.61 were obtained. S substituent was positive to improve selectivity.

[Peroxynitrite effect on the haemoglobin oxygen affinity in vitro in presence of different partial pressure of carbon dioxide].

PubMed

Stepuro, T L; Zinchuk, V V

2011-08-01

Peroxynitrite (ONOO-) besides its toxic possesses regulatory action that includes the modulation of oxygen binding properties of blood. The aim of this work was to estimate ONOO- effect on the haemoglobin oxygen affinity (HOA) in vitro in presence of different partial pressure of carbon dioxide (CO2). The ONOO- presence in venous blood in conditions of hypercapnia induced oxyhaemoglobin dissociation curve shift leftward while in hypocapnic conditions the result of a different character was obtained. The revealed effect of ONOO- is realized, possibly, through various modifications ofhaemoglobin whose formation is dependent on the CO2 pressure. The ONOO- influences the HOA in different manner that can be important in regulation of blood oxygenation in lungs and maintenance of oxygen consumption in tissues.

[11C]Harmine Binding to Brain Monoamine Oxidase A: Test-Retest Properties and Noninvasive Quantification.

PubMed

Zanderigo, Francesca; D'Agostino, Alexandra E; Joshi, Nandita; Schain, Martin; Kumar, Dileep; Parsey, Ramin V; DeLorenzo, Christine; Mann, J John

2018-02-08

Inhibition of the isoform A of monoamine oxidase (MAO-A), a mitochondrial enzyme catalyzing deamination of monoamine neurotransmitters, is useful in treatment of depression and anxiety disorders. [ 11 C]harmine, a MAO-A PET radioligand, has been used to study mood disorders and antidepressant treatment. However, [ 11 C]harmine binding test-retest characteristics have to date only been partially investigated. Furthermore, since MAO-A is ubiquitously expressed, no reference region is available, thus requiring arterial blood sampling during PET scanning. Here, we investigate [ 11 C]harmine binding measurements test-retest properties; assess effects of using a minimally invasive input function estimation on binding quantification and repeatability; and explore binding potentials estimation using a reference region-free approach. Quantification of [ 11 C]harmine distribution volume (V T ) via kinetic models and graphical analyses was compared based on absolute test-retest percent difference (TRPD), intraclass correlation coefficient (ICC), and identifiability. The optimal procedure was also used with a simultaneously estimated input function in place of the measured curve. Lastly, an approach for binding potentials quantification in absence of a reference region was evaluated. [ 11 C]harmine V T estimates quantified using arterial blood and kinetic modeling showed average absolute TRPD values of 7.7 to 15.6 %, and ICC values between 0.56 and 0.86, across brain regions. Using simultaneous estimation (SIME) of input function resulted in V T estimates close to those obtained using arterial input function (r = 0.951, slope = 1.073, intercept = - 1.037), with numerically but not statistically higher test-retest difference (range 16.6 to 22.0 %), but with overall poor ICC values, between 0.30 and 0.57. Prospective studies using [ 11 C]harmine are possible given its test-retest repeatability when binding is quantified using arterial blood. Results with SIME of input function show potential for simplifying data acquisition by replacing arterial catheterization with one arterial blood sample at 20 min post-injection. Estimation of [ 11 C]harmine binding potentials remains a challenge that warrants further investigation.

Influence of N-ethylmaleimide on cholinoceptors and responses in longitudinal muscles from guinea-pig ileum.

PubMed Central

Aronstam, R. S.; Carrier, G. O.

1982-01-01

1 The binding of carbamylcholine to membranes prepared from the longitudinal muscle of guinea-pig ileum was determined from its inhibition of the binding of [3H]-3-quinuclidinyl benzilate. Carbamylcholine binding was resolved into high and low affinity components with apparent dissociation constants of 0.11 +/- 0.02 and 11 +/- 1 microM; 42% of the receptors displayed high affinity carbamylcholine binding. 2 Alkylation of longitudinal muscle membranes with N-ethylmaleimide increased muscarinic receptor affinity for carbamylcholine in a manner consistent with a conversion of low affinity to high affinity receptors. After exposure the muscle membrane fragments to 1 mM N-ethylmaleimide for 20 min at 35 degrees C, carbamylcholine binding was resolved into two components with apparent dissociation constants of 0.11 +/- 0.01 and 9 +/- 2 microM, with 74% of the receptors displaying the higher affinity. 3 Exposure of longitudinal membranes mounted in an organ chamber to 1 mM N-ethylmaleimide for 30s depressed isometric contractions in response to acetylcholine by 80%, while contractions induced by K+ and Ba2+ were reduced by less than 20% and 10%, respectively. Acetylcholine dose-response curves were shifted to the right while Ba2+ curves were unaffected. 4 It is suggested that N-ethylmaleimide has a selective effect on muscarinic responses in the longitudinal muscle by disrupting processes occurring after receptor occupancy but before the induction of phospholipid turnover or calcium influx in the postsynaptic membrane. PMID:7126999

Differential Binding Models for Direct and Reverse Isothermal Titration Calorimetry.

PubMed

Herrera, Isaac; Winnik, Mitchell A

2016-03-10

Isothermal titration calorimetry (ITC) is a technique to measure the stoichiometry and thermodynamics from binding experiments. Identifying an appropriate mathematical model to evaluate titration curves of receptors with multiple sites is challenging, particularly when the stoichiometry or binding mechanism is not available. In a recent theoretical study, we presented a differential binding model (DBM) to study calorimetry titrations independently of the interaction among the binding sites (Herrera, I.; Winnik, M. A. J. Phys. Chem. B 2013, 117, 8659-8672). Here, we build upon our DBM and show its practical application to evaluate calorimetry titrations of receptors with multiple sites independently of the titration direction. Specifically, we present a set of ordinary differential equations (ODEs) with the general form d[S]/dV that can be integrated numerically to calculate the equilibrium concentrations of free and bound species S at every injection step and, subsequently, to evaluate the volume-normalized heat signal (δQ(V) = δq/dV) of direct and reverse calorimetry titrations. Additionally, we identify factors that influence the shape of the titration curve and can be used to optimize the initial concentrations of titrant and analyte. We demonstrate the flexibility of our updated DBM by applying these differentials and a global regression analysis to direct and reverse calorimetric titrations of gadolinium ions with multidentate ligands of increasing denticity, namely, diglycolic acid (DGA), citric acid (CIT), and nitrilotriacetic acid (NTA), and use statistical tests to validate the stoichiometries for the metal-ligand pairs studied.

Differential Cationization of Fatty Acids with Monovalent Cations Studied by ESI-MS/MS and Computational Approach.

PubMed

Sudarshana Reddy, B; Pavankumar, P; Sridhar, L; Saha, Soumen; Narahari Sastry, G; Prabhakar, S

2018-04-24

The intercellular and intracellular transport of charged species (Na + /K + ) entail interaction of the ions with neutral organic molecules and formation of adduct ions. The rate of transport of the ions across the cell membrane(s) may depend on the stability of the adduct ions, which in turn rely on structural aspects of the organic molecules that interact with the ions. Positive ion ESI mass spectra were recorded for the solutions containing fatty acids (FAs) and monovalent cations (X=Li + , Na + , K + , Rb + and Cs + ). Product ion spectra of the [FA+X] + ions were recorded at different collision energies. Theoretical studies were exploited under both gas phase and solvent phase to investigate the structural effects of the fatty acids during cationization. Stability of [FA+X] + adduct ions were further estimated by means of AIM topological analyses and interaction energy (IE) values. Positive ion ESI-MS analyses of the solution of FAs and X + ions showed preferential binding of the K + ions to FAs. The K + ion binding increased with the increase in number of double bonds of FAs, while decreased with increase in the number of carbons of FAs. Dissociation curves of [FA+X] + ions indicated the relative stability order of the [FA+X] + ions and it was in line with the observed trends in ESI-MS. The solvent phase computational studies divulged the mode of binding and the binding efficiencies of different FAs with monovalent cations. Among the studied monovalent cations, the cationization of FAs follow the order K + >Na + >Li + >Rb + >Cs + . The docosahexaenoic acid showed high efficiency in binding with K + ion. The K + ion binding efficiency of FAs depends on the number of double bonds in unsaturated FAs and the carbon chain length in saturated FAs. The cationization trends of FAs obtained from the ESI-MS, ESI-MS/MS analyses were in good agreement with solvent phase computational studies. This article is protected by copyright. All rights reserved.

Effect of Protein Binding on the Activity of Penicillins in Combination with Gentamicin Against Enterococci

PubMed Central

Glew, Richard H.; Moellering, Robert C.

1979-01-01

To assess the effect of protein binding by human serum on the synergistic interaction of penicillins with gentamicin, time-kill curves were determined for four penicillins alone and in combination with gentamicin against 10 blood isolates of enterococci. Killing curves demonstrated synergism with penicillin G plus gentamicin against all 10 strains in either broth or 50% human serum. In broth the combinations of nafcillin plus gentamicin and oxacillin plus gentamicin were synergistic against 10 of 10 strains and 4 of 10 strains, respectively. However, in serum, nafcillin plus gentamicin was synergistically bactericidal against only two strains and oxacillin plus gentamicin against none. Methicillin plus gentamicin was synergistic against none of the enterococci in either medium. Thus, the semisynthetic, penicillinase-resistant penicillins are unlikely to be effective in the therapy of patients with enterococcal endocarditis. PMID:426508

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

A simulation model of the oxygen alveolo-capillary exchange in normal and pathological conditions.

PubMed

Brighenti, Chiara; Gnudi, Gianni; Avanzolini, Guido

2003-05-01

This paper presents a mathematical model of the oxygen alveolo-capillary exchange to provide the capillary oxygen partial pressure profile in normal and pathological conditions. In fact, a thickening of the blood-gas barrier, heavy exercise or a low oxygen partial pressure (PO2) in the alveolar space can reduce the O2 alveolo-capillary exchange. Since the reversible binding between haemoglobin and oxygen makes it impossible to determine the closed form for the mathematical description of the PO2 profile along the pulmonary capillaries, an approximate analytical solution of the capillary PO2 profile is proposed. Simulation results are compared with the capillary PO2 profile obtained by numerical integration and by a piecewise linear interpolation of the oxyhaemoglobin dissociation curve. Finally, the proposed model is evaluated in a large range of physiopathological diffusive conditions. The good fit to numerical solutions in all experimental conditions seems to represent a substantial improvement with respect to the approach based on a linear approximation of the oxyhaemoglobin dissociation curve, and makes this model a candidate to be incorporated into the integrated descriptions of the entire respiratory system, where the datum of primary interest is the value of end capillary PO2.

Chemical system biology based molecular interactions to identify inhibitors against Q151M mutant of HIV-1 reverse transcriptase.

PubMed

Pandey, Rajan Kumar; Sharma, Drista; Ojha, Rupal; Bhatt, Tarun Kumar; Prajapati, Vijay Kumar

2018-05-09

The emergence of mutations leading to drug resistance is the main cause of therapeutic failure in the human HIV infection. Chemical system biology approach has drawn great attention to discover new antiretroviral hits with high efficacy and negligible toxicity, which can be used as a prerequisite for HIV drug resistance global action plan 2017-21. To discover potential hits, we docked 49 antiretroviral analogs (n = 6294) against HIV-1 reverse transcriptase Q151M mutant & its wild-type form and narrow downed their number in three sequential modes of docking using Schrödinger suite. Later on, 80 ligands having better docking score than reference ligands (tenofovir and lamivudine) were screened for ADME, toxicity prediction, and binding energy estimation. Simultaneously, the area under the curve (AUC) was estimated using receiver operating characteristics (ROC) curve analysis to validate docking protocols. Finally, single point energy and molecular dynamics simulation approaches were performed for best two ligands (L3 and L14). This study reveals the antiretroviral efficacy of obtained two best ligands and delivers the hits against HIV-1 reverse transcriptase Q151M mutant. Copyright © 2018 Elsevier B.V. All rights reserved.

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Pressure reversal of the action of octanol on postsynaptic membranes from Torpedo.

PubMed Central

Braswell, L. M.; Miller, K. W.; Sauter, J. F.

1984-01-01

Octanol increases the binding of [3H]-acetylcholine to the desensitized state of the nicotinic receptor in postsynaptic membranes prepared from Torpedo californica. This increase in binding results from an increase in the affinity of [3H]-acetylcholine for its receptor without any change in the number of sites or the shape of the acetylcholine binding curve. High pressures of helium (300 atm) decrease [3H]-acetylcholine binding by a mechanism that changes only the affinity of acetylcholine binding. Helium pressure reverses the effect of octanol on the affinity of [3H]-acetylcholine for its receptor. This pressure reversal of the action of octanol at a postsynaptic membrane is consistent either with pressure counteracting an octanol-induced membrane expansion or with independent mechanisms for the actions of octanol and pressure. The data do not conform with a mechanism in which pressure displaces octanol from a binding site on the receptor protein. PMID:6487895

Universal aspects of adhesion and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Smith, John R.; Ferrante, John

1990-01-01

Adhesive energies are computed for flat and atomically sharp tips as a function of the normal distance to the substrate. The dependence of binding energies on tip shape is investigated. The magnitudes of the binding energies for the atomic force microscope are found to depend sensitively on tip material, tip shape and the sample site being probed. The form of the energy-distance curve, however, is universal and independent of these variables, including tip shape.

Universal aspects of brittle fracture, adhesion, and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Ferrante, John; Smith, John R.

1989-01-01

This universal relation between binding energy and interatomic separation was originally discovered for adhesion at bimetallic interfaces involving the simple metals Al, Zn, Mg, and Na. It is shown here that the same universal relation extends to adhesion at transition-metal interfaces. Adhesive energies have been computed for the low-index interfaces of Al, Ni, Cu, Ag, Fe, and W, using the equivalent-crystal theory (ECT) and keeping the atoms in each semiinfinite slab fixed rigidly in their equilibrium positions. These adhesive energy curves can be scaled onto each other and onto the universal adhesion curve. The effect of tip shape on the adhesive forces in the atomic-force microscope (AFM) is studied by computing energies and forces using the ECT. While the details of the energy-distance and force-distance curves are sensitive to tip shape, all of these curves can be scaled onto the universal adhesion curve.

Empirical expression for DC magnetization curve of immobilized magnetic nanoparticles for use in biomedical applications

NASA Astrophysics Data System (ADS)

Elrefai, Ahmed L.; Sasayama, Teruyoshi; Yoshida, Takashi; Enpuku, Keiji

2018-05-01

We studied the magnetization (M-H) curve of immobilized magnetic nanoparticles (MNPs) used for biomedical applications. First, we performed numerical simulation on the DC M-H curve over a wide range of MNPs parameters. Based on the simulation results, we obtained an empirical expression for DC M-H curve. The empirical expression was compared with the measured M-H curves of various MNP samples, and quantitative agreements were obtained between them. We can also estimate the basic parameters of MNP from the comparison. Therefore, the empirical expression is useful for analyzing the M-H curve of immobilized MNPs for specific biomedical applications.

Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

PubMed Central

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

2015-01-01

SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

Expanding RNA binding specificity and affinity of engineered PUF domains.

PubMed

Zhao, Yang-Yang; Mao, Miao-Wei; Zhang, Wen-Jing; Wang, Jue; Li, Hai-Tao; Yang, Yi; Wang, Zefeng; Wu, Jia-Wei

2018-05-18

Specific manipulation of RNA is necessary for the research in biotechnology and medicine. The RNA-binding domains of Pumilio/fem-3 mRNA binding factors (PUF domains) are programmable RNA binding scaffolds used to engineer artificial proteins that specifically modulate RNAs. However, the native PUF domains generally recognize 8-nt RNAs, limiting their applications. Here, we modify the PUF domain of human Pumilio1 to engineer PUFs that recognize RNA targets of different length. The engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity than the canonical eight-repeat domains; however, the binding affinity reaches the peak at those with 9 and 10 repeats. Structural analysis on PUF with nine repeats reveals a higher degree of curvature, and the RNA binding unexpectedly and dramatically opens the curved structure. Investigation of the residues positioned in between two RNA bases demonstrates that tyrosine and arginine have favored stacking interactions. Further tests on the availability of the engineered PUFs in vitro and in splicing function assays indicate that our engineered PUFs bind RNA targets with high affinity in a programmable way.

Expanding RNA binding specificity and affinity of engineered PUF domains

PubMed Central

Zhao, Yang-Yang; Zhang, Wen-Jing; Wang, Jue; Li, Hai-Tao; Yang, Yi; Wang, Zefeng; Wu, Jia-Wei

2018-01-01

Abstract Specific manipulation of RNA is necessary for the research in biotechnology and medicine. The RNA-binding domains of Pumilio/fem-3 mRNA binding factors (PUF domains) are programmable RNA binding scaffolds used to engineer artificial proteins that specifically modulate RNAs. However, the native PUF domains generally recognize 8-nt RNAs, limiting their applications. Here, we modify the PUF domain of human Pumilio1 to engineer PUFs that recognize RNA targets of different length. The engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity than the canonical eight-repeat domains; however, the binding affinity reaches the peak at those with 9 and 10 repeats. Structural analysis on PUF with nine repeats reveals a higher degree of curvature, and the RNA binding unexpectedly and dramatically opens the curved structure. Investigation of the residues positioned in between two RNA bases demonstrates that tyrosine and arginine have favored stacking interactions. Further tests on the availability of the engineered PUFs in vitro and in splicing function assays indicate that our engineered PUFs bind RNA targets with high affinity in a programmable way. PMID:29490074

Zonal Rate Model for Axial and Radial Flow Membrane Chromatography. Part I: Knowledge Transfer Across Operating Conditions and Scales

PubMed Central

Ghosh, Pranay; Vahedipour, Kaveh; Lin, Min; Vogel, Jens H; Haynes, Charles A; von Lieres, Eric

2013-01-01

The zonal rate model (ZRM) has previously been applied for analyzing the performance of axial flow membrane chromatography capsules by independently determining the impacts of flow and binding related non-idealities on measured breakthrough curves. In the present study, the ZRM is extended to radial flow configurations, which are commonly used at larger scales. The axial flow XT5 capsule and the radial flow XT140 capsule from Pall are rigorously analyzed under binding and non-binding conditions with bovine serum albumin (BSA) as test molecule. The binding data of this molecule is much better reproduced by the spreading model, which hypothesizes different binding orientations, than by the well-known Langmuir model. Moreover, a revised cleaning protocol with NaCl instead of NaOH and minimizing the storage time has been identified as most critical for quantitatively reproducing the measured breakthrough curves. The internal geometry of both capsules is visualized by magnetic resonance imaging (MRI). The flow in the external hold-up volumes of the XT140 capsule was found to be more homogeneous as in the previously studied XT5 capsule. An attempt for model-based scale-up was apparently impeded by irregular pleat structures in the used XT140 capsule, which might lead to local variations in the linear velocity through the membrane stack. However, the presented approach is universal and can be applied to different capsules. The ZRM is shown to potentially help save valuable material and time, as the experiments required for model calibration are much cheaper than the predicted large-scale experiment at binding conditions. Biotechnol. Bioeng. 2013; 110: 1129–1141. © 2012 Wiley Periodicals, Inc. PMID:23097218

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

PubMed Central

Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

2015-01-01

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

SDS-binding assay based on tyrosine fluorescence as a tool to determine binding properties of human serum albumin in blood plasma

NASA Astrophysics Data System (ADS)

Zhdanova, Nadezda; Shirshin, Evgeny; Fadeev, Victor; Priezzhev, Alexander

2016-04-01

Among all plasma proteins human serum albumin (HSA) is the most studied one as it is the main transport protein and can bind a wide variety of ligands especially fatty acids (FAs). The concentration of FAs bound to HSA in human blood plasma differs by three times under abnormal conditions (fasting, physical exercises or in case of social important diseases). In the present study a surfactant sodium dodecyl sulfate (SDS) was used to simulate FAs binding to HSA. It was shown that the increase of Tyr fluorescence of human blood plasma due to SDS addition can be completely explained by HSA-SDS complex formation. Binding parameters of SDS-HSA complex (average number of sites and apparent constant of complex formation) were determined from titration curves based on tyrosine (Tyr) fluorescence.

Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements.

PubMed

Wierez-Kien, M; Craciun, A D; Pinon, A V; Roux, S Le; Gallani, J L; Rastei, M V

2018-04-01

The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically <10 3 nm 2 ) measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements

NASA Astrophysics Data System (ADS)

Wierez-Kien, M.; Craciun, A. D.; Pinon, A. V.; Le Roux, S.; Gallani, J. L.; Rastei, M. V.

2018-04-01

The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically <103 nm2) measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

Studying the hopping parameters of half-Heusler NaAuS using maximally localized Wannier function

NASA Astrophysics Data System (ADS)

Sihi, Antik; Lal, Sohan; Pandey, Sudhir K.

2018-04-01

Here, the electronic behavior of half-Heusler NaAuS is studied using PBEsol exchange correlation functional by plotting the band structure curve. These bands are reproduced using maximally localized Wannier function using WANNIER90. Tight-binding bands are nicely matched with density functional theory bands. By fitting the tight-binding model, hopping parameter for NaAuS is obtained by including Na 2s, 2p, Au 6s, 5p, 5d and S 3s, 3p orbitals within the energy interval of -5 to 16 eV around the Fermi level. In present study, hopping integrals for NaAuS are computed for the first primitive unit cell atoms as well as the first nearest neighbor primitive unit cell. The most dominating hopping integrals are found for Na (3s) - S (3s), Na (2px) - S (2px), Au (6s) - S (3px), Au (6s) - S (3py) and Au (6s) - S (3pz) orbitals. The hopping integrals for the first nearest neighbor primitive unit cell are also discussed in this manuscript. In future, these hopping integrals are very important to find the topological invariant for NaAuS compound.

Evaluating the Correlation between Anteroposterior and Mediolateral Compensatory Curves and their Influence on Dentoskeletal Morphology-An In vitro CBCT Study.

PubMed

Babu, K Suresh; Kumar, A Nanda; Kommi, Pradeep Babu; Krishnan, P Hari; Kumar, M Senthil; Sabapathy, R Senkutvan; Kumar, V Vijay

2017-08-01

To date, many orthodontist corrects malocclusion based on patients aesthetic concern and fails to correct the compensatory curves. This scenario is due to less insight on understanding relationship of compensatory curves and its correlation in treatment prognosis. The purpose of this study was to evaluate the correlation between the curve of Spee, curve of Monson and curve of Wilson, their influence on dentoskeletal morphology and their contribution to occlusal stability. This study included 104 non-orthodontic models. The study casts were subdivided into two groups, Group-I consist 52 non- orthodontic models with Class-I molar relationship and Group-II consist of 52 non- orthodontic models with Class-II molar relationship. Curve of Spee was measured with digital vernier caliper, curve of Monson estimated using specially made sphere (7″inch, 8″ inch and 9″inch) and curve of Wilson was evaluated using Cone Beam Computed Technology (CBCT). Mean value for curve of Spee obtained for Group I and Group II is 1.844 mm and 3.188 mm. For curve of Monson, the mean value obtained for Group I and Group-II is 7.65 inches and 7.40 inches. The mean degree obtained for the curve of Wilson for Group I and Group-II is 12.05 and 16.49. The result showed positive correlation between curve of Spee and curve of Wilson and no correlation between curve of Monson and curve of Wilson and no correlation between curve of Spee and curve of Monson. The Pearson correlation coefficient analysis from the study confirmed these results. The results showed positive correlation between curve of spee and curve of Wilson. The data found in this study can be applied clinically for Class I and Class II malocclusion patients on diagnosis and treatment planning.

Target molecules detection by waveguiding in a photonic silicon membrane

DOEpatents

Letant, Sonia E [Livermore, CA; Van Buuren, Anthony [Livermore, CA; Terminello, Louis [Danville, CA; Hart, Bradley R [Brentwood, CA

2006-12-26

Disclosed herein is a porous silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and calculate the concentration of bound target.

Target molecules detection by waveguiding in a photonic silicon membrane

DOEpatents

Letant, Sonia; Van Buuren, Anthony; Terminello, Louis

2004-08-31

Disclosed herein is a photonic silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls selectively bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and determine the concentration of bound target.

A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

PubMed Central

Lott, William B.; Pontius, Brian W.; von Hippel, Peter H.

1998-01-01

Evidence for a two-metal ion mechanism for cleavage of the HH16 hammerhead ribozyme is provided by monitoring the rate of cleavage of the RNA substrate as a function of La3+ concentration in the presence of a constant concentration of Mg2+. We show that a bell-shaped curve of cleavage activation is obtained as La3+ is added in micromolar concentrations in the presence of 8 mM Mg2+, with a maximal rate of cleavage being attained in the presence of 3 μM La3+. These results show that two-metal ion binding sites on the ribozyme regulate the rate of the cleavage reaction and, on the basis of earlier estimates of the Kd values for Mg2+ of 3.5 mM and >50 mM, that these sites bind La3+ with estimated Kd values of 0.9 and >37.5 μM, respectively. Furthermore, given the very different effects of these metal ions at the two binding sites, with displacement of Mg2+ by La3+ at the stronger (relative to Mg2+) binding site activating catalysis and displacement of Mg2+ by La3+ at the weaker (relative to Mg2+) (relative to Mg2+) binding site inhibiting catalysis, we show that the metal ions at these two sites play very different roles. We argue that the metal ion at binding site 1 coordinates the attacking 2′-oxygen species in the reaction and lowers the pKa of the attached proton, thereby increasing the concentration of the attacking alkoxide nucleophile in an equilibrium process. In contrast, the role of the metal ion at binding site 2 is to catalyze the reaction by absorbing the negative charge that accumulates at the leaving 5′-oxygen in the transition state. We suggest structural reasons why the Mg2+–La3+ ion combination is particularly suited to demonstrating these different roles of the two-metal ions in the ribozyme cleavage reaction. PMID:9435228

Anti-gravity and galaxy rotation curves

NASA Astrophysics Data System (ADS)

Sanders, R. H.

1984-07-01

A modification of Newtonian gravitational attraction which arises in the context of modern attempts to unify gravity with the other forces in nature can produce rotation curves for spiral galaxies which are nearly flat from 10 to 100 kpc, bind clusters of galaxies, and close the universe with the density of baryonic matter consistent with primordial nucleosynthesis. This is possible if a very low mass vector boson carries an effective anti-gravity force which on scales smaller than that of galaxies almost balances the normal attractive gravity force.

Radioimmunoassays and 2-site immunoradiometric "sandwich" assays: basic principles.

PubMed

Rodbard, D

1988-10-01

The "sandwich" or noncompetitive reagent-excess, 2-site immunoradiometric assay (2-site IRMA), ELISA, USERIA, and related techniques, have several advantages compared with the traditional or competitive radioimmunoassays. IRMAs can provide improved sensitivity and specificity. However, IRMAs present some practical problems with nonspecific binding, increased consumption of antibody, biphasic dose response curve, (high dose hook effect), and may require special techniques for dose response curve analysis. We anticipate considerable growth in the popularity and importance of 2-site IRMA.

Comparative Analysis of Virtual 3-D Visual Display Systems Contributions to Cross-Functional Team Collaboration in a Product Design Review Environment

DTIC Science & Technology

1998-01-01

including the surface they lie on and the edge curves that bind them. Also stored is topological information indicating how all these elements are connected...microchip. This technology researched by Texas Instruments is referred to as a Digital Micromirror Device (DMD) (Burdea & Coiffet, 1994). It has the...stereoscopic imaging system designed to resemble traditional designer drafting boards. The Visionarium uses a 180 degree curved screen providing users with

VizieR Online Data Catalog: Light curves for the eclipsing binary V1094 Tau (Maxted+, 2015)

NASA Astrophysics Data System (ADS)

Maxted, P. F. L.; Hutcheon, R. J.; Torres, G.; Lacy, C. H. S.; Southworth, J.; Smalley, B.; Pavlovski, K.; Marschall, L. A.; Clausen, J. V.

2015-04-01

Photometric light curves of the detached eclipsing binary V1094 Tau in the Stroemgren u-,v-,b- and y-bands, and in the Johnson V-band. The curves in the Stroemgren bands were obtained with the Stroemgren Automatic Telescope (SAT) at ESO, La Silla. The curves in the V-band were obtained with the NFO telescope in New Mexico and with the URSA telescope at the University of Arkansas. (6 data files).

Diffusion Monte Carlo method for evaluating Hamaker constants

NASA Astrophysics Data System (ADS)

Maezono, Ryo; Hongo, Kenta

We evaluated Hamaker's constants for Si6H12 (CHS) to investigate its wettability, which is industrially useful but no references available. The constant is fundamental for wettability, but not directly accessible by experiments. Ab initio estimations are therefore in demand, and surely give an impact for broader fields such as tribology where the wettability plays an important role. The evaluation of binding curves itself could be a big challenge if it is applied to a practical molecule such as CHS, because highly accurate descriptions of electron correlations in vdW bindings get tough for such larger sizes with anisotropy. We applied DMC to overcome this difficulty, showing a new direction for wettability issues. Since ab intio estimations rely on simple assumptions such as additivity (and hence we denote it as Aadd), it would include biases. Taking a benzene as a benchmark, we compared Aadd evaluated from several available binding curves with other reported AL (estimations based on Lifshitz theory). By the comparison, we get trends of biases in Aa dd due to non-additivity and anisotropy because AL is expected to capture these effects to some extent in macroscopic manner. The expected trends here surprisingly well explain the series of results for CHS.

Membrane Curvature and Lipid Composition Synergize To Regulate N-Ras Anchor Recruitment.

PubMed

Larsen, Jannik B; Kennard, Celeste; Pedersen, Søren L; Jensen, Knud J; Uline, Mark J; Hatzakis, Nikos S; Stamou, Dimitrios

2017-09-19

Proteins anchored to membranes through covalently linked fatty acids and/or isoprenoid groups play crucial roles in all forms of life. Sorting and trafficking of lipidated proteins has traditionally been discussed in the context of partitioning to membrane domains of different lipid composition. We recently showed that membrane shape/curvature can in itself mediate the recruitment of lipidated proteins. However, exactly how membrane curvature and composition synergize remains largely unexplored. Here we investigated how three critical structural parameters of lipids, namely acyl chain saturation, headgroup size, and acyl chain length, modulate the capacity of membrane curvature to recruit lipidated proteins. As a model system we used the lipidated minimal membrane anchor of the GTPase, N-Ras (tN-Ras). Our data revealed complex synergistic effects, whereby tN-Ras binding was higher on planar DOPC than POPC membranes, but inversely higher on curved POPC than DOPC membranes. This variation in the binding to both planar and curved membranes leads to a net increase in the recruitment by membrane curvature of tN-Ras when reducing the acyl chain saturation state. Additionally, we found increased recruitment by membrane curvature of tN-Ras when substituting PC for PE, and when decreasing acyl chain length from 14 to 12 carbons (DMPC versus DLPC). However, these variations in recruitment ability had different origins, with the headgroup size primarily influencing tN-Ras binding to planar membranes whereas the change in acyl chain length primarily affected binding to curved membranes. Molecular field theory calculations recapitulated these findings and revealed lateral pressure as an underlying biophysical mechanism dictating how curvature and composition synergize to modulate recruitment of lipidated proteins. Our findings suggest that the different compositions of cellular compartments could modulate the potency of membrane curvature to recruit lipidated proteins and thereby synergistically regulate the trafficking and sorting of lipidated proteins. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Staphylococcus aureus-Fibronectin Interactions with and without Fibronectin-Binding Proteins and Their Role in Adhesion and Desorption ▿

PubMed Central

Xu, Chun-Ping; Boks, Niels P.; de Vries, Joop; Kaper, Hans J.; Norde, Willem; Busscher, Henk J.; van der Mei, Henny C.

2008-01-01

Adhesion and residence-time-dependent desorption of two Staphylococcus aureus strains with and without fibronectin (Fn) binding proteins (FnBPs) on Fn-coated glass were compared under flow conditions. To obtain a better understanding of the role of Fn-FnBP binding, the adsorption enthalpies of Fn with staphylococcal cell surfaces were determined using isothermal titration calorimetry (ITC). Interaction forces between staphylococci and Fn coatings were measured using atomic force microscopy (AFM). The strain with FnBPs adhered faster and initially stronger to an Fn coating than the strain without FnBPs, and its Fn adsorption enthalpies were higher. The initial desorption was high for both strains but decreased substantially within 2 s. These time scales of staphylococcal bond ageing were confirmed by AFM adhesion force measurement. After exposure of either Fn coating or staphylococcal cell surfaces to bovine serum albumin (BSA), the adhesion of both strains to Fn coatings was reduced, suggesting that BSA suppresses not only nonspecific but also specific Fn-FnBP interactions. Adhesion forces and adsorption enthalpies were only slightly affected by BSA adsorption. This implies that under the mild contact conditions of convective diffusion in a flow chamber, adsorbed BSA prevents specific interactions but does allow forced Fn-FnBP binding during AFM or stirring in ITC. The bond strength energies calculated from retraction force-distance curves from AFM were orders of magnitude higher than those calculated from desorption data, confirming that a penetrating Fn-coated AFM tip probes multiple adhesins in the outermost cell surface that remain hidden during mild landing of an organism on an Fn-coated substratum, like that during convective diffusional flow. PMID:18952882

A physiologically based pharmacokinetic model to predict the pharmacokinetics of highly protein-bound drugs and the impact of errors in plasma protein binding.

PubMed

Ye, Min; Nagar, Swati; Korzekwa, Ken

2016-04-01

Predicting the pharmacokinetics of highly protein-bound drugs is difficult. Also, since historical plasma protein binding data were often collected using unbuffered plasma, the resulting inaccurate binding data could contribute to incorrect predictions. This study uses a generic physiologically based pharmacokinetic (PBPK) model to predict human plasma concentration-time profiles for 22 highly protein-bound drugs. Tissue distribution was estimated from in vitro drug lipophilicity data, plasma protein binding and the blood: plasma ratio. Clearance was predicted with a well-stirred liver model. Underestimated hepatic clearance for acidic and neutral compounds was corrected by an empirical scaling factor. Predicted values (pharmacokinetic parameters, plasma concentration-time profile) were compared with observed data to evaluate the model accuracy. Of the 22 drugs, less than a 2-fold error was obtained for the terminal elimination half-life (t1/2 , 100% of drugs), peak plasma concentration (Cmax , 100%), area under the plasma concentration-time curve (AUC0-t , 95.4%), clearance (CLh , 95.4%), mean residence time (MRT, 95.4%) and steady state volume (Vss , 90.9%). The impact of fup errors on CLh and Vss prediction was evaluated. Errors in fup resulted in proportional errors in clearance prediction for low-clearance compounds, and in Vss prediction for high-volume neutral drugs. For high-volume basic drugs, errors in fup did not propagate to errors in Vss prediction. This is due to the cancellation of errors in the calculations for tissue partitioning of basic drugs. Overall, plasma profiles were well simulated with the present PBPK model. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Binding of naproxen enantiomers to human serum albumin studied by fluorescence and room-temperature phosphorescence

NASA Astrophysics Data System (ADS)

Lammers, Ivonne; Lhiaubet-Vallet, Virginie; Ariese, Freek; Miranda, Miguel A.; Gooijer, Cees

2013-03-01

The interaction of the enantiomers of the non-steroidal anti-inflammatory drug naproxen (NPX) with human serum albumin (HSA) has been investigated using fluorescence and phosphorescence spectroscopy in the steady-state and time-resolved mode. The absorption, fluorescence excitation, and fluorescence emission spectra of (S)-NPX and (R)-NPX differ in shape in the presence of HSA, indicating that these enantiomers experience a different environment when bound. In solutions containing 0.2 M KI, complexation with HSA results in a strongly increased NPX fluorescence intensity and a decreased NPX phosphorescence intensity due to the inhibition of the collisional interaction with the heavy atom iodide. Fluorescence intensity curves obtained upon selective excitation of NPX show 8-fold different slopes for bound and free NPX. No significant difference in the binding constants of (3.8 ± 0.6) × 105 M-1 for (S)-NPX and (3.9 ± 0.6) × 105 M-1 for (R)-NPX was found. Furthermore, the addition of NPX quenches the phosphorescence of the single tryptophan in HSA (Trp-214) based on Dexter energy transfer. The short-range nature of this mechanism explains the upward curvature of the Stern-Volmer plot observed for HSA: At low concentrations NPX binds to HSA at a distance from Trp-214 and no quenching occurs, whereas at high NPX concentrations the phosphorescence intensity decreases due to dynamic quenching by NPX diffusing into site I from the bulk solution. The dynamic quenching observed in the Stern-Volmer plots based on the longest phosphorescence lifetime indicates an overall binding constant to HSA of about 3 × 105 M-1 for both enantiomers.

Validation of the Argentine version of the Memory Binding Test (MBT) for Early Detection of Mild Cognitive Impairment

PubMed Central

Roman, Fabian; Iturry, Mónica; Rojas, Galeno; Barceló, Ernesto; Buschke, Herman; Allegri, Ricardo F.

2016-01-01

ABSTRACT Background: "Forgetfulness" is frequent in normal aging and characteristic of the early stages of dementia syndromes. The episodic memory test is central for detecting amnestic mild cognitive impairment (MCI). The Memory Binding Test (MBT) is a simple, easy and brief memory test to detect the early stage of episodic memory impairment. Objective: To validate the Argentine version of the MBT in a Latin American population and to estimate the diagnostic accuracy as a tool for early detection of MCI. Methods: 88 subjects (46 healthy controls and 42 patients with amnestic MCI) matched for age and educational level were evaluated by an extensive neuropsychological battery and the memory binding test. Results: A significantly better performance was detected in the control group; all MBT scales were predictive of MCI diagnosis (p<.01). The MBT showed high sensitivity (69%) and high specificity (88%), with a PPV of 93% and a NPV of 55% for associative paired recall. A statistically significant difference (c2=14,164, p<.001) was obtained when comparing the area under the curve (AUC) of the MBT (0.88) and the MMSE (0.70). Conclusion: The Argentine version of the MBT correlated significantly with the MMSE and the memory battery and is a useful tool in the detection of MCI. The operating characteristics of the MBT are well suited, surpassing other tests commonly used for detecting MCI. PMID:29213458

Universal tight binding model for chemical reactions in solution and at surfaces. II. Water.

PubMed

Lozovoi, A Y; Sheppard, T J; Pashov, D L; Kohanoff, J J; Paxton, A T

2014-07-28

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice--leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

Identification of high-specificity H-NS binding site in LEE5 promoter of enteropathogenic Esherichia coli (EPEC).

PubMed

Bhat, Abhay Prasad; Shin, Minsang; Choy, Hyon E

2014-07-01

Histone-like nucleoid structuring protein (H-NS) is a small but abundant protein present in enteric bacteria and is involved in compaction of the DNA and regulation of the transcription. Recent reports have suggested that H-NS binds to a specific AT rich DNA sequence than to intrinsically curved DNA in sequence independent manner. We detected two high-specificity H-NS binding sites in LEE5 promoter of EPEC centered at -110 and -138, which were close to the proposed consensus H-NS binding motif. To identify H-NS binding sequence in LEE5 promoter, we took a random mutagenesis approach and found the mutations at around -138 were specifically defective in the regulation by H-NS. It was concluded that H-NS exerts maximum repression via the specific sequence at around -138 and subsequently contacts a subunit of RNAP through oligomerization.

Putative melatonin receptors in a human biological clock

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reppert, S.M.; Weaver, D.R.; Rivkees, S.A.

In vitro autoradiography with /sup 125/I-labeled melatonin was used to examine melatonin binding sites in human hypothalamus. Specific /sup 125/I-labeled melatonin binding was localized to the suprachiasmatic nuclei, the site of a putative biological clock, and was not apparent in other hypothalamic regions. Specific /sup 125/I-labeled melatonin binding was consistently found in the suprachiasmatic nuclei of hypothalami from adults and fetuses. Densitometric analysis of competition experiments with varying concentrations of melatonin showed monophasic competition curves, with comparable half-maximal inhibition values for the suprachiasmatic nuclei of adults (150 picomolar) and fetuses (110 picomolar). Micromolar concentrations of the melatonin agonist 6-chloromelatonin completelymore » inhibited specific /sup 125/I-labeled melatonin binding, whereas the same concentrations of serotonin and norepinephrine caused only a partial reduction in specific binding. The results suggest that putative melatonin receptors are located in a human biological clock.« less

Cholinergic Neurotransmission: Function and Dysfunction, International Cholinergic Symposium (8th) Held at Montreal (Quebec) on 26-30 July 1992

DTIC Science & Technology

1992-12-31

receptor were decreased. In the presence of nicotine 1.0pM, the Kd values of rat cerebral muscarinic receptor bound with its agonist P3H] oxotremorine -M...inhibitory effects of GTPrS on [1 3H] oxotremorine -M binding were potentiated.It is suggsted that the binding properties of brain muscarinic receptor...interval) the dose-response curves of M-agonists arecoline and oxotremorine for producing salivation shifted leftward. Above demonstrated phenomena

Characterization of Receptor Binding Profiles of Influenza A Viruses Using An Ellipsometry-Based Label-Free Glycan Microarray Assay Platform

PubMed Central

Fei, Yiyan; Sun, Yung-Shin; Li, Yanhong; Yu, Hai; Lau, Kam; Landry, James P.; Luo, Zeng; Baumgarth, Nicole; Chen, Xi; Zhu, Xiangdong

2015-01-01

A key step leading to influenza viral infection is the highly specific binding of a viral spike protein, hemagglutinin (HA), with an extracellular glycan receptor of a host cell. Detailed and timely characterization of virus-receptor binding profiles may be used to evaluate and track the pandemic potential of an influenza virus strain. We demonstrate a label-free glycan microarray assay platform for acquiring influenza virus binding profiles against a wide variety of glycan receptors. By immobilizing biotinylated receptors on a streptavidin-functionalized solid surface, we measured binding curves of five influenza A virus strains with 24 glycans of diverse structures and used the apparent equilibrium dissociation constants (avidity constants, 10–100 pM) as characterizing parameters of viral receptor profiles. Furthermore by measuring binding kinetic constants of solution-phase glycans to immobilized viruses, we confirmed that the glycan-HA affinity constant is in the range of 10 mM and the reaction is enthalpy-driven. PMID:26193329

Characterization of Receptor Binding Profiles of Influenza A Viruses Using An Ellipsometry-Based Label-Free Glycan Microarray Assay Platform.

PubMed

Fei, Yiyan; Sun, Yung-Shin; Li, Yanhong; Yu, Hai; Lau, Kam; Landry, James P; Luo, Zeng; Baumgarth, Nicole; Chen, Xi; Zhu, Xiangdong

2015-07-16

A key step leading to influenza viral infection is the highly specific binding of a viral spike protein, hemagglutinin (HA), with an extracellular glycan receptor of a host cell. Detailed and timely characterization of virus-receptor binding profiles may be used to evaluate and track the pandemic potential of an influenza virus strain. We demonstrate a label-free glycan microarray assay platform for acquiring influenza virus binding profiles against a wide variety of glycan receptors. By immobilizing biotinylated receptors on a streptavidin-functionalized solid surface, we measured binding curves of five influenza A virus strains with 24 glycans of diverse structures and used the apparent equilibrium dissociation constants (avidity constants, 10-100 pM) as characterizing parameters of viral receptor profiles. Furthermore by measuring binding kinetic constants of solution-phase glycans to immobilized viruses, we confirmed that the glycan-HA affinity constant is in the range of 10 mM and the reaction is enthalpy-driven.

Binding mechanism of PicoGreen to DNA characterized by magnetic tweezers and fluorescence spectroscopy.

PubMed

Wang, Ying; Schellenberg, Helene; Walhorn, Volker; Toensing, Katja; Anselmetti, Dario

2017-09-01

Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules. By means of stretching and overwinding single, torsionally constrained, nick-free double-stranded DNA molecules, we acquired force-extension and supercoiling curves which allow quantifying DNA contour length, persistence length and other thermodynamical binding parameters, respectively. The results of our magnetic tweezers single-molecule binding study were well supported through analyzing the fluorescent spectra of stained DNA. On the basis of our work, we could identify a concentration-dependent bimodal binding behavior, where, apparently, PicoGreen associates to DNA as an intercalator and minor-groove binder simultaneously.

Integrated analysis on static/dynamic aeroelasticity of curved panels based on a modified local piston theory

NASA Astrophysics Data System (ADS)

Yang, Zhichun; Zhou, Jian; Gu, Yingsong

2014-10-01

A flow field modified local piston theory, which is applied to the integrated analysis on static/dynamic aeroelastic behaviors of curved panels, is proposed in this paper. The local flow field parameters used in the modification are obtained by CFD technique which has the advantage to simulate the steady flow field accurately. This flow field modified local piston theory for aerodynamic loading is applied to the analysis of static aeroelastic deformation and flutter stabilities of curved panels in hypersonic flow. In addition, comparisons are made between results obtained by using the present method and curvature modified method. It shows that when the curvature of the curved panel is relatively small, the static aeroelastic deformations and flutter stability boundaries obtained by these two methods have little difference, while for curved panels with larger curvatures, the static aeroelastic deformation obtained by the present method is larger and the flutter stability boundary is smaller compared with those obtained by the curvature modified method, and the discrepancy increases with the increasing of curvature of panels. Therefore, the existing curvature modified method is non-conservative compared to the proposed flow field modified method based on the consideration of hypersonic flight vehicle safety, and the proposed flow field modified local piston theory for curved panels enlarges the application range of piston theory.

Comparison of Saccharomyces cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site.

PubMed

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R; Kenniston, Jon A; Mendrola, Jeannine M; Ferguson, Kathryn M; Lemmon, Mark A

2015-02-03

F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence. Copyright © 2015 Elsevier Ltd. All rights reserved.

Heterogeneity of binding of muscarinic receptor antagonists in rat brain homogenates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, J.H.; el-Fakahany, E.E.

1985-06-01

The binding properties of (-)-(/sup 3/H)quinuclidinyl benzilate and (/sup 3/H) N-methylscopolamine to muscarinic acetylcholine receptors have been investigated in rat brain homogenates. The binding of both antagonists demonstrated high affinity and saturability. Analysis of the binding data resulted in linear Scatchard plots. However, (-)-(/sup 3/H)quinuclidinyl benzilate showed a significantly higher maximal binding capacity than that of (/sup 3/H)N-methylscopolamine. Displacement of both ligands with several muscarinic receptor antagonists resulted in competition curves in accordance with the law of mass-action for quinuclidinyl benzilate, atropine and scopolamine. A similar profile was found for the quaternary ammonium analogs of atropine and scopolamine when (/supmore » 3/H)N-methylscopolamine was used to label the receptors. However, when these hydrophilic antagonists were used to displace (-)-(/sup 3/H) quinuclidinyl benzilate binding, they showed interaction with high- and low-affinity binding sites. On the other hand, the nonclassical muscarinic receptor antagonist, pirenzepine, was able to displace both ligands from two binding sites. The present data are discussed in terms of the relationship of this anomalous heterogenity of binding of these hydrophilic muscarinic receptor antagonists and the proposed M1 and M2 receptor subtypes.« less

Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site

DOE PAGES

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; ...

2015-01-22

F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here in this paper, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound tomore » an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. In conclusion, our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence.« less

Analysis of the curve of Spee and the curve of Wilson in adult Indian population: A three-dimensional measurement study.

PubMed

Surendran, Sowmya Velekkatt; Hussain, Sharmila; Bhoominthan, S; Nayar, Sanjna; Jayesh, Ragavendra

2016-01-01

When reconstructing the occlusal curvatures dentists often use a 4-inch radii arc as a rough standard based on Monson spherical theory. The use of an identical radius for the curve of Spee for all patients may not be appropriate because each patient is individually different. The validity of application of this theory in the Indian population and the present study has been undertaken. This study is an attempt to evaluate the curve of Spee and curve of Wilson in young Indian population using three dimensional analysis. This study compared the radius and the depth of right and left, maxillary and mandibular curves of Spee and the radius of maxillary and mandibular curves of Wilson in males and females. The cusp tips of canines, buccal cusp tips of premolars and molars and palatal/lingual cusp tips of second molars of 60 maxillary and 60 mandibular casts were obtained. Three-dimensional (x, y, z) coordinates of the cusp tips of the molars, premolars, and canines of the right and left sides of the maxilla and mandible were obtained with three dimensional coordinate measuring machine. The radius and the depth of right and left, maxillary and mandibular curves of Spee and the radius of maxillary and mandibular curves of Wilson were measured by means of computer software Metrologic-XG. Pearson's correlation test and Independent t-test were used to test the statistical significance (α=.05). The values of curve of Spee and curve of Wilson in Indian population obtained from this study were higher than the 4 inch (100 mm) radius proposed by Monson. These findings suggest ethnic differences in the radius of curve of Spee and curve of Wilson.

A weakly nonlinear theory for wave-vortex interactions in curved channel flow

NASA Technical Reports Server (NTRS)

Singer, Bart A.; Erlebacher, Gordon; Zang, Thomas A.

1992-01-01

A weakly nonlinear theory is developed to study the interaction of Tollmien-Schlichting (TS) waves and Dean vortices in curved channel flow. The predictions obtained from the theory agree well with results obtained from direct numerical simulations of curved channel flow, especially for low amplitude disturbances. Some discrepancies in the results of a previous theory with direct numerical simulations are resolved.

Marine derived compounds as binders of the White spot syndrome virus VP28 envelope protein: In silico insights from molecular dynamics and binding free energy calculations.

PubMed

Sivakumar, K C; Sajeevan, T P; Bright Singh, I S

2016-10-01

White spot syndrome virus (WSSV) remains as one of the most dreadful pathogen of the shrimp aquaculture industry owing to its high virulence. The cumulative mortality reaches up to 100% within in 2-10days in a shrimp farm. Currently, no chemotherapeutics are available to control WSSV. The viral envelope protein, VP28, located on the surface of the virus particle acts as a vital virulence factor in the initial phases of inherent WSSV infection in shrimp. Hence, inhibition of envelope protein VP28 could be a novel way to deal with infection by inhibiting its interaction in the endocytic pathway. In this direction, a timely attempt was made to recognize a potential drug candidate of marine origin against WSSV using VP28 as a target by employing in silico docking and molecular dynamic simulations. A virtual library of 388 marine bioactive compounds was extracted from reports published in Marine Drugs. The top ranking compounds from docking studies were chosen from the flexible docking based on the binding affinities (ΔGb). In addition, the MD simulation and binding free energy analysis were implemented to validate and capture intermolecular interactions. The results suggested that the two compounds obtained a negative binding free energy with -40.453kJ/mol and -31.031kJ/mol for compounds with IDs 30797199 and 144162 respectively. The RMSD curve indicated that 30797199 moves into the hydrophobic core, while the position of 144162 atoms changes abruptly during simulation and is mostly stabilized by water bridges. The shift in RMSD values of VP28 corresponding to ligand RMSD gives an insight into the ligand induced conformational changes in the protein. This study is first of its kind to elucidate the explicit binding of chemical inhibitor to WSSV major structural protein VP28. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bedload Rating and Flow Competence Curves Vary With Watershed and Bed Material Parameters

NASA Astrophysics Data System (ADS)

Bunte, K.; Abt, S. R.

2003-12-01

Bedload transport rating curves and flow competence curves (largest bedload size for specified flow) are usually not known for streams unless a large number of bedload samples has been collected and analyzed. However, this information is necessary for assessing instream flow needs and stream responses to watershed effects. This study therefore analyzed whether bedload transport rating and flow competence curves were related to stream parameters. Bedload transport rating curves and flow competence curves were obtained from extensive bedload sampling in six gravel- and cobble-bed mountain streams. Samples were collected using bedload traps and a large net sampler, both of which provide steep and relatively well-defined bedload rating and flow competence curves due to a long sampling duration, a large sampler opening and a large sampler capacity. The sampled streams have snowmelt regimes, steep (1-9%) gradients, and watersheds that are mainly forested and relatively undisturbed with basin area sizes of 8 to 105 km2. The channels are slightly incised and can contain flows of more than 1.5 times bankfull with little overbank flow. Exponents of bedload rating and flow competence curves obtained from these measurements were found to systematically increase with basin area size and decrease with the degree of channel armoring. By contrast, coefficients of bedload rating and flow competence curves decreased with basin size and increased with armoring. All of these relationships were well-defined (0.86 < r2 < 0.99). Data sets from other studies in coarse-bedded streams fit the indicated trend if the sampling device used allows measuring bedload transport rates over a wide range and if bedload supply is somewhat low. The existence of a general positive trend between bedload rating curve exponents and basin area, and a negative trend between coefficients and basin area, is confirmed by a large data set of bedload rating curves obtained from Helley-Smith samples. However, in this case, the trends only become visible as basin area sizes span a wide range (1 - 10,000 km2). The well-defined relationships obtained from the bedload trap and the large net sampler suggest that exponents and coefficients of bedload transport rating curves (and flow competence curves) are predictable from an easily obtainable parameter such as basin size. However, the relationships of bedload rating curve exponents and coefficients with basin size and armoring appear to be influenced by the sampling device used and the watershed sediment production.

A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva† †Electronic supplementary information (ESI) available: Optimization of Mg2+ and ATMND concentrations for our CBSA-based ATMND-binding assay; ATMND-reported calibration curve for CBSA-5325 at various cocaine concentrations; ATMND binding affinity for the cocaine-assembled CBSA-5325; K D of 38-GC and different 38-GC mutants for cocaine as characterized by ITC; stem length effects on cocaine-induced CBSA assembly; spectra of CBSA-5335-based fluorescence detection of cocaine in 1× binding buffer; characterization of cocaine binding affinity of CBSA-5335 and PSA using ITC; fluorescence detection of cocaine in saliva with our fluorophore/quencher modified CBSA-5335; calibration curve of our CBSA-5335-based fluorophore/quencher assay in 1× binding buffer and 10% saliva at cocaine concentrations ranging from 0 to 10 μM; bias and precision of the CBSA-5335-based fluorophore/quencher assay; comparison of amplification-free split-aptamer assays for cocaine detection; sequence ID and DNA sequences used in this work. See DOI: 10.1039/c6sc01833e Click here for additional data file.

PubMed Central

Yu, Haixiang; Canoura, Juan; Guntupalli, Bhargav; Lou, Xinhui

2017-01-01

Sensors employing split aptamers that reassemble in the presence of a target can achieve excellent specificity, but the accompanying reduction of target affinity mitigates any overall gains in sensitivity. We for the first time have developed a split aptamer that achieves enhanced target-binding affinity through cooperative binding. We have generated a split cocaine-binding aptamer that incorporates two binding domains, such that target binding at one domain greatly increases the affinity of the second domain. We experimentally demonstrate that the resulting cooperative-binding split aptamer (CBSA) exhibits higher target binding affinity and is far more responsive in terms of target-induced aptamer assembly compared to the single-domain parent split aptamer (PSA) from which it was derived. We further confirm that the target-binding affinity of our CBSA can be affected by the cooperativity of its binding domains and the intrinsic affinity of its PSA. To the best of our knowledge, CBSA-5335 has the highest cocaine affinity of any split aptamer described to date. The CBSA-based assay also demonstrates excellent performance in target detection in complex samples. Using this CBSA, we achieved specific, ultra-sensitive, one-step fluorescence detection of cocaine within fifteen minutes at concentrations as low as 50 nM in 10% saliva without signal amplification. This limit of detection meets the standards recommended by the European Union's Driving under the Influence of Drugs, Alcohol and Medicines program. Our assay also demonstrates excellent reproducibility of results, confirming that this CBSA-platform represents a robust and sensitive means for cocaine detection in actual clinical samples. PMID:28451157

18F-FPEB, a PET radiopharmaceutical for quantifying metabotropic glutamate 5 receptors: a first-in-human study of radiochemical safety, biokinetics, and radiation dosimetry.

PubMed

Wong, Dean F; Waterhouse, Rikki; Kuwabara, Hiroto; Kim, Jongho; Brašić, James R; Chamroonrat, Wichana; Stabins, Michael; Holt, Daniel P; Dannals, Robert F; Hamill, Terence G; Mozley, P David

2013-03-01

Identification of safe and valid PET radioligands for metabotropic glutamate receptor, type 5 (mGluR5), is essential to measure changes in brain mGluR5 in neuropsychiatric disorders, to confirm central mGluR5 occupancy of drug candidates, and to guide dose selection for obtaining an optimum therapeutic window. Here we present the results of a first-in-human study assessing the safety and effectiveness of a novel PET radiopharmaceutical, (18)F-3-fluoro-5-[(pyridin-3-yl)ethynyl]benzonitrile ((18)F-FPEB), for quantifying regional brain concentrations of mGluR5. Quantification of whole-body biokinetics was conducted in 6 healthy adults (3 men and 3 women). The radiation safety profile was estimated with OLINDA/EXM software. Subsequently, pairs of dynamic brain scans were obtained for 11 healthy men to identify optimal methods for derivation of regional distribution volume and binding potential and to determine the repeatability of measurement. The whole-body effective radiation dose was approximately 17 μSv/MBq (62 mrem/mCi), with the gallbladder receiving the highest dose of 190 μSv/MBq. In brain studies, time-activity curves showed high accumulation in the insula/caudate nucleus, moderate uptake in the thalamus, and the lowest concentration in the cerebellum/pons. The plasma reference graphical analysis method appeared optimal for (18)F-FPEB; it showed acceptable test-retest variability of nondisplaceable binding potential (<10%) and identified the highest nondisplaceable binding potential values (from ∼0.5 in the globus pallidus to ∼3.5 in the insula) for target regions. Safety assessments revealed no clinically meaningful changes in vital signs, electrocardiogram, or laboratory values. (18)F-FPEB is safe and well tolerated, and its regional cerebral distribution is consistent with previous reports in the literature for metabotropic glutamate receptors. The repeatability of measurement suggests that (18)F-FPEB is suitable for quantifying mGluR5 in humans.

EXPERIMENTAL MEASUREMENT AND INTERPRETATION OF VOLT-AMPERE CURVES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gingrich, J.E.; Warner, C.; Weeks, C.C.

1962-07-01

Cylindrical and parallel-plane cesium vapor thermionic converters were used for obtaining volt-ampere curves for systematic variations of emitter, collector, and cesium reservoir temperatures, with electrode spacings ranging from a few to many mean free paths, and with space charge conditions varying from electron-rich to ion-rich. The resulting curves exhibit much variety. The saturation currents agree well with the data of Houston and Aamodt for the space charge neutralized, few-mean-free-path cases. Apparent'' saturation currents for space charge limited cases were observed and were always less than the currents predicted by Houston and Aamodt. Several discontinuities in slope were observed in themore » reverse current portion of the curves and these have tentatively been identified with volume ionization of atoms in both the ground and excited states. Similar processes may be important for obtaining the ignited mode. The methods used to measure static and dynamic volt-ampere curves are described. The use of a controlled-current load has yielded a negative resistance'' region in the curves which show the ignited mode. The curves obtained with poor current control do not show this phenomenon. Extinction is considered from the standpoint of Kaufmann' s criterion for stability. (auth)« less

Poliovirus Mutants Resistant to Neutralization with Soluble Cell Receptors

NASA Astrophysics Data System (ADS)

Kaplan, Gerardo; Peters, David; Racaniello, Vincent R.

1990-12-01

Poliovirus mutants resistant to neutralization with soluble cellular receptor were isolated. Replication of soluble receptor-resistant (srr) mutants was blocked by a monoclonal antibody directed against the HeLa cell receptor for poliovirus, indicating that the mutants use this receptor to enter cells. The srr mutants showed reduced binding to HeLa cells and cell membranes. However, the reduced binding phenotype did not have a major impact on viral replication, as judged by plaque size and one-step growth curves. These results suggest that the use of soluble receptors as antiviral agents could lead to the selection of neutralization-resistant mutants that are able to bind cell surface receptors, replicate, and cause disease.

UV extinction properties of carina nebular dust

NASA Technical Reports Server (NTRS)

Massa, Derck

1993-01-01

I have performed an analysis of the UV extinction by dust along the line of sight to the young open cluster Tr 16. The observed curves are parameterized in order to extract quantitative information about the structure of the curves. Furthermore, by constructing differential extinction curves, obtained by differencing curves for stars which lie within a few arc seconds of each other on the sky, I was able to obtain a curve which is free of the effects of foreground extinction, and represents the extinction by the dust in the Tr 16 molecular cloud. I then show that this curve is nearly identical to one due to dust in the Orion molecular cloud. This result shows that dust in the Carina arm exhibits the same behavior as that in the local arm.

Rapid solid-phase immunoassay for 6-keto prostaglandin F1 alpha on microplates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schramm, W.; Smith, R.H.; Jackson, T.M.

1990-03-01

We describe, for the measurement of 6-keto prostaglandin F1 alpha in biological media, a solid-phase immunoassay with immobilized antibodies that requires a total processing time of less than 2 h with hands-on time less than 30 min for 40 samples. The method combines the convenience of the microplate format with the sensitivity of radiolabeled prostaglandin derivatives as tracers in a competitive immunoassay. The intra- and interassay variations at 50% displacement of the radiolabeled prostaglandin derivative as tracer were 9.0% and 11.8%, respectively. At 50% displacement of the radiolabeled tracer, the sensitivity is about 20 pg per well. Optimal incubation timemore » is between 60 and 90 min. Nonspecific binding was less than 1% if about 8 pg of tracer (approximately 25,000 counts/min per well) was used. Inhibition curves of samples in different dilutions were parallel to standard curves. The variation of bound radiolabeled prostaglandin derivative within the wells of one microplate (n = 96) was less than 3%. Human plasma samples and medium from tissue culture assayed for 6-keto prostaglandin F1 alpha correlated well with results obtained with a solid-phase assay based on use of magnetic particles (r = 0.99, n = 24) for culture-medium samples; r = 0.99; n = 26 for plasma samples.« less

Identification and differentiation of Campylobacter species by high-resolution melting curve analysis.

PubMed

Hoseinpour, Fatemeh; Foroughi, Azadeh; Nomanpour, Bizhan; Nasab, Rezvan Sobhani

2017-07-01

Campylobacter jejuni and Campylobacter coli are the important food-born zoonotic pathogen, also are leading causes of human food borne illnesses worldwide. cadF gene is expressed in all C. jejuni and C. coli strains and mediates cell binding to the cell matrix protein, Fibronectin. High-resolution melting (HRM) analysis is emerging as an efficient and robust method for discriminating DNA sequence variants. The goal of this study was to apply HRM analysis to identification of C. jejuni and C. coli. A total of 100 samples were obtained from chicken in Kermanshah, Iran. HRM analysis based on cadF gene and Eva Green was developed to the identification of Campylobacter to the species level. Fifty-five of 100 samples were positive as campylobacter (7 C. jejuni, 29 C. coli, 16 mixes and 3 unknown). Minor variations were observed in melting point temperatures of C. coli or C. jejuni isolates and this variation can be used to the differentiation between C. coli or C. jejuni isolates. The results of this study indicated that HRM curve analysis can be a suitable technique and rapid technique for distinguishing between C. jejuni and C. coli isolates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Studies on metal hydride electrodes containing no binder additives

NASA Astrophysics Data System (ADS)

Rogulski, Z.; Dłubak, J.; Karwowska, M.; Krebs, M.; Pytlik, E.; Schmalz, M.; Gumkowska, A.; Czerwiński, A.

Electrochemical properties of hydrogen storage alloys (AB 5 type: LaMm-Ni 4.1Al 0.3Mn 0.4Co 0.45) were studied in 6 M KOHaq using Limited Volume Electrode (LVE) method. Working electrodes were prepared by pressing alloy powder (without binding and conducting additives) into a metal net wire serving as a support and as a current collector. Cyclic voltammetry curves reveal well defined hydrogen sorption and desorption peaks which are separated from other faradic processes, such as surface oxidation. Voltammograms of LVE resemble the curves obtained by various authors for single particle metal alloy electrodes. Hydrogen diffusion coefficient calculated at room temperature for LV electrodes and for 100% state of charge reaches a constant value of ca. 3.3 × 10 -9 and 2.1 × 10 -10 cm 2 s -1, for chronoamperometric and chronopotentiometric measurements, respectively. A comparison of the electrodes with average alloy particle sizes of ca. 50 and 4 μm allows us to conclude that at room temperature hydrogen storage capability of AB 5 alloy studied is independent on the alloy particle size. On the other hand, reduction of the particle size increases alloy capacity at temperatures below -10 °C and reduces time of electrochemical activation of the electrode.

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

NASA Astrophysics Data System (ADS)

Sulea, Traian; Hogues, Hervé; Purisima, Enrico O.

2012-05-01

We carried out a prospective evaluation of the utility of the SIE (solvation interaction energy) scoring function for virtual screening and binding affinity prediction. Since experimental structures of the complexes were not provided, this was an exercise in virtual docking as well. We used our exhaustive docking program, Wilma, to provide high-quality poses that were rescored using SIE to provide binding affinity predictions. We also tested the combination of SIE with our latest solvation model, first shell of hydration (FiSH), which captures some of the discrete properties of water within a continuum model. We achieved good enrichment in virtual screening of fragments against trypsin, with an area under the curve of about 0.7 for the receiver operating characteristic curve. Moreover, the early enrichment performance was quite good with 50% of true actives recovered with a 15% false positive rate in a prospective calculation and with a 3% false positive rate in a retrospective application of SIE with FiSH. Binding affinity predictions for both trypsin and host-guest complexes were generally within 2 kcal/mol of the experimental values. However, the rank ordering of affinities differing by 2 kcal/mol or less was not well predicted. On the other hand, it was encouraging that the incorporation of a more sophisticated solvation model into SIE resulted in better discrimination of true binders from binders. This suggests that the inclusion of proper Physics in our models is a fruitful strategy for improving the reliability of our binding affinity predictions.

Calcium binding properties of calcium dependent protein kinase 1 (CaCDPK1) from Cicer arietinum.

PubMed

Dixit, Ajay Kumar; Jayabaskaran, Chelliah

2015-05-01

Calcium plays a crucial role as a secondary messenger in all aspects of plant growth, development and survival. Calcium dependent protein kinases (CDPKs) are the major calcium decoders, which couple the changes in calcium level to an appropriate physiological response. The mechanism by which calcium regulates CDPK protein is not well understood. In this study, we investigated the interactions of Ca(2+) ions with the CDPK1 isoform of Cicer arietinum (CaCDPK1) using a combination of biophysical tools. CaCDPK1 has four different EF hands as predicted by protein sequence analysis. The fluorescence emission spectrum of CaCDPK1 showed quenching with a 5 nm red shift upon addition of calcium, indicating conformational changes in the tertiary structure. The plot of changes in intensity against calcium concentrations showed a biphasic curve with binding constants of 1.29 μM and 120 μM indicating two kinds of binding sites. Isothermal calorimetric (ITC) titration with CaCl2 also showed a biphasic curve with two binding constants of 0.027 μM and 1.7 μM. Circular dichroism (CD) spectra showed two prominent peaks at 208 and 222 nm indicating that CaCDPK1 is a α-helical rich protein. Calcium binding further increased the α-helical content of CaCDPK1 from 75 to 81%. Addition of calcium to CaCDPK1 also increased fluorescence of 8-anilinonaphthalene-1-sulfonic acid (ANS) indicating exposure of hydrophobic surfaces. Thus, on the whole this study provides evidence for calcium induced conformational changes, exposure of hydrophobic surfaces and heterogeneity of EF hands in CaCDPK1. Copyright © 2015 Elsevier GmbH. All rights reserved.

Sodium modulates opioid receptors through a membrane component different from G-proteins. Demonstration by target size analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ott, S.; Costa, T.; Herz, A.

1988-07-25

The target size for opioid receptor binding was studied after manipulations known to affect the interactions between receptor and GTP-binding regulatory proteins (G-proteins). Addition of GTP or its analogs to the binding reaction, exposure of intact cells to pertussis toxin prior to irradiation, or treatment of irradiated membranes with N-ethylmaleimide did not change the target size (approximately equal to 100 kDa) for opioid receptors in NG 108-15 cells and rat brain. These data suggest that the 100-kDa species does not include an active subunit of a G-protein or alternatively that GTP does not promote the dissociation of the receptor-G-protein complex.more » The presence of Na+ (100 mM) in the radioligand binding assay induced a biphasic decay curve for agonist binding and a flattening of the monoexponential decay curve for a partial agonist. In both cases the effect was explained by an irradiation-induced loss of the low affinity state of the opioid receptor produced by the addition of Na+. This suggests that an allosteric inhibitor that mediates the effect of sodium on the receptor is destroyed at low doses of irradiation, leaving receptors which are no longer regulated by sodium. The effect of Na+ on target size was slightly increased by the simultaneous addition of GTP but was not altered by pertussis toxin treatment. Thus, the sodium unit is distinct from G-proteins and may represent a new component of the opioid receptor complex. Assuming a simple bimolecular model of one Na+ unit/receptor, the size of this inhibitor can be measured as 168 kDa.« less

Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible competitive inhibitor, tested by simulated progress curves.

PubMed

Moruno-Dávila, M A; Garrido-del Solo, C; García-Moreno, M; Havsteen, B H; Garcia-Sevilla, F; Garcia-Cánovas, F; Varón, R

2001-02-01

The use of suicide substrates remains a very important and useful method in enzymology for studying enzyme mechanisms and designing potential drugs. Suicide substrates act as modified substrates for the target enzymes and bind to the active site. Therefore the presence of a competitive reversible inhibitor decreases the rate of substrate-induced inactivation and protects the enzyme from this inactivation. This lowering on the inactivation rate has evident physiological advantages, since it allows the easy acquisition of experimental data and facilitates kinetic data analysis by providing another variable (inhibitor concentration). However despite the importance of the simultaneous action of a suicide substrate and a competitive reversible inhibition, to date no corresponding kinetic analysis has been carried out. Therefore we present a general kinetic analysis of a Michaelis-Menten reaction mechanism with double inhibition caused by both, a suicide substrate and a competitive reversible inhibitor. We assume rapid equilibrium of the reversible reaction steps involved, while the time course equations for the reaction product have been derived with the assumption of a limiting enzyme. The goodness of the analytical solutions has been tested by comparison with the simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested. In conclusion, we present a complete kinetic analysis of an enzyme reaction mechanism as described above in an attempt to fill a gap in the theoretical treatment of this type of system.

Controlling Surface Plasmons Through Covariant Transformation of the Spin-Dependent Geometric Phase Between Curved Metamaterials

NASA Astrophysics Data System (ADS)

Zhong, Fan; Li, Jensen; Liu, Hui; Zhu, Shining

2018-06-01

General relativity uses curved space-time to describe accelerating frames. The movement of particles in different curved space-times can be regarded as equivalent physical processes based on the covariant transformation between different frames. In this Letter, we use one-dimensional curved metamaterials to mimic accelerating particles in curved space-times. The different curved shapes of structures are used to mimic different accelerating frames. The different geometric phases along the structure are used to mimic different movements in the frame. Using the covariant principle of general relativity, we can obtain equivalent nanostructures based on space-time transformations, such as the Lorentz transformation and conformal transformation. In this way, many covariant structures can be found that produce the same surface plasmon fields when excited by spin photons. A new kind of accelerating beam, the Rindler beam, is obtained based on the Rindler metric in gravity. Very large effective indices can be obtained in such systems based on geometric-phase gradient. This general covariant design method can be extended to many other optical media.

Method bacterial endospore quantification using lanthanide dipicolinate luminescence

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri J. (Inventor); Kirby, James Patrick (Inventor); Ponce, Adrian (Inventor)

2007-01-01

A lanthanide is combined with a medium to be tested for endospores. The dipicolinic acid released from the endospores binds the lanthanides, which have distinctive emission (i.e., luminescence) spectra, and are detected using photoluminescence. The concentration of spores is determined by preparing a calibration curve generated from photoluminescence spectra of lanthanide complex mixed with spores of a known concentration. A lanthanide complex is used as the analysis reagent, and is comprised of lanthanide ions bound to multidentate ligands that increase the dipicolinic acid binding constant through a cooperative binding effect with respect to lanthanide chloride. The resulting combined effect of increasing the binding constant and eliminating coordinated water and multiple equilibria increase the sensitivity of the endospore assay by an estimated three to four orders of magnitude over prior art of endospore detection based on lanthanide luminescence.

Elevated urinary level of vitamin D-binding protein as a novel biomarker for diabetic nephropathy

PubMed Central

TIAN, XIAO-QIN; ZHAO, LI-MIN; GE, JIA-PU; ZHANG, YAN; XU, YAN-CHENG

2014-01-01

Improving the early prediction and detection of diabetic nephropathy (DN) remains a great challenge in disease management. The aim of this study was to evaluate the early detection power of urinary vitamin D-binding protein (VDBP) for the diagnosis of DN. Urine samples were obtained from 45 healthy volunteers and 105 diabetic patients with normoalbuminuria (DM group), microalbuminuria (DN1 group) and macroalbuminuria (DN2 group) (n=35 per group). The VDBP expression patterns in urine from patients and controls were quantified by western blot analysis. The excretion levels of urinary VDBP were quantified with enzyme-linked immunosorbent assay. The quantification results were obtained by correcting for creatinine expression and showed that urinary VDBP levels were significantly elevated in the patients of the DN1 and DN2 groups compared with those of the DM group and normal controls (1,011.33±325.30 and 1,406.34±239.66 compared with 466.54±213.63 and 125.48±98.27 ng/mg, respectively) (P<0.001). Receiver operating characteristic analysis of urinary VDBP levels for the diagnosis of DN rendered an optimum cut-off value of 552.243 ng/mg corresponding to 92.86% sensitivity and 85.00% specificity, which also showed an area under the ROC curve of 0.966. In conclusion, the findings of the present study suggest that urinary VDBP may be a potential biomarker for the early detection and prevention of DN. Further studies are required to examine the pathogenic mechanisms of elevated VDBP levels and their role in the diagnosis of DN. PMID:24396416

Characterization of [11C]Lu AE92686 as a PET radioligand for phosphodiesterase 10A in the nonhuman primate brain.

PubMed

Yang, Kai-Chun; Stepanov, Vladimir; Amini, Nahid; Martinsson, Stefan; Takano, Akihiro; Nielsen, Jacob; Bundgaard, Christoffer; Bang-Andersen, Benny; Grimwood, Sarah; Halldin, Christer; Farde, Lars; Finnema, Sjoerd J

2017-02-01

[ 11 C]Lu AE92686 is a positron emission tomography (PET) radioligand that has recently been validated for examining phosphodiesterase 10A (PDE10A) in the human striatum. [ 11 C]Lu AE92686 has high affinity for PDE10A (IC 50  = 0.39 nM) and may also be suitable for examination of the substantia nigra, a region with low density of PDE10A. Here, we report characterization of regional [ 11 C]Lu AE92686 binding to PDE10A in the nonhuman primate (NHP) brain. A total of 11 PET measurements, seven baseline and four following pretreatment with unlabeled Lu AE92686 or the structurally unrelated PDE10A inhibitor MP-10, were performed in five NHPs using a high resolution research tomograph (HRRT). [ 11 C]Lu AE92686 binding was quantified using a radiometabolite-corrected arterial input function and compartmental and graphical modeling approaches. Regional time-activity curves were best described with the two-tissue compartment model (2TCM). However, the distribution volume (V T ) values for all regions were obtained by the Logan plot analysis, as reliable cerebellar V T values could not be derived by the 2TCM. For cerebellum, a proposed reference region, V T values increased by ∼30 % with increasing PET measurement duration from 63 to 123 min, while V T values in target regions remained stable. Both pretreatment drugs significantly decreased [ 11 C]Lu AE92686 binding in target regions, while no significant effect on cerebellum was observed. Binding potential (BP ND ) values, derived with the simplified reference tissue model (SRTM), were 13-17 in putamen and 3-5 in substantia nigra and correlated well to values from the Logan plot analysis. The method proposed for quantification of [ 11 C]Lu AE92686 binding in applied studies in NHP is based on 63 min PET data and SRTM with cerebellum as a reference region. The study supports that [ 11 C]Lu AE92686 can be used for PET examinations of PDE10A binding also in substantia nigra.

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity

PubMed Central

Liu, Geng; Li, Dongli; Li, Zhang; Qiu, Si; Li, Wenhui; Chao, Cheng-chi; Yang, Naibo; Li, Handong; Cheng, Zhen; Song, Xin; Cheng, Le; Zhang, Xiuqing; Wang, Jian; Yang, Huanming

2017-01-01

Abstract Predicting peptide binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in the majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401, and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods. Furthermore, currently the most popularly used methods for predicting peptide binding affinity are inefficient in identifying neoantigens from a large quantity of whole genome and transcriptome sequencing data. Here we present a Position Specific Scoring Matrix (PSSM)-based software called PSSMHCpan to accurately and efficiently predict peptide binding affinity with a broad coverage of HLA class I alleles. We evaluated the performance of PSSMHCpan by analyzing 10-fold cross-validation on a training database containing 87 HLA alleles and obtained an average area under receiver operating characteristic curve (AUC) of 0.94 and accuracy (ACC) of 0.85. In an independent dataset (Peptide Database of Cancer Immunity) evaluation, PSSMHCpan is substantially better than the popularly used NetMHC-4.0, NetMHCpan-3.0, PickPocket, Nebula, and SMM with a sensitivity of 0.90, as compared to 0.74, 0.81, 0.77, 0.24, and 0.79. In addition, PSSMHCpan is more than 197 times faster than NetMHC-4.0, NetMHCpan-3.0, PickPocket, sNebula, and SMM when predicting neoantigens from 661 263 peptides from a breast tumor sample. Finally, we built a neoantigen prediction pipeline and identified 117 017 neoantigens from 467 cancer samples of various cancers from TCGA. PSSMHCpan is superior to the currently available methods in predicting peptide binding affinity with a broad coverage of HLA class I alleles. PMID:28327987

Centrifugation-assisted Assembly of Colloidal Silica into Crack-Free and Transferrable Films with Tunable Crystalline Structures

PubMed Central

Fan, Wen; Chen, Min; Yang, Shu; Wu, Limin

2015-01-01

Self-assembly of colloidal particles into colloidal films has many actual and potential applications. While various strategies have been developed to direct the assembly of colloidal particles, fabrication of crack-free and transferrable colloidal film with controllable crystal structures still remains a major challenge. Here we show a centrifugation-assisted assembly of colloidal silica spheres into free-standing colloidal film by using the liquid/liquid interfaces of three immiscible phases. Through independent control of centrifugal force and interparticle electrostatic repulsion, polycrystalline, single-crystalline and quasi-amorphous structures can be readily obtained. More importantly, by dehydration of silica particles during centrifugation, the spontaneous formation of capillary water bridges between particles enables the binding and pre-shrinkage of the assembled array at the fluid interface. Thus the assembled colloidal films are not only crack-free, but also robust and flexible enough to be easily transferred on various planar and curved substrates. PMID:26159121

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding.

PubMed

Newcomer, Rebecca L; Fraser, LaTasha C R; Teschke, Carolyn M; Alexandrescu, Andrei T

2015-12-15

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining (3)JNC' couplings transmitted through H-bonds, the temperature and urea-concentration dependence of (1)HN and (15)N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and (3)JNC' H-bond couplings, are identified with an accuracy of 90% by (1)HN temperature coefficients. The accuracy is improved to 95% when (15)N temperature coefficients are also included. In contrast, the urea dependence of (1)HN and (15)N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Calculations of proton-binding thermodynamics in proteins.

PubMed

Beroza, P; Case, D A

1998-01-01

Computational models of proton binding can range from the chemically complex and statistically simple (as in the quantum calculations) to the chemically simple and statistically complex. Much progress has been made in the multiple-site titration problem. Calculations have improved with the inclusion of more flexibility in regard to both the geometry of the proton binding and the larger scale protein motions associated with titration. This article concentrated on the principles of current calculations, but did not attempt to survey their quantitative performance. This is (1) because such comparisons are given in the cited papers and (2) because continued developments in understanding conformational flexibility and interaction energies will be needed to develop robust methods with strong predictive power. Nevertheless, the advances achieved over the past few years should not be underestimated: serious calculations of protonation behavior and its coupling to conformational change can now be confidently pursued against a backdrop of increasing understanding of the strengths and limitations of such models. It is hoped that such theoretical advances will also spur renewed experimental interest in measuring both overall titration curves and individual pKa values or pKa shifts. Exploration of the shapes of individual titration curves (as measured by Hill coefficients and other parameters) would also be useful in assessing the accuracy of computations and in drawing connections to functional behavior.

Electroencephalographic, behavioral and receptor binding correlates of phencyclinoids in the rat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mattia, A.; Marquis, K.L.; Leccese, A.P.

1988-08-01

The pharmacology and structure-activity relationship of phencyclidine (PCP)-like drugs (phencyclinoids) were studied using electroencephalographic (EEG), behavioral and receptor binding techniques. The effects of PCP, 1-phenylcyclohexylamine HCl, N-methyl-1-phenycyclohexylamine HCl, N-ethyl-1-phenylcyclohexylamine HCl, N-(s-butyl)-1-phenylcyclohexylamine HCL, 1-(1-phenylcyclo-hexyl)-pyrrolidine HCl, 1-(1-(2-thienyl)cyclohexyl) piperidine HCl, 1-(1-(2-thienyl)cyclohexyl)-pyrrolidine HCl, ketamine and (+/-)-SKF 10047 were evaluated on the direct EEG and EEG spectra after acute i.v. injections (0.1-17.8 mg/kg). Similarities and differences were noted in the EEG dose-response curves. At lower doses of PCP and its analogs, low-amplitude theta waves predominated; however, at higher doses, high-amplitude, lower-frequency waves predominated. Qualitatively, the N-piperidine derivatives were similar to PCP and differed primarily inmore » potency. The benzomorphan (+/-)-SKF 10047 produced only theta activity at doses up to 12.8 mg/kg. These EEG effects occurred in conjunction with overt behaviors including locomotion, stereotypy and ataxia, concurrently assessed via observer-based rating scales. A strong correlation (r = 0.98) was obtained between the EEG and behavioral effects and the IC50 values from (/sup 3/H)PCP displacement experiments using crude rat brain homogenates.« less

Measuring functioning hepatocytes using Tc-99m galactosylneoglycoalbumin (Tc-NGA)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stadalnik, R.C.; Vera, D.R.; Quadro, R.E.

1984-01-01

Tc-NGA is a synthetic ligand which binds only to hepatic binding protein (HBP), a receptor found only in the liver. It exhibits the properties of high tissue specificity, affinity-dependent uptake, and dose-dependent uptake. Tc-NGA provides an opportunity to study the functioning hepatocyte. The authors evaluated the usefulness of this technique in patients with hepatitis and hepatoma. After intravenous administration of 5 mCi Tc-NGA, dynamic images were acquired for 30 minutes followed by static views. Estimates of HBP concentrations were obtained by kinetic analysis of blood and liver time-activity curves. Kinetic estimates (reduced chi-squares < 3.0) of HBP correlated well withmore » the clinical course and histology. For example, a patient with hepatoma whose calculated receptor population (functioning hepatocytes) was 3.0 +- 0.9 x 10/sup -7/ mole, which is the normal range, is doing well undergoing chemotherapy. Liver biopsy demonstrated normal liver tissue except for the hepatoma. Another patient with hepatoma who had a severely depressed receptor population, 1.2 +- 0.2 x 10/sup -8/ mole, expired one week after the study. Liver biopsy demonstrated practically no normal tissue. Thus, by means of a complementary, receptor radiopharmaceutical and mathematical model, one should be able to quantitatively follow hepatocyte function and predict response to a therapeutic regimen.« less

Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.

PubMed

Fang, Baishan; Niu, Jin; Ren, Hong; Guo, Yingxia; Wang, Shizhen

2014-01-01

Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.

MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

PubMed Central

Nagy, Alexander; Černíková, Lenka; Vitásková, Eliška; Křivda, Vlastimil; Dán, Ádám; Dirbáková, Zuzana; Jiřincová, Helena; Procházka, Bohumír; Sedlák, Kamil; Havlíčková, Martina

2016-01-01

In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence. PMID:27031831

Ligand and membrane-binding behavior of the phosphatidylinositol transfer proteins PITPα and PITPβ.

PubMed

Baptist, Matilda; Panagabko, Candace; Cockcroft, Shamshad; Atkinson, Jeffrey

2016-12-01

Phosphatidylinositol transfer proteins (PITPs) are believed to be lipid transfer proteins because of their ability to transfer either phosphatidylinositol (PI) or phosphatidylcholine (PC) between membrane compartments, in vitro. However, the detailed mechanism of this transfer process is not fully established. To further understand the transfer mechanism of PITPs we examined the interaction of PITPs with membranes using dual polarization interferometry (DPI), which measures protein binding affinity on a flat immobilized lipid surface. In addition, a fluorescence resonance energy transfer (FRET)-based assay was also employed to monitor how quickly PITPs transfer their ligands to lipid vesicles. DPI analysis revealed that PITPβ had a higher affinity to membranes compared with PITPα. Furthermore, the FRET-based transfer assay revealed that PITPβ has a higher ligand transfer rate compared with PITPα. However, both PITPα and PITPβ demonstrated a preference for highly curved membrane surfaces during ligand transfer. In other words, ligand transfer rate was higher when the accepting vesicles were highly curved.

Evaluation of Hamaker coefficients using Diffusion Monte Carlo method

NASA Astrophysics Data System (ADS)

Maezono, Ryo; Hongo, Kenta

We evaluated the Hamaker's constant for Cyclohexasilane to investigate its wettability, which is used as an ink of 'liquid silicon' in 'printed electronics'. Taking three representative geometries of the dimer coalescence (parallel, lined, and T-shaped), we evaluated these binding curves using diffusion Monte Carlo method. The parallel geometry gave the most long-ranged exponent, ~ 1 /r6 , in its asymptotic behavior. Evaluated binding lengths are fairly consistent with the experimental density of the molecule. The fitting of the asymptotic curve gave an estimation of Hamaker's constant being around 100 [zJ]. We also performed a CCSD(T) evaluation and got almost similar result. To check its justification, we applied the same scheme to Benzene and compared the estimation with those by other established methods, Lifshitz theory and SAPT (Symmetry-adopted perturbation theory). The result by the fitting scheme turned to be twice larger than those by Lifshitz and SAPT, both of which coincide with each other. It is hence implied that the present evaluation for Cyclohexasilane would be overestimated.

Thermoluminscence of irradiated herbs and spices

NASA Astrophysics Data System (ADS)

Mamoon, A.; Abdul-Fattah, A. A.; Abulfaraj, W. H.

1994-07-01

Several types of herbs and spices from the local market were irradiated with different doses of γ radiations. Doses varied from a few kilograys to 10 kilograys. Thermoluminescence of the irradiated samples and their controls was investigated. For the same type of herb or spice glow curves of different magnitudes, corresponding somewhat to the doses given, were obtained from the irradiated samples. Most control samples gave little or insignificant glow. Glow curves from different herbs and spices irradiated with the same doses were not similar in the strength of the glow signal given. Samples of the black pepper obtained from different packages sometimes give glow curves of very different intensities. Samples from irradiated black pepper were found to show little fading of their glow curves even at 9 months postirradiation. All irradiations were done under the same experimental conditions and at a dose rate of approximately 1 kGy h-1. The glow curves were obtained using a heating rate of about 9°C s-1 and a constant nitrogen flow rate.

Estimation of suspended-sediment rating curves and mean suspended-sediment loads

USGS Publications Warehouse

Crawford, Charles G.

1991-01-01

A simulation study was done to evaluate: (1) the accuracy and precision of parameter estimates for the bias-corrected, transformed-linear and non-linear models obtained by the method of least squares; (2) the accuracy of mean suspended-sediment loads calculated by the flow-duration, rating-curve method using model parameters obtained by the alternative methods. Parameter estimates obtained by least squares for the bias-corrected, transformed-linear model were considerably more precise than those obtained for the non-linear or weighted non-linear model. The accuracy of parameter estimates obtained for the biascorrected, transformed-linear and weighted non-linear model was similar and was much greater than the accuracy obtained by non-linear least squares. The improved parameter estimates obtained by the biascorrected, transformed-linear or weighted non-linear model yield estimates of mean suspended-sediment load calculated by the flow-duration, rating-curve method that are more accurate and precise than those obtained for the non-linear model.

Cooperative Allosteric Ligand Binding in Calmodulin

NASA Astrophysics Data System (ADS)

Nandigrami, Prithviraj

Conformational dynamics is often essential for a protein's function. For example, proteins are able to communicate the effect of binding at one site to a distal region of the molecule through changes in its conformational dynamics. This so called allosteric coupling fine tunes the sensitivity of ligand binding to changes in concentration. A conformational change between a "closed" (apo) and an "open" (holo) conformation upon ligation often produces this coupling between binding sites. Enhanced sensitivity between the unbound and bound ensembles leads to a sharper binding curve. There are two basic conceptual frameworks that guide our visualization about ligand binding mechanisms. First, a ligand can stabilize the unstable "open" state from a dynamic ensemble of conformations within the unbound basin. This binding mechanism is called conformational selection. Second, a ligand can weakly bind to the low-affinity "closed" state followed by a conformational transition to the "open" state. In this dissertation, I focus on molecular dynamics simulations to understand microscopic origins of ligand binding cooperativity. A minimal model of allosteric binding transitions must include ligand binding/unbinding events, while capturing the transition mechanism between two distinct meta-stable free energy basins. Due in part to computational timescales limitations, work in this dissertation describes large-scale conformational transitions through a simplified, coarse-grained model based on the energy basins defined by the open and closed conformations of the protein Calmodulin (CaM). CaM is a ubiquitous calcium-binding protein consisting of two structurally similar globular domains connected by a flexible linker. The two domains of CaM, N-terminal domain (nCaM) and C-terminal domain (cCaM) consists of two helix-loop-helix motifs (the EF-hands) connected by a flexible linker. Each domain of CaM consists of two binding loops and binds 2 calcium ions each. The intact domain binds up to 4 calcium ions. The simulations use a coupled molecular dynamics/monte carlo scheme where the protein dynamics is simulated explicitly, while ligand binding/unbinding are treated implicitly. In the model, ligand binding/unbinding events coupled with a conformational change of the protein within the grand canonical ensemble. Here, ligand concentration is controlled through the chemical potential (micro). This allows us to use a simple thermodynamic model to analyze the simulated data and quantify binding cooperativity. Simulated binding titration curves are calculated through equilibrium simulations at different values of micro. First, I study domain opening transitions of isolated nCaM and cCaM in the absence of calcium. This work is motivated by results from a recent analytic variational model that predicts distinct domain opening transition mechanism for the domains of CaM. This is a surprising result because the domains have the same folded state topology. In the simulations, I find the two domains of CaM have distinct transition mechanism over a broad range of temperature, in harmony with the analytic predictions. In particular, the simulated transition mechanism of nCaM follows a two-state behavior, while domain opening in cCaM involves global unfolding and refolding of the tertiary structure. The unfolded intermediate also appears in the landscape of nCaM, but at a higher temperature than it appears in cCaM's energy landscape. This is consistent with nCaM's higher thermal stability. Under approximate physiological conditions, majority of the sampled transitions in cCaM involves unfolding and refolding during conformational change. Kinetically, the transient unfolding and refolding in cCaM significantly slows the domain opening and closing rates in cCaM. Second, I investigate the structural origins of binding affinity and allosteric cooperativity of binding 2 calcium-ions to each domain of CaM. In my work, I predict the order of binding strength of CaM's loops. I analyze simulated binding curves within the framework of the classic Monod-Wyman-Changeux (MWC) model of allostery to extract the binding free energies to the closed and open ensembles. The simulations predict that cCaM binds calcium with higher affinity and greater cooperativity than nCaM. Where it is possible to compare, these predictions are in good agreement with experimental results. The analysis of the simulations offers a rationale for why the two domains differ in cooperativity: the higher cooperativity of cCaM is due to larger difference in affinity of its binding loops. Third, I extend the work to investigate structural origins of binding cooperativity of 4 calcium-ions to intact CaM. I characterize the microscopic cooperativities of each ligation state and provide a kinetic description of the binding mechanism. Due to the heterogeneous nature of CaM's loops, as predicted in our simulations of isolated domains, I focus on investigating the influence of this heterogeneity on the kinetic flux of binding pathways as a function of concentration. The formalism developed for Network Models of protein folding kinetics, is used to evaluate the directed flux of all possible pathways between unligated and fully loaded CaM. (Abstract shortened by ProQuest.).

Membrane Bending by Protein Crowding

NASA Astrophysics Data System (ADS)

Stachowiak, Jeanne

2014-03-01

From endosomes and synaptic vesicles to the cristae of the mitochondria and the annulus of the nuclear pore, highly curved membranes are fundamental to the structure and physiology of living cells. The established view is that specific families of proteins are able to bend membranes by binding to them. For example, inherently curved proteins are thought to impose their structure on the membrane surface, while membrane-binding proteins with hydrophobic motifs are thought to insert into the membrane like wedges, driving curvature. However, computational models have recently revealed that these mechanisms would require specialized membrane-bending proteins to occupy nearly 100% of a curved membrane surface, an improbable physiological situation given the immense density and diversity of membrane-bound proteins, and the low expression levels of these specialized proteins within curved regions of the membrane. How then does curvature arise within the complex and crowded environment of cellular membranes? Our recent work using proteins involved in clathrin-mediated endocytosis, as well as engineered protein-lipid interactions, has suggested a new hypothesis - that lateral pressure generated by collisions between membrane-bound proteins can drive membrane bending. Specifically, by correlating membrane bending with quantitative optical measurements of protein density on synthetic membrane surfaces and simple physical models of collisions among membrane-bound proteins, we have demonstrated that protein-protein steric interactions can drive membrane curvature. These findings suggest that a simple imbalance in the concentration of membrane-bound proteins across a membrane surface can drive a membrane to bend, providing an efficient mechanism by which essentially any protein can contribute to shaping membranes.

Cato Guldberg and Peter Waage, the history of the Law of Mass Action, and its relevance to clinical pharmacology.

PubMed

Ferner, Robin E; Aronson, Jeffrey K

2016-01-01

We have traced the historical link between the Law of Mass Action and clinical pharmacology. The Law evolved from the work of the French chemist Claude Louis Berthollet, was first formulated by Cato Guldberg and Peter Waage in 1864 and later clarified by the Dutch chemist Jacobus van 't Hoff in 1877. It has profoundly influenced our qualitative and quantitative understanding of a number of physiological and pharmacological phenomena. According to the Law of Mass Action, the velocity of a chemical reaction depends on the concentrations of the reactants. At equilibrium the concentrations of the chemicals involved bear a constant relation to each other, described by the equilibrium constant, K. The Law of Mass Action is relevant to various physiological and pharmacological concepts, including concentration-effect curves, dose-response curves, and ligand-receptor binding curves, all of which are important in describing the pharmacological actions of medications, the Langmuir adsorption isotherm, which describes the binding of medications to proteins, activation curves for transmembrane ion transport, enzyme inhibition and the Henderson-Hasselbalch equation, which describes the relation between pH, as a measure of acidity and the concentrations of the contributory acids and bases. Guldberg and Waage recognized the importance of dynamic equilibrium, while others failed to do so. Their ideas, over 150 years old, are embedded in and still relevant to clinical pharmacology. Here we explain the ideas and in a subsequent paper show how they are relevant to understanding adverse drug reactions. © 2015 The British Pharmacological Society.

Kinetics of the biodegradation of phenol in wastewaters from the chemical industry by covalently immobilized Trichosporon cutaneum cells.

PubMed

Yotova, Lyubov; Tzibranska, Irene; Tileva, Filadia; Markx, G H; Georgieva, Nelly

2009-03-01

A simple method for the preparation of the biocatalyst with whole cells is presented, and the applicability of the technique for biodegradation of phenol in wastewater from the chemical industries using the basidomycetes yeast Trichosporon cutaneum is explored. Kinetic studies of the influence of other compounds contained in wastewater as naphthalene, benzene, toluene and pyridine indicate that apart from oil fraction, which is removed, the phenol concentration is the only major factor limiting the growth of immobilized cells. Mathematical models are applied to describe the kinetic behavior of immobilized yeast cells. From the analysis of the experimental curves was shown that the obtained values for the apparent rate parameters vary depending on the substrate concentration (mu(maxapp) from 0.35 to 0.09 h(-1) and K (sapp) from 0.037 to 0.4 g dm(-3)). The inhibitory effect of the phenol on the obtained yield coefficients was investigated too. It has been shown that covalent immobilization of T. cutaneum whole cells to plastic carrier beads is possible, and that cell viability and phenol degrading activity are maintained after the chemical modification of cell walls during the binding procedure. The results obtained indicate a possible future application of immobilized T. cutaneum for destroying phenol in industrial wastewaters.

Spectroscopic and biological activity studies of the chromium-binding peptide EEEEGDD.

PubMed

Arakawa, Hirohumi; Kandadi, Machender R; Panzhinskiy, Evgeniy; Belmore, Kenneth; Deng, Ge; Love, Ebony; Robertson, Preshus M; Commodore, Juliette J; Cassady, Carolyn J; Nair, Sreejayan; Vincent, John B

2016-06-01

While trivalent chromium has been shown at high doses to have pharmacological effects improving insulin resistance in rodent models of insulin resistance, the mechanism of action of chromium at a molecular level is not known. The chromium-binding and transport agent low-molecular-weight chromium-binding substance (LMWCr) has been proposed to be the biologically active form of chromium. LMWCr has recently been shown to be comprised of a heptapeptide of the sequence EEEEDGG. The binding of Cr(3+) to this heptapeptide has been examined. Mass spectrometric and a variety of spectroscopic studies have shown that multiple chromic ions bind to the peptide in an octahedral fashion through carboxylate groups and potentially small anionic ligands such as oxide and hydroxide. A complex of Cr and the peptide when administered intravenously to mice is able to decrease area under the curve in intravenous glucose tolerance tests. It can also restore insulin-stimulated glucose uptake in myotubes rendered insulin resistant by treating them with a high-glucose media.

Capillary pressure curves for low permeability chalk obtained by NMR imaging of core saturation profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norgaard, J.V.; Olsen, D.; Springer, N.

1995-12-31

A new technique for obtaining water-oil capillary pressure curves, based on NMR imaging of the saturation distribution in flooded cores is presented. In this technique, a steady state fluid saturation profile is developed by flooding the core at a constant flow rate. At the steady state situation where the saturation distribution no longer changes, the local pressure difference between the wetting and non-wetting phases represents the capillary pressure. The saturation profile is measured using an NMR technique and for a drainage case, the pressure in the non-wetting phase is calculated numerically. The paper presents the NMR technique and the proceduremore » for calculating the pressure distribution in the sample. Inhomogeneous samples produce irregular saturation profiles, which may be interpreted in terms of variation in permeability, porosity, and capillary pressure. Capillary pressure curves for North Sea chalk obtained by the new technique show good agreement with capillary pressure curves obtained by traditional techniques.« less

Real-time quantitative polymerase chain reaction analysis of patients with refractory chronic periodontitis.

PubMed

Marconcini, Simone; Covani, Ugo; Barone, Antonio; Vittorio, Orazio; Curcio, Michele; Barbuti, Serena; Scatena, Fabrizio; Felli, Lamberto; Nicolini, Claudio

2011-07-01

Periodontitis is a complex multifactorial disease and is typically polygenic in origin. Genes play a fundamental part in each biologic process forming complex networks of interactions. However, only some genes have a high number of interactions with other genes in the network and may, therefore, be considered to play an important role. In a preliminary bioinformatic analysis, five genes that showed a higher number of interactions were identified and termed leader genes. In the present study, we use real-time quantitative polymerase chain reaction (PCR) technology to evaluate the expression levels of leader genes in the leukocytes of 10 patients with refractory chronic periodontitis and compare the expression levels with those of the same genes in 24 healthy patients. Blood was collected from 24 healthy human subjects and 10 patients with refractory chronic periodontitis and placed into heparinized blood collection tubes by personnel trained in phlebotomy using a sterile technique. Blood leukocyte cells were immediately lysed by using a kit for total RNA purification from human whole blood. Complementary DNA (cDNA) synthesis was obtained from total RNA and then real-time quantitative PCR was performed. PCR efficiencies were calculated with a relative standard curve derived from a five cDNA dilution series in triplicate that gave regression coefficients >0.98 and efficiencies >96%. The standard curves were obtained using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and growth factor receptor binding protein 2 (GRB2), casitas B-lineage lymphoma (CBL), nuclear factor-KB1 (NFKB1), and REL-A (gene for transcription factor p65) gene primers and amplified with 1.6, 8, 40, 200, and 1,000 ng/μL total cDNA. Curves obtained for each sample showed a linear relationship between RNA concentrations and the cycle threshold value of real-time quantitative PCR for all genes. Data were expressed as mean ± SE (SEM). The groups were compared to the analysis of variance. A probability value <0.01 was considered statistically significant. The present study agrees with the preliminary bioinformatics analysis. In our experiments, the association of pathology with the genes was statistically significant for GRB2 and CBL (P <0.01), and it was not statistically significant for REL-A and NFKB1. This article lends support to our preliminary hypothesis that assigned an important role in refractory aggressive periodontitis to leader genes.

Tensile stress-strain behavior of boron/aluminum laminates

NASA Technical Reports Server (NTRS)

Sova, J. A.; Poe, C. C., Jr.

1978-01-01

The tensile stress-strain behavior of five types of boron/aluminum laminates was investigated. Longitudinal and transverse stress-strain curves were obtained for monotonic loading to failure and for three cycles of loading to successively higher load levels. The laminate strengths predicted by assuming that the zero deg plies failed first correlated well with the experimental results. The stress-strain curves for all the boron/aluminum laminates were nonlinear except at very small strains. Within the small linear regions, elastic constants calculated from laminate theory corresponded to those obtained experimentally to within 10 to 20 percent. A limited amount of cyclic loading did not affect the ultimate strength and strain for the boron/aluminum laminates. The laminates, however, exhibited a permanent strain on unloading. The Ramberg-Osgood equation was fitted to the stress-strain curves to obtain average curves for the various laminates.

Binding of basic amphipathic peptides to neutral phospholipid membranes: a thermodynamic study applied to dansyl-labeled melittin and substance P analogues.

PubMed

Pérez-Payá, E; Porcar, I; Gómez, C M; Pedrós, J; Campos, A; Abad, C

1997-08-01

A thermodynamic approach is proposed to quantitatively analyze the binding isotherms of peptides to model membranes as a function of one adjustable parameter, the actual peptide charge in solution z(p)+. The main features of this approach are a theoretical expression for the partition coefficient calculated from the molar free energies of the peptide in the aqueous and lipid phases, an equation proposed by S. Stankowski [(1991) Biophysical Journal, Vol. 60, p. 341] to evaluate the activity coefficient of the peptide in the lipid phase, and the Debye-Hückel equation that quantifies the activity coefficient of the peptide in the aqueous phase. To assess the validity of this approach we have studied, by means of steady-state fluorescence spectroscopy, the interaction of basic amphipathic peptides such as melittin and its dansylcadaverine analogue (DNC-melittin), as well as a new fluorescent analogue of substance P, SP (DNC-SP) with neutral phospholipid membranes. A consistent quantitative analysis of each binding curve was achieved. The z(p)+ values obtained were always found to be lower than the physical charge of the peptide. These z(p)+ values can be rationalized by considering that the peptide charged groups are strongly associated with counterions in buffer solution at a given ionic strength. The partition coefficients theoretically derived using the z(p)+ values were in agreement with those deduced from the Gouy-Chapman formalism. Ultimately, from the z(p)+ values the molar free energies for the free and lipid-bound states of the peptides have been calculated.

Characterization of the adenosine receptor in cultured embryonic chick atrial myocytes: Coupling to modulation of contractility and adenylate cyclase activity and identification by direct radioligand binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, B.T.

1989-06-01

Adenosine receptors in a spontaneously contracting atrial myocyte culture from 14-day chick embryos were characterized by radioligand binding studies and by examining the involvement of G-protein in coupling these receptors to a high-affinity state and to the adenylate cyclase and the myocyte contractility. Binding of the antagonist radioligand (3H)-8-cyclopentyl-1,3-diproylxanthine ((3H)CPX) was rapid, reversible and saturable and was to a homogeneous population of sites with a Kd value of 2.1 +/- 0.2 nM and an apparent maximum binding of 26.2 +/- 3 fmol/mg of protein (n = 10, +/- S.E.). Guanyl-5-yl-(beta, gamma-imido)diphosphate had no effect on either the Kd or themore » maximum binding and CPX reversed the N6-R-phenyl-2-propyladenosine-induced inhibition of adenylate cyclase activity and contractility, indicating that (3H) CPX is an antagonist radioligand. Competition curves for (3H) CPX binding by a series of reference adenosine agonists were consistent with labeling of an A1 adenosine receptor and were better fit by a two-site model than by a one-site model. ADP-ribosylation of the G-protein by the endogenous NAD+ in the presence of pertussis toxin shifted the competition curves from bi to monophasic with Ki values similar to those of the KL observed in the absence of prior pertussis intoxication. The adenosine agonists were capable of inhibiting both the adenylate cyclase activity and myocyte contractility in either the absence or the presence of isoproterenol. The A1 adenosine receptor-selective antagonist CPX reversed these agonist effects. The order of ability of the reference adenosine receptor agonists in causing these inhibitory effects was similar to the order of potency of the same agonists in inhibiting the specific (3H)CPX binding (N6-R-phenyl-2-propyladenosine greater than N6-S-phenyl-2-propyladenosine or N-ethyladenosine-5'-uronic acid).« less

Alzheimer disease identification using amyloid imaging and reserve variables

PubMed Central

Roe, C.M.; Mintun, M.A.; Ghoshal, N.; Williams, M.M.; Grant, E.A.; Marcus, D.S.; Morris, J.C.

2010-01-01

Objective: Several factors may influence the relationship between Alzheimer disease (AD) lesions and the expression of dementia, including those related to brain and cognitive reserve. Other factors may confound the association between AD pathology and dementia. We tested whether factors thought to influence the association of AD pathology and dementia help to accurately identify dementia of the Alzheimer type (DAT) when considered together with amyloid imaging. Methods: Participants with normal cognition (n = 180) and with DAT (n = 25), aged 50 years or older, took part in clinical, neurologic, and psychometric assessments. PET with the Pittsburgh compound B (PiB) tracer was used to measure brain amyloid, yielding a mean cortical binding potential (MCBP) reflecting PiB uptake. Logistic regression was used to generate receiver operating characteristic curves, and the areas under those curves (AUC), to compare the predictive accuracy of using MCBP alone vs MCBP together with other variables selected using a stepwise selection procedure to identify participants with DAT vs normal cognition. Results: The AUC resulting from MCBP alone was 0.84 (95% confidence interval [CI] = 0.73–0.94; cross-validated AUC = 0.80, 95% CI = 0.68–0.92). The AUC for the predictive equation generated by a stepwise model including education, normalized whole brain volume, physical health rating, gender, and use of medications that may interfere with cognition was 0.94 (95% CI = 0.90–0.98; cross-validated AUC = 0.91, 95% CI = 0.85–0.96), an improvement (p = 0.025) over that yielded using MCBP alone. Conclusion: Results suggest that factors reported to influence associations between AD pathology and dementia can improve the predictive accuracy of amyloid imaging for the identification of symptomatic AD. GLOSSARY A β = amyloid-β; AD = Alzheimer disease; AUC = area under receiver operating characteristic curve; BP = binding potential; CDR = Clinical Dementia Rating; CI = confidence interval; DAT = dementia of the Alzheimer type; DV = distribution volume; MCBP = mean cortical binding potential; nWBV = normalized whole brain volume; OR = odds ratio; PiB = Pittsburgh compound B; ROC = receiver operating characteristic curve; ROI = region of interest. PMID:20603484

VizieR Online Data Catalog: WASP-22, WASP-41, WASP-42, WASP-55 (Southworth+, 2016)

NASA Astrophysics Data System (ADS)

Southworth, J.; Tregloan-Reed, J.; Andersen, M. I.; Calchi Novati, S.; Ciceri, S.; Colque, J. P.; D'Ago, G.; Dominik, M.; Evans, D. F.; Gu, S.-H.; Herrera-Cordova, A.; Hinse, T. C.; Jorgensen, U. G.; Juncher, D.; Kuffmeier, M.; Mancini, L.; Peixinho, N.; Popovas, A.; Rabus, M.; Skottfelt, J.; Tronsgaard, R.; Unda-Sanzana, E.; Wang, X.-B.; Wertz, O.; Alsubai, K. A.; Andersen, J. M.; Bozza, V.; Bramich, D. M.; Burgdorf, M.; Damerdji, Y.; Diehl, C.; Elyiv, A.; Figuera Jaimes, R.; Haugbolle, T.; Hundertmark, M.; Kains, N.; Kerins, E.; Korhonen, H.; Liebig, C.; Mathiasen, M.; Penny, M. T.; Rahvar, S.; Scarpetta, G.; Schmidt, R. W.; Snodgrass, C.; Starkey, D.; Surdej, J.; Vilela, C.; von Essen, C.; Wang, Y.

2018-05-01

17 light curves of transits of the extrasolar planetary systems WASP-22, WASP-41, WASP-42 and WASP-55 are presented. 13 of the light curves were obtained using the Danish 1.54m telescope at ESO La Silla, Chile, in the Bessell R or Bessell I passbands. The other 4 light curves were obtained using the 84cm telescope at Observatorio Cerro Armazones, Chile, using either an R filter or no filter. The errorbars for each transit have been scaled so the best-fitting model (obtained using the JKTEBOP code) has a reduced chi-squared value of 1.0. (4 data files).

Demonstration of clomipramine and venlafaxine occupation at serotonin reuptake sites in man in vivo.

PubMed

Malizia, A L; Melichar, J M; Brown, D J; Gunn, R N; Reynolds, A; Jones, T; Nutt, D J

1997-01-01

We describe the use of 11CRTI-55 and the Multiple Objects Coincidences Counter (MOCC) to detect in-vivo binding to peripheral serotonin reuptake sites (left chest comprising platelet and lung serotonin reuptake sites) in man. Displacement and preloading experiments with clomipramine and venlafaxine in two healthy volunteers demonstrated that 11CRTI-55 binding is decreased in a dose-dependent fashion by both these drugs which bind to the serotonin transporter. In addition parallel data from the total head curve (representing 11CRTI-55 binding to central serotonin and dopamine (DA) reuptake sites) suggest that prior blockade of the serotonin transporter may be a useful strategy to maximize radioactive counts in the head when measuring the DA transporter. The MOCC is likely to be useful to determine sequential indices of relative serotonin reuptake blockade in patients on treatment.

A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies.

PubMed

Zahn, Raphael; Osmanović, Dino; Ehret, Severin; Araya Callis, Carolina; Frey, Steffen; Stewart, Murray; You, Changjiang; Görlich, Dirk; Hoogenboom, Bart W; Richter, Ralf P

2016-04-08

The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.

Programmable calculator software for computation of the plasma binding of ligands.

PubMed

Conner, D P; Rocci, M L; Larijani, G E

1986-01-01

The computation of the extent of plasma binding of a ligand to plasma constituents using radiolabeled ligand and equilibrium dialysis is complex and tedious. A computer program for the HP-41C Handheld Computer Series (Hewlett-Packard) was developed to perform these calculations. The first segment of the program constructs a standard curve for quench correction of post-dialysis plasma and buffer samples, using either external standard ratio (ESR) or sample channels ratio (SCR) techniques. The remainder of the program uses the counts per minute, SCR or ESR, and post-dialysis volume of paired plasma and buffer samples generated from the dialysis procedure to compute the extent of binding after correction for background radiation, counting efficiency, and intradialytic shifts of fluid between plasma and buffer compartments during dialysis. This program greatly simplifies the analysis of equilibrium dialysis data and has been employed in the analysis of dexamethasone binding in normal and uremic sera.

Relation between heat of vaporization, ion transport, molar volume, and cation-anion binding energy for ionic liquids.

PubMed

Borodin, Oleg

2009-09-10

A number of correlations between heat of vaporization (H(vap)), cation-anion binding energy (E(+/-)), molar volume (V(m)), self-diffusion coefficient (D), and ionic conductivity for 29 ionic liquids have been investigated using molecular dynamics (MD) simulations that employed accurate and validated many-body polarizable force fields. A significant correlation between D and H(vap) has been found, while the best correlation was found for -log(DV(m)) vs H(vap) + 0.28E(+/-). A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids. A deviation of some ILs from the reported master curve is explained based upon ion packing and proposed diffusion pathways. No general correlations were found between the ion diffusion coefficient and molecular volume or the diffusion coefficient and cation/anion binding energy.

Comparison of cannabinoid binding sites in guinea-pig forebrain and small intestine

PubMed Central

Ross, Ruth A; Brockie, Heather C; Fernando, Susanthi R; Saha, Bijali; Razdan, Raj K; Pertwee, Roger G

1998-01-01

We have investigated the nature of cannabinoid receptors in guinea-pig small intestine by establishing whether this tissue contains cannabinoid receptors with similar binding properties to those of brain CB1 receptors. The cannabinoids used were the CB1-selective antagonist SR141716A, the CB2-selective antagonist SR144528, the novel cannabinoid receptor ligand, 6′-azidohex-2′-yne-Δ8-tetrahydrocannabinol (O-1184), and the agonists CP55940, which binds equally well to CB1 and CB2 receptors, and WIN55212-2, which shows marginal CB2 selectivity.[3H]-CP55940 (1 nM) underwent extensive specific binding both to forebrain membranes (76.3%) and to membranes obtained by sucrose density gradient fractionation of homogenates of myenteric plexus-longitudinal muscle of guinea-pig small intestine (65.2%).Its binding capacity (Bmax) was higher in forebrain (4281 fmol mg−1) than in intestinal membranes (2092 fmol mg−1). However, the corresponding KD values were not significantly different from each other (2.29 and 1.75 nM respectively). Nor did the Ki values for its displacement by CP55940, WIN55212-2, O-1184, SR141716A and SR144528 from forebrain membranes (0.87, 4.15, 2.85, 5.32 and 371.9 respectively) differ significantly from the corresponding Ki values determined in experiments with intestinal membranes (0.99, 5.03, 3.16, 4.95 and 361.5 nM respectively).The Bmax values of [3H]-CP55940 and [3H]-SR141716A in forebrain membranes did not differ significantly from each other (4281 and 5658 fmol mg−1) but were both greater than the Bmax of [3H]-WIN55212-2 (2032 fmol mg−1).O-1184 (10 or 100 nM) produced parallel dextral shifts in the log concentration-response curves of WIN55212-2 and CP55940 for inhibition of electrically-evoked contractions of the myenteric plexus-longitudinal muscle preparation, its KD values being 0.20 nM (against WIN55212-2) and 0.89 nM (against CP55940).We conclude that cannabinoid binding sites in guinea-pig small intestine closely resemble CB1 binding sites of guinea-pig brain and that O-1184 behaves as a cannabinoid receptor antagonist in the guinea-pig myenteric plexus-longitudinal muscle preparation. PMID:9863666

Numerical investigation on effect of blade shape for stream water wheel performance.

NASA Astrophysics Data System (ADS)

Yah, N. F.; Oumer, A. N.; Aziz, A. A.; Sahat, I. M.

2018-04-01

Stream water wheels are one of the oldest and commonly used types of wheels for the production of energy. Moreover, they are economical, efficient and sustainable. However, few amounts of research works are available in the open literature. This paper aims to develop numerical model for investigation of the effect of blade shape on the performance of stream water wheel. The numerical model was simulated using Computational Fluid Dynamics (CFD) method and the developed model was validated by comparing the simulation results with experimental data obtained from literature. The performance of straight, curved type 1 and curved type 2 was observed and the power generated by each blade design was identified. The inlet velocity was set to 0.3 m/s static pressure outlet. The obtained results indicate that the highest power was generated by the Curved type 2 compared to straight blade and curved type 1. From the CFD result, Curved type 1 was able to generate 0.073 Watt while Curved type 2 generate 0.064 Watt. The result obtained were consistent with the experiment result hence can be used the numerical model as a guide to numerically predict the water wheel performance

Chronic lithium treatment up-regulates cell surface Na(V)1.7 sodium channels via inhibition of glycogen synthase kinase-3 in adrenal chromaffin cells: enhancement of Na(+) influx, Ca(2+) influx and catecholamine secretion after lithium withdrawal.

PubMed

Yanagita, Toshihiko; Maruta, Toyoaki; Nemoto, Takayuki; Uezono, Yasuhito; Matsuo, Kiyotaka; Satoh, Shinya; Yoshikawa, Norie; Kanai, Tasuku; Kobayashi, Hideyuki; Wada, Akihiko

2009-09-01

In cultured bovine adrenal chromaffin cells expressing Na(V)1.7 isoform of voltage-dependent Na(+) channels, we have previously reported that lithium chloride (LiCl) inhibits function of Na(+) channels independent of glycogen synthase kinase-3 (GSK-3) (Yanagita et al., 2007). Here, we further examined the effects of chronic lithium treatment on Na(+) channels. LiCl treatment (1-30 mM, > or = 12 h) increased cell surface [(3)H]saxitoxin ([(3)H]STX) binding by approximately 32% without altering the affinity of [(3)H]STX binding. This increase was prevented by cycloheximide and actinomycin D. SB216763 and SB415286 (GSK-3 inhibitors) also increased cell surface [(3)H]STX binding by approximately 31%. Simultaneous treatment with LiCl and SB216763 or SB415286 did not produce an increased effect on [(3)H]STX binding compared with either treatment alone. LiCl increased Na(+) channel alpha-subunit mRNA level by 32% at 24 h. LiCl accelerated alpha-subunit gene transcription by 35% without altering alpha-subunit mRNA stability. In LiCl-treated cells, LiCl inhibited veratridine-induced (22)Na(+) influx as in untreated cells. However, washout of LiCl after chronic treatment enhanced veratridine-induced (22)Na(+) influx, (45)Ca(2+) influx and catecholamine secretion by approximately 30%. Washout of LiCl after 24 h treatment shifted concentration-response curve of veratridine upon (22)Na(+) influx upward, without altering its EC(50) value. Ptychodiscus brevis toxin-3 allosterically enhanced veratridine-induced (22)Na(+) influx by two-fold in untreated and LiCl-treated cells. Whole-cell patch-clamp analysis indicated that I-V curve and steady-state inactivation/activation curves were comparable between untreated and LiCl-treated cells. Thus, GSK-3 inhibition by LiCl up-regulated cell surface Na(V)1.7 via acceleration of alpha-subunit gene transcription, enhancing veratridine-induced Na(+) influx, Ca(2+) influx and catecholamine secretion.

A room-temperature phase transition in maximum microcline - Heat capacity measurements

USGS Publications Warehouse

Openshaw, R.E.; Hemingway, B.S.; Robie, R.A.; Krupka, K.M.

1979-01-01

The thermal hysteresis in heat capacity measurements recently reported (Openshaw et al., 1976) for a maximum microcline prepared from Amelia albite by fused-salt ion-exchange is described in detail. The hysteresis is characterized by two limiting and reproducible curves which differ by 1% of the measured heat capacities. The lower curve, denoted curve B, represents the values obtained before the sample had been cooled below 300 K. Measurements made immediately after cooling the sample below 250 K followed a second parallel curve, curve A, to at least 370 K. Values intermediate to the two limiting curves were also obtained. The transitions from the B to the A curve were rapid and observed to occur three times. The time required to complete the transition from the A to the B curve increased from 39 h to 102 h in the two times it was observed to occur. The hysteresis is interpreted as evidence of a phase change in microcline at 300??10 K The heat effect associated with the phase change has not been evaluated. ?? 1979 Springer-Verlag.

A dose-response curve for biodosimetry from a 6 MV electron linear accelerator

PubMed Central

Lemos-Pinto, M.M.P.; Cadena, M.; Santos, N.; Fernandes, T.S.; Borges, E.; Amaral, A.

2015-01-01

Biological dosimetry (biodosimetry) is based on the investigation of radiation-induced biological effects (biomarkers), mainly dicentric chromosomes, in order to correlate them with radiation dose. To interpret the dicentric score in terms of absorbed dose, a calibration curve is needed. Each curve should be constructed with respect to basic physical parameters, such as the type of ionizing radiation characterized by low or high linear energy transfer (LET) and dose rate. This study was designed to obtain dose calibration curves by scoring of dicentric chromosomes in peripheral blood lymphocytes irradiated in vitro with a 6 MV electron linear accelerator (Mevatron M, Siemens, USA). Two software programs, CABAS (Chromosomal Aberration Calculation Software) and Dose Estimate, were used to generate the curve. The two software programs are discussed; the results obtained were compared with each other and with other published low LET radiation curves. Both software programs resulted in identical linear and quadratic terms for the curve presented here, which was in good agreement with published curves for similar radiation quality and dose rates. PMID:26445334

Muscarinic binding sites in cultured bovine pulmonary arterial endothelial cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aronstam, R.S.; Catravas, J.D.; Ryan, U.S.

The authors have previously reported a) the presence of muscarinic binding sites on cultured bovine pulmonary arterial endothelial cells (BPAE; 2,000 sites/cell) and b) that acetylcholine inhibits the release of thromboxane B/sub 2/ fro BPAE. Since the authors findings could reflect muscarinic receptors (mAChR) on BPAE, they have further investigated the nature of BPAE muscarinic binding sites and contrast them to those of known functional mAChR. Muscarinic binding sites on BPAE resembled mAChR in that a) the binding of 3 nM /sup 3/H QNB was inhibited by muscarinic agonists and antagonists; b) /sup 3/H QNB binding was 30 times moremore » sensitive to R(-)- than to S(+)-QNB; c) carbamylcholine binding was resolved into high and low affinity components (IC50's = 0.04 and 2 ..mu..M; d) 5'-guanylylimidodiphosphate (100 ..mu..M) shifted agonist binding curves to the right by a factor of 3; 4) the atropine-sensitive binding of /sup 3/H oxotremorine-M (/sup 3/H-OXO-M) was depressed by the guanine nucleotide (IC50 + 60 ..mu..M). However, although gallamine allosterically regulates mAChR binding in other tissues, it did not affect the rates of dissociation of /sup 3/H QNB, /sup 3/H methylscopolamine or /sup 3/H OXO-M from BPAE binding sites. Thus, BPAE muscarinic binding sites posses many but not all of the properties associated with functional mAChR.« less

The HOPS/Class C Vps Complex Tethers High-Curvature Membranes via a Direct Protein-Membrane Interaction.

PubMed

Ho, Ruoya; Stroupe, Christopher

2016-10-01

Membrane tethering is a physical association of two membranes before their fusion. Many membrane tethering factors have been identified, but the interactions that mediate inter-membrane associations remain largely a matter of conjecture. Previously, we reported that the homotypic fusion and protein sorting/Class C vacuolar protein sorting (HOPS/Class C Vps) complex, which has two binding sites for the yeast vacuolar Rab GTPase Ypt7p, can tether two low-curvature liposomes when both membranes bear Ypt7p. Here, we show that HOPS tethers highly curved liposomes to Ypt7p-bearing low-curvature liposomes even when the high-curvature liposomes are protein-free. Phosphorylation of the curvature-sensing amphipathic lipid-packing sensor (ALPS) motif from the Vps41p HOPS subunit abrogates tethering of high-curvature liposomes. A HOPS complex without its Vps39p subunit, which contains one of the Ypt7p binding sites in HOPS, lacks tethering activity, though it binds high-curvature liposomes and Ypt7p-bearing low-curvature liposomes. Thus, HOPS tethers highly curved membranes via a direct protein-membrane interaction. Such high-curvature membranes are found at the sites of vacuole tethering and fusion. There, vacuole membranes bend sharply, generating large areas of vacuole-vacuole contact. We propose that HOPS localizes via the Vps41p ALPS motif to these high-curvature regions. There, HOPS binds via Vps39p to Ypt7p in an apposed vacuole membrane. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Application of Geodetic VLBI Data to Obtaining Long-Term Light Curves for Astrophysics

NASA Technical Reports Server (NTRS)

Kijima, Masachika

2010-01-01

The long-term light curve is important to research on binary black holes and disk instability in AGNs. The light curves have been drawn mainly using single dish data provided by the University of Michigan Radio Observatory and the Metsahovi Radio Observatory. Hence, thus far, we have to research on limited sources. I attempt to draw light curves using VLBI data for those sources that have not been monitored by any observatories with single dish. I developed software, analyzed all geodetic VLBI data available at the IVS Data Centers, and drew the light curves at 8 GHz. In this report, I show the tentative results for two AGNs. I compared two light curves of 4C39.25, which were drawn based on single dish data and on VLBI data. I confirmed that the two light curves were consistent. Furthermore, I succeeded in drawing the light curve of 0454-234 with VLBI data, which has not been monitored by any observatory with single dish. In this report, I suggest that the geodetic VLBI archive data is useful to obtain the long-term light curves at radio bands for astrophysics.

Direct recording of cardiac output- and venous return-curves in the dog heart-lung preparation for a graphical analysis of the effects of cardioactive drugs.

PubMed

Ishikawa, N; Taki, K; Hojo, Y; Hagino, Y; Shigei, T

1978-09-01

The dog heart-lung preparations were prepared. The "equilibrium point", which could be defined as the point at which the cardiac output (CO)-curve and the venous return (VR)-curve crossed, when the CO and VR were plotted against the right atrial pressure, was recorded directly by utilizing an X-Y recorder. The CO-curve was obtained, as a locus of the equilibrium point, by raising and lowering the level of blood in the venous reservoir (competence test). The meaning of the procedure was shown to increase or decrease the mean systemic pressure, and to cause the corresponding parallel shift in the VR-curve. The VR-curve was obtained by changing myocardial contractility. When heart failure was induced by pentobarbital or by chloroform, the equilibrium point shifted downwards to the right, depicting the VR-curve. During development of the failure, the slopes of CO-curves decreased gradually. Effects of cinobufagin and norepinephrine were also analyzed. Utilization of the X-Y recorder enabled us to settle the uniform experimental conditions more easily, and to follow the effects of drugs continuously on a diagram equating the CO- and VR-curves (Gyton's scheme).

Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation

PubMed Central

Joynt, Suzanne; Morillo, Victor; Leng, Fenfei

2009-01-01

HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)2 is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5′-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3′ (FL-AT-1) and 5′-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3′ (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to ∼200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar. PMID:19450485

Importance of nasal clipping in screening investigations of flow volume curve.

PubMed

Yanev, I

1992-01-01

Comparative analysis of some basic lung indices obtained from a screening investigation of the flow volume curve by using two techniques, with a nose clip and without a nose clip, was made on a cohort of 86 workers in a factory shop for the production of bearings. We found no statistically significant differences between the indices obtained by the two techniques. Our study showed that the FVC and FEV1 obtained in workers without using nose clips were equal to or better than those obtained using nose clips in 60% of the workers. The reproducibility of the two methods was similar. The analysis of the data has shown that the flow volume curve investigation gives better results when performed without a nose clip, especially in industrial conditions.

Plastometric tests for plasticine as physical modelling material

NASA Astrophysics Data System (ADS)

Wójcik, Łukasz; Lis, Konrad; Pater, Zbigniew

2016-12-01

This paper presents results of plastometric tests for plasticine, used as material for physical modelling of metal forming processes. The test was conducted by means of compressing by flat dies of cylindrical billets at various temperatures. The aim of the conducted research was comparison of yield stresses and course of material flow curves. Tests were made for plasticine in black and white colour. On the basis of the obtained experimental results, the influence of forming parameters change on flow curves course was determined. Sensitivity of yield stresses change in function of material deformation, caused by forging temperature change within the scope of 0&C ÷ 20&C and differentiation of strain rate for ˙ɛ = 0.563; ˙ɛ = 0.0563; ˙ɛ = 0.0056s-1,was evaluated. Experimental curves obtained in compression test were described by constitutive equations. On the basis of the obtained results the function which most favourably describes flow curves was chosen.

A systematic methodology for creep master curve construction using the stepped isostress method (SSM): a numerical assessment

NASA Astrophysics Data System (ADS)

Miranda Guedes, Rui

2018-02-01

Long-term creep of viscoelastic materials is experimentally inferred through accelerating techniques based on the time-temperature superposition principle (TTSP) or on the time-stress superposition principle (TSSP). According to these principles, a given property measured for short times at a higher temperature or higher stress level remains the same as that obtained for longer times at a lower temperature or lower stress level, except that the curves are shifted parallel to the horizontal axis, matching a master curve. These procedures enable the construction of creep master curves with short-term experimental tests. The Stepped Isostress Method (SSM) is an evolution of the classical TSSP method. Higher reduction of the required number of test specimens to obtain the master curve is achieved by the SSM technique, since only one specimen is necessary. The classical approach, using creep tests, demands at least one specimen per each stress level to produce a set of creep curves upon which TSSP is applied to obtain the master curve. This work proposes an analytical method to process the SSM raw data. The method is validated using numerical simulations to reproduce the SSM tests based on two different viscoelastic models. One model represents the viscoelastic behavior of a graphite/epoxy laminate and the other represents an adhesive based on epoxy resin.

Effect of temperature on the acid-base properties of the alumina surface: microcalorimetry and acid-base titration experiments.

PubMed

Morel, Jean-Pierre; Marmier, Nicolas; Hurel, Charlotte; Morel-Desrosiers, Nicole

2006-06-15

Sorption reactions on natural or synthetic materials that can attenuate the migration of pollutants in the geosphere could be affected by temperature variations. Nevertheless, most of the theoretical models describing sorption reactions are at 25 degrees C. To check these models at different temperatures, experimental data such as the enthalpies of sorption are thus required. Highly sensitive microcalorimeters can now be used to determine the heat effects accompanying the sorption of radionuclides on oxide-water interfaces, but enthalpies of sorption cannot be extracted from microcalorimetric data without a clear knowledge of the thermodynamics of protonation and deprotonation of the oxide surface. However, the values reported in the literature show large discrepancies and one must conclude that, amazingly, this fundamental problem of proton binding is not yet resolved. We have thus undertaken to measure by titration microcalorimetry the heat effects accompanying proton exchange at the alumina-water interface at 25 degrees C. Based on (i) the surface sites speciation provided by a surface complexation model (built from acid-base titrations at 25 degrees C) and (ii) results of the microcalorimetric experiments, calculations have been made to extract the enthalpic variations associated respectively to first and second deprotonation of the alumina surface. Values obtained are deltaH1 = 80+/-10 kJ mol(-1) and deltaH2 = 5+/-3 kJ mol(-1). In a second step, these enthalpy values were used to calculate the alumina surface acidity constants at 50 degrees C via the van't Hoff equation. Then a theoretical titration curve at 50 degrees C was calculated and compared to the experimental alumina surface titration curve. Good agreement between the predicted acid-base titration curve and the experimental one was observed.

Poster — Thur Eve — 03: Application of the non-negative matrix factorization technique to [{sup 11}C]-DTBZ dynamic PET data for the early detection of Parkinson's disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Dong-Chang; Jans, Hans; McEwan, Sandy

2014-08-15

In this work, a class of non-negative matrix factorization (NMF) technique known as alternating non-negative least squares, combined with the projected gradient method, is used to analyze twenty-five [{sup 11}C]-DTBZ dynamic PET/CT brain data. For each subject, a two-factor model is assumed and two factors representing the striatum (factor 1) and the non-striatum (factor 2) tissues are extracted using the proposed NMF technique and commercially available factor analysis software “Pixies”. The extracted factor 1 and 2 curves represent the binding site of the radiotracer and describe the uptake and clearance of the radiotracer by soft tissues in the brain, respectively.more » The proposed NMF technique uses prior information about the dynamic data to obtain sample time-activity curves representing the striatum and the non-striatum tissues. These curves are then used for “warm” starting the optimization. Factor solutions from the two methods are compared graphically and quantitatively. In healthy subjects, radiotracer uptake by factors 1 and 2 are approximately 35–40% and 60–65%, respectively. The solutions are also used to develop a factor-based metric for the detection of early, untreated Parkinson's disease. The metric stratifies healthy subjects from suspected Parkinson's patients (based on the graphical method). The analysis shows that both techniques produce comparable results with similar computational time. The “semi-automatic” approach used by the NMF technique allows clinicians to manually set a starting condition for “warm” starting the optimization in order to facilitate control and efficient interaction with the data.« less

Global invariants of paths and curves for the group of all linear similarities in the two-dimensional Euclidean space

NASA Astrophysics Data System (ADS)

Khadjiev, Djavvat; Ören, Idri˙s; Pekşen, Ömer

Let E2 be the 2-dimensional Euclidean space, LSim(2) be the group of all linear similarities of E2 and LSim+(2) be the group of all orientation-preserving linear similarities of E2. The present paper is devoted to solutions of problems of global G-equivalence of paths and curves in E2 for the groups G = LSim(2),LSim+(2). Complete systems of global G-invariants of a path and a curve in E2 are obtained. Existence and uniqueness theorems are given. Evident forms of a path and a curve with the given global invariants are obtained.

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.

PubMed

Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S; Honig, Barry

2014-01-01

We present OnTheFly (http://bhapp.c2b2.columbia.edu/OnTheFly/index.php), a database comprising a systematic collection of transcription factors (TFs) of Drosophila melanogaster and their DNA-binding sites. TFs predicted in the Drosophila melanogaster genome are annotated and classified and their structures, obtained via experiment or homology models, are provided. All known preferred TF DNA-binding sites obtained from the B1H, DNase I and SELEX methodologies are presented. DNA shape parameters predicted for these sites are obtained from a high throughput server or from crystal structures of protein-DNA complexes where available. An important feature of the database is that all DNA-binding domains and their binding sites are fully annotated in a eukaryote using structural criteria and evolutionary homology. OnTheFly thus provides a comprehensive view of TFs and their binding sites that will be a valuable resource for deciphering non-coding regulatory DNA.

Binding free energy prediction in strongly hydrophobic biomolecular systems.

PubMed

Charlier, Landry; Nespoulous, Claude; Fiorucci, Sébastien; Antonczak, Serge; Golebiowski, Jérome

2007-11-21

We present a comparison of various computational approaches aiming at predicting the binding free energy in ligand-protein systems where the ligand is located within a highly hydrophobic cavity. The relative binding free energy between similar ligands is obtained by means of the thermodynamic integration (TI) method and compared to experimental data obtained through isothermal titration calorimetry measurements. The absolute free energy of binding prediction was obtained on a similar system (a pyrazine derivative bound to a lipocalin) by TI, potential of mean force (PMF) and also by means of the MMPBSA protocols. Although the TI protocol performs poorly either with an explicit or an implicit solvation scheme, the PMF calculation using an implicit solvation scheme leads to encouraging results, with a prediction of the binding affinity being 2 kcal mol(-1) lower than the experimental value. The use of an implicit solvation scheme appears to be well suited for the study of such hydrophobic systems, due to the lack of water molecules within the binding site.

Application of Impedance Microbiology for Evaluating Potential Acidifying Performances of Starter Lactic Acid Bacteria to Employ in Milk Transformation.

PubMed

Bancalari, Elena; Bernini, Valentina; Bottari, Benedetta; Neviani, Erasmo; Gatti, Monica

2016-01-01

Impedance microbiology is a method that enables tracing microbial growth by measuring the change in the electrical conductivity. Different systems, able to perform this measurement, are available in commerce and are commonly used for food control analysis by mean of measuring a point of the impedance curve, defined "time of detection." With this work we wanted to find an objective way to interpret the metabolic significance of impedance curves and propose it as a valid approach to evaluate the potential acidifying performances of starter lactic acid bacteria to be employed in milk transformation. To do this it was firstly investigated the possibility to use the Gompertz equation to describe the data coming from the impedance curve obtained by mean of BacTrac 4300®. Lag time (λ), maximum specific M% rate (μmax), and maximum value of M% (Yend) have been calculated and, given the similarity of the impedance fitted curve to the bacterial growth curve, their meaning has been interpreted. Potential acidifying performances of eighty strains belonging to Lactobacillus helveticus, Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis , and Streptococcus thermophilus species have been evaluated by using the kinetics parameters, obtained from Excel add-in DMFit version 2.1. The novelty and importance of our findings, obtained by means of BacTrac 4300®, is that they can also be applied to data obtained from other devices. Moreover, the meaning of λ, μmax, and Yend that we have extrapolated from Modified Gompertz equation and discussed for lactic acid bacteria in milk, can be exploited also to other food environment or other bacteria, assuming that they can give a curve and that curve is properly fitted with Gompertz equation.

Application of Impedance Microbiology for Evaluating Potential Acidifying Performances of Starter Lactic Acid Bacteria to Employ in Milk Transformation

PubMed Central

Bancalari, Elena; Bernini, Valentina; Bottari, Benedetta; Neviani, Erasmo; Gatti, Monica

2016-01-01

Impedance microbiology is a method that enables tracing microbial growth by measuring the change in the electrical conductivity. Different systems, able to perform this measurement, are available in commerce and are commonly used for food control analysis by mean of measuring a point of the impedance curve, defined “time of detection.” With this work we wanted to find an objective way to interpret the metabolic significance of impedance curves and propose it as a valid approach to evaluate the potential acidifying performances of starter lactic acid bacteria to be employed in milk transformation. To do this it was firstly investigated the possibility to use the Gompertz equation to describe the data coming from the impedance curve obtained by mean of BacTrac 4300®. Lag time (λ), maximum specific M% rate (μmax), and maximum value of M% (Yend) have been calculated and, given the similarity of the impedance fitted curve to the bacterial growth curve, their meaning has been interpreted. Potential acidifying performances of eighty strains belonging to Lactobacillus helveticus, Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis, and Streptococcus thermophilus species have been evaluated by using the kinetics parameters, obtained from Excel add-in DMFit version 2.1. The novelty and importance of our findings, obtained by means of BacTrac 4300®, is that they can also be applied to data obtained from other devices. Moreover, the meaning of λ, μmax, and Yend that we have extrapolated from Modified Gompertz equation and discussed for lactic acid bacteria in milk, can be exploited also to other food environment or other bacteria, assuming that they can give a curve and that curve is properly fitted with Gompertz equation. PMID:27799925

Using Changes in Binding Globulins to Assess Oral Contraceptive Compliance

PubMed Central

Westhoff, Carolyn; Petrie, K.A.; Cremers, S.

2012-01-01

Background Validity of oral contraceptive pill (OCP) clinical trial results depends on participant compliance. Ethinyl estradiol (EE2) induces increases in hepatic binding globulin (BG) levels. Measuring these BG increases may provide an effective and convenient approach to distinguishing non-compliant from compliant OCP users in research settings. This analysis evaluated the usefulness of measuring increases in corticosteroid, sex hormone and thyroxine binding globulins (CBG, SHBG, TBG) as measures of OCP compliance. Methods We used frozen serum from a trial that compared ovarian suppression between normal weight and obese women randomized to one of two OCPs containing EE2 and levonorgestrel (LNG). Based on serial LNG measurements during the trial, 17% of participants were non-compliant. We matched non-compliant participants with compliant participants by age, BMI, ethnicity and OCP formulation. We measured CBG, SHBG and TBG levels, and compared change from baseline to 3-month follow-up between the non-compliant and compliant participants. Construction of receiver operator characteristic (ROC) curves allowed comparison of various BG measures. Results Changes in CBG and TBG distinguished OCP non-compliant users from compliant users (area under the ROC curve (AUROC), 0.86 and 0.89, p < 0.01). Changes in SHBG were less discriminating (AUROC 0.69) Conclusions EE2 induced increases in CBG and TBG provide a sensitive integrated marker of compliance with an LNG-containing OCP. PMID:22795088

Local anesthetics disrupt energetic coupling between the voltage-sensing segments of a sodium channel.

PubMed

Muroi, Yukiko; Chanda, Baron

2009-01-01

Local anesthetics block sodium channels in a state-dependent fashion, binding with higher affinity to open and/or inactivated states. Gating current measurements show that local anesthetics immobilize a fraction of the gating charge, suggesting that the movement of voltage sensors is modified when a local anesthetic binds to the pore of the sodium channel. Here, using voltage clamp fluorescence measurements, we provide a quantitative description of the effect of local anesthetics on the steady-state behavior of the voltage-sensing segments of a sodium channel. Lidocaine and QX-314 shifted the midpoints of the fluorescence-voltage (F-V) curves of S4 domain III in the hyperpolarizing direction by 57 and 65 mV, respectively. A single mutation in the S6 of domain IV (F1579A), a site critical for local anesthetic block, abolished the effect of QX-314 on the voltage sensor of domain III. Both local anesthetics modestly shifted the F-V relationships of S4 domain IV toward hyperpolarized potentials. In contrast, the F-V curve of the S4 domain I was shifted by 11 mV in the depolarizing direction upon QX-314 binding. These antagonistic effects of the local anesthetic indicate that the drug modifies the coupling between the voltage-sensing domains of the sodium channel. Our findings suggest a novel role of local anesthetics in modulating the gating apparatus of the sodium channel.

An accurate redetermination of the 118Sn binding energy

NASA Astrophysics Data System (ADS)

Borzakov, S. B.; Chrien, R. E.; Faikow-Stanczyk, H.; Grigoriev, Yu. V.; Panteleev, Ts. Ts.; Pospisil, S.; Smotritsky, L. M.; Telezhnikov, S. A.

2002-03-01

The energy of well-known strong γ line from 198Au, the "gold standard", has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined, which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, Bn, from complicated (n, γ) spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taken into account by a Monte-Carlo simulation. The procedure was used in obtaining Bn for 118Sn. The γ-ray spectrum from thermal neutron radiative capture by 117Sn has been measured on the IBR-2 pulsed reactor. γ-rays were detected by a 72 cm 3 HPGe detector. For a better determination of Bn it was important to determine Bn for 64Cu. This value was obtained from two γ-spectra. One spectrum was measured on the IBR-2 by the same detector. The other spectrum was measured with a pair spectrometer at the Brookhaven High Flux Beam Reactor. From these two spectra, Bn for 64Cu was determined to be equal to 7915.52(8) keV. This result essentially differs from the previous value of 7915.96(11) keV. The mean value of the two most precise results of the Bn for 118Sn, was determined to be 9326.35(9) keV. The Bn for 57Fe was determined to be 7646.08(9) keV.

Recombinant expression of Intrepicalcin from the scorpion Vaejovis intrepidus and its effect on skeletal ryanodine receptors.

PubMed

Vargas-Jaimes, Leonel; Xiao, Liang; Zhang, Jing; Possani, Lourival D; Valdivia, Héctor H; Quintero-Hernández, Verónica

2017-04-01

Scorpion venoms contain toxins that modulate ionic channels, among which are the calcins, a small group of short, basic peptides with an Inhibitor Cystine Knot (ICK) motif that target calcium release channels/ryanodine receptors (RyRs) with high affinity and selectivity. Here we describe the heterologous expression of Intrepicalcin, identified by transcriptomic analysis of venomous glands from Vaejovis intrepidus. Recombinant Intrepicalcin was obtained in Escherichia coli BL21-DE3 (periplasm) by fusing the Intrepicalcin gene to sequences coding for signal-peptide, thioredoxin, His-tag and enterokinase cleavage site. [ 3 H]Ryanodine binding, used as a functional index of RyR activity, revealed that recombinant Intrepicalcin activates skeletal RyR (RyR1) dose-dependently with K d =17.4±4.0nM. Intrepicalcin significantly augments the bell-shaped [Ca 2+ ]-[ 3 H]ryanodine binding curve at all [Ca 2+ ] ranges, as is characteristic of the calcins. In single channel recordings, Intrepicalcin induces the appearance of a subconductance state in RyR1 with a fractional value ∼55% of the full conductance state, very close to that of Vejocalcin. Furthermore, Intrepicalcin stimulates Ca 2+ release at an initial dose=45.3±2.5nM, and depletes ~50% of Ca 2+ load from skeletal sarcoplasmic reticulum vesicles. We conclude that active recombinant Intrepicalcin was successfully obtained without the need of manual oxidation, enabling it to target RyR1s with high affinity. This is the first calcin heterologously expressed in the periplasma of Escherichia coli BL21-DE3, shown to be pharmacologically effective, thus paving the way for the generation of Intrepicalcin variants that are required for structure-function relationship studies of calcins and RyRs. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of Uncertainties in Stage-Discharge Curve for an Experimental Himalayan Watershed

NASA Astrophysics Data System (ADS)

Kumar, V.; Sen, S.

2016-12-01

Various water resource projects developed on rivers originating from the Himalayan region, the "Water Tower of Asia", plays an important role on downstream development. Flow measurements at the desired river site are very critical for river engineers and hydrologists for water resources planning and management, flood forecasting, reservoir operation and flood inundation studies. However, an accurate discharge assessment of these mountainous rivers is costly, tedious and frequently dangerous to operators during flood events. Currently, in India, discharge estimation is linked to stage-discharge relationship known as rating curve. This relationship would be affected by a high degree of uncertainty. Estimating the uncertainty of rating curve remains a relevant challenge because it is not easy to parameterize. Main source of rating curve uncertainty are errors because of incorrect discharge measurement, variation in hydraulic conditions and depth measurement. In this study our objective is to obtain best parameters of rating curve that fit the limited record of observations and to estimate uncertainties at different depth obtained from rating curve. The rating curve parameters of standard power law are estimated for three different streams of Aglar watershed located in lesser Himalayas by maximum-likelihood estimator. Quantification of uncertainties in the developed rating curves is obtained from the estimate of variances and covariances of the rating curve parameters. Results showed that the uncertainties varied with catchment behavior with error varies between 0.006-1.831 m3/s. Discharge uncertainty in the Aglar watershed streams significantly depend on the extent of extrapolation outside the range of observed water levels. Extrapolation analysis confirmed that more than 15% for maximum discharges and 5% for minimum discharges are not strongly recommended for these mountainous gauging sites.

Decomposition and correction overlapping peaks of LIBS using an error compensation method combined with curve fitting.

PubMed

Tan, Bing; Huang, Min; Zhu, Qibing; Guo, Ya; Qin, Jianwei

2017-09-01

The laser induced breakdown spectroscopy (LIBS) technique is an effective method to detect material composition by obtaining the plasma emission spectrum. The overlapping peaks in the spectrum are a fundamental problem in the qualitative and quantitative analysis of LIBS. Based on a curve fitting method, this paper studies an error compensation method to achieve the decomposition and correction of overlapping peaks. The vital step is that the fitting residual is fed back to the overlapping peaks and performs multiple curve fitting processes to obtain a lower residual result. For the quantitative experiments of Cu, the Cu-Fe overlapping peaks in the range of 321-327 nm obtained from the LIBS spectrum of five different concentrations of CuSO 4 ·5H 2 O solution were decomposed and corrected using curve fitting and error compensation methods. Compared with the curve fitting method, the error compensation reduced the fitting residual about 18.12-32.64% and improved the correlation about 0.86-1.82%. Then, the calibration curve between the intensity and concentration of the Cu was established. It can be seen that the error compensation method exhibits a higher linear correlation between the intensity and concentration of Cu, which can be applied to the decomposition and correction of overlapping peaks in the LIBS spectrum.

Transformation-invariant and nonparametric monotone smooth estimation of ROC curves.

PubMed

Du, Pang; Tang, Liansheng

2009-01-30

When a new diagnostic test is developed, it is of interest to evaluate its accuracy in distinguishing diseased subjects from non-diseased subjects. The accuracy of the test is often evaluated by receiver operating characteristic (ROC) curves. Smooth ROC estimates are often preferable for continuous test results when the underlying ROC curves are in fact continuous. Nonparametric and parametric methods have been proposed by various authors to obtain smooth ROC curve estimates. However, there are certain drawbacks with the existing methods. Parametric methods need specific model assumptions. Nonparametric methods do not always satisfy the inherent properties of the ROC curves, such as monotonicity and transformation invariance. In this paper we propose a monotone spline approach to obtain smooth monotone ROC curves. Our method ensures important inherent properties of the underlying ROC curves, which include monotonicity, transformation invariance, and boundary constraints. We compare the finite sample performance of the newly proposed ROC method with other ROC smoothing methods in large-scale simulation studies. We illustrate our method through a real life example. Copyright (c) 2008 John Wiley & Sons, Ltd.

Phage display selection of peptides that target calcium-binding proteins.

PubMed

Vetter, Stefan W

2013-01-01

Phage display allows to rapidly identify peptide sequences with binding affinity towards target proteins, for example, calcium-binding proteins (CBPs). Phage technology allows screening of 10(9) or more independent peptide sequences and can identify CBP binding peptides within 2 weeks. Adjusting of screening conditions allows selecting CBPs binding peptides that are either calcium-dependent or independent. Obtained peptide sequences can be used to identify CBP target proteins based on sequence homology or to quickly obtain peptide-based CBP inhibitors to modulate CBP-target interactions. The protocol described here uses a commercially available phage display library, in which random 12-mer peptides are displayed on filamentous M13 phages. The library was screened against the calcium-binding protein S100B.

Analytical models of calcium binding in a calcium channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jinn-Liang; Eisenberg, Bob

2014-08-21

The anomalous mole fraction effect of L-type calcium channels is analyzed using a Fermi like distribution with the experimental data of Almers and McCleskey [J. Physiol. 353, 585 (1984)] and the atomic resolution model of Lipkind and Fozzard [Biochemistry 40, 6786 (2001)] of the selectivity filter of the channel. Much of the analysis is algebraic, independent of differential equations. The Fermi distribution is derived from the configuration entropy of ions and water molecules with different sizes, different valences, and interstitial voids between particles. It allows us to calculate potentials and distances (between the binding ion and the oxygen ions ofmore » the glutamate side chains) directly from the experimental data using algebraic formulas. The spatial resolution of these results is comparable with those of molecular models, but of course the accuracy is no better than that implied by the experimental data. The glutamate side chains in our model are flexible enough to accommodate different types of binding ions in different bath conditions. The binding curves of Na{sup +} and Ca{sup 2+} for [CaCl{sub 2}] ranging from 10{sup −8} to 10{sup −2} M with a fixed 32 mM background [NaCl] are shown to agree with published Monte Carlo simulations. The Poisson-Fermi differential equation—that includes both steric and correlation effects—is then used to obtain the spatial profiles of energy, concentration, and dielectric coefficient from the solvent region to the filter. The energy profiles of ions are shown to depend sensitively on the steric energy that is not taken into account in the classical rate theory. We improve the rate theory by introducing a steric energy that lumps the effects of excluded volumes of all ions and water molecules and empty spaces between particles created by Lennard-Jones type and electrostatic forces. We show that the energy landscape varies significantly with bath concentrations. The energy landscape is not constant.« less

Curved-flow, rolling-flow, and oscillatory pure-yawing wind-tunnel test methods for determination of dynamic stability derivatives

NASA Technical Reports Server (NTRS)

Chambers, J. R.; Grafton, S. B.; Lutze, F. H.

1981-01-01

The test capabilities of the Stability Wind Tunnel of the Virginia Polytechnic Institute and State University are described, and calibrations for curved and rolling flow techniques are given. Oscillatory snaking tests to determine pure yawing derivatives are considered. Representative aerodynamic data obtained for a current fighter configuration using the curved and rolling flow techniques are presented. The application of dynamic derivatives obtained in such tests to the analysis of airplane motions in general, and to high angle of attack flight conditions in particular, is discussed.

New Modelling of Localized Necking in Sheet Metal Stretching

NASA Astrophysics Data System (ADS)

Bressan, José Divo

2011-01-01

Present work examines a new mathematical model to predict the onset of localized necking in the industrial processes of sheet metal forming such as biaxial stretching. Sheet metal formability is usually assessed experimentally by testing such as the Nakajima test to obtain the Forming Limit Curve, FLC, which is an essential material parameter necessary to numerical simulations by FEM. The Forming Limit Diagram or "Forming Principal Strain Map" shows the experimental FLC which is the plot of principal true strains in the sheet metal surface, ɛ1 and ɛ2, occurring at critical points obtained in laboratory formability tests or in the fabrication process. Two types of undesirable rupture mechanisms can occur in sheet metal forming products: localized necking and shear induced fracture. Therefore, two kinds of limit strain curves can be plotted: the local necking limit curve FLC-N and the shear fracture limit curve FLC-S. Localized necking is theoretically anticipated to initiate at a thickness defect ƒin = hib/hia inside the grooved sheet thickness hia, but only at the instability point of maximum load. The inception of grooving on the sheet surface evolves from instability point to localized necking and final rupture, during further sheet metal straining. Work hardening law is defined for a strain and strain rate material by the effective stress σ¯ = σo(1+βɛ¯)n???ɛM. The average experimental hardening law curve for tensile tests at 0°, 45° and 90°, assuming isotropic plasticity, was used to analyze the plasticity behavior during the biaxial stretching of sheet metals. Theoretical predicted curves of local necking limits are plotted in the positive quadrant of FPSM for different defect values ƒin and plasticity parameters. Limit strains are obtained from a software developed by the author. Some experimental results of forming limit curve obtained from experiments for IF steel sheets are compared with the theoretical predicted curves: the correlation is good.

A comparative study of electric load curve changes in an urban low-voltage substation in Spain during the economic crisis (2008-2013).

PubMed

Lara-Santillán, Pedro M; Mendoza-Villena, Montserrat; Fernández-Jiménez, L Alfredo; Mañana-Canteli, Mario

2014-01-01

This paper presents a comparative study of the electricity consumption (EC) in an urban low-voltage substation before and during the economic crisis (2008-2013). This low-voltage substation supplies electric power to near 400 users. The EC was measured for an 11-year period (2002-2012) with a sampling time of 1 minute. The study described in the paper consists of detecting the changes produced in the load curves of this substation along the time due to changes in the behaviour of consumers. The EC was compared using representative curves per time period (precrisis and crisis). These representative curves were obtained after a computational process, which was based on a search for days with similar curves to the curve of a determined (base) date. This similitude was assessed by the proximity on the calendar, day of the week, daylight time, and outdoor temperature. The last selection parameter was the error between the nearest neighbour curves and the base date curve. The obtained representative curves were linearized to determine changes in their structure (maximum and minimum consumption values, duration of the daily time slot, etc.). The results primarily indicate an increase in the EC in the night slot during the summer months in the crisis period.

What Do We Learn from Binding Features? Evidence for Multilevel Feature Integration

ERIC Educational Resources Information Center

Colzato, Lorenza S.; Raffone, Antonino; Hommel, Bernhard

2006-01-01

Four experiments were conducted to investigate the relationship between the binding of visual features (as measured by their after-effects on subsequent binding) and the learning of feature-conjunction probabilities. Both binding and learning effects were obtained, but they did not interact. Interestingly, (shape-color) binding effects…

Ligand Binding to WW Tandem Domains of YAP2 Transcriptional Regulator Is Under Negative Cooperativity

PubMed Central

Schuchardt, Brett J.; Mikles, David C.; Hoang, Lawrence M.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

2014-01-01

YAP2 transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well-documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. PMID:25283809

Sensing Membrane Stresses by Protein Insertions

PubMed Central

Campelo, Felix; Kozlov, Michael M.

2014-01-01

Protein domains shallowly inserting into the membrane matrix are ubiquitous in peripheral membrane proteins involved in various processes of intracellular membrane shaping and remodeling. It has been suggested that these domains sense membrane curvature through their preferable binding to strongly curved membranes, the binding mechanism being mediated by lipid packing defects. Here we make an alternative statement that shallow protein insertions are universal sensors of the intra-membrane stresses existing in the region of the insertion embedding rather than sensors of the curvature per se. We substantiate this proposal computationally by considering different independent ways of the membrane stress generation among which some include changes of the membrane curvature whereas others do not alter the membrane shape. Our computations show that the membrane-binding coefficient of shallow protein insertions is determined by the resultant stress independently of the way this stress has been produced. By contrast, consideration of the correlation between the insertion binding and the membrane curvature demonstrates that the binding coefficient either increases or decreases with curvature depending on the factors leading to the curvature generation. To validate our computational model, we treat quantitatively the experimental results on membrane binding by ALPS1 and ALPS2 motifs of ArfGAP1. PMID:24722359

Fluorescence analysis of competition of phenylbutazone and methotrexate in binding to serum albumin in combination treatment in rheumatology

NASA Astrophysics Data System (ADS)

Maciążek-Jurczyk, M.; Sułkowska, A.; Bojko, B.; Równicka, J.; Sułkowski, W. W.

2009-04-01

Combination of several drugs is often necessary especially during long-them therapy. The competition between drugs can cause a decrease of the amount of a drug bound to albumin. This results in an increase of the free, biological active fraction of the drug. The aim of the presented study was to describe the competition between phenylbutazone (Phe) and methotrexate (MTX), two drugs recommended for the treatment of rheumatology in binding to bovine (BSA) and human (HSA) serum albumin in the high affinity binding site. Fluorescence analysis was used to estimate the effect of drugs on the protein fluorescence and to define the binding and quenching properties of drugs-serum albumin complexes. The effect of the displacement of one drug from the complex of the other with serum albumin has been described on the basis of the comparison of the quenching curves and binding constants for the binary and ternary systems. The conclusion that both Phe and MTX form a binding site in the same subdomain (IIA) points to the necessity of using a monitoring therapy owning to the possible increase of the uncontrolled toxic effects.

Single molecule junction conductance and binding geometry

NASA Astrophysics Data System (ADS)

Kamenetska, Maria

This Thesis addresses the fundamental problem of controlling transport through a metal-organic interface by studying electronic and mechanical properties of single organic molecule-metal junctions. Using a Scanning Tunneling Microscope (STM) we image, probe energy-level alignment and perform STM-based break junction (BJ) measurements on molecules bound to a gold surface. Using Scanning Tunneling Microscope-based break-junction (STM-BJ) techniques, we explore the effect of binding geometry on single-molecule conductance by varying the structure of the molecules, metal-molecule binding chemistry and by applying sub-nanometer manipulation control to the junction. These experiments are performed both in ambient conditions and in ultra high vacuum (UHV) at cryogenic temperatures. First, using STM imaging and scanning tunneling spectroscopy (STS) measurements we explore binding configurations and electronic properties of an amine-terminated benzene derivative on gold. We find that details of metal-molecule binding affect energy-level alignment at the interface. Next, using the STM-BJ technique, we form and rupture metal-molecule-metal junctions ˜104 times to obtain conductance-vs-extension curves and extract most likely conductance values for each molecule. With these measurements, we demonstrated that the control of junction conductance is possible through a choice of metal-molecule binding chemistry and sub-nanometer positioning. First, we show that molecules terminated with amines, sulfides and phosphines bind selectively on gold and therefore demonstrate constant conductance levels even as the junction is elongated and the metal-molecule attachment point is modified. Such well-defined conductance is also obtained with paracyclophane molecules which bind to gold directly through the pi system. Next, we are able to create metal-molecule-metal junctions with more than one reproducible conductance signatures that can be accessed by changing junction geometry. In the case of pyridine-linked molecules, conductance can be reliably switched between two distinct conductance states using sub-nanometer mechanical manipulation. Using a methyl sulfide linker attached to an oligoene backbone, we are able to create a 3-nm-long molecular potentiometer, whose resistance can be tuned exponentially with Angstom-scale modulations in metal-molecule configuration. These experiments points to a new paradigm for attaining reproducible electrical characteristics of metal-organic devices which involves controlling linker-metal chemistry rather than fabricating identically structured metal-molecule interfaces. By choosing a linker group which is either insensitive to or responds reproducibly to changes in metal-molecule configuration, one can design single molecule devices with functionality more complex than a simple resistor. These ambient temperature experiments were combined with UHV conductance measurements performed in a commercial STM on amine-terminated benzene derivatives which conduct through a non-resonant tunneling mechanism, at temperatures varying from 5 to 300 Kelvin. Our results indicate that while amine-gold binding remains selective irrespective of environment, conductance is not temperature independent, in contrast to what is expected for a tunneling mechanism. Furthermore, using temperature-dependent measurements in ambient conditions we find that HOMO-conducting amines and LUMO-conducting pyridines show opposite dependence of conductance on temperature. These results indicate that energy-level alignment between the molecule and the electrodes changes as a result of varying electrode structure at different temperatures. We find that temperature can serve as a knob with which to tune transport properties of single molecule-metal junctions.

Quadratic canonical transformation theory and higher order density matrices.

PubMed

Neuscamman, Eric; Yanai, Takeshi; Chan, Garnet Kin-Lic

2009-03-28

Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT's accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H(2)O and N(2) binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.

Universal binding energy relations in metallic adhesion

NASA Technical Reports Server (NTRS)

Ferrante, J.; Smith, J. R.; Rose, J. J.

1984-01-01

Rose, Smith, and Ferrante have discovered scaling relations which map the adhesive binding energy calculated by Ferrante and Smith onto a single universal binding energy curve. These binding energies are calculated for all combinations of Al(111), Zn(0001), Mg(0001), and Na(110) in contact. The scaling involves normalizing the energy by the maximum binding energy and normalizing distances by a suitable combination of Thomas-Fermi screening lengths. Rose et al. have also found that the calculated cohesive energies of K, Ba, Cu, Mo, and Sm scale by similar simple relations, suggesting the universal relation may be more general than for the simple free electron metals for which it was derived. In addition, the scaling length was defined more generally in order to relate it to measurable physical properties. Further this universality can be extended to chemisorption. A simple and yet quite accurate prediction of a zero temperature equation of state (volume as a function of pressure for metals and alloys) is presented. Thermal expansion coefficients and melting temperatures are predicted by simple, analytic expressions, and results compare favorably with experiment for a broad range of metals.

A rigorous multiple independent binding site model for determining cell-based equilibrium dissociation constants.

PubMed

Drake, Andrew W; Klakamp, Scott L

2007-01-10

A new 4-parameter nonlinear equation based on the standard multiple independent binding site model (MIBS) is presented for fitting cell-based ligand titration data in order to calculate the ligand/cell receptor equilibrium dissociation constant and the number of receptors/cell. The most commonly used linear (Scatchard Plot) or nonlinear 2-parameter model (a single binding site model found in commercial programs like Prism(R)) used for analysis of ligand/receptor binding data assumes only the K(D) influences the shape of the titration curve. We demonstrate using simulated data sets that, depending upon the cell surface receptor expression level, the number of cells titrated, and the magnitude of the K(D) being measured, this assumption of always being under K(D)-controlled conditions can be erroneous and can lead to unreliable estimates for the binding parameters. We also compare and contrast the fitting of simulated data sets to the commonly used cell-based binding equation versus our more rigorous 4-parameter nonlinear MIBS model. It is shown through these simulations that the new 4-parameter MIBS model, when used for cell-based titrations under optimal conditions, yields highly accurate estimates of all binding parameters and hence should be the preferred model to fit cell-based experimental nonlinear titration data.

Constitutive activity of the δ-opioid receptor expressed in C6 glioma cells: identification of non-peptide δ-inverse agonists

PubMed Central

Neilan, Claire L; Akil, Huda; Woods, James H; Traynor, John R

1999-01-01

G-protein coupled receptors can exhibit constitutive activity resulting in the formation of active ternary complexes in the absence of an agonist. In this study we have investigated constitutive activity in C6 glioma cells expressing either the cloned δ-(OP1) receptor (C6δ), or the cloned μ-(OP3) opioid receptor (C6μ).Constitutive activity was measured in the absence of Na+ ions to provide an increased signal. The degree of constitutive activity was defined as the level of [35S]-GTPγS binding that could be inhibited by pre-treatment with pertussis toxin (PTX). In C6δ cells the level of basal [35S]-GTPγS binding was reduced by 51.9±6.1 fmols mg−1 protein, whereas in C6μ and C6 wild-type cells treatment with PTX reduced basal [35S]-GTPγS binding by only 10.0±3.5 and 8.6±3.1 fmols mg−1 protein respectively.The δ-antagonists N,N-diallyl-Tyr-Aib-Aib-Phe-Leu-OH (ICI 174,864), 7-benzylidenenaltrexone (BNTX) and naltriben (NTB), in addition to clocinnamox (C-CAM), acted as δ-opioid receptor inverse agonists. Naloxone, buprenorphine, and naltrindole were neutral antagonists. Furthermore, naltrindole blocked the reduction in [35S]-GTPγS binding caused by the inverse agonists. The inverse agonists did not inhibit basal [35S]-GTPγS binding in C6μ or C6 wild-type cell membranes.Competition binding assays in C6δ cell membranes revealed a leftward shift in the displacement curve of [3H]-naltrindole by ICI 174,864 and C-CAM in the presence of NaCl and the GTP analogue, GppNHp. There was no change in the displacement curve for BNTX or NTB under these conditions.These data confirm the presence of constitutive activity associated with the δ-opioid receptor and identify three novel, non-peptide, δ-opioid inverse agonists. PMID:10516632

Accelerated pharmacokinetic map determination for dynamic contrast enhanced MRI using frequency-domain based Tofts model.

PubMed

Vajuvalli, Nithin N; Nayak, Krupa N; Geethanath, Sairam

2014-01-01

Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) is widely used in the diagnosis of cancer and is also a promising tool for monitoring tumor response to treatment. The Tofts model has become a standard for the analysis of DCE-MRI. The process of curve fitting employed in the Tofts equation to obtain the pharmacokinetic (PK) parameters is time-consuming for high resolution scans. Current work demonstrates a frequency-domain approach applied to the standard Tofts equation to speed-up the process of curve-fitting in order to obtain the pharmacokinetic parameters. The results obtained show that using the frequency domain approach, the process of curve fitting is computationally more efficient compared to the time-domain approach.

Inhibition of [11C]mirtazapine binding by alpha2-adrenoceptor antagonists studied by positron emission tomography in living porcine brain.

PubMed

Smith, Donald F; Dyve, Suzan; Minuzzi, Luciano; Jakobsen, Steen; Munk, Ole L; Marthi, Katalin; Cumming, Paul

2006-06-15

We have developed [(11)C]mirtazapine as a ligand for PET studies of antidepressant binding in living brain. However, previous studies have determined neither optimal methods for quantification of [(11)C]mirtazapine binding nor the pharmacological identity of this binding. To obtain that information, we have now mapped the distribution volume (V(d)) of [(11)C]mirtazapine relative to the arterial input in the brain of three pigs, in a baseline condition and after pretreatment with excess cold mirtazapine (3 mg/kg). Baseline V(d) ranged from 6 ml/ml in cerebellum to 18 ml/ml in frontal cortex, with some evidence for a small self-displaceable binding component in the cerebellum. Regional binding potentials (pBs) obtained by a constrained two-compartment model, using the V(d) observation in cerebellum, were consistently higher than pBs obtained by other arterial input or reference tissue methods. We found that adequate quantification of pB was obtained using the simplified reference tissue method. Concomitant PET studies with [(15)O]-water indicated that mirtazapine challenge increased CBF uniformly in cerebellum and other brain regions, supporting the use of this reference tissue for calculation of [(11)C]mirtazapine pB. Displacement by mirtazapine was complete in the cerebral cortex, but only 50% in diencephalon, suggesting the presence of multiple binding sites of differing affinities in that tissue. Competition studies with yohimbine and RX 821002 showed decreases in [(11)C]mirtazapine pB throughout the forebrain; use of the multireceptor version of the Michaelis-Menten equation indicated that 42% of [(11)C]mirtazapine binding in cortical regions is displaceable by yohimbine. Thus, PET studies confirm that [(11)C]mirtazapine affects alpha(2)-adrenoceptor binding sites in living brain. (c) 2006 Wiley-Liss, Inc.

Evaluation of the antagonism of nicotine by mecamylamine and pempidine in the brain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, T.J.

1989-01-01

Antagonists have been crucial in the characterization of nicotine's pharmacology. Initial evidence for the existence of central nicotinic receptors was based on the fact that nicotine produced a number of behavioral effects that were antagonized by ganglionic blockers that crossed the blood-brain barrier, such as mecamylamine and pempidine. These compounds are thought to be noncompetitive antagonists due to the fact that they do not compete for agonist binding to brain homogenate in vitro. However, pharmacological evidence in support of noncompetitive antagonism is lacking. Dose-response curves for nicotine were determined in the presence of various doses of pempidine for depression ofmore » spontaneous activity and antinociception in mice. Pempidine was found to shift the dose response curves for these effects of nicotine in a manner consistent with noncompetitive antagonism. A number of mecamylamine analogs were investigated for antagonism of these central effects of nicotine as well. These studies revealed that the N-, 2-, and 3-methyls were crucial for optimal efficacy and potency and suggests that these compounds possess a specific mechanism of action, possibly involving a receptor. Furthermore, the structure-activity relationships for the mecamylamine analogs were found to be different than that previously reported for the agonists, suggesting that they do not act at the same site. The binding of ({sup 3} H)-L-nicotine and ({sup 3}H)-pempidine was studied in vitro to mouse brain homogentate and in situ to rat brain slices. The in situ binding of ({sup 3}H)-L-nicotine to rat brain slices was quantitated autoradiographically to discrete brain areas in the presence and absence of 1, 10 and 100 {mu}M nicotine and pempidine. Pempidine did not effectively displace ({sup 3}H)-L-nicotine binding.« less

Agonist activation of α7 nicotinic acetylcholine receptors via an allosteric transmembrane site

PubMed Central

Gill, JasKiran K.; Savolainen, Mari; Young, Gareth T.; Zwart, Ruud; Sher, Emanuele; Millar, Neil S.

2011-01-01

Conventional nicotinic acetylcholine receptor (nAChR) agonists, such as acetylcholine, act at an extracellular “orthosteric” binding site located at the interface between two adjacent subunits. Here, we present evidence of potent activation of α7 nAChRs via an allosteric transmembrane site. Previous studies have identified a series of nAChR-positive allosteric modulators (PAMs) that lack agonist activity but are able to potentiate responses to orthosteric agonists, such as acetylcholine. It has been shown, for example, that TQS acts as a conventional α7 nAChR PAM. In contrast, we have found that a compound with close chemical similarity to TQS (4BP-TQS) is a potent allosteric agonist of α7 nAChRs. Whereas the α7 nAChR antagonist metyllycaconitine acts competitively with conventional nicotinic agonists, metyllycaconitine is a noncompetitive antagonist of 4BP-TQS. Mutation of an amino acid (M253L), located in a transmembrane cavity that has been proposed as being the binding site for PAMs, completely blocks agonist activation by 4BP-TQS. In contrast, this mutation had no significant effect on agonist activation by acetylcholine. Conversely, mutation of an amino acid located within the known orthosteric binding site (W148F) has a profound effect on agonist potency of acetylcholine (resulting in a shift of ∼200-fold in the acetylcholine dose-response curve), but had little effect on the agonist dose-response curve for 4BP-TQS. Computer docking studies with an α7 homology model provides evidence that both TQS and 4BP-TQS bind within an intrasubunit transmembrane cavity. Taken together, these findings provide evidence that agonist activation of nAChRs can occur via an allosteric transmembrane site. PMID:21436053

Cardiovascular and haematological responses of Atlantic cod (Gadus morhua) to acute temperature increase.

PubMed

Gollock, M J; Currie, S; Petersen, L H; Gamperl, A K

2006-08-01

For fish to survive large acute temperature increases (i.e. >10.0 degrees C) that may bring them close to their critical thermal maximum (CTM), oxygen uptake at the gills and distribution by the cardiovascular system must increase to match tissue oxygen demand. To examine the effects of an acute temperature increase ( approximately 1.7 degrees C h(-1) to CTM) on the cardiorespiratory physiology of Atlantic cod, we (1) carried out respirometry on 10.0 degrees C acclimated fish, while simultaneously measuring in vivo cardiac parameters using Transonic probes, and (2) constructed in vitro oxygen binding curves on whole blood from 7.0 degrees C acclimated cod at a range of temperatures. Both cardiac output (Q) and heart rate (fh) increased until near the fish's CTM (22.2+/-0.2 degrees C), and then declined rapidly. Q(10) values for Q and fh were 2.48 and 2.12, respectively, and increases in both parameters were tightly correlated with O(2) consumption. The haemoglobin (Hb)-oxygen binding curve at 24.0 degrees C showed pronounced downward and rightward shifts compared to 20.0 degrees C and 7.0 degrees C, indicating that both binding capacity and affinity decreased. Further, Hb levels were lower at 24.0 degrees C than at 20.0 degrees C and 7.0 degrees C. This was likely to be due to cell swelling, as electrophoresis of Hb samples did not suggest protein denaturation, and at 24.0 degrees C Hb samples showed peak absorbance at the expected wavelength (540 nm). Our results show that cardiac function is unlikely to limit metabolic rate in Atlantic cod from Newfoundland until close to their CTM, and we suggest that decreased blood oxygen binding capacity may contribute to the plateau in oxygen consumption.

Continuous relaxation and retardation spectrum method for viscoelastic characterization of asphalt concrete

NASA Astrophysics Data System (ADS)

Bhattacharjee, Sudip; Swamy, Aravind Krishna; Daniel, Jo S.

2012-08-01

This paper presents a simple and practical approach to obtain the continuous relaxation and retardation spectra of asphalt concrete directly from the complex (dynamic) modulus test data. The spectra thus obtained are continuous functions of relaxation and retardation time. The major advantage of this method is that the continuous form is directly obtained from the master curves which are readily available from the standard characterization tests of linearly viscoelastic behavior of asphalt concrete. The continuous spectrum method offers efficient alternative to the numerical computation of discrete spectra and can be easily used for modeling viscoelastic behavior. In this research, asphalt concrete specimens have been tested for linearly viscoelastic characterization. The linearly viscoelastic test data have been used to develop storage modulus and storage compliance master curves. The continuous spectra are obtained from the fitted sigmoid function of the master curves via the inverse integral transform. The continuous spectra are shown to be the limiting case of the discrete distributions. The continuous spectra and the time-domain viscoelastic functions (relaxation modulus and creep compliance) computed from the spectra matched very well with the approximate solutions. It is observed that the shape of the spectra is dependent on the master curve parameters. The continuous spectra thus obtained can easily be implemented in material mix design process. Prony-series coefficients can be easily obtained from the continuous spectra and used in numerical analysis such as finite element analysis.

Enhanced Charge Carrier Transport and Device Performance Through Dual-Cesium Doping in Mixed-Cation Perovskite Solar Cells with Near Unity Free Carrier Ratios.

PubMed

Ye, Tao; Petrović, Miloš; Peng, Shengjie; Yoong, Jeremy Lee Kong; Vijila, Chellappan; Ramakrishna, Seeram

2017-01-25

PbI 2 -enriched mixed perovskite film [FA 0.81 MA 0.15 Pb(I 0.836 Br 0.15 ) 3 ] has been widely studied due to its great potential in perovskite solar cell (PSC) applications. Herein, a FA 0.81 MA 0.15 Pb(I 0.836 Br 0.15 ) 3 film has been fabricated with the temperature-dependent optical absorption spectra utilized to determine its exciton binding energy. A ∼13 meV exciton binding energy is estimated, and a near-unity fraction of free carriers out of the total photoexcitons has been obtained in the solar cell operating regime at equilibrium state. PSCs are fabricated with this mixed perovskite film, but a significant electron transport barrier at the TiO 2 -perovskite interface limited their performance. Cs 2 CO 3 and CsI are then utilized as functional enhancers with which to substantially balance the electron and hole transport and increase the carriers (both electrons and holes) mobilities in PSCs, resulting in much-improved solar-cell performance. The modified PSCs exhibit reproducible power conversion efficiency (PCE) values with little hysteresis effect in the J-V curves, achieving PCEs up to 19.5% for the Cs 2 CO 3 -modified PSC and 20.6% when subsequently further doped with CsI.

Design of Remote GPRS-based Gas Data Monitoring System

NASA Astrophysics Data System (ADS)

Yan, Xiyue; Yang, Jianhua; Lu, Wei

2018-01-01

In order to solve the problem of remote data transmission of gas flowmeter, and realize unattended operation on the spot, an unattended remote monitoring system based on GPRS for gas data is designed in this paper. The slave computer of this system adopts embedded microprocessor to read data of gas flowmeter through rs-232 bus and transfers it to the host computer through DTU. In the host computer, the VB program dynamically binds the Winsock control to receive and parse data. By using dynamic data exchange, the Kingview configuration software realizes history trend curve, real time trend curve, alarm, print, web browsing and other functions.

Interaction between quinoline yellow and human serum albumin: Spectroscopic, chemometrics and molecular docking studies.

PubMed

Wang, Rui; Hu, Xing; Pan, Junhui; Gong, Deming; Zhang, Guowen

2018-05-23

Quinoline yellow (QY), a widely used synthetic colorant in food industry, has caused extensive concern due to its potential harm to human health. In the present work, the interaction between food colourant quinoline yellow (QY) and human serum albumin (HSA) was characterized by multispectroscopic methods, chemometrics algorithm and molecular modeling studies. The concentration profiles and the pure spectra for the components (QY, HSA and QY-HSA complex) obtained through analyzing the expanded UV-vis absorption data matrix by multivariate curve resolution-alternating least squares confirmed the QY-HSA interaction process. QY quenched the fluorescence of HSA due to the formation of QY-HSA complex and moderate affinity stabilized the complex. Hydrophobic forces and hydrogen bonding played major roles in the binding of QY to HSA. Site-specific marker-induced displacement results suggested that QY bound to the subdomain IIA of HSA which was corroborated by the molecular docking results. Decreases of HSA surface hydrophobicity and free sulfhydryl groups content indicated that QY caused a contraction of the peptide strand in HSA and hided the hydrophobic patches of the protein. The analysis of UV-vis absorption, circular dichroism and three-dimensional fluorescence spectroscopy found that QY led to the microenvironmental perturbations around the fluorophores and secondary structure changes of HSA. This work showed that QY could bind to HSA and affect the structural and functional properties of this protein, which provided new insights into the binding mechanism of QY with HSA and comprehensive understanding for the toxicity of QY in biological process. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Avoiding false positives and optimizing identification of true ...

EPA Pesticide Factsheets

The potential for chemicals to affect endocrine signaling is commonly evaluated via in vitro receptor binding and gene activation, but these assays, especially antagonism assays, have potential artifacts that must be addressed for accurate interpretation. Results are presented from screening 94 chemicals from 54 chemical groups for estrogen receptor (ER) activation in a competitive rainbow trout ER (rtER) binding assay and a trout liver slice vitellogenin mRNA expression assay. Results from true competitive agonists and antagonists, and inactive chemicals with little or no indication of ER binding or gene activation were easily interpreted. However, results for numerous industrial chemicals were more challenging to interpret, including chemicals with: (1) apparent competitive binding curves but no gene activation, (2) apparent binding and gene inhibition with evidence of either cytotoxicity or changes in assay media pH, (3) apparent binding but non-competitive gene inhibition of unknown cause, or (4) no rtER binding and gene inhibition not due to competitive ER interaction but due to toxicity, pH change, or some unknown cause. The use of endpoints such as toxicity, pH, precipitate formation, and determination of inhibitor dissociation constants (Ki) for interpreting the results of antagonism and binding assays for diverse chemicals is presented. Of the 94 chemicals tested for antagonism only two, tamoxifen and ICI-182,780, were found to be true competitive

Ca sup 2+ binding capacity of cytoplasmic proteins from rod photoreceptors is mainly due to arrestin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huppertz, B.; Weyand, I.; Bauer, P.J.

1990-06-05

Arrestin (also called S-antigen or 48-kDa protein) binds to photoexcited and phosphorylated rhodopsin and, thereby, blocks competitively the activation of transducin. Using Ca{sup 2+} titration in the presence of the indicator arsenazo III and {sup 45}Ca{sup 2+} autoradiography, we show that arrestin is a Ca2(+)-binding protein. The Ca{sup 2+} binding capacity of arresting-containing protein extracts from bovine rod outer segments is about twice as high as that of arrestin-depleted extracts. The difference in the Ca{sup 2+} binding of arrestin-containing and arrestin-depleted protein extracts was attributed to arrestin. Both, these difference-measurements of protein extracts and the measurements of purified arrestin yieldmore » dissociation constants for the Ca{sup 2+} binding of arrestin between 2 and 4 microM. The titration curves are consistent with a molar ratio of one Ca{sup 2+} binding site per arrestin. No Ca{sup 2+} binding in the micromolar range was found in extracts containing mainly transducin and cGMP-phosphodiesterase. Since arrestin is one of the most abundant proteins in rod photoreceptors occurring presumably up to millimolar concentrations in rod outer segments, we suggest that aside from its function to prevent the activation of transducin, arrestin acts probably as an intracellular Ca{sup 2+} buffer.« less

Analysis of molecular determinants of affinity and relative efficacy of a series of R- and S-2-(dipropylamino)tetralins at the 5-HT1A serotonin receptor

PubMed Central

Alder, J Tracy; Hacksell, Uli; Strange, Philip G

2003-01-01

Factors influencing agonist affinity and relative efficacy have been studied for the 5-HT1A serotonin receptor using membranes of CHO cells expressing the human form of the receptor and a series of R-and S-2-(dipropylamino)tetralins (nonhydroxylated and monohydroxylated (5-OH, 6-OH, 7-OH, 8-OH) species). Ligand binding studies were used to determine dissociation constants for agonist binding to the 5-HT1A receptor: Ki values for agonists were determined in competition versus the binding of the agonist [3H]-8-OH DPAT. Competition data were all fitted best by a one-binding site model.Ki values for agonists were also determined in competition versus the binding of the antagonist [3H]-NAD-199. Competition data were all fitted best by a two-binding site model, and agonist affinities for the higher (Kh) and lower affinity (Kl) sites were determined. The ability of the agonists to activate the 5-HT1A receptor was determined using stimulation of [35S]-GTPγS binding. Maximal effects of agonists (Emax) and their potencies (EC50) were determined from concentration/response curves for stimulation of [35S]-GTPγS binding. Kl/Kh determined from ligand binding assays correlated with the relative efficacy (relative Emax) of agonists determined in [35S]-GTPγS binding assays. There was also a correlation between Kl/Kh and Kl/EC50 for agonists determined from ligand binding and [35S]-GTPγS binding assays. Simulations of agonist binding and effect data were performed using the Ternary Complex Model in order to assess the use of Kl/Kh for predicting the relative efficacy of agonists. PMID:12684269

How actin binds and assembles onto plasma membranes from Dictyostelium discoideum

PubMed Central

1988-01-01

We have shown previously (Schwartz, M. A., and E. J. Luna. 1986. J. Cell Biol. 102: 2067-2075) that actin binds with positive cooperativity to plasma membranes from Dictyostelium discoideum. Actin is polymerized at the membrane surface even at concentrations well below the critical concentration for polymerization in solution. Low salt buffer that blocks actin polymerization in solution also prevents actin binding to membranes. To further explore the relationship between actin polymerization and binding to membranes, we prepared four chemically modified actins that appear to be incapable of polymerizing in solution. Three of these derivatives also lost their ability to bind to membranes. The fourth derivative (EF actin), in which histidine-40 is labeled with ethoxyformic anhydride, binds to membranes with reduced affinity. Binding curves exhibit positive cooperativity, and cross- linking experiments show that membrane-bound actin is multimeric. Thus, binding and polymerization are tightly coupled, and the ability of these membranes to polymerize actin is dramatically demonstrated. EF actin coassembles weakly with untreated actin in solution, but coassembles well on membranes. Binding by untreated actin and EF actin are mutually competitive, indicating that they bind to the same membrane sites. Hill plots indicate that an actin trimer is the minimum assembly state required for tight binding to membranes. The best explanation for our data is a model in which actin oligomers assemble by binding to clustered membrane sites with successive monomers on one side of the actin filament bound to the membrane. Individual binding affinities are expected to be low, but the overall actin-membrane avidity is high, due to multivalency. Our results imply that extracellular factors that cluster membrane proteins may create sites for the formation of actin nuclei and thus trigger actin polymerization in the cell. PMID:3392099

An Experimental Investigation of Mechanical Properties in Clay Brick Masonry by Partial Replacement of Fine Aggregate with Clay Brick Waste

NASA Astrophysics Data System (ADS)

Kumavat, Hemraj Ramdas

2016-09-01

The compressive stress-strain behavior and mechanical properties of clay brick masonry and its constituents clay bricks and mortar, have been studied by several laboratory tests. Using linear regression analysis, a analytical model has been proposed for obtaining the stress-strain curves for masonry that can be used in the analysis and design procedures. The model requires only the compressive strengths of bricks and mortar as input data, which can be easily obtained experimentally. Development of analytical model from the obtained experimental results of Young's modulus and compressive strength. Simple relationships have been identified for obtaining the modulus of elasticity of bricks, mortar, and masonry from their corresponding compressive strengths. It was observed that the proposed analytical model clearly demonstrates a reasonably good prediction of the stress-strain curves when compared with the experimental curves.

Recession curve analysis for groundwater levels: case study in Latvia

NASA Astrophysics Data System (ADS)

Gailuma, A.; VÄ«tola, I.; Abramenko, K.; Lauva, D.; Vircavs, V.; Veinbergs, A.; Dimanta, Z.

2012-04-01

Recession curve analysis is powerful and effective analysis technique in many research areas related with hydrogeology where observations have to be made, such as water filtration and absorption of moisture, irrigation and drainage, planning of hydroelectric power production and chemical leaching (elution of chemical substances) as well as in other areas. The analysis of the surface runoff hydrograph`s recession curves, which is performed to conceive the after-effects of interaction of precipitation and surface runoff, has approved in practice. The same method for analysis of hydrograph`s recession curves can be applied for the observations of the groundwater levels. There are manually prepared hydrograph for analysis of recession curves for observation wells (MG2, BG2 and AG1) in agricultural monitoring sites in Latvia. Within this study from the available monitoring data of groundwater levels were extracted data of declining periods, splitted by month. The drop-down curves were manually (by changing the date) moved together, until to find the best match, thereby obtaining monthly drop-down curves, representing each month separately. Monthly curves were combined and manually joined, for obtaining characterizing drop-down curves of the year for each well. Within the process of decreased recession curve analysis, from the initial curve was cut out upward areas, leaving only the drops of the curve, consequently, the curve is transformed more closely to the groundwater flow, trying to take out the impact of rain or drought periods from the curve. Respectively, the drop-down curve is part of the data, collected with hydrograph, where data with the discharge dominates, without considering impact of precipitation. Using the recession curve analysis theory, ready tool "A Visual Basic Spreadsheet Macro for Recession Curve Analysis" was used for selection of data and logarithmic functions matching (K. Posavec et.al., GROUND WATER 44, no. 5: 764-767, 2006), as well as functions were developed by manual processing of data. For displaying data the mathematical model of data equalization was used, finding the corresponding or closest logarithmic function of the recession for the graph. Obtained recession curves were similar but not identical. With full knowledge of the fluctuations of ground water level, it is possible to indirectly (without taking soil samples) determine the filtration coefficient: more rapid decline in the recession curve correspond for the better filtration conditions. This research could be very useful in construction planning, road constructions, agriculture etc. Acknowledgments The authors gratefully acknowledge the funding from ESF Project "Establishment of interdisciplinary scientist group and modeling system for groundwater research" (Agreement No. 2009/0212/1DP/1.1.1.2.0/09/APIA/VIAA/060EF7)

A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

PubMed Central

Zahn, Raphael; Osmanović, Dino; Ehret, Severin; Araya Callis, Carolina; Frey, Steffen; Stewart, Murray; You, Changjiang; Görlich, Dirk; Hoogenboom, Bart W; Richter, Ralf P

2016-01-01

The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior – a key element for the transport selectivity of the NPC – was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface. DOI: http://dx.doi.org/10.7554/eLife.14119.001 PMID:27058170

The influence of fatty acids on theophylline binding to human serum albumin. Comparative fluorescence study

NASA Astrophysics Data System (ADS)

Maciążek-Jurczyk, M.; Sułkowska, A.; Bojko, B.; Równicka-Zubik, J.; Szkudlarek-Haśnik, A.; Zubik-Skupień, I.; Góra, A.; Dubas, M.; Korzonek-Szlacheta, I.; Wielkoszyński, T.; Żurawiński, W.; Sosada, K.

2012-04-01

Theophylline, popular diuretic, is used to treat asthma and bronchospasm. In blood it forms complexes with albumin, which is also the main transporter of fatty acids. The aim of the present study was to describe the influence of fatty acids (FA) on binding of theophylline (Th) to human serum albumin (HSA) in the high affinity binding sites. Binding parameters have been obtained on the basis of the fluorescence analysis. The data obtained for the complex of Th and natural human serum albumin (nHSA) obtained from blood of obese patients qualified for surgical removal of stomach was compared with our previous studies on the influence of FA on the complex of Th and commercially available defatted human serum albumin (dHSA).

CCD photometry of 2060 Chiron, 1991 January

NASA Technical Reports Server (NTRS)

Buratti, B. J.; Marcialis, R. L.; Howell, E. S.; Nolan, M. C.

1991-01-01

Observations of 2060 Chiron was performed on 7 to 8 Jan. 1991 with the Mt. Palomar 1.52 m telescope in the Gunn-R passband. On-chip field stars were used to perform differential reductions. The repeatability of the 5.9 hour light curve was excellent, both within a night and from night to night. No evidence for short-term secular variations similar to those seen last year by both Luu and Jewitt (1990) and Buratti and Dunbar (1991) is seen in the new light curve. Chiron's rotational light curve appears strikingly similar to that obtained a year earlier by Luu and Jewitt (1990), both in amplitude and shape. Both light curves show strongly correlated changes over a timescale of perhaps 15 minutes. These same features were marginally visible in the 1986 light curve. Such behavior is believed to be evidence that Chiron may be more aspherical than the 4 percent intensity variation might otherwise indicate, and favors a viewing geometry where the subearth latitude is rather low. Chiron was much fainter in 1985, when a partial light curve was obtained by Marcialis. Due to the lower sampling rate of these early data, no conclusions can be made regarding the high-frequency light curve structure back then. All three of these light curves differ significantly from that obtained by Buratti and Dunbar (1991), one week before the observations of Luu and Jewitt. The Chiron field was calibrated using Landolt standards on Ut 15 Mar. 1991. A mean R-magnitude of 15.6 + or - 0.1 was found. Variability of 2060 Chiron was demonstrated over timescales of minutes, hours, and years. An intense campaign was urged to monitor the photometric behavior of Chiron throughout the 1990s.

CSI 2264: Characterizing Young Stars In NGC 2264 With Short-Duration Periodic Flux Dips in Their Light Curves

DTIC Science & Technology

2015-04-01

curve (it was not observed by CoRoT in 2008). We have subsequently obtained optical and IR spectra of it from SOAR (see Appendix) that indicate a spectral...CoRoT light curve. We also obtained a SOAR optical spectrum of Mon-1131. Based on measures of the depths of the TiO bands in that spectrum, we...scales in Table 4, one from Table 6 of Pecaut & Mamajek (2013; PM13), and one from Cohen & Kuhi ( 1979 ; CK79). For many of the stars, the calculation

On measuring the scattering coefficient in a nondiffuse sound field

NASA Astrophysics Data System (ADS)

Kanev, N. G.

2017-11-01

The laws of sound decay in a cubic room, one wall of which is absorbing and the other scattering, are obtained. It is shown that under certain conditions, sound decay in a room occurs nonexponentially and the shape of the decay curve depends on the scattering coefficient of the walls. This makes it possible to suggest a method for measuring the scattering coefficient by the analysis the decay curve when the walls have sound-scattering materials and structures. Expressions are obtained for approximating the measured decay curve, and the boundaries of the method's applicability are determined.

Modeling of light dynamic cone penetration test - Panda 3 ® in granular material by using 3D Discrete element method

NASA Astrophysics Data System (ADS)

Tran, Quoc Anh; Chevalier, Bastien; Benz, Miguel; Breul, Pierre; Gourvès, Roland

2017-06-01

The recent technological developments made on the light dynamic penetration test Panda 3 ® provide a dynamic load-penetration curve σp - sp for each impact. This curve is influenced by the mechanical and physical properties of the investigated granular media. In order to analyze and exploit the load-penetration curve, a numerical model of penetration test using 3D Discrete Element Method is proposed for reproducing tests in dynamic conditions in granular media. All parameters of impact used in this model have at first been calibrated by respecting mechanical and geometrical properties of the hammer and the rod. There is a good agreement between experimental results and the ones obtained from simulations in 2D or 3D. After creating a sample, we will simulate the Panda 3 ®. It is possible to measure directly the dynamic load-penetration curve occurring at the tip for each impact. Using the force and acceleration measured in the top part of the rod, it is possible to separate the incident and reflected waves and then calculate the tip's load-penetration curve. The load-penetration curve obtained is qualitatively similar with that obtained by experimental tests. In addition, the frequency analysis of the measured signals present also a good compliance with that measured in reality when the tip resistance is qualitatively similar.

Metal binding characterization and conformational studies using Raman microscopy of resin-bound poly(aspartic acid).

PubMed

Stair, Jacqueline L; Holcombe, James A

2007-03-01

The metal binding capacities, conditional stability constants, and secondary structure of immobilized polyaspartic acid (PLAsp) (n = 6, 20, and 30) on TentaGel resin were determined when binding Mg2+, Co2+, Cd2+, and Ni2+. Metal binding to the synthesized peptides was evaluated using breakthrough curves from a packed microcolumn and flame atomic absorption spectrophotometry (FAAS) detection. The metal capacities reached values of 590, 2160, and 3710 mumol of metal/g of resin for the 6-mer, 20-mer, and 30-mer, respectively, and this resulted in 2-3 residues per metal for all peptides and metals tested. Surprisingly, the concentrated environment of the resin along with the spatial distribution of attachment groups allowed for most residues to participate in metal binding regardless of the peptide length. Conditional stability constants calculated using single metal binding isotherms indicated that binding strength decreased as the chain length increased on the resin. Raman microscopy on single beads was used to determine PLAsp secondary structure, and all peptides were of a mixed conformation (i.e., beta-sheets, alpha-helices, random chain, etc.) during neutral conditioning and metal binding. Uniquely, the longer 20-mer and 30-mer peptides showed a distinct change from a mixed conformation to beta-sheets and alpha-helices during metal release with acid. This study confirms that metal release by longer immobilized peptides is often assisted by a conformational change, which easily spoils the binding cavity, while shorter peptides may release metal primarily by H+ displacement.

MRTD: man versus machine

NASA Astrophysics Data System (ADS)

van Rheenen, Arthur D.; Taule, Petter; Thomassen, Jan Brede; Madsen, Eirik Blix

2018-04-01

We present Minimum-Resolvable Temperature Difference (MRTD) curves obtained by letting an ensemble of observers judge how many of the six four-bar patterns they can "see" in a set of images taken with different bar-to-background contrasts. The same images are analyzed using elemental signal analysis algorithms and machine-analysis based MRTD curves are obtained. We show that by adjusting the minimum required signal-to-noise ratio the machine-based MRTDs are very similar to the ones obtained with the help of the human observers.

Enantioselective binding of L, D-phenylalanine to ct DNA

NASA Astrophysics Data System (ADS)

Zhang, Lijin; Xu, Jianhua; Huang, Yan; Min, Shungeng

2009-10-01

The enantioselective binding of L, D-phenylalanine to calf thymus DNA was studied by absorption, circular dichroism, fluorescence quenching, viscosity, salt effect and emission experiments. The results obtained from absorption, circular dichroism, fluorescence quenching and viscosity experiments excluded the intercalative binding and salt effect experiments did not support electrostatic binding. So the binding of L, D-phenylalanine to ct DNA should be groove binding. Furthermore, the emission spectra revealed that the binding is enantioselective.

Enantioselective binding of L,D-phenylalanine to ct DNA.

PubMed

Zhang, Lijin; Xu, Jianhua; Huang, Yan; Min, Shungeng

2009-10-15

The enantioselective binding of L,D-phenylalanine to calf thymus DNA was studied by absorption, circular dichroism, fluorescence quenching, viscosity, salt effect and emission experiments. The results obtained from absorption, circular dichroism, fluorescence quenching and viscosity experiments excluded the intercalative binding and salt effect experiments did not support electrostatic binding. So the binding of l,d-phenylalanine to ct DNA should be groove binding. Furthermore, the emission spectra revealed that the binding is enantioselective.

Analytic functions for potential energy curves, dipole moments, and transition dipole moments of LiRb molecule.

PubMed

You, Yang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang; Wang, Li-Zhi

2016-01-15

The analytic potential energy functions (APEFs) of the X(1)Σ(+), 2(1)Σ(+), a(3)Σ(+), and 2(3)Σ(+) states of the LiRb molecule are obtained using Morse long-range potential energy function with damping function and nonlinear least-squares method. These calculations were based on the potential energy curves (PECs) calculated using the multi-reference configuration interaction (MRCI) method. The reliability of the APEFs is confirmed using the curves of their first and second derivatives. By using the obtained APEFs, the rotational and vibrational energy levels of the states are determined by solving the Schrödinger equation of nuclear movement. The spectroscopic parameters, which are deduced using Dunham expansion, and the obtained rotational and vibrational levels are compared with the reported theoretical and experimental values. The correlation effect of the electrons of the inner shell remarkably improves the results compared with the experimental spectroscopic parameters. For the first time, the APEFs for the dipole moments and transition dipole moments of the states have been determined based on the curves obtained from the MRCI calculations. Copyright © 2015 Elsevier B.V. All rights reserved.

A Comparative Study of Electric Load Curve Changes in an Urban Low-Voltage Substation in Spain during the Economic Crisis (2008–2013)

PubMed Central

Lara-Santillán, Pedro M.; Mendoza-Villena, Montserrat; Fernández-Jiménez, L. Alfredo; Mañana-Canteli, Mario

2014-01-01

This paper presents a comparative study of the electricity consumption (EC) in an urban low-voltage substation before and during the economic crisis (2008–2013). This low-voltage substation supplies electric power to near 400 users. The EC was measured for an 11-year period (2002–2012) with a sampling time of 1 minute. The study described in the paper consists of detecting the changes produced in the load curves of this substation along the time due to changes in the behaviour of consumers. The EC was compared using representative curves per time period (precrisis and crisis). These representative curves were obtained after a computational process, which was based on a search for days with similar curves to the curve of a determined (base) date. This similitude was assessed by the proximity on the calendar, day of the week, daylight time, and outdoor temperature. The last selection parameter was the error between the nearest neighbour curves and the base date curve. The obtained representative curves were linearized to determine changes in their structure (maximum and minimum consumption values, duration of the daily time slot, etc.). The results primarily indicate an increase in the EC in the night slot during the summer months in the crisis period. PMID:24895677

Detection of Naja atra Cardiotoxin Using Adenosine-Based Molecular Beacon.

PubMed

Shi, Yi-Jun; Chen, Ying-Jung; Hu, Wan-Ping; Chang, Long-Sen

2017-01-07

This study presents an adenosine (A)-based molecular beacon (MB) for selective detection of Naja atra cardiotoxin (CTX) that functions by utilizing the competitive binding between CTX and the poly(A) stem of MB to coralyne. The 5'- and 3'-end of MB were labeled with a reporter fluorophore and a non-fluorescent quencher, respectively. Coralyne induced formation of the stem-loop MB structure through A₂-coralyne-A₂ coordination, causing fluorescence signal turn-off due to fluorescence resonance energy transfer between the fluorophore and quencher. CTX3 could bind to coralyne. Moreover, CTX3 alone induced the folding of MB structure and quenching of MB fluorescence. Unlike that of snake venom α-neurotoxins, the fluorescence signal of coralyne-MB complexes produced a bell-shaped concentration-dependent curve in the presence of CTX3 and CTX isotoxins; a turn-on fluorescence signal was noted when CTX concentration was ≤80 nM, while a turn-off fluorescence signal was noted with a further increase in toxin concentrations. The fluorescence signal of coralyne-MB complexes yielded a bell-shaped curve in response to varying concentrations of N. atra crude venom but not those of Bungarus multicinctus and Protobothrops mucrosquamatus venoms. Moreover, N. nigricollis venom also functioned as N. atra venom to yield a bell-shaped concentration-dependent curve of MB fluorescence signal, again supporting that the hairpin-shaped MB could detect crude venoms containing CTXs. Taken together, our data validate that a platform composed of coralyne-induced stem-loop MB structure selectively detects CTXs.

Gene Scanning of an Internalin B Gene Fragment Using High-Resolution Melting Curve Analysis as a Tool for Rapid Typing of Listeria monocytogenes

PubMed Central

Pietzka, Ariane T.; Stöger, Anna; Huhulescu, Steliana; Allerberger, Franz; Ruppitsch, Werner

2011-01-01

The ability to accurately track Listeria monocytogenes strains involved in outbreaks is essential for control and prevention of listeriosis. Because current typing techniques are time-consuming, cost-intensive, technically demanding, and difficult to standardize, we developed a rapid and cost-effective method for typing of L. monocytogenes. In all, 172 clinical L. monocytogenes isolates and 20 isolates from culture collections were typed by high-resolution melting (HRM) curve analysis of a specific locus of the internalin B gene (inlB). All obtained HRM curve profiles were verified by sequence analysis. The 192 tested L. monocytogenes isolates yielded 15 specific HRM curve profiles. Sequence analysis revealed that these 15 HRM curve profiles correspond to 18 distinct inlB sequence types. The HRM curve profiles obtained correlated with the five phylogenetic groups I.1, I.2, II.1, II.2, and III. Thus, HRM curve analysis constitutes an inexpensive assay and represents an improvement in typing relative to classical serotyping or multiplex PCR typing protocols. This method provides a rapid and powerful screening tool for simultaneous preliminary typing of up to 384 samples in approximately 2 hours. PMID:21227395

A reusable evanescent wave immunosensor for highly sensitive detection of bisphenol A in water samples

NASA Astrophysics Data System (ADS)

Xiao-Hong, Zhou; Lan-Hua, Liu; Wei-Qi, Xu; Bao-Dong, Song; Jian-Wu, Sheng; Miao, He; Han-Chang, Shi

2014-04-01

This paper proposed a compact and portable planar waveguide evanescent wave immunosensor (EWI) for highly sensitive detection of BPA. The incident light is coupled into the planar waveguide chip via a beveled angle through undergoing total internal reflection, where the evanescent wave field forms and excites the binding fluorophore-tagged antibodies on the chip surface. Typical calibration curves obtained for BPA has detection limits of 0.03 μg/L. Linear response for BPA ranged from 0.124 μg/L-9.60 μg/L with 50% inhibition concentration for BPA of 1.09 +/- 0.25 μg/L. The regeneration of the planar optical waveguide chip allows the performance of more than 300 assay cycles within an analysis time of about 20 min for each assay cycle. By application of effective pretreatment procedure, the recoveries of BPA in real water samples gave values from 88.3% +/- 8.5% to 103.7% +/- 3.5%, confirming its application potential in the measurement of BPA in reality.

Human antibody fragments specific for the epidermal growth factor receptor selected from large non-immunised phage display libraries.

PubMed

Souriau, Christelle; Rothacker, Julie; Hoogenboom, Hennie R; Nice, Edouard

2004-09-01

Antibodies to EGFR have been shown to display anti-tumour effects mediated in part by inhibition of cellular proliferation and angiogenesis, and by enhancement of apoptosis. Humanised antibodies are preferred for clinical use to reduce complications with HAMA and HAHA responses frequently seen with murine and chimaeric antibodies. We have used depletion and subtractive selection strategies on cells expressing the EGFR to sample two large antibody fragment phage display libraries for the presence of human antibodies which are specific for the EGFR. Four Fab fragments and six scFv fragments were identified, with affinities of up to 2.2nM as determined by BIAcore analysis using global fitting of the binding curves to obtain the individual rate constants (ka and kd). This overall approach offers a generic screening method for the identification of growth factor specific antibodies and antibody fragments from large expression libraries and has potential for the rapid development of new therapeutic and diagnostic reagents.

Diethylaminoethyl (DEAE) binding fraction from Taenia solium metacestode improves the neurocysticercosis serodiagnosis.

PubMed

Ribeiro, Vanessa da S; Nunes, Daniela da S; Gonzaga, Henrique T; da Cunha-Junior, Jair P; Costa-Cruz, Julia M

2014-07-01

Neurocysticercosis (NC) is one of the most important diseases caused by parasites affecting the central nervous system. We fractionated by ion-exchange chromatography using diethylaminoethyl (DEAE)-sepharose resin the total saline extract (S) from Taenia solium metacestodes and evaluated obtained fractions (DEAE S1 and DEAE S2) by enzyme-linked immunosorbent assay (ELISA, n = 123) and immunoblotting (IB, n = 22) to detect human NC in serum. Diagnostic parameters were established by ROC and TG ROC curves for ELISA tests. IB was qualitatively analyzed. S and DEAE S1 presented sensitivity of 87. 5% and DEAE S2 90%. The best specificity was observed for DEAE S2 (90.4%). In IB, using DEAE S2 samples from NC patients presented bands of 20-25, 43-45, 55-50, 60-66, 82, 89, and 140 kDa. The great diagnostic parameters reached by DEAE S2 suggest the potential applicability of this fraction in NC immunodiagnosis.

Experimental study of a generic high-speed civil transport

NASA Technical Reports Server (NTRS)

Belton, Pamela S.; Campbell, Richard L.

1992-01-01

An experimental study of generic high-speed civil transport was conducted in the NASA Langley 8-ft Transonic Pressure Tunnel. The data base was obtained for the purpose of assessing the accuracy of various levels of computational analysis. Two models differing only in wingtip geometry were tested with and without flow-through nacelles. The baseline model has a curved or crescent wingtip shape, while the second model has a more conventional straight wingtip shape. The study was conducted at Mach numbers from 0.30 to 1.19. Force data were obtained on both the straight wingtip model and the curved wingtip model. Only the curved wingtip model was instrumented for measuring pressures. Selected longitudinal, lateral, and directional data are presented for both models. Selected pressure distributions for the curved wingtip model are also presented.

Fast gradient HPLC method to determine compounds binding to human serum albumin. Relationships with octanol/water and immobilized artificial membrane lipophilicity.

PubMed

Valko, Klara; Nunhuck, Shenaz; Bevan, Chris; Abraham, Michael H; Reynolds, Derek P

2003-11-01

A fast gradient HPLC method (cycle time 15 min) has been developed to determine Human Serum Albumin (HSA) binding of discovery compounds using chemically bonded protein stationary phases. The HSA binding values were derived from the gradient retention times that were converted to the logarithm of the equilibrium constants (logK HSA) using data from a calibration set of molecules. The method has been validated using literature plasma protein binding data of 68 known drug molecules. The method is fully automated, and has been used for lead optimization in more than 20 company projects. The HSA binding data obtained for more than 4000 compounds were suitable to set up global and project specific quantitative structure binding relationships that helped compound design in early drug discovery. The obtained HSA binding of known drug molecules were compared to the Immobilized Artificial Membrane binding data (CHI IAM) obtained by our previously described HPLC-based method. The solvation equation approach has been used to characterize the normal binding ability of HSA, and this relationship shows that compound lipophilicity is a significant factor. It was found that the selectivity of the "baseline" lipophilicity governing HSA binding, membrane interaction, and octanol/water partition are very similar. However, the effect of the presence of positive or negative charges have very different effects. It was found that negatively charged compounds bind more strongly to HSA than it would be expected from the lipophilicity of the ionized species at pH 7.4. Several compounds showed stronger HSA binding than can be expected from their lipophilicity alone, and comparison between predicted and experimental binding affinity allows the identification of compounds that have good complementarities with any of the known binding sites. Copyright 2003 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 92:2236-2248, 2003

UV Thermal Melting Curves of tRNA[superscript Phe] in the Presence of Ligands

ERIC Educational Resources Information Center

Kirk, Sarah R.; Silverstein, Todd P.; McFarlane Holman, Karen L.

2008-01-01

This laboratory project is one component of a semester-long advanced biochemistry laboratory course that uses several complementary techniques to study tRNA[superscript Phe] conformational changes induced by ligand binding. In this article we describe a set of experiments in which the thermal unfolding of tRNA[superscript Phe] is studied with…

Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process

PubMed Central

Wickstrom, Lauren; He, Peng; Gallicchio, Emilio; Levy, Ronald M.

2013-01-01

Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies. PMID:25147485

The Welfare Effects of Monopoly versus Competition: A Clarification of Textbook Presentations.

ERIC Educational Resources Information Center

Lamdin, Douglas J.

1992-01-01

Addresses effects of monopoly and competition on societal welfare. Discusses inadequacy of economics textbooks. Concludes that most texts fail to explain the shape of monopolists' underlying cost curves. Argues that the monopolist's long run marginal cost curve cannot be obtained by horizontal summation of the long run marginal cost curves of…

Extracting information from S-curves of language change

PubMed Central

Ghanbarnejad, Fakhteh; Gerlach, Martin; Miotto, José M.; Altmann, Eduardo G.

2014-01-01

It is well accepted that adoption of innovations are described by S-curves (slow start, accelerating period and slow end). In this paper, we analyse how much information on the dynamics of innovation spreading can be obtained from a quantitative description of S-curves. We focus on the adoption of linguistic innovations for which detailed databases of written texts from the last 200 years allow for an unprecedented statistical precision. Combining data analysis with simulations of simple models (e.g. the Bass dynamics on complex networks), we identify signatures of endogenous and exogenous factors in the S-curves of adoption. We propose a measure to quantify the strength of these factors and three different methods to estimate it from S-curves. We obtain cases in which the exogenous factors are dominant (in the adoption of German orthographic reforms and of one irregular verb) and cases in which endogenous factors are dominant (in the adoption of conventions for romanization of Russian names and in the regularization of most studied verbs). These results show that the shape of S-curve is not universal and contains information on the adoption mechanism. PMID:25339692

Modeling of a Robust Confidence Band for the Power Curve of a Wind Turbine.

PubMed

Hernandez, Wilmar; Méndez, Alfredo; Maldonado-Correa, Jorge L; Balleteros, Francisco

2016-12-07

Having an accurate model of the power curve of a wind turbine allows us to better monitor its operation and planning of storage capacity. Since wind speed and direction is of a highly stochastic nature, the forecasting of the power generated by the wind turbine is of the same nature as well. In this paper, a method for obtaining a robust confidence band containing the power curve of a wind turbine under test conditions is presented. Here, the confidence band is bound by two curves which are estimated using parametric statistical inference techniques. However, the observations that are used for carrying out the statistical analysis are obtained by using the binning method, and in each bin, the outliers are eliminated by using a censorship process based on robust statistical techniques. Then, the observations that are not outliers are divided into observation sets. Finally, both the power curve of the wind turbine and the two curves that define the robust confidence band are estimated using each of the previously mentioned observation sets.

Modeling of a Robust Confidence Band for the Power Curve of a Wind Turbine

PubMed Central

Hernandez, Wilmar; Méndez, Alfredo; Maldonado-Correa, Jorge L.; Balleteros, Francisco

2016-01-01

Having an accurate model of the power curve of a wind turbine allows us to better monitor its operation and planning of storage capacity. Since wind speed and direction is of a highly stochastic nature, the forecasting of the power generated by the wind turbine is of the same nature as well. In this paper, a method for obtaining a robust confidence band containing the power curve of a wind turbine under test conditions is presented. Here, the confidence band is bound by two curves which are estimated using parametric statistical inference techniques. However, the observations that are used for carrying out the statistical analysis are obtained by using the binning method, and in each bin, the outliers are eliminated by using a censorship process based on robust statistical techniques. Then, the observations that are not outliers are divided into observation sets. Finally, both the power curve of the wind turbine and the two curves that define the robust confidence band are estimated using each of the previously mentioned observation sets. PMID:27941604

Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

PubMed

Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

2014-12-01

YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. © 2014 FEBS.

Kif2C Minimal Functional Domain Has Unusual Nucleotide Binding Properties That Are Adapted to Microtubule Depolymerization*

PubMed Central

Wang, Weiyi; Jiang, Qiyang; Argentini, Manuela; Cornu, David; Gigant, Benoît; Knossow, Marcel; Wang, Chunguang

2012-01-01

The kinesin-13 Kif2C hydrolyzes ATP and uses the energy released to disassemble microtubules. The mechanism by which this is achieved remains elusive. Here we show that Kif2C-(sN+M), a monomeric construct consisting of the motor domain with the proximal part of the N-terminal Neck extension but devoid of its more distal, unstructured, and highly basic part, has a robust depolymerase activity. When detached from microtubules, the Kif2C-(sN+M) nucleotide-binding site is occupied by ATP at physiological concentrations of adenine nucleotides. As a consequence, Kif2C-(sN+M) starts its interaction with microtubules in that state, which differentiates kinesin-13s from motile kinesins. Moreover, in this ATP-bound conformational state, Kif2C-(sN+M) has a higher affinity for soluble tubulin compared with microtubules. We propose a mechanism in which, in the first step, the specificity of ATP-bound Kif2C for soluble tubulin causes it to stabilize a curved conformation of tubulin heterodimers at the ends of microtubules. Data from an ATPase-deficient Kif2C mutant suggest that, then, ATP hydrolysis precedes and is required for tubulin release to take place. Finally, comparison with Kif2C-Motor indicates that the binding specificity for curved tubulin and, accordingly, the microtubule depolymerase activity are conferred to the motor domain by its N-terminal Neck extension. PMID:22403406

Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease

PubMed Central

Altman, Michael D.; Nalivaika, Ellen A.; Prabu-Jeyabalan, Moses; Schiffer, Celia A.; Tidor, Bruce

2009-01-01

Drug resistance in HIV-1 protease, a barrier to effective treatment, is generally caused by mutations in the enzyme that disrupt inhibitor binding but still allow for substrate processing. Structural studies with mutant, inactive enzyme, have provided detailed information regarding how the substrates bind to the protease yet avoid resistance mutations; insights obtained inform the development of next generation therapeutics. Although structures have been obtained of complexes between substrate peptide and inactivated (D25N) protease, thermodynamic studies of peptide binding have been challenging due to low affinity. Peptides that bind tighter to the inactivated protease than the natural substrates would be valuable for thermodynamic studies as well as to explore whether the structural envelope observed for substrate peptides is a function of weak binding. Here, two computational methods — namely, charge optimization and protein design — were applied to identify peptide sequences predicted to have higher binding affinity to the inactivated protease, starting from an RT–RH derived substrate peptide. Of the candidate designed peptides, three were tested for binding with isothermal titration calorimetry, with one, containing a single threonine to valine substitution, measured to have more than a ten-fold improvement over the tightest binding natural substrate. Crystal structures were also obtained for the same three designed peptide complexes; they show good agreement with computational prediction. Thermodynamic studies show that binding is entropically driven, more so for designed affinity enhanced variants than for the starting substrate. Structural studies show strong similarities between natural and tighter-binding designed peptide complexes, which may have implications in understanding the molecular mechanisms of drug resistance in HIV-1 protease. PMID:17729291

Adapting Shape Parameters for Cubic Bezier Curves

NASA Technical Reports Server (NTRS)

Isacoff, D.; Bailey, M. J.

1985-01-01

Bezier curves are an established tool in Computer Aided Geometric Design. One of the drawbacks of the Bezier method is that the curves often bear little resemblance to their control polygons. As a result, it becomes increasingly difficult to obtain anything but a rough outline of the desired shape. One possible solution is tomanipulate the curve itself instead of the control polygon. The standard cubic Bezier curve form has introduced into it two shape parameters, gamma 1 and 2. These parameters give the user the ability to manipulate the curve while the control polygon retains its original form, thereby providing a more intuitive feel for the necessary changes to the curve in order to achieve the desired shape.

21 CFR 862.1685 - Thyroxine-binding globulin test system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... globulin test system is a device intended to measure thyroxine (thyroid)-binding globulin (TBG), a plasma protein which binds thyroxine, in serum and plasma. Measurements obtained by this device are used in the...

21 CFR 862.1685 - Thyroxine-binding globulin test system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... globulin test system is a device intended to measure thyroxine (thyroid)-binding globulin (TBG), a plasma protein which binds thyroxine, in serum and plasma. Measurements obtained by this device are used in the...

21 CFR 862.1685 - Thyroxine-binding globulin test system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... globulin test system is a device intended to measure thyroxine (thyroid)-binding globulin (TBG), a plasma protein which binds thyroxine, in serum and plasma. Measurements obtained by this device are used in the...

21 CFR 862.1685 - Thyroxine-binding globulin test system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... globulin test system is a device intended to measure thyroxine (thyroid)-binding globulin (TBG), a plasma protein which binds thyroxine, in serum and plasma. Measurements obtained by this device are used in the...

21 CFR 862.1685 - Thyroxine-binding globulin test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... globulin test system is a device intended to measure thyroxine (thyroid)-binding globulin (TBG), a plasma protein which binds thyroxine, in serum and plasma. Measurements obtained by this device are used in the...

Regional Myocardial Blood Volume and Flow: First-Pass MR Imaging with Polylysine-Gd-DTPA

PubMed Central

Wilke, Norbert; Kroll, Keith; Merkle, Hellmut; Wang, Ying; Ishibashi, Yukata; Xu, Ya; Zhang, Jiani; Jerosch-Herold, Michael; Mühler, Andreas; Stillman, Arthur E.; Bassingthwaighte, James B.; Bache, Robert; Ugurbil, Kamil

2010-01-01

The authors investigated the utility of an intravascular magnetic resonance (MR) contrast agent, poly-L-lysine-gadolinium diethylenetriaminepentaacetic acid (DTPA), for differentiating acutely ischemic from normally perfused myocardium with first-pass MR imaging. Hypoperfused regions, identified with microspheres, on the first-pass images displayed significantly decreased signal intensities compared with normally perfused myocardium (P < .0007). Estimates of regional myocardial blood content, obtained by measuring the ratio of areas under the signal intensity-versus-time curves in tissue regions and the left ventricular chamber, averaged 0.12 mL/g ± 0.04 (n = 35), compared with a value of 0.11 mL/g ± 0.05 measured with radiolabeled albumin in the same tissue regions. To obtain MR estimates of regional myocardial blood flow, in situ calibration curves were used to transform first-pass intensity-time curves into content-time curves for analysis with a multiple-pathway, axially distributed model. Flow estimates, obtained by automated parameter optimization, averaged 1.2 mL/min/g ± 0.5 [n = 29), compared with 1.3 mL/min/g ± 0.3 obtained with tracer microspheres in the same tissue specimens at the same time. The results represent a combination of T1-weighted first-pass imaging, intravascular relaxation agents, and a spatially distributed perfusion model to obtain absolute regional myocardial blood flow and volume. PMID:7766986

Stimulation of iodine organification in porcine thyroid cells by thyroid stimulators.

PubMed

Ginsberg, J; Shewring, G; Howells, R; Smith, B R; Hall, R

Several Graves' sera were simultaneously assessed in a bioassay based on the ability of porcine thyroid cells to organify 125I and in a radioreceptor assay for TSH receptor binding activity. Both assay systems were sensitive to 1 mcU/ml (final concentration) of unlabelled bovine TSH. Six Graves' sera were studied in detail over a wide (0-1.0 mcl sera) dose response range in repeat determinations. Two sera exhibited parallel binding and stimulating. However, two sera revealed significant inhibition of 125I-TSH binding prior to the demonstration of stimulation and the other two sera showed stimulatory capabilities before significant binding was evident. IgG was prepared from one serum by ammonium sulphate precipitation and chromatography on Sepharose 6B and then subjected to preparative isoelectric focusing. The isoelectric distribution of the two activities were found to be identical with major peaks of activity at pl=9.5 and pl=8.5. In summary: 1) each Graves' sera exhibits different dose-response curves with respect to binding and stimulation, 2) at certain concentrations of sera, only binding or stimulation were evident, 3) neither assay was consistently more sensitive for the presence of Graves' immunoglobulins, 4) for one Graves' sera, binding and stimulation could not be separated by isoelectric focusing. These studies would suggest each Graves' immunoglobulin has inherently different characteristics in its interaction with the TSH receptor.

Experimental characterisation and modelling of deformation- induced microstructure in an A6061 aluminium alloy

NASA Astrophysics Data System (ADS)

Kreyca, J. F.; Falahati, A.; Kozeschnik, E.

2016-03-01

For industry, the mechanical properties of a material in form of flow curves are essential input data for finite element simulations. Current practice is to obtain flow curves experimentally and to apply fitting procedures to obtain constitutive equations that describe the material response to external loading as a function of temperature and strain rate. Unfortunately, the experimental procedure for characterizing flow curves is complex and expensive, which is why the prediction of flow-curves by computer modelling becomes increasingly important. In the present work, we introduce a state parameter based model that is capable of predicting the flow curves of an A6061 aluminium alloy in different heat-treatment conditions. The model is implemented in the thermo-kinetic software package MatCalc and takes into account precipitation kinetics, subgrain formation, dynamic recovery by spontaneous annihilation and dislocation climb. To validate the simulation results, a series of compression tests is performed on the thermo-mechanical simulator Gleeble 1500.

Resistance Curves in the Tensile and Compressive Longitudinal Failure of Composites

NASA Technical Reports Server (NTRS)

Camanho, Pedro P.; Catalanotti, Giuseppe; Davila, Carlos G.; Lopes, Claudio S.; Bessa, Miguel A.; Xavier, Jose C.

2010-01-01

This paper presents a new methodology to measure the crack resistance curves associated with fiber-dominated failure modes in polymer-matrix composites. These crack resistance curves not only characterize the fracture toughness of the material, but are also the basis for the identification of the parameters of the softening laws used in the analytical and numerical simulation of fracture in composite materials. The method proposed is based on the identification of the crack tip location by the use of Digital Image Correlation and the calculation of the J-integral directly from the test data using a simple expression derived for cross-ply composite laminates. It is shown that the results obtained using the proposed methodology yield crack resistance curves similar to those obtained using FEM-based methods in compact tension carbon-epoxy specimens. However, it is also shown that the Digital Image Correlation based technique can be used to extract crack resistance curves in compact compression tests for which FEM-based techniques are inadequate.

Photometric followup investigations on LAMOST survey target Ly And

NASA Astrophysics Data System (ADS)

Lu, Hong-peng; Zhang, Li-yun; Han, Xianming L.; Pi, Qing-feng; Wang, Dai-mei

2017-02-01

We present a low-dispersion spectrum and two sets of CCD photometric light curves of the eclipsing binary LY And for the first time. The spectrum of LY And was classified as G2. We derived an updated ephemeris based on all previously available and our newly acquired minimum light times. Our analyses of LY And light curve minimum times reveals that the differences between calculated and observed minimum times for LY And can be represented by an upward parabolic curve, which means its orbital period is increasing with a rate of 1.88 (± 0.13) × 10-7 days/year. This increase in orbital period may be interpreted as mass transfer from the primary component to the secondary component, with a rate of dM1/dt = -4.54 × 10-8M⊙/year. By analyzing our CCD photometric light curves obtained in 2015, we obtained its photometric solution with the Wilson-Devinney program. This photometric solution also fits very well our light curves obtained in 2014. Our photometric solution shows that LY And is a contact eclipsing binary and its contact factor is f = (17.8 ± 1.9)%. Furthermore, both our spectroscopic and photometric data show no obvious chromospheric activity of LY And.

Further Results on the Production of Neutral Mesons by Photons

DOE R&D Accomplishments Database

Panofsky, W. K. H.; Steinberger, J.; Steller, J.

1951-10-01

Further measurements have been made on the photoproduction of neutral mesons using the gamma-gamma coincidence technique. New data have been obtained on the gamma-gamma correlation curves in beryllium. The angular distribution of the photo mesons in Be has been determined and found to be strongly peaked forward. The dependence on the atomic number A of production has been found to obey an A{sup 2/3} law. Some data obtained for production in hydrogen show that the pi-zero and pi-plus production cross sections are comparable and that the pi-zero excitation curve starts more slowly from threshold than does the pi-plus photo excitation curve.

A new graphic plot analysis for determination of neuroreceptor binding in positron emission tomography studies.

PubMed

Ito, Hiroshi; Yokoi, Takashi; Ikoma, Yoko; Shidahara, Miho; Seki, Chie; Naganawa, Mika; Takahashi, Hidehiko; Takano, Harumasa; Kimura, Yuichi; Ichise, Masanori; Suhara, Tetsuya

2010-01-01

In positron emission tomography (PET) studies with radioligands for neuroreceptors, tracer kinetics have been described by the standard two-tissue compartment model that includes the compartments of nondisplaceable binding and specific binding to receptors. In the present study, we have developed a new graphic plot analysis to determine the total distribution volume (V(T)) and nondisplaceable distribution volume (V(ND)) independently, and therefore the binding potential (BP(ND)). In this plot, Y(t) is the ratio of brain tissue activity to time-integrated arterial input function, and X(t) is the ratio of time-integrated brain tissue activity to time-integrated arterial input function. The x-intercept of linear regression of the plots for early phase represents V(ND), and the x-intercept of linear regression of the plots for delayed phase after the equilibrium time represents V(T). BP(ND) can be calculated by BP(ND)=V(T)/V(ND)-1. Dynamic PET scanning with measurement of arterial input function was performed on six healthy men after intravenous rapid bolus injection of [(11)C]FLB457. The plot yielded a curve in regions with specific binding while it yielded a straight line through all plot data in regions with no specific binding. V(ND), V(T), and BP(ND) values calculated by the present method were in good agreement with those by conventional non-linear least-squares fitting procedure. This method can be used to distinguish graphically whether the radioligand binding includes specific binding or not.

Peculiarities of binding composition production in vortex jet mill

NASA Astrophysics Data System (ADS)

Zagorodnyuk, L. Kh; Lesovik, V. S.; Sumskoy, D. A.; Elistratkin, M. Yu; Makhortov, D. S.

2018-03-01

The article investigates the disintegration of perlite production waste in a vortex jet mill; the regularities of milling were established. Binding compositions were obtained at different ratios of cement vs. perlite sand production waste in the vortex jet mill in various milling regimes. The peculiarities of milling processes were studied, and technological and physicomechanical properties of the binding compositions were determined as well. The microstructure of the cement stones made of activated Portland cement and binding compositions in the vortex jet mill was elucidated by electron microscopy. The open pores of the cement-binding compositions prepared using perlite fillers were found to be filled by newgrowths at different stages of collective growth. The microstructure of the binding compositions is dense due to rationally proportioned composition, effective mineral filler— perlite waste — that creates additional substrates for internal composite microstructure formation, mechanochemical activation of raw mixture, which allows obtaining composites with required properties.

Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature.

PubMed

Takemura, Kazuhiro; Hanawa-Suetsugu, Kyoko; Suetsugu, Shiro; Kitao, Akio

2017-07-28

The BAR domain superfamily proteins sense or induce curvature in membranes. The inverse-BAR domain (I-BAR) is a BAR domain that forms a straight "zeppelin-shaped" dimer. The mechanisms by which IRSp53 I-BAR binds to and deforms a lipid membrane are investigated here by all-atom molecular dynamics simulation (MD), binding energy analysis, and the effects of mutation experiments on filopodia on HeLa cells. I-BAR adopts a curved structure when crystallized, but adopts a flatter shape in MD. The binding of I-BAR to membrane was stabilized by ~30 salt bridges, consistent with experiments showing that point mutations of the interface residues have little effect on the binding affinity whereas multiple mutations have considerable effect. Salt bridge formation increases the local density of lipids and deforms the membrane into a concave shape. In addition, the point mutations that break key intra-molecular salt bridges within I-BAR reduce the binding affinity; this was confirmed by expressing these mutants in HeLa cells and observing their effects. The results indicate that the stiffness of I-BAR is important for membrane deformation, although I-BAR does not act as a completely rigid template.

Experimental study of a generic high-speed civil transport: Tabulated data

NASA Technical Reports Server (NTRS)

Belton, Pamela S.; Campbell, Richard L.

1992-01-01

An experimental study of a generic high-speed civil transport was conducted in LaRC's 8-Foot Transonic Pressure Tunnel. The data base was obtained for the purpose of assessing the accuracy of various levels of computational analysis. Two models differing only in wing tip geometry were tested with and without flow-through nacelles. The baseline model has a curved or crescent wing tip shape while the second model has a more conventional straight wing tip shape. The study was conducted at Mach numbers from 0.30-1.19. Force data were obtained on both the straight and curved wing tip models. Only the curved wing tip model was instrumented for measuring pressures. Longitudinal and lateral-directional aerodynamic data are presented without analysis in tabulated form. Pressure coefficients for the curved wing tip model are also presented in tabulated form.

Application of Curved MPR Algorithm to High Resolution 3 Dimensional T2 Weighted CISS Images for Virtual Uncoiling of Membranous Cochlea as an Aid for Cochlear Morphometry.

PubMed

Kumar, Joish Upendra; Kavitha, Y

2017-02-01

With the use of various surgical techniques, types of implants, the preoperative assessment of cochlear dimensions is becoming increasingly relevant prior to cochlear implantation. High resolution CISS protocol MRI gives a better assessment of membranous cochlea, cochlear nerve, and membranous labyrinth. Curved Multiplanar Reconstruction (MPR) algorithm provides better images that can be used for measuring dimensions of membranous cochlea. To ascertain the value of curved multiplanar reconstruction algorithm in high resolution 3-Dimensional T2 Weighted Gradient Echo Constructive Interference Steady State (3D T2W GRE CISS) imaging for accurate morphometry of membranous cochlea. Fourteen children underwent MRI for inner ear assessment. High resolution 3D T2W GRE CISS sequence was used to obtain images of cochlea. Curved MPR reconstruction algorithm was used to virtually uncoil the membranous cochlea on the volume images and cochlear measurements were done. Virtually uncoiled images of membranous cochlea of appropriate resolution were obtained from the volume data obtained from the high resolution 3D T2W GRE CISS images, after using curved MPR reconstruction algorithm mean membranous cochlear length in the children was 27.52 mm. Maximum apical turn diameter of membranous cochlea was 1.13 mm, mid turn diameter was 1.38 mm, basal turn diameter was 1.81 mm. Curved MPR reconstruction algorithm applied to CISS protocol images facilitates in getting appropriate quality images of membranous cochlea for accurate measurements.

On the analytical determination of relaxation modulus of viscoelastic materials by Prony's interpolation method

NASA Technical Reports Server (NTRS)

Rodriguez, Pedro I.

1986-01-01

A computer implementation to Prony's curve fitting by exponential functions is presented. The method, although more than one hundred years old, has not been utilized to its fullest capabilities due to the restriction that the time range must be given in equal increments in order to obtain the best curve fit for a given set of data. The procedure used in this paper utilizes the 3-dimensional capabilities of the Interactive Graphics Design System (I.G.D.S.) in order to obtain the equal time increments. The resultant information is then input into a computer program that solves directly for the exponential constants yielding the best curve fit. Once the exponential constants are known, a simple least squares solution can be applied to obtain the final form of the equation.

Detection and quantification of a toxic salt substitute (LiCl) by using laser induced breakdown spectroscopy (LIBS).

PubMed

Sezer, Banu; Velioglu, Hasan Murat; Bilge, Gonca; Berkkan, Aysel; Ozdinc, Nese; Tamer, Ugur; Boyaci, Ismail Hakkı

2018-01-01

The use of Li salts in foods has been prohibited due to their negative effects on central nervous system; however, they might still be used especially in meat products as Na substitutes. Lithium can be toxic and even lethal at higher concentrations and it is not approved in foods. The present study focuses on Li analysis in meatballs by using laser induced breakdown spectroscopy (LIBS). Meatball samples were analyzed using LIBS and flame atomic absorption spectroscopy. Calibration curves were obtained by utilizing Li emission lines at 610nm and 670nm for univariate calibration. The results showed that Li calibration curve at 670nm provided successful determination of Li with 0.965 of R 2 and 4.64ppm of limit of detection (LOD) value. While Li Calibration curve obtained using emission line at 610nm generated R 2 of 0.991 and LOD of 22.6ppm, calibration curve obtained at 670nm below 1300ppm generated R 2 of 0.965 and LOD of 4.64ppm. Copyright © 2017. Published by Elsevier Ltd.

Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation

PubMed Central

Das, Amit; Chakrabarti, J.; Ghosh, Mahua

2013-01-01

We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically. PMID:23528087

Evaluation of the Efficiency of the Reticulocyte Hemoglobin Content on Diagnosis for Iron Deficiency Anemia in Chinese Adults.

PubMed

Cai, Jie; Wu, Meng; Ren, Jie; Du, Yali; Long, Zhangbiao; Li, Guoxun; Han, Bing; Yang, Lichen

2017-05-02

Our aim was to evaluate the cut-off value and efficiency of using reticulocyte hemoglobin content as a marker to diagnose iron deficiency anemia in Chinese adults. 140 adults who needed bone marrow aspiration for diagnosis at the hematology department of the Peking Union Medical College Hospital were enrolled according to the inclusive and exclusive criteria. Venous blood samples were collected to detect complete blood count, including hemoglobin, reticulocyte hemoglobin content, hematocrit, mean cellular volume, corpuscular hemoglobin concentration, hemoglobin content, free erythrocyte protoporphyrin; iron indexes of serum ferritin, serum transferrin receptor, and unsaturated iron-binding capacity; and inflammation markers of C-reactive protein and α-acid glycoprotein. Bone marrow samples were obtained for the bone marrow iron staining, which was used as the standard for the evaluation of iron status in this study. Subjects were divided into three groups according to hemoglobin levels and bone marrow iron staining results: the IDA (iron deficiency anemia) group, the NIDA (non-iron deficiency anemia) group, and the control group. The differences of the above-mentioned indexes were compared among the three groups and the effect of inflammation was also considered. The cut-off value of reticulocyte hemoglobin content was determined by receiver operation curves. The IDA group ( n = 56) had significantly lower reticulocyte hemoglobin content, mean cellular volume, corpuscular hemoglobin concentration, hemoglobin content, and serum ferritin; and higher free erythrocyte protoporphyrin, unsaturated iron-binding capacity, and serum transferrin receptor ( p < 0.05) compared with the NIDA group ( n = 38) and control group ( n = 46). Hematocrit, serum ferritin, and unsaturated iron-binding capacity were significantly affected by inflammation while reticulocyte hemoglobin content and other parameters were not. The cut-off value of reticulocyte hemoglobin content for diagnosing iron deficiency anemia was 27.2 pg, with a sensitivity of 87.5% and a specificity of 92.9%. The cut-off values for mean cellular volume, serum ferritin, and serum transferrin receptor were 76.6, 12.9, and 4.89 mg/L, respectively. Reticulocyte hemoglobin content had the largest area under the curve of 0.929, while those for mean cellular volume, serum ferritin, serum transferrin receptor were 0.922, 0.887, and 0.900, respectively. Reticulocyte hemoglobin content has a high sensitivity and specificity in the diagnosis of iron deficiency anemia, and its comprehensive diagnostic efficacy is better than other traditional indicators-such as serum ferritin and serum transferrin receptor.

The binding of aluminum to mugineic acid and related compounds as studied by potentiometric titration.

PubMed

Yoshimura, Etsuro; Kohdr, Hicham; Mori, Satoshi; Hider, Robert C

2011-08-01

The phytosiderophores, mugineic acid (MA) and epi-hydroxymugineic acid (HMA), together with a related compound, nicotianamine (NA), were investigated for their ability to bind Al(III). Potentiometric titration analysis demonstrated that MA and HMA bind Al(III), in contrast to NA which does not under normal physiological conditions. With MA and HMA, in addition to the Al complex (AlL), the protonated (AlLH) and deprotonated (AlLH(-1)) complexes were identified from an analysis of titration curves, where L denotes the phytosiderophore form in which all the carboxylate functions are ionized. The equilibrium formation constants of the Al(III) phytosiderophore complexes are much smaller than those of the corresponding Fe(III) complexes. The higher selectivity of phytosiderophores for Fe(III) over Al(III) facilitates Fe(III) acquisition in alkaline conditions where free Al(III) levels are higher than free Fe(III) levels.

In Vitro Adsorption and in Vivo Pharmacokinetic Interaction between Doxycycline and Frequently Used Mycotoxin Binders in Broiler Chickens.

PubMed

De Mil, Thomas; Devreese, Mathias; Broekaert, Nathan; Fraeyman, Sophie; De Backer, Patrick; Croubels, Siska

2015-05-06

Mycotoxin binders are readily mixed in feeds to prevent uptake of mycotoxins by the animal. Concerns were raised for nonspecific binding with orally administered veterinary drugs by the European Food Safety Authority in 2010. This paper describes the screening for in vitro adsorption of doxycycline-a broad-spectrum tetracycline antibiotic-to six different binders that were able to bind >75% of the doxycycline. Next, an in vivo pharmacokinetic interaction study of doxycycline with two of the binders, which demonstrated significant in vitro binding, was performed in broiler chickens using an oral bolus model. It was shown that two montmorillonite-based binders were able to lower the area under the plasma concentration-time curve of doxycycline by >60% compared to the control group. These results may indicate a possible risk for reduced efficacy of doxycycline when used concomitantly with montmorillonite-based mycotoxin binders.

The tightly bound nuclei in the liquid drop model

NASA Astrophysics Data System (ADS)

Sree Harsha, N. R.

2018-05-01

In this paper, we shall maximise the binding energy per nucleon function in the semi-empirical mass formula of the liquid drop model of the atomic nuclei to analytically prove that the mean binding energy per nucleon curve has local extrema at A ≈ 58.6960, Z ≈ 26.3908 and at A ≈ 62.0178, Z ≈ 27.7506. The Lagrange method of multipliers is used to arrive at these results, while we have let the values of A and Z take continuous fractional values. The shell model that shows why 62Ni is the most tightly bound nucleus is outlined. A brief account on stellar nucleosynthesis is presented to show why 56Fe is more abundant than 62Ni and 58Fe. We believe that the analytical proof presented in this paper can be a useful tool to the instructors to introduce the nucleus with the highest mean binding energy per nucleon.

Research on Al-alloy sheet forming formability during warm/hot sheet hydroforming based on elliptical warm bulging test

NASA Astrophysics Data System (ADS)

Cai, Gaoshen; Wu, Chuanyu; Gao, Zepu; Lang, Lihui; Alexandrov, Sergei

2018-05-01

An elliptical warm/hot sheet bulging test under different temperatures and pressure rates was carried out to predict Al-alloy sheet forming limit during warm/hot sheet hydroforming. Using relevant formulas of ultimate strain to calculate and dispose experimental data, forming limit curves (FLCS) in tension-tension state of strain (TTSS) area are obtained. Combining with the basic experimental data obtained by uniaxial tensile test under the equivalent condition with bulging test, complete forming limit diagrams (FLDS) of Al-alloy are established. Using a quadratic polynomial curve fitting method, material constants of fitting function are calculated and a prediction model equation for sheet metal forming limit is established, by which the corresponding forming limit curves in TTSS area can be obtained. The bulging test and fitting results indicated that the sheet metal FLCS obtained were very accurate. Also, the model equation can be used to instruct warm/hot sheet bulging test.

Extracting transient Rayleigh wave and its application in detecting quality of highway roadbed

USGS Publications Warehouse

Liu, J.; Xia, J.; Luo, Y.; Li, X.; Xu, S.; ,

2004-01-01

This paper first explains the tau-p mapping method of extracting Rayleigh waves (LR waves) from field shot gathers. It also explains a mathematical model of physical character parameters of quality of high-grade roads. This paper then discusses an algorithm of computing dispersion curves using adjacent channels. Shear velocity and physical character parameters are obtained by inversion of dispersion curves. The algorithm using adjacent channels to calculating dispersion curves eliminates average effects that exist by using multi-channels to obtain dispersion curves so that it improves longitudinal and transverse resolution of LR waves and precision of non-invasive detection, and also broadens its application fields. By analysis of modeling results of detached computation of the ground roll and real examples of detecting density and pressure strength of a high-grade roadbed, and by comparison of shallow seismic image method with borehole cores, we concluded that: 1 the abnormal scale and configuration obtained by LR waves are mostly the same as the result of shallow seismic image method; 2 an average relative error of density obtained from LR waves inversion is 1.6% comparing with borehole coring; 3 transient LR waves in detecting density and pressure strength of a high-grade roadbed is feasible and effective.

Choline+ is a low-affinity ligand for alpha 1-adrenoceptors.

PubMed

Unelius, L; Cannon, B; Nedergaard, J

1994-10-07

The effect of choline+, a commonly used Na+ substitute, on ligand binding to alpha 1-adrenoceptors was investigated. It was found that replacement of 25% of the Na+ in a Krebs-Ringer bicarbonate buffer with choline+ led to a 3-fold decrease in the apparent affinity of [3H]prazosin for its binding site (i.e. the alpha 1-receptor) in a membrane preparation from brown adipose tissue, while no decrease in the total number of binding sites was observed. Similar effects were seen in membrane preparations from liver and brain. In competition experiments, it was found that choline+ could inhibit [3H]prazosin binding; from the inhibition curve, an affinity (Ki) of 31 mM choline+ for the [3H]prazosin-binding site could be calculated. In fully choline(+)-substituted buffers, where the level of [3H]prazosin binding was substantially reduced, both phentolamine and norepinephrine could still compete with [3H]prazosin for its binding site, with virtually unaltered affinity; thus choline+ did not substantially affect the characteristics of those receptors to which it did not bind. Choline+ did not affect the binding characteristics of the beta 1/beta 2 radioligand [3H]CGP-12177; thus, the effect on alpha 1-receptors was not due to general, unspecific effects on the membrane preparations. It is concluded that choline+ possesses characteristics similar to those of a competitive ligand for the alpha 1-adrenoceptor; it has a low affinity but the competitive type of interaction of choline may nonetheless under experimental conditions interfere with agonist interaction with the alpha 1-receptor.

Theoretical kinetic studies of models for binding myosin subfragment-1 to regulated actin: Hill model versus Geeves model.

PubMed Central

Chen , Y; Yan, B; Chalovich, J M; Brenner, B

2001-01-01

It was previously shown that a one-dimensional Ising model could successfully simulate the equilibrium binding of myosin S1 to regulated actin filaments (T. L. Hill, E. Eisenberg and L. Greene, Proc. Natl. Acad. Sci. U.S.A. 77:3186-3190, 1980). However, the time course of myosin S1 binding to regulated actin was thought to be incompatible with this model, and a three-state model was subsequently developed (D. F. McKillop and M. A. Geeves, Biophys. J. 65:693-701, 1993). A quantitative analysis of the predicted time course of myosin S1 binding to regulated actin, however, was never done for either model. Here we present the procedure for the theoretical evaluation of the time course of myosin S1 binding for both models and then show that 1) the Hill model can predict the "lag" in the binding of myosin S1 to regulated actin that is observed in the absence of Ca++ when S1 is in excess of actin, and 2) both models generate very similar families of binding curves when [S1]/[actin] is varied. This result shows that, just based on the equilibrium and pre-steady-state kinetic binding data alone, it is not possible to differentiate between the two models. Thus, the model of Hill et al. cannot be ruled out on the basis of existing pre-steady-state and equilibrium binding data. Physical mechanisms underlying the generation of the lag in the Hill model are discussed. PMID:11325734

Specific binding of nicergoline on an alpha1-like adrenoreceptor in the rat retina.

PubMed

Lograno, M D; Tricarico, D; Masciopinto, V; Scuderl, A C

2000-02-01

Systemic treatment with nicergoline, an ergoline derivative showing alpha1-antagonist properties, causes vasodilatation in the eye without apparent untoward cardiovascular effects. In the present work we investigated the ability of nicergoline to inhibit the binding of radiolabelled prazosin in the rat retina and cortex. We found that nicergoline inhibited [3H]prazosin binding in both tissues, being more potent than unlabelled prazosin in the retinal tissue. The competition curves of the ergoline derivative were well fitted by a one-site model in the cortical tissue, with an IC50 (concentration of the drugs needed to inhibit the binding of labelled prazosin by 50%) of 2.54 x 10(-8) M, and by a two-site model in the retinal tissue, with IC50 values of 7.08 x 10(-12) M and 1.82 x 10(-5) M. 2-(2,6 dimetoxyphenoxyethyl) aminomethyl-1,4-benzodioxane hydrochloride (WB4101) and phentolamine, selective ligands for the high-affinity binding site for prazosin, in particular the alpha1A-site, fully inhibited prazosin binding in the cortex but only partially inhibited prazosin binding in the retina, being less potent in this tissue than either nicergoline or prazosin. Our results suggest that a binding component of alpha1-adrenoreceptors is expressed to a lesser extent in the retina than the cortex, leading to a reduced response of the retinal tissue to prazosin, and more particularly to WB4101 and phentolamine. The selective binding of the nicergoline on this retinal adrenoreceptor may explain the peculiar efficacy of the drug in ocular pathophysiology.

Principles of quantitation of viral loads using nucleic acid sequence-based amplification in combination with homogeneous detection using molecular beacons.

PubMed

Weusten, Jos J A M; Carpay, Wim M; Oosterlaken, Tom A M; van Zuijlen, Martien C A; van de Wiel, Paul A

2002-03-15

For quantitative NASBA-based viral load assays using homogeneous detection with molecular beacons, such as the NucliSens EasyQ HIV-1 assay, a quantitation algorithm is required. During the amplification process there is a constant growth in the concentration of amplicons to which the beacon can bind while generating a fluorescence signal. The overall fluorescence curve contains kinetic information on both amplicon formation and beacon binding, but only the former is relevant for quantitation. In the current paper, mathematical modeling of the relevant processes is used to develop an equation describing the fluorescence curve as a function of the amplification time and the relevant kinetic parameters. This equation allows reconstruction of RNA formation, which is characterized by an exponential increase in concentrations as long as the primer concentrations are not rate limiting and by linear growth over time after the primer pool is depleted. During the linear growth phase, the actual quantitation is based on assessing the amplicon formation rate from the viral RNA relative to that from a fixed amount of calibrator RNA. The quantitation procedure has been successfully applied in the NucliSens EasyQ HIV-1 assay.

Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves

PubMed Central

Idili, Andrea

2017-01-01

Abstract DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson–Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers. PMID:28605461

Light-curve Analysis of Neon Novae

NASA Astrophysics Data System (ADS)

Hachisu, Izumi; Kato, Mariko

2016-01-01

We analyzed light curves of five neon novae, QU Vul, V351 Pup, V382 Vel, V693 CrA, and V1974 Cyg, and determined their white dwarf (WD) masses and distance moduli on the basis of theoretical light curves composed of free-free and photospheric emission. For QU Vul, we obtained a distance of d ˜ 2.4 kpc, reddening of E(B - V) ˜ 0.55, and WD mass of MWD = 0.82-0.96 {M}⊙ . This suggests that an oxygen-neon WD lost a mass of more than ˜ 0.1 {M}⊙ since its birth. For V351 Pup, we obtained d˜ 5.5 {{kpc}}, E(B-V)˜ 0.45, and {M}{{WD}}=0.98-1.1 {M}⊙ . For V382 Vel, we obtained d˜ 1.6 {{kpc}}, E(B-V)˜ 0.15, and {M}{{WD}}=1.13-1.28 {M}⊙ . For V693 CrA, we obtained d˜ 7.1 {{kpc}}, E(B-V)˜ 0.05, and {M}{{WD}}=1.15-1.25 {M}⊙ . For V1974 Cyg, we obtained d˜ 1.8 {{kpc}}, E(B-V)˜ 0.30, and {M}{{WD}}=0.95-1.1 {M}⊙ . For comparison, we added the carbon-oxygen nova V1668 Cyg to our analysis and obtained d˜ 5.4 {{kpc}}, E(B-V)˜ 0.30, and {M}{{WD}}=0.98-1.1 {M}⊙ . In QU Vul, photospheric emission contributes 0.4-0.8 mag at most to the optical light curve compared with free-free emission only. In V351 Pup and V1974 Cyg, photospheric emission contributes very little (0.2-0.4 mag at most) to the optical light curve. In V382 Vel and V693 CrA, free-free emission dominates the continuum spectra, and photospheric emission does not contribute to the optical magnitudes. We also discuss the maximum magnitude versus rate of decline relation for these novae based on the universal decline law.

Prediction of in vivo drug-drug interactions based on mechanism-based inhibition from in vitro data: inhibition of 5-fluorouracil metabolism by (E)-5-(2-Bromovinyl)uracil.

PubMed

Kanamitsu, S I; Ito, K; Okuda, H; Ogura, K; Watabe, T; Muro, K; Sugiyama, Y

2000-04-01

The fatal drug-drug interaction between sorivudine, an antiviral drug, and 5-fluorouracil (5-FU) has been shown to be caused by a mechanism-based inhibition. In this interaction, sorivudine is converted by gut flora to (E)-5-(2-bromovinyl)uracil (BVU), which is metabolically activated by dihydropyrimidine dehydrogenase (DPD), and the activated BVU irreversibly binds to DPD itself, thereby inactivating it. In an attempt to predict this interaction in vivo from in vitro data, inhibition of 5-FU metabolism by BVU was investigated by using rat and human hepatic cytosol and human recombinant DPD. Whichever enzyme was used, increased inhibition was observed that depended on the preincubation time of BVU and enzyme in the presence of NADPH and BVU concentration. The kinetic parameters obtained for inactivation represented by k(inact) and K'(app) were 2.05 +/- 1.52 min(-1), 69.2 +/- 60.8 microM (rat hepatic cytosol), 2.39 +/- 0.13 min(-1), 48.6 +/- 11.8 microM (human hepatic cytosol), and 0.574 +/- 0.121 min(-1), 2.20 +/- 0.57 microM (human recombinant DPD). The drug-drug interaction in vivo was predicted quantitatively based on a physiologically based pharmacokinetic model, using pharmacokinetic parameters obtained from the literature and kinetic parameters for the enzyme inactivation obtained in the in vitro studies. In rats, DPD was predicted to be completely inactivated by administration of BVU and the area under the curve of 5-FU was predicted to increase 11-fold, which agreed well with the reported data. In humans, a 5-fold increase in the area under the curve of 5-FU was predicted after administration of sorivudine, 150 mg/day for 5 days. Mechanism-based inhibition of drug metabolism is supposed to be very dangerous. We propose that such in vitro studies should be carried out during the drug-developing phase so that in vivo drug-drug interactions can be predicted.

Kinetic Modeling of the Tau PET Tracer 18F-AV-1451 in Human Healthy Volunteers and Alzheimer Disease Subjects.

PubMed

Barret, Olivier; Alagille, David; Sanabria, Sandra; Comley, Robert A; Weimer, Robby M; Borroni, Edilio; Mintun, Mark; Seneca, Nicholas; Papin, Caroline; Morley, Thomas; Marek, Ken; Seibyl, John P; Tamagnan, Gilles D; Jennings, Danna

2017-07-01

18 F-AV-1451 is currently the most widely used of several experimental tau PET tracers. The objective of this study was to evaluate 18 F-AV-1451 binding with full kinetic analysis using a metabolite-corrected arterial input function and to compare parameters derived from kinetic analysis with SUV ratio (SUVR) calculated over different imaging time intervals. Methods: 18 F-AV-1451 PET brain imaging was completed in 16 subjects: 4 young healthy volunteers (YHV), 4 aged healthy volunteers (AHV), and 8 Alzheimer disease (AD) subjects. Subjects were imaged for 3.5 h, with arterial blood samples obtained throughout. PET data were analyzed using plasma and reference tissue-based methods to estimate the distribution volume, binding potential (BP ND ), and SUVR. BP ND and SUVR were calculated using the cerebellar cortex as a reference region and were compared across the different methods and across the 3 groups (YHV, AHV, and AD). Results: AD demonstrated increased 18 F-AV-1451 retention compared with YHV and AHV based on both invasive and noninvasive analyses in cortical regions in which paired helical filament tau accumulation is expected in AD. A correlation of R 2 > 0.93 was found between BP ND (130 min) and SUVR-1 at all time intervals. Cortical SUVR curves reached a relative plateau around 1.0-1.2 for YHV and AHV by approximately 50 min, but increased in AD by up to approximately 20% at 110-130 min and approximately 30% at 160-180 min relative to 80-100 min. Distribution volume (130 min) was lower by 30%-35% in the YHV than AHV. Conclusion: Our data suggest that although 18 F-AV-1451 SUVR curves do not reach a plateau and are still increasing in AD, an SUVR calculated over an imaging window of 80-100 min (as currently used in clinical studies) provides estimates of paired helical filament tau burden in good correlation with BP ND , whereas SUVR sensitivity to regional cerebral blood changes needs further investigation. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Pharmacological characterization of the cysteinyl-leukotriene antagonists CGP 45715A (iralukast) and CGP 57698 in human airways in vitro

PubMed Central

Capra, Valérie; Bolla, Manlio; Angelo Belloni, Pier; Mezzetti, Maurizio; Carlo Folco, G; Nicosia, Simonetta; Enrico Rovati, G

1998-01-01

Cysteinyl-leukotrienes (cysteinyl-LTs) are important mediators in the pathogenesis of asthma. They cause bronchoconstriction, mucus hypersecretion, increase in microvascular permeability, plasma extravasation and eosinophil recruitment. We investigated the pharmacological profile of the cysteinyl-LT antagonists CGP 45715A (iralukast), a structural analogue of LTD4 and CGP 57698, a quinoline type antagonist, in human airways in vitro, by performing binding studies on human lung parenchyma membranes and functional studies on human isolated bronchial strips. Competition curves vs [3H]-LTD4 on human lung parenchyma membranes demonstrated that: (a) both antagonists were able to compete for the two sites labelled by [3H]-LTD4; (b) as in all the G-protein coupled receptors, iralukast and CGP 57698 did not discriminate between the high and the low affinity states of the CysLT receptor labelled by LTD4 (Ki1=Ki2=16.6 nM±36% CV and Ki1= Ki2=5.7 nM±19% CV, respectively); (c) iralukast, but not CGP 57698, displayed a slow binding kinetic, because preincubation (15 min) increased its antagonist potency. In functional studies: (a) iralukast and CGP 57698 antagonized LTD4-induced contraction of human bronchi, with pA2 values of 7.77±4.3% CV and 8.51±1.6% CV, respectively, and slopes not significantly different from unity; (b) the maximal LTD4 response in the presence of CGP 57698 was actually increased, thus clearly deviating from apparent simple competition. Both antagonists significantly inhibited antigen-induced contraction of human isolated bronchial strips in a concentration-dependent manner, lowering the upper plateau of the anti-IgE curves. In conclusion, the results of the present in vitro investigation indicate that iralukast and CGP 57698 are potent antagonists of LTD4 in human airways, with affinities in the nanomolar range, similar to those obtained for ICI 204,219 and ONO 1078, two of the most clinically advanced CysLT receptor antagonists. Thus, these compounds might be useful drugs for the therapy of asthma and other allergic diseases. PMID:9504401

A theory of adhesion at a bimetallic interface - Overlap effects.

NASA Technical Reports Server (NTRS)

Ferrante, J.; Smith, J. R.

1973-01-01

A preliminary calculation of the chemical bonding adhesive interaction between metal surfaces is provided. In this first theory the Hohenberg and Kohn formalism is used to give the bimetallic adhesive binding energy versus separation. The close-packed planes of Al, Mg, and Zn are considered. The effect of simple overlap of the metal-vacuum distributions is determined. The importance of registry between contact surfaces is ascertained. A minimum in the binding energy curve is exhibited for all combinations. The theoretical predictions agree with trends in bond strengths taken from available experimental data. An insight into the mechanisms involved in metallic transfer is given. The relationship between adhesive energies, cohesive energies, and surface energies is discussed.

Relative loading on biplane wings

NASA Technical Reports Server (NTRS)

Diehl, Walter S

1934-01-01

Recent improvements in stress analysis methods have made it necessary to revise and to extend the loading curves to cover all conditions of flight. This report is concerned with a study of existing biplane data by combining the experimental and theoretical data to derive a series of curves from which the lift curves of the individual wings of a biplane may be obtained.

VizieR Online Data Catalog: K2-141 b radial velocity and light curve (Barragan+, 2018)

NASA Astrophysics Data System (ADS)

Barragan, O.; Gandolfi, D.; Dai, F.; Livingston, J.; Persson, C. M.; Hirano, T.; Narita, N.; Csizmadia, Sz.; Winn, J. N.; Nespral, D.; Prieto-Arranz, J.; Smith, A. M. S.; Nowak, G.; Albrecht, S.; Antoniciello, G.; Bo Justesen, A.; Cabrera, J.; Cochran, W. D.; Deeg, H..; Eigmuller, P.; Endl, M.; Erikson, A.; Fridlund, M.; Fukui, A.; Grziwa, S.; Guenther, E.; Hatzes, A. P.; Hidalgo, D.; Johnson, M. C.; Korth, J.; Palle, E.; Patzold, M.; Rauer, H.; Tanaka, Y.; van Eylen, V.

2018-01-01

Light curve and radial velocities for K2-141 (EPIC 246393474). Light curve comes from campaing 12 of the extended Kepler mission, K2. Radial velocity data was obtained with HARPS at th3 3.6m telescope, ESO. FIES data comes from observations at the Nordic Optical Telescope (NOT). (3 data files).

Extracting information from S-curves of language change.

PubMed

Ghanbarnejad, Fakhteh; Gerlach, Martin; Miotto, José M; Altmann, Eduardo G

2014-12-06

It is well accepted that adoption of innovations are described by S-curves (slow start, accelerating period and slow end). In this paper, we analyse how much information on the dynamics of innovation spreading can be obtained from a quantitative description of S-curves. We focus on the adoption of linguistic innovations for which detailed databases of written texts from the last 200 years allow for an unprecedented statistical precision. Combining data analysis with simulations of simple models (e.g. the Bass dynamics on complex networks), we identify signatures of endogenous and exogenous factors in the S-curves of adoption. We propose a measure to quantify the strength of these factors and three different methods to estimate it from S-curves. We obtain cases in which the exogenous factors are dominant (in the adoption of German orthographic reforms and of one irregular verb) and cases in which endogenous factors are dominant (in the adoption of conventions for romanization of Russian names and in the regularization of most studied verbs). These results show that the shape of S-curve is not universal and contains information on the adoption mechanism. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

SB265610 is an allosteric, inverse agonist at the human CXCR2 receptor

PubMed Central

Bradley, ME; Bond, ME; Manini, J; Brown, Z; Charlton, SJ

2009-01-01

Background and purpose: In several previous studies, the C-X-C chemokine receptor (CXCR)2 antagonist 1-(2-bromo-phenyl)-3-(7-cyano-3H-benzotriazol-4-yl)-urea (SB265610) has been described as binding competitively with the endogenous agonist. This is in contrast to many other chemokine receptor antagonists, where the mechanism of antagonism has been described as allosteric. Experimental approach: To determine whether it displays a unique mechanism among the chemokine receptor antagonists, the mode of action of SB265610 was investigated at the CXCR2 receptor using radioligand and [35S]-GTPγS binding approaches in addition to chemotaxis of human neutrophils. Key results: In equilibrium saturation binding studies, SB265610 depressed the maximal binding of [125I]-interleukin-8 ([125I]-IL-8) without affecting the Kd. In contrast, IL-8 was unable to prevent binding of [3H]-SB265610. Kinetic binding experiments demonstrated that this was not an artefact of irreversible or slowly reversible binding. In functional experiments, SB265610 caused a rightward shift of the concentration-response curves to IL-8 and growth-related oncogene α, but also a reduction in maximal response elicited by each agonist. Fitting these data to an operational allosteric ternary complex model suggested that, once bound, SB265610 completely blocks receptor activation. SB265610 also inhibited basal [35S]-GTPγS binding in this preparation. Conclusions and implications: Taken together, these data suggest that SB265610 behaves as an allosteric inverse agonist at the CXCR2 receptor, binding at a region distinct from the agonist binding site to prevent receptor activation, possibly by interfering with G protein coupling. PMID:19422399

Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

PubMed Central

Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

2009-01-01

We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as charge optimization or component analysis, can be computed to high accuracy using the presented BEM approach, in compute times comparable to traditional finite-difference methods. PMID:18567005

Estimation of Rapidly Exchangeable Cellular Thyroxine from the Plasma Disappearance Curves of Simultaneously Administered Thyroxine-131I and Albumin-125I*

PubMed Central

Oppenheimer, Jack H.; Bernstein, Gerald; Hasen, Julian

1967-01-01

A mathematical analysis of the plasma disappearance curves of simultaneously injected thyroxine-131I and albumin-125I allows the development of simple formulas for estimating the pool size and transfer kinetics of rapidly exchangeable intracellular thyroxine in man. Evidence is presented that the early distribution kinetics of albumin-125I can be used to represent the expansion of the thyroxine-131I-plasma protein complex into the extracellular compartment. Calculations indicate that approximately 37% of total body extrathyroidal thyroxine is within such exchangeable tissue stores. The average cellular clearance of thyroxine is 42.7 ml per minute, a value far in excess of the metabolic clearance of this hormone. Results of external measurements over the hepatic area and studies involving hepatic biopsies indicate that the liver is an important but probably not the exclusive component of the intracellular compartment. The partition of thyroxine between cellular and extracellular compartments is determined by the balance of tissue and plasma protein binding factors. The fractional transfer constants are inversely related to the strength of binding of each compartment and directly proportional to the permeability characteristic of the hypothetical membrane separating compartments. Appropriate numerical values for these factors are assigned. An increased fractional entrance of thyroxine-131I into the cellular compartment was noted in a patient with congenital decrease in the maximal binding capacity of thyroxine-binding globulin and in three patients after the infusion of 5,5-diphenylhydantoin. Decreased intracellular space and impaired permeability characteristics were observed in five patients with hepatic disease. Studies of the rate of entrance of thyroxine-131I and albumin-125I into the pleural effusion of a patient with congestive heart failure suggested that transcapillary passage of thyroxine independent of its binding protein is not a predominant factor in the total distribution kinetics of thyroxine-131I. The thesis is advanced that the distribution of thyroxine, both within the extracellular compartment and between the extracellular and intracellular compartments, is accomplished largely by the carrier protein and the direct transfer of thyroxine from one binding site to another. The concept of free thyroxine is reassessed in terms of this formulation. PMID:4960936

Beyond conventional dose-response curves: Sensorgram comparison in SPR allows single concentration activity and similarity assessment.

PubMed

Gassner, C; Karlsson, R; Lipsmeier, F; Moelleken, J

2018-05-30

Previously we have introduced two SPR-based assay principles (dual-binding assay and bridging assay), which allow the determination of two out of three possible interaction parameters for bispecific molecules within one assay setup: two individual interactions to both targets, and/or one simultaneous/overall interaction, which potentially reflects the inter-dependency of both individual binding events. However, activity and similarity are determined by comparing report points over a concentration range, which also mirrors the way data is generated by conventional ELISA-based methods So far, binding kinetics have not been specifically considered in generic approaches for activity assessment. Here, we introduce an improved slope-ratio model which, together with a sensorgram comparison based similarity assessment, allows the development of a detailed, USP-conformal ligand binding assay using only a single sample concentration. We compare this novel analysis method to the usual concentration-range approach for both SPR-based assay principles and discuss its impact on data quality and increased sample throughput. Copyright © 2018 Elsevier B.V. All rights reserved.

Protein Binding and Astringent Taste of a Polymeric Procyanidin, 1,2,3,4,6-Penta-O-galloyl-β-D-glucopyranose, Castalagin and Grandinin

PubMed Central

Hofmann, Thomas; Glabasnia, Arne; Schwarz, Bernd; Wisman, Kimberly N.; Gangwer, Kelly A.; Hagerman, Ann E.

2008-01-01

The objective of the present investigation was to examine oral astringency and protein binding activity of four structurally well-defined tannins, namely procyanidin (epicatechin16(4→8)catechin), pentagalloyl glucose (1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose), castalagin, and grandinin, representing the three main structural categories of tannins, the proanthocyanidins, the gallotannins, and the ellagitannins. Astringency threshold and dose response were determined by the half-tongue test using a trained human panel. Protein binding stoichiometry and relative affinity were determined using radioiodinated bovine serum albumin in precipitation or competitive binding assays. Procyanidin and pentagalloyl glucose were perceived as highly astringent compounds and had relatively steep dose response curves but castalagin and grandinin had a lower mass threshold for detection. In vitro, procyanidin was the most effective protein precipitating agent, and grandinin the least. Increasing the temperature increased protein precipitation by the hydrolysable tannins, especially grandinin. All four polyphenols had higher relative affinity for proline-rich proteins than for bovine serum albumin. PMID:17147439

Reconstruction of quadratic curves in 3D using two or more perspective views: simulation studies

NASA Astrophysics Data System (ADS)

Kumar, Sanjeev; Sukavanam, N.; Balasubramanian, R.

2006-01-01

The shapes of many natural and man-made objects have planar and curvilinear surfaces. The images of such curves usually do not have sufficient distinctive features to apply conventional feature-based reconstruction algorithms. In this paper, we describe a method of reconstruction of a quadratic curve in 3-D space as an intersection of two cones containing the respective projected curve images. The correspondence between this pair of projections of the curve is assumed to be established in this work. Using least-square curve fitting, the parameters of a curve in 2-D space are found. From this we are reconstructing the 3-D quadratic curve. Relevant mathematical formulations and analytical solutions for obtaining the equation of reconstructed curve are given. The result of the described reconstruction methodology are studied by simulation studies. This reconstruction methodology is applicable to LBW decision in cricket, path of the missile, Robotic Vision, path lanning etc.

Multimodal determination of Rayleigh dispersion and attenuation curves using the circle fit method

NASA Astrophysics Data System (ADS)

Verachtert, R.; Lombaert, G.; Degrande, G.

2018-03-01

This paper introduces the circle fit method for the determination of multi-modal Rayleigh dispersion and attenuation curves as part of a Multichannel Analysis of Surface Waves (MASW) experiment. The wave field is transformed to the frequency-wavenumber (fk) domain using a discretized Hankel transform. In a Nyquist plot of the fk-spectrum, displaying the imaginary part against the real part, the Rayleigh wave modes correspond to circles. The experimental Rayleigh dispersion and attenuation curves are derived from the angular sweep of the central angle of these circles. The method can also be applied to the analytical fk-spectrum of the Green's function of a layered half-space in order to compute dispersion and attenuation curves, as an alternative to solving an eigenvalue problem. A MASW experiment is subsequently simulated for a site with a regular velocity profile and a site with a soft layer trapped between two stiffer layers. The performance of the circle fit method to determine the dispersion and attenuation curves is compared with the peak picking method and the half-power bandwidth method. The circle fit method is found to be the most accurate and robust method for the determination of the dispersion curves. When determining attenuation curves, the circle fit method and half-power bandwidth method are accurate if the mode exhibits a sharp peak in the fk-spectrum. Furthermore, simulated and theoretical attenuation curves determined with the circle fit method agree very well. A similar correspondence is not obtained when using the half-power bandwidth method. Finally, the circle fit method is applied to measurement data obtained for a MASW experiment at a site in Heverlee, Belgium. In order to validate the soil profile obtained from the inversion procedure, force-velocity transfer functions were computed and found in good correspondence with the experimental transfer functions, especially in the frequency range between 5 and 80 Hz.

On the reduction of occultation light curves. [stellar occultations by planets

NASA Technical Reports Server (NTRS)

Wasserman, L.; Veverka, J.

1973-01-01

The two basic methods of reducing occultation light curves - curve fitting and inversion - are reviewed and compared. It is shown that the curve fitting methods have severe problems of nonuniqueness. In addition, in the case of occultation curves dominated by spikes, it is not clear that such solutions are meaningful. The inversion method does not suffer from these drawbacks. Methods of deriving temperature profiles from refractivity profiles are then examined. It is shown that, although the temperature profiles are sensitive to small errors in the refractivity profile, accurate temperatures can be obtained, particularly at the deeper levels of the atmosphere. The ambiguities that arise when the occultation curve straddles the turbopause are briefly discussed.

Development and validation of a bioassay to evaluate binding of adalimumab to cell membrane-anchored TNFα using flow cytometry detection.

PubMed

Camacho-Sandoval, Rosa; Sosa-Grande, Eréndira N; González-González, Edith; Tenorio-Calvo, Alejandra; López-Morales, Carlos A; Velasco-Velázquez, Marco; Pavón-Romero, Lenin; Pérez-Tapia, Sonia Mayra; Medina-Rivero, Emilio

2018-06-05

Physicochemical and structural properties of proteins used as active pharmaceutical ingredients of biopharmaceuticals are determinant to carry out their biological activity. In this regard, the assays intended to evaluate functionality of biopharmaceuticals provide confirmatory evidence that they contain the appropriate physicochemical properties and structural conformation. The validation of the methodologies used for the assessment of critical quality attributes of biopharmaceuticals is a key requirement for manufacturing under GMP environments. Herein we present the development and validation of a flow cytometry-based methodology for the evaluation of adalimumab's affinity towards membrane-bound TNFα (mTNFα) on recombinant CHO cells. This in vitro methodology measures the interaction between an in-solution antibody and its target molecule onto the cell surface through a fluorescent signal. The characteristics evaluated during the validation exercise showed that this methodology is suitable for its intended purpose. The assay demonstrated to be accurate (r 2  = 0.92, slope = 1.20), precise (%CV ≤ 18.31) and specific (curve fitting, r 2  = 0.986-0.997) to evaluate binding of adalimumab to mTNFα. The results obtained here provide evidence that detection by flow cytometry is a viable alternative for bioassays used in the pharmaceutical industry. In addition, this methodology could be standardized for the evaluation of other biomolecules acting through the same mechanism of action. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Photometric flow analysis system for biomedical investigations of iron/transferrin speciation in human serum.

PubMed

Strzelak, Kamil; Rybkowska, Natalia; Wiśniewska, Agnieszka; Koncki, Robert

2017-12-01

The Multicommutated Flow Analysis (MCFA) system for the estimation of clinical iron parameters: Serum Iron (SI), Unsaturated Iron Binding Capacity (UIBC) and Total Iron Binding Capacity (TIBC) has been proposed. The developed MCFA system based on simple photometric detection of iron with chromogenic agent (ferrozine) enables a speciation of transferrin (determination of free and Fe-bound protein) in human serum. The construction of manifold was adapted to the requirements of measurements under changing conditions. In the course of studies, a different effect of proteins on SI and UIBC determination has been proven. That was in turn the reason to perform two kinds of calibration methods. For measurements in acidic medium for SI/holotransferrin determination, the calibration curve method was applied, characterized by limit of determination and limit of quantitation on the level of 3.4 μmol L -1 and 9.1 μmol L -1 , respectively. The determination method for UIBC parameter (related to apotransferrin level) in physiological medium of pH 7.4 forced the use of standard addition method due to the strong influence of proteins on obtaining analytical signals. These two different methodologies, performed in the presented system, enabled the estimation of all three clinical iron/transferrin parameters in human serum samples. TIBC corresponding to total transferrin level was calculated as a sum of SI and UIBC. Copyright © 2017 Elsevier B.V. All rights reserved.

[Effects of glycerol on the spectral properties of sodium caseinate].

PubMed

Li, Yan; Chang, Fen-fen; Gao, Huan-yuan; Cao, Qing; Jin, Li-e

2015-01-01

Although the immigration of water molecule, and diffusion and traversing of oxygen can be prevented by the edible film prepared through sodium caseinate, which plays a good protection role for the food, the strong hydrophilicity makes its watertightness and mechanical properties become inferior. Because the toughness and water resistance of SC films can be enhanced by glycerol (G) as an additive, it is necessary to elucidate the interaction between G and SC through the spectral characteristics such as fluorescence spectra, infrared spectra and UV spectra. The results show that the fluorescence intensity of SC decreases due to the addition of G. The binding constant obtained by the double logarithmic regression curve analysis is 1. 127 x 10(3) L . mol-1 and the number of binding sites reaches 1. 161. It indicates that the weak chemical bond is primary between G and SC molecules; From IR the absorption peaks of SC are almost the same before and after adding G. However, there is a certain difference among their absorption intensities. It reveals that the secondary structure of SC is affected, β folding length decreases, α helix, random coil structure, β angle structure increases, and the intermolecular hydrogen bond is strengthened; From UV the peptide bond structure of SC is not changed after the addition of G, but the polymer with larger molecular weight, which is formed by non-covalent bond, makes the peak intensity decrease. The research gives the mode of G and SC from the molecular level.

Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

PubMed

Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

2016-01-01

We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

MM Herculis - An eclipsing binary of the RS CVn

NASA Technical Reports Server (NTRS)

Sowell, J. R.; Hall, D. S.; Henry, G. W.; Burke, E. W., Jr.; Milone, E. F.

1983-01-01

V, B and U differential photoelectric photometry has been obtained for the RS Canum Venaticorum-class eclipsing binary star MM Her, with the light outside the eclipse being Fourier-analyzed to study wave migration and amplitude. These, together with the mean light level of the system, have been monitored from 1976 through 1980. Observations within the eclipse have revealed eclipses to be partial, rather than total as previously thought. The geometric elements of the presently rectified light curve are forced on the pre-1980 light curves and found to be compatible. With these elements, and previously obtained double line radial velocity curves, new absolute dimensions of 1.18 solar masses and 1.58 solar radii are calculated for the hotter star and 1.27 solar masses and 2.83 solar radii for the cooler star. The plotting of color indices on the color-color curve indicates G2V and K2IV spectral types.

[Kinematics Modeling and Analysis of Central-driven Robot for Upper Limb Rehabilitation after Stroke].

PubMed

Yi, Jinhua; Yu, Hongliu; Zhang, Ying; Hu, Xin; Shi, Ping

2015-12-01

The present paper proposed a central-driven structure of upper limb rehabilitation robot in order to reduce the volume of the robotic arm in the structure, and also to reduce the influence of motor noise, radiation and other adverse factors on upper limb dysfunction patient. The forward and inverse kinematics equations have been obtained with using the Denavit-Hartenberg (D-H) parameter method. The motion simulation has been done to obtain the angle-time curve of each joint and the position-time curve of handle under setting rehabilitation path by using Solid Works software. Experimental results showed that the rationality with the central-driven structure design had been verified by the fact that the handle could move under setting rehabilitation path. The effectiveness of kinematics equations had been proved, and the error was less than 3° by comparing the angle-time curves obtained from calculation with those from motion simulation.

Photometric and spectroscopic investigation of the oscillating Algol type binary: EW Boo

NASA Astrophysics Data System (ADS)

Doğruel, Mustafa Burak; Gürol, Birol

2015-10-01

We obtained the physical and geometrical parameters of the EW Boo system, which exhibits short period and small amplitude pulsations as well as brightness variations due to orbital motion of components. Towards this end we carried out photometric observations at Ankara University Kreiken Observatory (AUKO) as well as spectroscopic observations at TUBITAK National Observatory (TNO). The light and radial velocity curves obtained from these observations have been simultaneously analyzed with PHOEBE and the absolute parameters of the system along with the geometric parameters of the components have been determined. Using model light curves of EW Boo, light curve regions in which the pulsations are active have been determined and as a result of analyses performed in the frequency region, characteristic parameters of pulsations have been obtained. We find that the results are compatible with current parameters of similar systems in the literature. The evolutionary status of the components is propounded and discussed.

Dynamic deformation of soft soil media: Experimental studies and mathematical modeling

NASA Astrophysics Data System (ADS)

Balandin, V. V.; Bragov, A. M.; Igumnov, L. A.; Konstantinov, A. Yu.; Kotov, V. L.; Lomunov, A. K.

2015-05-01

A complex experimental-theoretical approach to studying the problem of high-rate strain of soft soil media is presented. This approach combines the following contemporary methods of dynamical tests: the modified Hopkinson-Kolsky method applied tomedium specimens contained in holders and the method of plane wave shock experiments. The following dynamic characteristics of sand soils are obtained: shock adiabatic curves, bulk compressibility curves, and shear resistance curves. The obtained experimental data are used to study the high-rate strain process in the system of a split pressure bar, and the constitutive relations of Grigoryan's mathematical model of soft soil medium are verified by comparing the results of computational and natural test experiments of impact and penetration.

Accounting for unintended binding events in the analysis of quartz crystal microbalance kinetic data.

PubMed

Heller, Gabriella T; Zwang, Theodore J; Sarapata, Elizabeth A; Haber, Michael A; Sazinsky, Matthew H; Radunskaya, Ami E; Johal, Malkiat S

2014-05-01

Previous methods for analyzing protein-ligand binding events using the quartz crystal microbalance with dissipation monitoring (QCM-D) fail to account for unintended binding that inevitably occurs during surface measurements and obscure kinetic information. In this article, we present a system of differential equations that accounts for both reversible and irreversible unintended interactions. This model is tested on three protein-ligand systems, each of which has different features, to establish the feasibility of using the QCM-D for protein binding analysis. Based on this analysis, we were able to obtain kinetic information for the intended interaction that is consistent with those obtained in literature via bulk-phase methods. In the appendix, we include a method for decoupling these from the intended binding events and extracting relevant affinity information. Copyright © 2014 Elsevier B.V. All rights reserved.

Receptor Binding Sites for Substance P, but not Substance K or Neuromedin K, are Expressed in High Concentrations by Arterioles, Venules, and Lymph Nodules in Surgical Specimens Obtained from Patients with Ulcerative Colitis and Crohn Disease

NASA Astrophysics Data System (ADS)

Mantyh, Christopher R.; Gates, Troy S.; Zimmerman, Robert P.; Welton, Mark L.; Passaro, Edward P.; Vigna, Steven R.; Maggio, John E.; Kruger, Lawrence; Mantyh, Patrick W.

1988-05-01

Several lines of evidence indicate that tachykinin neuropeptides [substance P (SP), substance K (SK), and neuromedin K (NK)] play a role in regulating the inflammatory and immune responses. To test this hypothesis in a human inflammatory disease, quantitative receptor autoradiography was used to examine possible abnormalities in tachykinin binding sites in surgical specimens from patients with inflammatory bowel disease. Surgical specimens of colon were obtained from patients with ulcerative colitis (n = 4) and Crohn disease (n = 4). Normal tissue was obtained from uninvolved areas of extensive resections for carcinoma (n = 6). In all cases, specimens were obtained <5 min after removal to minimize influences associated with degradation artifacts and were processed for quantitative receptor autoradiography by using 125I-labeled Bolton--Hunter conjugates of NK, SK, and SP. In the normal colon a low concentration of SP receptor binding sites is expressed by submucosal arterioles and venules and a moderate concentration is expressed by the external circular muscle, whereas SK receptor binding sites are expressed in low concentrations by the external circular and longitudinal muscle. In contrast, specific NK binding sites were not observed in any area of the human colon. In colon tissue obtained from ulcerative colitis and Crohn disease patients, however, very high concentrations of SP receptor binding sites are expressed by arterioles and venules located in the submucosa, muscularis mucosa, external circular muscle, external longitudinal muscle, and serosa. In addition, very high concentrations of SP receptor binding sites are expressed within the germinal center of lymph nodules, whereas the concentrations of SP and SK binding sites expressed by the external muscle layers are not altered significantly. These results demonstrate that receptor binding sites for SP, but not SK or NK, are ectopically expressed in high concentrations (1000-2000 times normal) by cells involved in mediating inflammatory and immune responses. These data suggest that SP may be involved in the pathophysiology of inflammatory bowel disease and might provide some insight into the interaction between the nervous system and the regulation of inflammation and the immune response in human inflammatory disease.

Sandwich enzyme-linked immunosorbent assay for naringin.

PubMed

Qu, Huihua; Wang, Xueqian; Qu, Baoping; Kong, Hui; Zhang, Yue; Shan, Wenchao; Cheng, Jinjun; Wang, Qingguo; Zhao, Yan

2016-01-15

Among the currently used immunoassay techniques, sandwich ELISA exhibits higher specificity, lower cross-reactivity, and a wider working range compared to the corresponding competitive assays. However, it is difficult to obtain a pair of antibodies that can simultaneously bind to two epitopes of a molecule with a molecular weight of less than 1000 Da. Naringin (Nar) is a flavonoid with a molecular mass of 580 Da. The main aim of this study was to develop a sandwich ELISA for detecting Nar. Two hybridomas secreting anti-Nar monoclonal antibodies (mAbs) were produced by fusing splenocytes from a mouse immunised against Nar-bovine serum albumin (BSA) conjugated with a hypoxanthine-aminopterin-thymidine (HAT)-sensitive mouse myeloma cell line; a sandwich ELISA for detecting Nar was developed using these two well-characterised anti-Nar mAbs. The performance of the sandwich assay was further evaluated by limit of detection (LOD), limit of quantification (LOQ), recovery, and interference analyses. A dose-response curve to Nar was obtained with an LOD of 6.78 ng mL(-1) and an LOQ of 13.47 ng mL(-1). The inter-assay and intra-assay coefficients of variation were 4.32% and 7.48%, respectively. The recovery rate of Nar from concentrated Fructus aurantii granules was 83.63%. A high correlation was obtained between HPLC and sandwich ELISA. These results demonstrate that the sandwich ELISA method has higher specificity for Nar than indirect competitive ELISA. Copyright © 2015 Elsevier B.V. All rights reserved.

Function and dynamics of aptamers: A case study on the malachite green aptamer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Tianjiao

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH - is sterically excluded frommore » the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. MD simulation also provided a 3D-structure model of unoccupied MGA that has not yet been obtained by biophysical measurements. These predictions were consistent with biochemical and biophysical measurements of the MGA-MG interaction including RNase I footprinting, melting curves, thermodynamic and kinetic constants measurement. This work shows that MD simulation can be used to extend our understanding of the dynamics of aptamer-target interaction which is not evident from static 3D-structures. To conclude, I have developed a novel concept to control molecular reactivity by an aptamer based on steric protection and a strategy to study the dynamics of aptamer-target interaction by combining MD simulation and experimental verification. The former has potential application in controlling metabolic reactions and protein modifications by small reactants and the latter may serve as a general approach to study the dynamics of aptamer-target interaction for new insights into mechanisms of aptamer-target recognition.« less

Dislocation based controlling of kinematic hardening contribution to simulate primary and secondary stages of uniaxial ratcheting

NASA Astrophysics Data System (ADS)

Bhattacharjee, S.; Dhar, S.; Acharyya, S. K.

2017-07-01

The primary and secondary stages of the uniaxial ratcheting curve for the C-Mn steel SA333 have been investigated. Stress controlled uniaxial ratcheting experiments were conducted with different mean stresses and stress amplitudes to obtain curves showing the evolution of ratcheting strain with number of cycles. In stage-I of the ratcheting curve, a large accumulation of ratcheting strain occurs, but at a decreasing rate. In contrast, in stage-II a smaller accumulation of ratcheting strain is found and the ratcheting rate becomes almost constant. Transmission electron microscope observations reveal that no specific dislocation structures are developed during the early stages of ratcheting. Rather, compared with the case of low cycle fatigue, it is observed that sub-cell formation is delayed in the case of ratcheting. The increase in dislocation density as a result of the ratcheting strain is obtained using the Orowan equation. The ratcheting strain is obtained from the shift of the plastic strain memory surface. The dislocation rearrangement is incorporated in a functional form of dislocation density, which is used to calibrate the parameters of a kinematic hardening law. The observations are formulated in a material model, plugged into the ABAQUS finite element (FE) platform as a user material subroutine. Finally the FE-simulated ratcheting curves are compared with the experimental curves.

Optimization and validation of moving average quality control procedures using bias detection curves and moving average validation charts.

PubMed

van Rossum, Huub H; Kemperman, Hans

2017-02-01

To date, no practical tools are available to obtain optimal settings for moving average (MA) as a continuous analytical quality control instrument. Also, there is no knowledge of the true bias detection properties of applied MA. We describe the use of bias detection curves for MA optimization and MA validation charts for validation of MA. MA optimization was performed on a data set of previously obtained consecutive assay results. Bias introduction and MA bias detection were simulated for multiple MA procedures (combination of truncation limits, calculation algorithms and control limits) and performed for various biases. Bias detection curves were generated by plotting the median number of test results needed for bias detection against the simulated introduced bias. In MA validation charts the minimum, median, and maximum numbers of assay results required for MA bias detection are shown for various bias. Their use was demonstrated for sodium, potassium, and albumin. Bias detection curves allowed optimization of MA settings by graphical comparison of bias detection properties of multiple MA. The optimal MA was selected based on the bias detection characteristics obtained. MA validation charts were generated for selected optimal MA and provided insight into the range of results required for MA bias detection. Bias detection curves and MA validation charts are useful tools for optimization and validation of MA procedures.

Evaluation of variability and quality control procedures for a receptor-binding assay for paralytic shellfish poisoning toxins.

PubMed

Ruberu, S R; Langlois, G W; Masuda, M; Perera, S Kusum

2012-01-01

The receptor-binding assay (RBA) method for determining saxatoxin (STX) and its numerous analogues, which cause paralytic shellfish poisoning (PSP) in humans, was evaluated in a single laboratory study. Each step of the assay preparation procedure including the performance of the multi-detector TopCount® instrument was evaluated for its contribution to method variability. The overall inherent RBA variability was determined to be 17%. Variability within the 12 detectors was observed; however, there was no reproducible pattern in detector performance. This observed variability among detectors could be attributed to other factors, such as pipetting errors. In an attempt to reduce the number of plates rejected due to excessive variability in the method's quality control parameters, a statistical approach was evaluated using either Grubbs' test or the Student's t-test for rejecting outliers in the measurement of triplicate wells. This approach improved the ratio of accepted versus rejected plates, saving cost and time for rerunning the assay. However, the potential reduction in accuracy and the lack of improvement in precision suggests caution when using this approach. The current study has recommended an alternate quality control procedure for accepting or rejecting plates in place of the criteria currently used in the published assay, or the alternative of outlier testing. The recommended procedure involves the development of control charts to monitor the critical parameters identified in the published method (QC sample, EC₅₀, slope of calibration curve), with the addition of a fourth critical parameter which is the top value (100% binding) of the calibration curve.

Concentration-Dependent Interactions of the Organophosphates Chlorpyrifos Oxon and Methyl Paraoxon with Human Recombinant Acetylcholinesterase

PubMed Central

Kaushik, R.; Rosenfeld, Clint A.; Sultatos, L.G.

2007-01-01

For many decades it has been thought that oxygen analogs (oxons) of organophosphorus insecticides phosphylate the catalytic site of acetylcholinesterase by a mechanism that follows simple Michaelis-Menten kinetics. More recently, the interactions of at least some oxons have been shown to be far more complex, and likely involve binding of oxons to a second site on acetylcholinesterase that modulates the inhibitory capacity of other oxon molecules at the catalytic site. The current study has investigated the interactions of chlorpyrifos oxon and methyl paraoxon with human recombinant acetylcholinesterase. Both chlorpyrifos oxon and methyl paraoxon were found to have ki’s that change as a function of oxon concentration. Furthermore, 10 nM chlorpyrifos oxon resulted in a transient increase in acetylthiocholine hydrolysis, followed by inhibition. Moreover, in the presence of 100 nM chlorpyrifos oxon, acetylthiocholine was found to influence both the Kd (binding affinity) and k2 (phosphorylation constant) of this oxon. Collectively, these results demonstrate that the interactions of chlorpyrifos oxon and methyl paraoxon with acetylcholinesterase cannot be described by simple Michaelis-Menten kinetics, but instead support the hypothesis that these oxons bind to a secondary site on acetylcholinesterase, leading to activation/inhibition of the catalytic site, depending on the nature of the substrate and inhibitor. Additionally, these data raise questions regarding the adequacy of estimating risk of low levels of insecticide exposure from direct extrapolation of insecticide dose-response curves since the capacity of individual oxon molecules at low oxon levels could be greater than individual oxon molecules in vivo associated with the dose response curve. PMID:17467020

Prediction of ttt curves of cold working tool steels using support vector machine model

NASA Astrophysics Data System (ADS)

Pillai, Nandakumar; Karthikeyan, R., Dr.

2018-04-01

The cold working tool steels are of high carbon steels with metallic alloy additions which impart higher hardenability, abrasion resistance and less distortion in quenching. The microstructure changes occurring in tool steel during heat treatment is of very much importance as the final properties of the steel depends upon these changes occurred during the process. In order to obtain the desired performance the alloy constituents and its ratio plays a vital role as the steel transformation itself is complex in nature and depends very much upon the time and temperature. The proper treatment can deliver satisfactory results, at the same time process deviation can completely spoil the results. So knowing time temperature transformation (TTT) of phases is very critical which varies for each type depending upon its constituents and proportion range. To obtain adequate post heat treatment properties the percentage of retained austenite should be lower and metallic carbides obtained should be fine in nature. Support vector machine is a computational model which can learn from the observed data and use these to predict or solve using mathematical model. Back propagation feedback network will be created and trained for further solutions. The points on the TTT curve for the known transformations curves are used to plot the curves for different materials. These data will be trained to predict TTT curves for other steels having similar alloying constituents but with different proportion range. The proposed methodology can be used for prediction of TTT curves for cold working steels and can be used for prediction of phases for different heat treatment methods.

Aleatory Uncertainty and Scale Effects in Computational Damage Models for Failure and Fragmentation

DTIC Science & Technology

2014-09-01

larger specimens, small specimens have, on average, higher strengths. Equivalently, because curves for small specimens fall below those of larger...the material strength associated with each realization parameter R in Equation (7), and strength distribution curves associated with multiple...effects in brittle media [58], which applies micromorphological dimensional analysis to obtain a universal curve which closely fits rate-dependent

Perceptibility curve test for digital radiographs before and after correction for attenuation and correction for attenuation and visual response.

PubMed

Li, G; Welander, U; Yoshiura, K; Shi, X-Q; McDavid, W D

2003-11-01

Two digital image processing methods, correction for X-ray attenuation and correction for attenuation and visual response, have been developed. The aim of the present study was to compare digital radiographs before and after correction for attenuation and correction for attenuation and visual response by means of a perceptibility curve test. Radiographs were exposed of an aluminium test object containing holes ranging from 0.03 mm to 0.30 mm with increments of 0.03 mm. Fourteen radiographs were exposed with the Dixi system (Planmeca Oy, Helsinki, Finland) and twelve radiographs were exposed with the F1 iOX system (Fimet Oy, Monninkylä, Finland) from low to high exposures covering the full exposure ranges of the systems. Radiographs obtained from the Dixi and F1 iOX systems were 12 bit and 8 bit images, respectively. Original radiographs were then processed for correction for attenuation and correction for attenuation and visual response. Thus, two series of radiographs were created. Ten viewers evaluated all the radiographs in the same random order under the same viewing conditions. The object detail having the lowest perceptible contrast was recorded for each observer. Perceptibility curves were plotted according to the mean of observer data. The perceptibility curves for processed radiographs obtained with the F1 iOX system are higher than those for originals in the exposure range up to the peak, where the curves are basically the same. For radiographs exposed with the Dixi system, perceptibility curves for processed radiographs are higher than those for originals for all exposures. Perceptibility curves show that for 8 bit radiographs obtained from the F1 iOX system, the contrast threshold was increased in processed radiographs up to the peak, while for 12 bit radiographs obtained with the Dixi system, the contrast threshold was increased in processed radiographs for all exposures. When comparisons were made between radiographs corrected for attenuation and corrected for attenuation and visual response, basically no differences were found. Radiographs processed for correction for attenuation and correction for attenuation and visual response may improve perception, especially for 12 bit originals.

Temporal Evolution of the Gamma-ray Burst Afterglow Spectrum for an Observer: GeV-TeV Synchrotron Self-Compton Light Curve

NASA Astrophysics Data System (ADS)

Fukushima, Takuma; To, Sho; Asano, Katsuaki; Fujita, Yutaka

2017-08-01

We numerically simulate the gamma-ray burst (GRB) afterglow emission with a one-zone time-dependent code. The temporal evolutions of the decelerating shocked shell and energy distributions of electrons and photons are consistently calculated. The photon spectrum and light curves for an observer are obtained taking into account the relativistic propagation of the shocked shell and the curvature of the emission surface. We find that the onset time of the afterglow is significantly earlier than the previous analytical estimate. The analytical formulae of the shock propagation and light curve for the radiative case are also different from our results. Our results show that even if the emission mechanism is switching from synchrotron to synchrotron self-Compton, the gamma-ray light curves can be a smooth power law, which agrees with the observed light curve and the late detection of a 32 GeV photon in GRB 130427A. The uncertainty of the model parameters obtained with the analytical formula is discussed, especially in connection with the closure relation between spectral index and decay index.

Ultrasonic velocity profiling rheometry based on a widened circular Couette flow

NASA Astrophysics Data System (ADS)

Shiratori, Takahisa; Tasaka, Yuji; Oishi, Yoshihiko; Murai, Yuichi

2015-08-01

We propose a new rheometry for characterizing the rheological properties of fluids. The technique produces flow curves, which represent the relationship between the fluid shear rate and shear stress. Flow curves are obtained by measuring the circumferential velocity distribution of tested fluids in a circular Couette system, using an ultrasonic velocity profiling technique. By adopting a widened gap of concentric cylinders, a designed range of the shear rate is obtained so that velocity profile measurement along a single line directly acquires flow curves. To reduce the effect of ultrasonic noise on resultant flow curves, several fitting functions and variable transforms are examined to best approximate the velocity profile without introducing a priori rheological models. Silicone oil, polyacrylamide solution, and yogurt were used to evaluate the applicability of this technique. These substances are purposely targeted as examples of Newtonian fluids, shear thinning fluids, and opaque fluids with unknown rheological properties, respectively. We find that fourth-order Chebyshev polynomials provide the most accurate representation of flow curves in the context of model-free rheometry enabled by ultrasonic velocity profiling.

Predicting permanent and transient protein-protein interfaces.

PubMed

La, David; Kong, Misun; Hoffman, William; Choi, Youn Im; Kihara, Daisuke

2013-05-01

Protein-protein interactions (PPIs) are involved in diverse functions in a cell. To optimize functional roles of interactions, proteins interact with a spectrum of binding affinities. Interactions are conventionally classified into permanent and transient, where the former denotes tight binding between proteins that result in strong complexes, whereas the latter compose of relatively weak interactions that can dissociate after binding to regulate functional activity at specific time point. Knowing the type of interactions has significant implications for understanding the nature and function of PPIs. In this study, we constructed amino acid substitution models that capture mutation patterns at permanent and transient type of protein interfaces, which were found to be different with statistical significance. Using the substitution models, we developed a novel computational method that predicts permanent and transient protein binding interfaces (PBIs) in protein surfaces. Without knowledge of the interacting partner, the method uses a single query protein structure and a multiple sequence alignment of the sequence family. Using a large dataset of permanent and transient proteins, we show that our method, BindML+, performs very well in protein interface classification. A very high area under the curve (AUC) value of 0.957 was observed when predicted protein binding sites were classified. Remarkably, near prefect accuracy was achieved with an AUC of 0.991 when actual binding sites were classified. The developed method will be also useful for protein design of permanent and transient PBIs. Copyright © 2013 Wiley Periodicals, Inc.

International Validation of Two Human Recombinant Estrogen ...

EPA Pesticide Factsheets

An international validation study has been successfully completed for 2 competitive binding assays using human recombinant ERa. Assays evaluated included the Freyberger-Wilson (FW) assay using a full length human ER, and the Chemical Evaluation and Research Institute (CERI) assay using a ligand-binding domain of the human ER. Twenty three compounds were tested in 6 laboratories for the FW assay and 5 for the CERJ assay, which included three controls (used with every run), 9 uncoded, and 14 coded chemicals across 3 subtasks. The overall goal of this validation study was to demonstrate the ability of each of the two assays to reliably classify the test chemicals as binders or non-binders. Laboratories had little trouble with the ER binders that produced a full binding curve when using either the CERI or FW assays. As is typical with all ER competitive binding assays, the weak binders proved to be more challenging. However, overall results from both the FW and CERI assays were consistent and in agreement with expected classifications regardless of the form of the hrER (i.e., full length ER versus an ER ligand binding domain) or the subtle differences in the protocols for conducting each assay. The reproducibility and accuracy for classification of chemicals as potential ER binders and non- binders using the FW and CERI hrER binding assays were comparable to that of the U.S.EPA’s existing ER binding test guideline OPPTS 890.1250, while providing an improved, highe

Protein Binding: Do We Ever Learn?▿

PubMed Central

Zeitlinger, Markus A.; Derendorf, Hartmut; Mouton, Johan W.; Cars, Otto; Craig, William A.; Andes, David; Theuretzbacher, Ursula

2011-01-01

Although the influence of protein binding (PB) on antibacterial activity has been reported for many antibiotics and over many years, there is currently no standardization for pharmacodynamic models that account for the impact of protein binding of antimicrobial agents in vitro. This might explain the somewhat contradictory results obtained from different studies. Simple in vitro models which compare the MIC obtained in protein-free standard medium versus a protein-rich medium are prone to methodological pitfalls and may lead to flawed conclusions. Within in vitro test systems, a range of test conditions, including source of protein, concentration of the tested antibiotic, temperature, pH, electrolytes, and supplements may influence the impact of protein binding. As new antibiotics with a high degree of protein binding are in clinical development, attention and action directed toward the optimization and standardization of testing the impact of protein binding on the activity of antibiotics in vitro become even more urgent. In addition, the quantitative relationship between the effects of protein binding in vitro and in vivo needs to be established, since the physiological conditions differ. General recommendations for testing the impact of protein binding in vitro are suggested. PMID:21537013

Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, WC; Zhuang, ZB; Gao, MR

2015-01-08

The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearlymore » increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.« less

Two active molecular phenotypes of the tachykinin NK1 receptor revealed by G-protein fusions and mutagenesis.

PubMed

Holst, B; Hastrup, H; Raffetseder, U; Martini, L; Schwartz, T W

2001-06-08

The NK1 neurokinin receptor presents two non-ideal binding phenomena, two-component binding curves for all agonists and significant differences between agonist affinity determined by homologous versus heterologous competition binding. Whole cell binding with fusion proteins constructed between either Galpha(s) or Galpha(q) and the NK1 receptor with a truncated tail, which secured non-promiscuous G-protein interaction, demonstrated monocomponent agonist binding closely corresponding to either of the two affinity states found in the wild-type receptor. High affinity binding of both substance P and neurokinin A was observed in the tail-truncated Galpha(s) fusion construct, whereas the lower affinity component was displayed by the tail-truncated Galpha(q) fusion. The elusive difference between the affinity determined in heterologous versus homologous binding assays for substance P and especially for neurokinin A was eliminated in the G-protein fusions. An NK1 receptor mutant with a single substitution at the extracellular end of TM-III-(F111S), which totally uncoupled the receptor from Galpha(s) signaling, showed binding properties that were monocomponent and otherwise very similar to those observed in the tail-truncated Galpha(q) fusion construct. Thus, the heterogenous pharmacological phenotype displayed by the NK1 receptor is a reflection of the occurrence of two active conformations or molecular phenotypes representing complexes with the Galpha(s) and Galpha(q) species, respectively. We propose that these molecular forms do not interchange readily, conceivably because of the occurrence of microdomains or "signal-transductosomes" within the cell membrane.

Theory of melting at high pressures: Amending density functional theory with quantum Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shulenburger, L.; Desjarlais, M. P.; Mattsson, T. R.

We present an improved first-principles description of melting under pressure based on thermodynamic integration comparing Density Functional Theory (DFT) and quantum Monte Carlo (QMC) treatments of the system. The method is applied to address the longstanding discrepancy between density functional theory (DFT) calculations and diamond anvil cell (DAC) experiments on the melting curve of xenon, a noble gas solid where van der Waals binding is challenging for traditional DFT methods. The calculations show excellent agreement with data below 20 GPa and that the high-pressure melt curve is well described by a Lindemann behavior up to at least 80 GPa, amore » finding in stark contrast to DAC data.« less

Theory of melting at high pressures: Amending density functional theory with quantum Monte Carlo

DOE PAGES

Shulenburger, L.; Desjarlais, M. P.; Mattsson, T. R.

2014-10-01

We present an improved first-principles description of melting under pressure based on thermodynamic integration comparing Density Functional Theory (DFT) and quantum Monte Carlo (QMC) treatments of the system. The method is applied to address the longstanding discrepancy between density functional theory (DFT) calculations and diamond anvil cell (DAC) experiments on the melting curve of xenon, a noble gas solid where van der Waals binding is challenging for traditional DFT methods. The calculations show excellent agreement with data below 20 GPa and that the high-pressure melt curve is well described by a Lindemann behavior up to at least 80 GPa, amore » finding in stark contrast to DAC data.« less

The effect of 2,3-diphosphoglycerate on the oxygen dissociation curve of human haemoglobin.

PubMed Central

Goodford, P J; Norrington, F E; Paterson, R A; Wootton, R

1977-01-01

1. Oxygen dissociation curves for concentrated human haemoglobin solutions (1.6 mmol dm-3 in haem) have been measured by mixing known quantities of oxy- and deoxyhaemoglobin solutions and measuring the resulting partial pressure of oxygen with an oxygen electrode. 2. Observations in the presence of 2,3-diphosphoglycerate support previous conclusions derived from experiments at low haemoglobin concentrations, the validity of which has been questioned. 3. The two affinity state model of Monod, Wyman & Changeux (1965) does not fully describe the actions of 2,3-diphosphoglycerate and a model in which this allosteric effector not only binds preferentially to the T state but also lowers the oxygen affinity of this state gives an improved fit to the data. PMID:604451

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, G.F.; Marks, B.H.

This study examines the beta adrenergic receptors of the rabbit detrusor smooth muscle, employing (/sup 125/I)iodocyanopindolol (ICYP) as a ligand for the binding of beta adrenergic receptors. Saturation binding experiments on the isolated membrane fraction yielded a KD for ICYP of 14.7 pM and a maximum binding of 147.6 fmol/mg of protein. Displacement of labeled ICYP by a series of beta adrenergic agents yielded the following KD values for the combined high and low affinity binding sites: I-propranolol, 0.76 nM; ICI 118,551, 1.7 nM; zinterol, 38.0 nM; metoprolol, 3.5 microM; and practolol, 61.4 microM. When these displacement experimental results weremore » compared to KD values from other reported binding studies with ICYP for beta adrenoreceptors, both the order of potency and the KD values indicated primarily beta-2 adrenergic receptor subtypes. Computer program Scatfit analysis of the displacement curves indicated a single slope and affinity constant for all five beta adrenergic agents. Hofstee plots for zinterol, ICI 118,551 and metoprolol, however, were not linear and indicated that minor populations of beta-1 adrenoreceptors were also present as both high and low affinity binding sites could be defined. It is concluded that the primary receptor population is beta-2 and that this tissue is heterogenous with a small population of beta-1 adrenoreceptors representing approximately 13 to 23% of the total beta adrenoreceptor population.« less

Regulation of uterine progesterone receptors by the nonsteroidal anti-androgen hydroxyflutamide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandrasekhar, Y.; Armstrong, D.T.

1991-07-01

The authors have recently reported that the anti-androgen hydroxyflutamide causes delayed implantation and exhibits antideciduogenic activity in the rat. The present experiments were conducted to examine whether hydroxyflutamide binds to the uterine progesterone receptors and/or alters the progesterone binding sites in the uterus. Cytosol and nuclear fractions from decidualized rat uterus were incubated with (3H)-R5020 without or with increasing concentrations of radioinert R5020, RU486, dihydrotestosterone, or hydroxyflutamide. From the log-dose inhibition curves, the relative binding affinity of both hydroxyflutamide and dihydrotestosterone was less than 0.1% and 2%, compared with R5020 (100%) for displacing (3H)-R5020 bound to uterine cytosol and nuclearmore » fractions, respectively. Injection of estradiol-17 beta (1 microgram/rat) to ovariectomized prepubertal rats induced a 1.85-fold increase in uterine weight by 24 h. Hydroxyflutamide at 2.5 or 5.0 mg did not significantly alter the estrogen-induced increase in uterine weight. Compared to vehicle alone, estrogen induced an approximately 5-fold increase in uterine cytosolic progesterone binding sites. Hydroxyflutamide at both 2.5- and 5.0-mg doses significantly attenuated the estrogen-induced elevation in uterine progesterone binding sites. These studies demonstrate that hydroxyflutamide does not bind with high affinity to progesterone receptors, but suppresses the estrogen-induced elevation in progesterone receptor levels in the uterus.« less

A FEM-based method to determine the complex material properties of piezoelectric disks.

PubMed

Pérez, N; Carbonari, R C; Andrade, M A B; Buiochi, F; Adamowski, J C

2014-08-01

Numerical simulations allow modeling piezoelectric devices and ultrasonic transducers. However, the accuracy in the results is limited by the precise knowledge of the elastic, dielectric and piezoelectric properties of the piezoelectric material. To introduce the energy losses, these properties can be represented by complex numbers, where the real part of the model essentially determines the resonance frequencies and the imaginary part determines the amplitude of each resonant mode. In this work, a method based on the Finite Element Method (FEM) is modified to obtain the imaginary material properties of piezoelectric disks. The material properties are determined from the electrical impedance curve of the disk, which is measured by an impedance analyzer. The method consists in obtaining the material properties that minimize the error between experimental and numerical impedance curves over a wide range of frequencies. The proposed methodology starts with a sensitivity analysis of each parameter, determining the influence of each parameter over a set of resonant modes. Sensitivity results are used to implement a preliminary algorithm approaching the solution in order to avoid the search to be trapped into a local minimum. The method is applied to determine the material properties of a Pz27 disk sample from Ferroperm. The obtained properties are used to calculate the electrical impedance curve of the disk with a Finite Element algorithm, which is compared with the experimental electrical impedance curve. Additionally, the results were validated by comparing the numerical displacement profile with the displacements measured by a laser Doppler vibrometer. The comparison between the numerical and experimental results shows excellent agreement for both electrical impedance curve and for the displacement profile over the disk surface. The agreement between numerical and experimental displacement profiles shows that, although only the electrical impedance curve is considered in the adjustment procedure, the obtained material properties allow simulating the displacement amplitude accurately. Copyright © 2014 Elsevier B.V. All rights reserved.

Characterization of nicotine binding to the rat brain P/sub 2/ preparation: the identification of multiple binding sites which include specific up-regulatory site(s)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sloan, J.W.

1984-01-01

These studies show that nicotine binds to the rat brain P/sub 2/ preparation by saturable and reversible processes. Multiple binding sites were revealed by the configuration of saturation, kinetic and Scatchard plots. A least squares best fit of Scatchard data using nonlinear curve fitting programs confirmed the presence of a very high affinity site, an up-regulatory site, a high affinity site and one or two low affinity sites. Stereospecificity was demonstrated for the up-regulatory site where (+)-nicotine was more effective and for the high affinity site where (-)-nicotine had a higher affinity. Drugs which selectively up-regulate nicotine binding site(s) havemore » been identified. Further, separate very high and high affinity sites were identified for (-)- and (+)-(/sup 3/H)nicotine, based on evidence that the site density for the (-)-isomer is 10 times greater than that for the (+)-isomer at these sites. Enhanced nicotine binding has been shown to be a statistically significant phenomenon which appears to be a consequence of drugs binding to specific site(s) which up-regulate binding at other site(s). Although Scatchard and Hill plots indicate positive cooperatively, up-regulation more adequately describes the function of these site(s). A separate up-regulatory site is suggested by the following: (1) Drugs vary markedly in their ability to up-regulate binding. (2) Both the affinity and the degree of up-regulation can be altered by structural changes in ligands. (3) Drugs with specificity for up-regulation have been identified. (4) Some drugs enhance binding in a dose-related manner. (5) Competition studies employing cold (-)- and (+)-nicotine against (-)- and (+)-(/sup 3/H)nicotine show that the isomers bind to separate sites which up-regulate binding at the (-)- and (+)-nicotine high affinity sites and in this regard (+)-nicotine is more specific and efficacious than (-)-nicotine.« less

Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

PubMed

Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

2016-11-25

The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

First archaeointensity catalogue and intensity secular variation curve for Iberia spanning the last 3000 years

NASA Astrophysics Data System (ADS)

Molina-Cardín, Alberto; Campuzano, Saioa A.; Rivero, Mercedes; Osete, María Luisa; Gómez-Paccard, Miriam; Pérez-Fuentes, José Carlos; Pavón-Carrasco, F. Javier; Chauvin, Annick; Palencia-Ortas, Alicia

2017-04-01

In this work we present the first archaeomagnetic intensity database for the Iberian Peninsula covering the last 3 millennia. In addition to previously published archaeointensities (about 100 data), we present twenty new high-quality archaeointensities. The new data have been obtained following the Thellier and Thellier method including pTRM-checks and have been corrected for the effect of the anisotropy of thermoremanent magnetization upon archaeointensity estimates. Importantly, about 50% of the new data obtained correspond to the first millennium BC, a period for which there was not possible to develop an intensity palaeosecular variation curve before due to the lack of high-quality archaeointensity data. The different qualities of the data included in the Iberian dataset have been evaluated following different palaeomagnetic criteria, such as the number of specimens analysed, the laboratory protocol applied and the kind of material analysed. Finally, we present the first intensity palaeosecular variation curve for the Iberian Peninsula centred at Madrid for the last 3000 years. In order to obtain the most reliable secular variation curve, it has been generated using only selected high-quality data from the catalogue.

Stretching a Curved Surface in a Viscous Fluid

NASA Astrophysics Data System (ADS)

Sajid, M.; N., Ali; T., Javed; Z., Abbas

2010-02-01

This work is concerned with the viscous flow due to a curved stretching sheet. The similarity solution of the problem is obtained numerically by a shooting method using the Runge-Kutta algorithm. The physical quantities of interest like the fluid velocity and skin friction coefficient are obtained and discussed under the influence of dimensionless curvature. It is evident from the results that dimensionless curvature causes an increase in boundary layer thickness and a decrease in the skin friction coefficient.

Simultaneous realization of slow and fast acoustic waves using a fractal structure of Koch curve.

PubMed

Ding, Jin; Fan, Li; Zhang, Shu-Yi; Zhang, Hui; Yu, Wei-Wei

2018-01-24

An acoustic metamaterial based on a fractal structure, the Koch curve, is designed to simultaneously realize slow and fast acoustic waves. Owing to the multiple transmitting paths in the structure resembling the Koch curve, the acoustic waves travelling along different paths interfere with each other. Therefore, slow waves are created on the basis of the resonance of a Koch-curve-shaped loop, and meanwhile, fast waves even with negative group velocities are obtained due to the destructive interference of two acoustic waves with opposite phases. Thus, the transmission of acoustic wave can be freely manipulated with the Koch-curve shaped structure.

Convection, diffusion and reaction in a surface-based biosensor: modeling of cooperativity and binding site competition on the surface and in the hydrogel.

PubMed

Lebedev, Konstantin; Mafé, Salvador; Stroeve, Pieter

2006-04-15

We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.

Binding of benzocaine in batrachotoxin-modified Na+ channels. State- dependent interactions

PubMed Central

1994-01-01

Hille (1977. Journal of General Physiology. 69:497-515) first proposed a modulated receptor hypothesis (MRH) to explain the action of benzocaine in voltage-gated Na+ channels. Using the MRH as a framework, we examined benzocaine binding in batrachotoxin (BTX)-modified Na+ channels under voltage-clamp conditions using either step or ramp command signals. We found that benzocaine binding is strongly voltage dependent. At -70 mV, the concentration of benzocaine that inhibits 50% of BTX-modified Na+ currents in GH3 cells (IC50) is 0.2 mM, whereas at +50 mV, the IC50 is 1.3 mM. Dose-response curves indicate that only one molecule of benzocaine is required to bind with one BTX-modified Na+ channel at -70 mV, whereas approximately two molecules are needed at +50 mV. Upon treatment with the inactivation modifier chloramine-T, the binding affinity of benzocaine is reduced significantly at -70 mV, probably as a result of the removal of the inactivated state of BTX- modified Na+ channels. The same treatment, however, enhances the binding affinity of cocaine near this voltage. External Na+ ions appear to have little effect on benzocaine binding, although they do affect cocaine binding. We conclude that two mechanisms underlie the action of local anesthetics in BTX-modified Na+ channels. Unlike open-channel blockers such as cocaine and bupivacaine, neutral benzocaine binds preferentially with BTX-modified Na+ channels in a closed state. Furthermore, benzocaine can be modified chemically so that it behaves like an open-channel blocker. This compound also elicits a use- dependent block in unmodified Na+ channels after repetitive depolarizations, whereas benzocaine does not. The implications of these findings for the MRH theory will be discussed. PMID:8195785

Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics

NASA Astrophysics Data System (ADS)

Bhakat, Soumendranath; Söderhjelm, Pär

2017-01-01

The funnel metadynamics method enables rigorous calculation of the potential of mean force along an arbitrary binding path and thereby evaluation of the absolute binding free energy. A problem of such physical paths is that the mechanism characterizing the binding process is not always obvious. In particular, it might involve reorganization of the solvent in the binding site, which is not easily captured with a few geometrically defined collective variables that can be used for biasing. In this paper, we propose and test a simple method to resolve this trapped-water problem by dividing the process into an artificial host-desolvation step and an actual binding step. We show that, under certain circumstances, the contribution from the desolvation step can be calculated without introducing further statistical errors. We apply the method to the problem of predicting host-guest binding free energies in the SAMPL5 blind challenge, using two octa-acid hosts and six guest molecules. For one of the hosts, well-converged results are obtained and the prediction of relative binding free energies is the best among all the SAMPL5 submissions. For the other host, which has a narrower binding pocket, the statistical uncertainties are slightly higher; longer simulations would therefore be needed to obtain conclusive results.

High pressure melting curve of platinum up to 35 GPa

NASA Astrophysics Data System (ADS)

Patel, Nishant N.; Sunder, Meenakshi

2018-04-01

Melting curve of Platinum (Pt) has been measured up to 35 GPa using our laboratory based laser heated diamond anvil cell (LHDAC) facility. Laser speckle method has been employed to detect onset of melting. High pressure melting curve of Pt obtained in the present study has been compared with previously reported experimental and theoretical results. The melting curve measured agrees well within experimental error with the results of Kavner et al. The experimental data fitted with simon equation gives (∂Tm/∂P) ˜25 K/GPa at P˜1 MPa.

The Designs of Fins Air-Cooled Cylinders

DTIC Science & Technology

1939-06-28

4 (a). EMer part of figure 4 clearly shows that, for one pnir of values of s and t, the heat transfer is a maximum. The peak values of the curves of...specified s” curves. Similarly, the peak values of the curves of constant values of t shown in &ure 4 (b) and of similar cwwes plotted for othm values of... picking the values of optimum g and t from these curves: PIots of tk type shown in figure 4 were obtained for - other \\ralues of M and Aplpa,/m by means

Bandwidth increasing mechanism by introducing a curve fixture to the cantilever generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Weiqun, E-mail: weiqunliu@home.swjtu.edu.cn; Liu, Congzhi; Ren, Bingyu

2016-07-25

A nonlinear wideband generator architecture by clamping the cantilever beam generator with a curve fixture is proposed. Devices with different nonlinear stiffness can be obtained by properly choosing the fixture curve according to the design requirements. Three available generator types are presented and discussed for polynomial curves. Experimental investigations show that the proposed mechanism effectively extends the operation bandwidth with good power performance. Especially, the simplicity and easy feasibility allow the mechanism to be widely applied for vibration generators in different scales and environments.

Empirical constraints on closure temperatures from a single diffusion coefficient

NASA Astrophysics Data System (ADS)

Lee, J. K. W.

The elucidation of thermal histories by geochronological and isotopic means is based fundamentally on solid-state diffusion and the concept of closure temperatures. Because diffusion is thermally activated, an analytical solution of the closure temperature (Tc*) can only be obtained if the diffusion coefficient D of the diffusion process is measured at two or more different temperatures. If the diffusion coefficient is known at only one temperature, however, the true closure temperature (Tc*) cannot be calculated analytically because there exist an infinite number of possible (apparent) closure temperatures (Tc) which can be generated by this single datum. By introducing further empirical constraints to limit the range of possible closure temperatures, however, mathematical analysis of a modified form of the closure temperature equation shows that it is possible to make both qualitative and quantitative estimates of Tc* given knowledge of only one diffusion coefficient DM measured at one temperature TM. Qualitative constraints of the true closure temperature Tc* are obtained from the shapes of curves on a graph of the apparent Tc (Tc) vs. activation energy E, in which each curve is based on a single diffusion coefficient measurement DM at temperature TM. Using a realistic range of E, the concavity of the curve shows whether TM is less than, approximately equal to, or greater than Tc*. Quantitative estimates are obtained by considering two dimensionless parameters [lnÊRT^c vs. Tc*/TM] derived from these curves. When these parameters are plotted for known argon diffusion data and for a given diffusion size and cooling rate, it is found that the resultant curves are almost identical for all of the commonly dated K-Ar minerals - biotite, phlogopite, muscovite, hornblende and orthoclase - in spite of differences in their diffusion parameters. A common curve for Ar diffusion can be derived by least-squares fitting of all the Ar diffusion data and provides a way of predicting a ``model'' closure temperature Tcm from a single diffusion coefficient DM at temperature TM. Preliminary diffusion data for a labradorite lead to a Tcm of 507+/-17°C and a corresponding activation energy of about 65kcal/mol, given a grain size of 200μm and a cooling rate of 5°C/Ma. Curves for He diffusion in silicates (augite, quartz and sanidine) also overlap to a significant degree, both among themselves and with the Ar model curve, suggesting that a single model curve may be a good representation of noble gas closure temperatures in silicates. An analogous model curve for a selection of 18O data can also be constructed, but this curve differs from the Ar model curve. A single model curve for cationic species does not appear to exist, however, suggesting that chemical bonding relationships between the ionic size/charge and crystal structure may influence the closure temperatures of diffusing cations. An indication of the degree of overlap among the various curves for Ar, He, 18O and cations is also obtained by considering the dimensionless parameter E/RTc*; for the noble gases and 18O, E/RTc* values for the respective minerals are very similar, whereas for cations, there is significant dispersion. Given these constraints, this may be a potential method of estimating closure temperatures for certain diffusing species when there are limited diffusion data.

Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design

PubMed Central

2012-01-01

The aim of fragment-based drug design (FBDD) is to identify molecular fragments that bind to alternate subsites within a given binding pocket leading to cooperative binding when linked. In this study, the binding of fragments to human phenylethanolamine N-methyltransferase is used to illustrate how (a) current protocols may fail to detect fragments that bind cooperatively, (b) theoretical approaches can be used to validate potential hits, and (c) apparent false positives obtained when screening against cocktails of fragments may in fact indicate promising leads. PMID:24900472

[Screening specific recognition motif of RNA-binding proteins by SELEX in combination with next-generation sequencing technique].

PubMed

Zhang, Lu; Xu, Jinhao; Ma, Jinbiao

2016-07-25

RNA-binding protein exerts important biological function by specifically recognizing RNA motif. SELEX (Systematic evolution of ligands by exponential enrichment), an in vitro selection method, can obtain consensus motif with high-affinity and specificity for many target molecules from DNA or RNA libraries. Here, we combined SELEX with next-generation sequencing to study the protein-RNA interaction in vitro. A pool of RNAs with 20 bp random sequences were transcribed by T7 promoter, and target protein was inserted into plasmid containing SBP-tag, which can be captured by streptavidin beads. Through only one cycle, the specific RNA motif can be obtained, which dramatically improved the selection efficiency. Using this method, we found that human hnRNP A1 RRMs domain (UP1 domain) bound RNA motifs containing AGG and AG sequences. The EMSA experiment indicated that hnRNP A1 RRMs could bind the obtained RNA motif. Taken together, this method provides a rapid and effective method to study the RNA binding specificity of proteins.

Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors.

PubMed

Sun, Meijian; Wang, Xia; Zou, Chuanxin; He, Zenghui; Liu, Wei; Li, Honglin

2016-06-07

RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA interactions of RNA-binding proteins. Newly developed discriminative descriptors will help to improve the prediction accuracy of these prediction methods and provide further meaningful information for researchers. In this work, we designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the two features were powerful for identifying RNA-binding protein residues. Using these two features and other excellent structure- and sequence-based features, a random forest classifier was constructed to predict RNA-binding residues. The area under the receiver operating characteristic curve (AUC) of five-fold cross-validation for our method on training set RBP195 was 0.900, and when applied to the test set RBP68, the prediction accuracy (ACC) was 0.868, and the F-score was 0.631. The good prediction performance of our method revealed that the two newly designed descriptors could be discriminative for inferring protein residues interacting with RNAs. To facilitate the use of our method, a web-server called RNAProSite, which implements the proposed method, was constructed and is freely available at http://lilab.ecust.edu.cn/NABind .

Effect of H2 binding on the nonadiabatic transition probability between singlet and triplet states of the [NiFe]-hydrogenase active site.

PubMed

Kaliakin, Danil S; Zaari, Ryan R; Varganov, Sergey A

2015-02-12

We investigate the effect of H2 binding on the spin-forbidden nonadiabatic transition probability between the lowest energy singlet and triplet electronic states of [NiFe]-hydrogenase active site model, using a velocity averaged Landau-Zener theory. Density functional and multireference perturbation theories were used to provide parameters for the Landau-Zener calculations. It was found that variation of the torsion angle between the terminal thiolate ligands around the Ni center induces an intersystem crossing between the lowest energy singlet and triplet electronic states in the bare active site and in the active site with bound H2. Potential energy curves between the singlet and triplet minima along the torsion angle and H2 binding energies to the two spin states were calculated. Upon H2 binding to the active site, there is a decrease in the torsion angle at the minimum energy crossing point between the singlet and triplet states. The probability of nonadiabatic transitions at temperatures between 270 and 370 K ranges from 35% to 32% for the active site with bound H2 and from 42% to 38% for the bare active site, thus indicating the importance of spin-forbidden nonadiabatic pathways for H2 binding on the [NiFe]-hydrogenase active site.

Dimeric, trimeric and tetrameric complexes of immunoglobulin G fix complement.

PubMed Central

Wright, J K; Tschopp, J; Jaton, J C; Engel, J

1980-01-01

The binding of pure dimers, trimers and tetramers of randomly cross-linked non-immune rabbit immunoglobulin G to the first component and subcomponent of the complement system, C1 and C1q respectively, was studied. These oligomers possessed open linear structures. All three oligomers fixed complement with decreasing affinity in the order: tetramer, trimer, dimer. Complement fixation by dimeric immunoglobulin exhibited the strongest concentration-dependence. No clear distinction between a non-co-operative and a co-operative binding mechanism could be achieved, although the steepness of the complement-fixation curves for dimers and trimers was better reflected by the co-operative mechanism. Intrinsic binding constants were about 10(6)M-1 for dimers, 10(7)M-1 for trimers and 3 X 10(9)M-1 for tetramers, assuming non-co-operative binding. The data are consistent with a maximum valency of complement component C1 for immunoglobulin G protomers in the range 6-18. The binding of dimers to purified complement subcomponent C1q was demonstrated by sedimentation-velocity ultracentrifugation. Mild reduction of the complexes by dithioerythritol caused the immunoglobulin to revert to the monomeric state (S20,w = 6.2-6.5S) with concomitant loss of complement-fixing ability. Images Fig. 2. PMID:6985362

Esr Spectra of Alkali-Metal Atoms on Helium Nanodroplets: a Theoretical Model for the Prediction of Helium Induced Hyperfine Structure Shifts

NASA Astrophysics Data System (ADS)

Hauser, Reas W.; Filatov, Michael; Ernst, Wolfgang E.

2013-06-01

We predict He-droplet-induced changes of the isotropic HFS constant a_{HFS} of the alkali-metal atoms M = Li, Na, K and Rb on the basis of a model description. Optically detected electron spin resonance spectroscopy has allowed high resolution measurements that show the influence of the helium droplet and its size on the unpaired electron spin density at the alkali nucleus. Our theoretical approach to describe this dependence is based on a combination of two well established techniques: Results of relativistic coupled-cluster calculations on the alkali-He dimers (energy and HFS constant as functions of the binding length) are mapped onto the doped-droplet-situation with the help of helium-density functional theory. We simulate doped droplets He_{N} with N ranging from 50 to 10000, using the diatomic alkali-He-potential energy curves as input. From the obtained density profiles we evaluate average distances between the dopant atom and its direct helium neighborhood. The distances are then set in relation to the variation of the HFS constant with binding length in the simplified alkali-He-dimer model picture. This method yields reliable relative shifts but involves a systematic absolute error. Hence, the absolute values of the shifts are tied to one experimentally determined HFS constant for ^{85}Rb-He_{N = 2000}. With this parameter choice we obtain results in good agreement with the available experimental data for Rb and K^{a,b} confirming the predicted 1/N trend of the functional dependence^{c}. M. Koch, G. Auböck, C. Callegari, and W. E. Ernst, Phys. Rev. Lett. 103, 035302-1-4 (2009) M. Koch, C. Callegari, and W. E. Ernst, Mol. Phys. 108 (7), 1005-1011 (2010) A. W. Hauser, T. Gruber, M. Filatov, and W. E. Ernst, ChemPhysChem (2013) online DOI: 10.1002/cphc.201200697

Dual-Tracer PET Using Generalized Factor Analysis of Dynamic Sequences

PubMed Central

Fakhri, Georges El; Trott, Cathryn M.; Sitek, Arkadiusz; Bonab, Ali; Alpert, Nathaniel M.

2013-01-01

Purpose With single-photon emission computed tomography, simultaneous imaging of two physiological processes relies on discrimination of the energy of the emitted gamma rays, whereas the application of dual-tracer imaging to positron emission tomography (PET) imaging has been limited by the characteristic 511-keV emissions. Procedures To address this limitation, we developed a novel approach based on generalized factor analysis of dynamic sequences (GFADS) that exploits spatio-temporal differences between radiotracers and applied it to near-simultaneous imaging of 2-deoxy-2-[18F]fluoro-D-glucose (FDG) (brain metabolism) and 11C-raclopride (D2) with simulated human data and experimental rhesus monkey data. We show theoretically and verify by simulation and measurement that GFADS can separate FDG and raclopride measurements that are made nearly simultaneously. Results The theoretical development shows that GFADS can decompose the studies at several levels: (1) It decomposes the FDG and raclopride study so that they can be analyzed as though they were obtained separately. (2) If additional physiologic/anatomic constraints can be imposed, further decomposition is possible. (3) For the example of raclopride, specific and nonspecific binding can be determined on a pixel-by-pixel basis. We found good agreement between the estimated GFADS factors and the simulated ground truth time activity curves (TACs), and between the GFADS factor images and the corresponding ground truth activity distributions with errors less than 7.3±1.3 %. Biases in estimation of specific D2 binding and relative metabolism activity were within 5.9±3.6 % compared to the ground truth values. We also evaluated our approach in simultaneous dual-isotope brain PET studies in a rhesus monkey and obtained accuracy of better than 6 % in a mid-striatal volume, for striatal activity estimation. Conclusions Dynamic image sequences acquired following near-simultaneous injection of two PET radiopharmaceuticals can be separated into components based on the differences in the kinetics, provided their kinetic behaviors are distinct. PMID:23636489

Measurement of regional cerebral blood flow with copper-62-PTSM and a three-compartment model.

PubMed

Okazawa, H; Yonekura, Y; Fujibayashi, Y; Mukai, T; Nishizawa, S; Magata, Y; Ishizu, K; Tamaki, N; Konishi, J

1996-07-01

We evaluated quantitatively 62Cu-labeled pyruvaldehyde bis(N4-methylthiosemicarbazone) copper II (62Cu-PTSM) as a brain perfusion tracer for positron emission tomography (PET). For quantitative measurement, the octanol extraction method is needed to correct for arterial radioactivity in estimating the lipophilic input function, but the procedure is not practical for clinical studies. To measure regional cerebral blood flow (rCBF) by 62Cu-PTSM with simple arterial blood sampling, a standard curve of the octanol extraction ratio and a three-compartment model were applied. We performed both 15O-labeled water PET and 62 Cu-PTSM PET with dynamic data acquisition and arterial sampling in six subjects. Data obtained in 10 subjects studied previously were used for the standard octanol extraction curve. Arterial activity was measured and corrected to obtain the true input function using the standard curve. Graphical analysis (Gjedde-Patlak plot) with the data for each subject fitted by a straight regression line suggested that 62Cu-PTSM can be analyzed by the three-compartment model with negligible K4. Using this model, K1-K3 were estimated from curve fitting of the cerebral time-activity curve and the corrected input function. The fractional uptake of 62Cu-PTSM was corrected to rCBF with the individual extraction at steady state calculated from K1-K3. The influx rates (Ki) obtained from three-compartment model and graphical analyses were compared for the validation of the model. A comparison of rCBF values obtained from 62Cu-PTSM and 150-water studies demonstrated excellent correlation. The results suggest the potential feasibility of quantitation of cerebral perfusion with 62Cu-PTSM accompanied by dynamic PET and simple arterial sampling.

Reverberation Mapping of the Kepler-Field AGN KA1858+4850

NASA Technical Reports Server (NTRS)

Pei, Liuyi; Barth, Aaron J.; Aldering, Greg S.; Briley, Michael M.; Carroll, Carla J.; Carson, Daniel J.; Cenko, S., Bradley; Clubb, Kelsey I.; Cohen, Daniel P.; Cucchiara, Antonino;

Reverberation Mapping of the KEPLER Field AGN KA1858+4850

NASA Astrophysics Data System (ADS)

Pei, Liuyi; Barth, Aaron J.; Aldering, Greg S.; Briley, Michael M.; Carroll, Carla J.; Carson, Daniel J.; Cenko, S. Bradley; Clubb, Kelsey I.; Cohen, Daniel P.; Cucchiara, Antonino; Desjardins, Tyler D.; Edelson, Rick; Fang, Jerome J.; Fedrow, Joseph M.; Filippenko, Alexei V.; Fox, Ori D.; Furniss, Amy; Gates, Elinor L.; Gregg, Michael; Gustafson, Scott; Horst, J. Chuck; Joner, Michael D.; Kelly, Patrick L.; Lacy, Mark; Laney, C. David; Leonard, Douglas C.; Li, Weidong; Malkan, Matthew A.; Margon, Bruce; Neeleman, Marcel; Nguyen, My L.; Prochaska, J. Xavier; Ross, Nathaniel R.; Sand, David J.; Searcy, Kinchen J.; Shivvers, Isaac S.; Silverman, Jeffrey M.; Smith, Graeme H.; Suzuki, Nao; Smith, Krista Lynne; Tytler, David; Werk, Jessica K.; Worseck, Gábor

2014-11-01

KA1858+4850 is a narrow-line Seyfert 1 galaxy at redshift 0.078 and is among the brightest active galaxies monitored by the Kepler mission. We have carried out a reverberation mapping campaign designed to measure the broad-line region size and estimate the mass of the black hole in this galaxy. We obtained 74 epochs of spectroscopic data using the Kast Spectrograph at the Lick 3 m telescope from 2012 February to November, and obtained complementary V-band images from five other ground-based telescopes. We measured the Hβ light curve lag with respect to the V-band continuum light curve using both cross-correlation techniques (CCF) and continuum light curve variability modeling with the JAVELIN method and found rest-frame lags of τ CCF = 13.53+2.03-2.32 days and τ JAVELIN = 13.15+1.08-1.00 days. The Hβ rms line profile has a width of σline = 770 ± 49 km s-1. Combining these two results and assuming a virial scale factor of f = 5.13, we obtained a virial estimate of M{BH} = 8.06+1.59-1.72 × 106 {M}⊙ for the mass of the central black hole and an Eddington ratio of L/L Edd ≈ 0.2. We also obtained consistent but slightly shorter emission-line lags with respect to the Kepler light curve. Thanks to the Kepler mission, the light curve of KA1858+4850 has among the highest cadences and signal-to-noise ratios ever measured for an active galactic nucleus; thus, our black hole mass measurement will serve as a reference point for relations between black hole mass and continuum variability characteristics in active galactic nuclei.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conroy, W.G.

Structural relatedness between the variable region of anti-ligand antibodies and opioid binding sites allowed the generation of anti-idiotypic antibodies which recognized opioid receptors. The IgG{sub 3}k antibodies which bound to opioid receptors were obtained when an anti-morphine antiserum was the idiotype. Both antibodies bound to opioid receptors, but only one of these blocked the binding of ({sup 3}H)naloxone. The antibody which did not inhibit the binding of ({sup 3}H)naloxone was itself displaced from the receptor by opioid ligands. The unique binding properties displayed by this antibody indicated that anti-idiotypic antibodies are not always a perfect image of the original ligand,more » and therefore may be more useful than typical ligands as probes for the receptor. An auto-anti-idiotypic technique was successfully used to obtain anti-opioid receptor antibodies. Another IgG{sub 3}k antibody that blocked the binding of ({sup 3}H)naloxone to rat brain opioid receptors was obtained when a mouse was immunized with naloxone conjugated to bovine serum albumin. These data confirmed that an idiotype-anti-idiotype network which can generate an anti-receptor antibody normally functions when an opioid ligand is introduced into an animal in an immunogenic form.« less

Mobility-based correction for accurate determination of binding constants by capillary electrophoresis-frontal analysis.

PubMed

Qian, Cheng; Kovalchik, Kevin A; MacLennan, Matthew S; Huang, Xiaohua; Chen, David D Y

2017-06-01

Capillary electrophoresis frontal analysis (CE-FA) can be used to determine binding affinity of molecular interactions. However, its current data processing method mandate specific requirement on the mobilities of the binding pair in order to obtain accurate binding constants. This work shows that significant errors are resulted when the mobilities of the interacting species do not meet these requirements. Therefore, the applicability of CE-FA in many real word applications becomes questionable. An electrophoretic mobility-based correction method is developed in this work based on the flux of each species. A simulation program and a pair of model compounds are used to verify the new equations and evaluate the effectiveness of this method. Ibuprofen and hydroxypropyl-β-cyclodextrinare used to demonstrate the differences in the obtained binding constant by CE-FA when different calculation methods are used, and the results are compared with those obtained by affinity capillary electrophoresis (ACE). The results suggest that CE-FA, with the mobility-based correction method, can be a generally applicable method for a much wider range of applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.

PubMed

Sprouffske, Kathleen; Wagner, Andreas

2016-04-19

Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis. Growthcurver summarizes the growth characteristics of microbial growth curve experiments conducted in a plate reader. The data are fitted to a standard form of the logistic equation, and the parameters have clear interpretations on population-level characteristics, like doubling time, carrying capacity, and growth rate. Growthcurver is an easy-to-use R package available for installation from the Comprehensive R Archive Network (CRAN). The source code is available under the GNU General Public License and can be obtained from Github (Sprouffske K, Growthcurver sourcecode, 2016).

Localized Principal Component Analysis based Curve Evolution: A Divide and Conquer Approach

PubMed Central

Appia, Vikram; Ganapathy, Balaji; Yezzi, Anthony; Faber, Tracy

2014-01-01

We propose a novel localized principal component analysis (PCA) based curve evolution approach which evolves the segmenting curve semi-locally within various target regions (divisions) in an image and then combines these locally accurate segmentation curves to obtain a global segmentation. The training data for our approach consists of training shapes and associated auxiliary (target) masks. The masks indicate the various regions of the shape exhibiting highly correlated variations locally which may be rather independent of the variations in the distant parts of the global shape. Thus, in a sense, we are clustering the variations exhibited in the training data set. We then use a parametric model to implicitly represent each localized segmentation curve as a combination of the local shape priors obtained by representing the training shapes and the masks as a collection of signed distance functions. We also propose a parametric model to combine the locally evolved segmentation curves into a single hybrid (global) segmentation. Finally, we combine the evolution of these semilocal and global parameters to minimize an objective energy function. The resulting algorithm thus provides a globally accurate solution, which retains the local variations in shape. We present some results to illustrate how our approach performs better than the traditional approach with fully global PCA. PMID:25520901

Comparative magnetic and thermoanalytical study of two enstatite chondrites: Adhi Kot and Atlanta

NASA Astrophysics Data System (ADS)

Krol, Elizabeth; Lang, Bruno

1993-03-01

With allowance for the discussion of classification of enstatite chondrites and their relation to aubrites, the obtained magnetic and thermoanalytical data is submitted to be considered as additive arguments. Our study covered the Adhi Kot (EH4) and Atlanta (EL6). meteorites belonging to two distinct groups of enstatite chondrites. Applying AF demagnetization the intensity of natural remanent magnetization (NRM) was measured and the mean magnetic susceptibility of the samples was determined. The differential thermal (DTA) and thermogravimetric (TG) curves were obtained for meteorites under study. For measurements of the intensity of NRM, a superconducting cryomagnetometer SQUID (2 G Enterprise, USA), while magnetic susceptibility Kappabridge KLY-2 (Czechoslovakia) were used. The abbreviated magnetic data sheets are given. The values 786 x 10-4A/mkg and 196.1 x 10-4A/mkg were obtained as NRM intensities for Atlanta and Adhi Kot respectively, while 17.4 x 10-6 SIu/kg and 43.4 x 10-6 SIu/kg for their susceptibilities. Both meteorites proved to be strongly magnetized. The demagnetization down to 3.2 percent of NMR was received for Atlanta at AF field intensity of 250 Oe. For Adhi Kot at this level rested 13.2 percent of NRM intensity, this sample being demagnetized without change of direction till 750 Oe field. The demagnetization curves are similar to those obtained for Abee (EL4) chondrite by Sugiura and Strangway. Against Abee the Adhi Kot exhibited a little bit steeper downfall, and in both cases dominate one component of magnetization. The DTA and TG curves were obtained with Rigaku-Denki thermoanalytical instrument. The DTA curves exhibit striking similarity in their shape and relatively close temperature values for various features. The same is valid for TG curves. The higher values for TG for Adhi Kot express its higher content of oxydable (Fe, Ni) whose oxidation in air is reached at 1000-1200 C.

Comparative magnetic and thermoanalytical study of two enstatite chondrites: Adhi Kot and Atlanta

NASA Technical Reports Server (NTRS)

Krol, Elizabeth; Lang, Bruno

1993-01-01

With allowance for the discussion of classification of enstatite chondrites and their relation to aubrites, the obtained magnetic and thermoanalytical data is submitted to be considered as additive arguments. Our study covered the Adhi Kot (EH4) and Atlanta (EL6). meteorites belonging to two distinct groups of enstatite chondrites. Applying AF demagnetization the intensity of natural remanent magnetization (NRM) was measured and the mean magnetic susceptibility of the samples was determined. The differential thermal (DTA) and thermogravimetric (TG) curves were obtained for meteorites under study. For measurements of the intensity of NRM, a superconducting cryomagnetometer SQUID (2 G Enterprise, USA), while magnetic susceptibility Kappabridge KLY-2 (Czechoslovakia) were used. The abbreviated magnetic data sheets are given. The values 786 x 10(exp -4)A/mkg and 196.1 x 10(exp -4)A/mkg were obtained as NRM intensities for Atlanta and Adhi Kot respectively, while 17.4 x 10(exp -6) SIu/kg and 43.4 x 10(exp -6) SIu/kg for their susceptibilities. Both meteorites proved to be strongly magnetized. The demagnetization down to 3.2 percent of NMR was received for Atlanta at AF field intensity of 250 Oe. For Adhi Kot at this level rested 13.2 percent of NRM intensity, this sample being demagnetized without change of direction till 750 Oe field. The demagnetization curves are similar to those obtained for Abee (EL4) chondrite by Sugiura and Strangway. Against Abee the Adhi Kot exhibited a little bit steeper downfall, and in both cases dominate one component of magnetization. The DTA and TG curves were obtained with Rigaku-Denki thermoanalytical instrument. The DTA curves exhibit striking similarity in their shape and relatively close temperature values for various features. The same is valid for TG curves. The higher values for TG for Adhi Kot express its higher content of oxydable (Fe, Ni) whose oxidation in air is reached at 1000-1200 C.

Expression, crosslinking, and developing modulus master curves of recombinant resilin.

PubMed

Khandaker, Md Shahriar K; Dudek, Daniel M; Beers, Eric P; Dillard, David A

2017-05-01

Resilin is a disordered elastomeric protein found in specialized regions of insect cuticles, where low stiffness and high resilience are required. Having a wide range of functions that vary among insect species, resilin operates across a wide frequency range, from 5Hz for locomotion to 13kHz for sound production. We synthesize and crosslink a recombinant resilin from clone-1 (exon-1+exon-2) of the gene, and determine the water content (approximately 80wt%) and dynamic mechanical properties, along with estimating surface energies relevant for adhesion. Dynamic moduli master curves have been developed, by applying the time-temperature superposition principle (TTSP) and time-temperature concentration superposition principle (TTCSP), and compared with reported master curves for natural resilin from locusts, dragonflies, and cockroaches. To our knowledge, this is the first time dynamic moduli master curves have been developed to explore the dynamic mechanical properties of recombinant resilin and compare with resilin behavior. The resulting master curves show that the synthetic resilin undergoes a pronounced transition with increasing ethanol concentrations, with the storage modulus increasing by approximately three orders of magnitude. Although possibly a glass transition, alternate explanations include the formation of intramolecular hydrogen bonds or that the chitin binding domain (ChBD) in exon-2 might change the secondary structure of the normally disordered exon-1 into more ordered conformations that limit deformation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Projecting diffusion along the normal bundle of a plane curve

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valero-Valdés, Carlos; Herrera-Guzmán, Rafael

2014-05-15

The purpose of this paper is to provide new formulas for the effective diffusion coefficient of a generalized Fick-Jacob's equation obtained by projecting the two-dimensional diffusion equation along the normal directions of an arbitrary curve on the plane.

Sensing of hydrophobic cavity of serum albumin by an adenosine analogue: fluorescence correlation and ensemble spectroscopic studies.

PubMed

Nag, Moupriya; Bera, Kallol; Chakraborty, Sandipan; Basak, Soumen

2013-10-05

Adenosine is a naturally occurring purine nucleoside that plays important role in various biochemical processes. We have studied the binding of TNP-Ado (trinitrophenylated-adenosine), a fluorescent analogue of adenosine (which itself is a weak fluorophore), with a model transport protein, bovine serum albumin (BSA). The binding affinity was determined using Fluorescence correlation spectroscopy (FCS) and compared with its value obtained from macroscopic fluorescence spectroscopic studies. Fluorescence and circular dichroism (CD) spectroscopies were employed together with molecular docking study to locate the probable binding site of TNP-Ado on BSA and its effect on the conformation and stability of BSA. Fluorescence studies showed that TNP-Ado binds to BSA in 1:1 stoichiometry via an entropically favoured process. Induced CD spectra revealed that a chiro-optical switching of TNP-Ado occurs upon binding to BSA. Results on urea-induced denaturation of BSA and docking study suggested that the binding site for the ligand is in the hydrophobic subdomain IIA of BSA, consistent with the results of other measurements. This study establishes TNP-Ado as a sensor of hydrophobic regions in proteins like serum albumin, having the capability of detecting a minimum concentration of 140ng/ml protein. FCS measurement of binding interaction of rhodamine-labeled TNP-Ado (RTNP-Ado) with BSA yielded an association constant of KFCS=(1.03±0.06) × 10(4)M(-1). The association constants (Ka) obtained for binding of BSA with rhodamine-free (i.e. TNP-Ado) and rhodamine-labeled (RTNP-Ado) ligands, obtained using the ensemble spectroscopic technique, were (2.3±0.06) × 10(5)M(-1) and (3.4±0.03) × 10(4)M(-1), respectively. The difference between the values of Ka for the free and labeled ligands suggests that fluorescent labeling of small molecules perceptibly interferes with the binding process. On the other hand, the difference in Ka obtained by FCS and ensemble techniques is due to the fact that while the former measures the change in the diffusion constant (i.e. size) of RTNP-Ado upon binding to BSA, the latter focuses on the change of tryptophan emission properties of BSA due to the presence of bound RTNP-Ado. Copyright © 2013 Elsevier B.V. All rights reserved.

Implementation Learning and Forgetting Curve to Scheduling in Garment Industry

NASA Astrophysics Data System (ADS)

Muhamad Badri, Huda; Deros, Baba Md; Syahri, M.; Saleh, Chairul; Fitria, Aninda

2016-02-01

The learning curve shows the relationship between time and the cumulative number of units produced which using the mathematical description on the performance of workers in performing repetitive works. The problems of this study is level differences in the labors performance before and after the break which affects the company's production scheduling. The study was conducted in the garment industry, which the aims is to predict the company production scheduling using the learning curve and forgetting curve. By implementing the learning curve and forgetting curve, this paper contributes in improving the labors performance that is in line with the increase in maximum output 3 hours productive before the break are 15 unit product with learning curve percentage in the company is 93.24%. Meanwhile, the forgetting curve improving maximum output 3 hours productive after the break are 11 unit product with the percentage of forgetting curve in the company is 92.96%. Then, the obtained 26 units product on the productive hours one working day is used as the basic for production scheduling.

Thermochemistry of the specific binding of C12 surfactants to bovine serum albumin.

PubMed

Nielsen, A D; Borch, K; Westh, P

2000-06-15

The specific binding to bovine serum albumin (BSA) of anionic and non-ionic surfactants with C12 acyl chains has been studied by high sensitivity isothermal titration calorimetry. This method proved particularly effective in resolving the binding of anionic surfactants into separate classes of sites with different affinity. For sodium dodecylsulfate (SDS) the measured binding curves could be rationalized as association to two classes (high affinity/low affinity) of sites comprising, respectively, three and six similar (i.e. thermodynamically equivalent), independent sites. Changes in the thermodynamic functions enthalpy, standard free energy, standard entropy and heat capacity could be discerned for each class of binding site, as well as for micelle formation. These data suggest that binding to low affinity sites (in analogy with micelle formation) exhibits energetic parameters; in particular, a large negative change in heat capacity, which is characteristic of hydrophobic interactions. The thermodynamics of high affinity binding, on the other hand, is indicative of other dominant forces; most likely electrostatic interactions. Other anionic ligands investigated (laurate and dodecyl benzylsulfonate) showed a behavior similar to SDS, the most significant difference being the high affinity binding of the alkylbenzyl sulfonate. For this ligand, the thermodynamic data is indicative of a more loosely associated complex than for SDS and laurate. BSA was found to bind one or two of the non-ionic surfactants (NIS) hepta- or penta(ethylene glycol) monododecyl ether (C12EO7 and C12EO5) with binding constants about three orders of magnitude lower than for SDS. Hence, the free energy of the surfactant in the weakly bound BSA-NIS complex is only slightly favored over the micellar state. The binding process is characterized by very large exothermic enthalpy changes (larger than for the charged surfactants) and a large, positive increment in heat capacity. These observations cannot be reconciled with a molecular picture based on simple hydrophobic condensation onto non-polar patches on the protein surface.

Characterization of (/sup 3/H)pirenzepine binding to muscarinic cholinergic receptors solubilized from rat brain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luthin, G.R.; Wolfe, B.B.

Membranes prepared from rat cerebral cortex were solubilized in buffer containing 1% digitonin. Material present in the supernatant after centrifugation at 147,000 X g was shown to contain binding sites for both (/sup 3/H)quinuclidinyl benzilate ((/sup 3/H)QNB) and (/sup 3/H)pirenzepine ((/sup 3/H)PZ). Recovery of binding sites was approximately 25% of the initial membrane-bound (/sup 3/H)QNB binding sites. The Kd values for (/sup 3/H)QNB and (/sup 3/H)PZ binding to solubilized receptors were 0.3 nM and 0.1 microM, respectively. As has been observed previously in membrane preparations, (/sup 3/H)PZ appeared to label fewer solubilized binding sites than did (/sup 3/H)QNB. Maximum bindingmore » values for (/sup 3/H)PZ and (/sup 3/H)QNB binding to solubilized receptors were approximately 400 and 950 fmol/mg of protein, respectively. Competition curves for PZ inhibiting the binding of (/sup 3/H)QNB, however, had Hill slopes of 1, with a Ki value of 0.24 microM. The k1 and k-1 for (/sup 3/H)PZ binding were 3.5 X 10(6) M-1 min-1 and 0.13 min-1, respectively. The muscarinic receptor antagonists atropine, scopolamine and PZ inhibited the binding of (/sup 3/H)QNB and (/sup 3/H)PZ to solubilized receptors with Hill slopes of 1, as did the muscarinic receptor agonist oxotremorine. The muscarinic receptor agonist carbachol competed for (/sup 3/H)QNB and (/sup 3/H)PZ binding with a Hill slope of less than 1 in cerebral cortex, but not in cerebellum. GTP did not alter the interactions of carbachol or oxotremorine with the solubilized receptor. Together, these data suggest that muscarinic receptor sites solubilized from rat brain retain their abilities to interact selectively with muscarinic receptor agonists and antagonists.« less

Estimation of Mechanical Properties of Stainless Steel AISI 410 by Small-Punch Testing (Erickson Test)

NASA Astrophysics Data System (ADS)

Hassan, A.-P.

2014-07-01

The small-punch testing (SPT) method is used for determining the mechanical properties of AISI 410 (0.14% C, 12% Cr) stainless steel. A thin disc-shaped specimen with known mechanical properties is pressed with a small ball until the appearance of cracks in the former. The load - displacement curves are recorded. Computation of the yield strength and fracture energy by the curve obtained and by known formulas shows good convergence with the characteristics obtained by standard testing.

Photometric geodesy of main-belt asteroids. I - Lightcurves of 26 large, rapid rotators

NASA Technical Reports Server (NTRS)

Weidenschilling, S. J.; Chapman, C. R.; Davis, D. R.; Greenberg, R.; Levy, D. H.

1987-01-01

A 'photometric geodesy' program is selected on the basis of light-curve data from five years' observations of large, rapidly rotating asteroids, where the observing protocol was designed to obtain precise, absolute photometry at a wide variety of orbital longitudes and phase angles. A total of 257 complete or partial light-curves are obtained for 26 asteroids; the data set will allow the future determination of pole positions and shapes, as well as to constrain the geophysical traits of these bodies.

Color quench correction for low level Cherenkov counting.

PubMed

Tsroya, S; Pelled, O; German, U; Marco, R; Katorza, E; Alfassi, Z B

2009-05-01

The Cherenkov counting efficiency varies strongly with color quenching, thus correction curves must be used to obtain correct results. The external (152)Eu source of a Quantulus 1220 liquid scintillation counting (LSC) system was used to obtain a quench indicative parameter based on spectra area ratio. A color quench correction curve for aqueous samples containing (90)Sr/(90)Y was prepared. The main advantage of this method over the common spectra indicators is its usefulness also for low level Cherenkov counting.

VizieR Online Data Catalog: Light curves of WASP-52 (Mancini+, 2017)

NASA Astrophysics Data System (ADS)

Mancini, L.; Southworth, J.; Raia, G.; Tregloan-Reed, J.; Molliere, P.; Bozza, V.; Bretton, M.; Bruni, I.; Ciceri, S.; D'Ago, G.; Dominik, M.; Hinse, T. C.; Hundertmark, M.; Jorgensen, U. G.; Korhonen, H.; Rabus, M.; Rahvar, S.; Starkey, D.; Calchi Novati, S.; Figuera Jaimes, R.; Henning, T.; Juncher, D.; Haugbolle, T.; Kains, N.; Popovas, A.; Schmidt, R. W.; Skottfelt, J.; Snodgrass, C.; Surdej, J.; Wertz, O.

2018-03-01

Light curves of transit events of the extrasolar planet WASP-52b. One of the datasets was obtained using the Cassini 1.52m Telescope (Gunn r) at the Astronomical Observatory of Bologna in Loiano (Italy). Three of the datasets were obtained using the Zeiss 1.23m telescope (Cousins R and Cousins I) at the German-Spanish Astronomical Centre at Calar Alto (Spain). Four of the datasets were obtained using the MPG 2.2m telescope (Sloan g, Sloan r, Sloan i, Sloan z) at the ESO Observatory in La Silla (Chile). Four of the datasets were obtained using the 1.54m Danish Telescope at the ESO Observatory in La Silla (Chile). (2 data files).

A tool for calculating binding-site residues on proteins from PDB structures.

PubMed

Hu, Jing; Yan, Changhui

2009-08-03

In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB) that consists of the protein of interest and its interacting partner(s) and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. The developed tool is very useful for the research on protein binding site analysis and prediction.

Determination of albumin in bronchoalveolar lavage fluid by flow-injection fluorometry using chromazurol S.

PubMed

Sato, Takaji; Saito, Yoshihiro; Chikuma, Masahiko; Saito, Yutaka; Nagai, Sonoko

2008-03-01

A highly sensitive flow injection fluorometry for the determination of albumin was developed and applied to the determination of albumin in human bronchoalveolar lavage fluids (BALF). This method is based on binding of chromazurol S (CAS) to albumin. The calibration curve was linear in the range of 5-200 microg/ml of albumin. A highly linear correlation (r=0.986) was observed between the albumin level in BALF samples (n=25) determined by the proposed method and by a conventional fluorometric method using CAS (CAS manual method). The IgG interference was lower in the CAS flow injection method than in the CAS manual method. The albumin level in BALF collected from healthy volunteers (n=10) was 58.5+/-13.1 microg/ml. The albumin levels in BALF samples obtained from patients with sarcoidosis and idiopathic pulmonary fibrosis were increased. This finding shows that the determination of albumin levels in BALF samples is useful for investigating lung diseases and that CAS flow injection method is promising in the determination of trace albumin in BALF samples, because it is sensitive and precise.

A kinetic model to explain the maximum in alpha-amylase activity measurements in the presence of small carbohydrates.

PubMed

Baks, Tim; Janssen, Anja E M; Boom, Remko M

2006-06-20

The effect of the presence of several small carbohydrates on the measurement of the alpha-amylase activity was determined over a broad concentration range. At low carbohydrate concentrations, a distinct maximum in the alpha-amylase activity versus concentration curves was observed in several cases. At higher concentrations, all carbohydrates show a decreasing alpha-amylase activity at increasing carbohydrate concentrations. A general kinetic model has been developed that can be used to describe and explain these phenomena. This model is based on the formation of a carbohydrate-enzyme complex that remains active. It is assumed that this complex is formed when a carbohydrate binds to alpha-amylase without blocking the catalytic site and its surrounding subsites. Furthermore, the kinetic model incorporates substrate inhibition and substrate competition. Depending on the carbohydrate type and concentration, the measured alpha-amylase activity can be 75% lower than the actual alpha-amylase activity. The model that has been developed can be used to correct for these effects in order to obtain the actual amount of active enzyme. 2006 Wiley Periodicals, Inc.

A reusable evanescent wave immunosensor for highly sensitive detection of bisphenol A in water samples

PubMed Central

Xiao-hong, Zhou; Lan-hua, Liu; Wei-qi, Xu; Bao-dong, Song; Jian-wu, Sheng; Miao, He; Han-chang, Shi

2014-01-01

This paper proposed a compact and portable planar waveguide evanescent wave immunosensor (EWI) for highly sensitive detection of BPA. The incident light is coupled into the planar waveguide chip via a beveled angle through undergoing total internal reflection, where the evanescent wave field forms and excites the binding fluorophore-tagged antibodies on the chip surface. Typical calibration curves obtained for BPA has detection limits of 0.03 μg/L. Linear response for BPA ranged from 0.124 μg/L–9.60 μg/L with 50% inhibition concentration for BPA of 1.09 ± 0.25 μg/L. The regeneration of the planar optical waveguide chip allows the performance of more than 300 assay cycles within an analysis time of about 20 min for each assay cycle. By application of effective pretreatment procedure, the recoveries of BPA in real water samples gave values from 88.3% ± 8.5% to 103.7% ± 3.5%, confirming its application potential in the measurement of BPA in reality. PMID:24699239

Rectification of graphene self-switching diodes: First-principles study

NASA Astrophysics Data System (ADS)

Ghaziasadi, Hassan; Jamasb, Shahriar; Nayebi, Payman; Fouladian, Majid

2018-05-01

The first principles calculations based on self-consistent charge density functional tight-binding have performed to investigate the electrical properties and rectification behavior of the graphene self-switching diodes (GSSD). The devices contained two structures called CG-GSSD and DG-GSSD which have metallic or semiconductor gates depending on their side gates have a single or double hydrogen edge functionalized. We have relaxed the devices and calculated I-V curves, transmission spectrums and maximum rectification ratios. We found that the DG-MSM devices are more favorable and more stable. Also, the DG-MSM devices have better maximum rectification ratios and current. Moreover, by changing the side gates widths and behaviors from semiconductor to metal, the threshold voltages under forward bias changed from +1.2 V to +0.3 V. Also, the maximum currents are obtained from 1.12 μA to 10.50 μA. Finally, the MSM and SSS type of all devices have minimum and maximum values of voltage threshold and maximum rectification ratios, but the 769-DG devices don't obey this rule.

On the interactions of nitriles and fluoro-substituted pyridines with silicon tetrafluoride: Computations and thin film IR spectroscopy

NASA Astrophysics Data System (ADS)

Hora, Nicholas J.; Wahl, Benjamin M.; Soares, Camilla; Lara, Skylee A.; Lanska, John R.; Phillips, James A.

2018-04-01

The nature of the interactions between silicon tetrafluoride and series of nitrogen bases, including nitriles (RCN, with R > CH3), pyridine, and various fluoro-substituted pyridines, has been investigated via quantum-chemical computations, low-temperature IR spectroscopy, and bulk reactivity experiments. Using (primarily) M06 with the 6-311+G(2df,2pd) basis set, we obtained equilibrium structures, binding energies, harmonic frequencies, and N-Si potentials in the gas-phase and in bulk dielectric media for an extensive series of 1:1 molecular complexes, including: C6H5CH2CN-SiF4, CH3CH2CN-SiF4, (CH3)3CCN-SiF4, C5H5N-SiF4, 4-FC5H4N-SiF4, 3,5-C5F2H3N-SiF4, 2,6-C5F2H3N-SiF4 and 3,4,5-C5F3H2N-SiF4. In addition, for the analogous 2:1 complexes of pyridine and 3,5-difluororpyridine, we obtained equilibrium structures, binding energies, and harmonic frequencies. The N-Si distances in the 1:1 nitrile complexes are fairly long, ranging from 2.84 Å to 2.88 Å, and the binding energies range from 4.0 to 4.2 kcal/mol (16.7-17.6 kJ/mol). Also, computations predict extremely anharmonic N-Si potentials, for which the inner portions of the curve are preferentially stabilized in dielectric media, which predict an enhancement of these interactions in condensed-phases. However, we see no evidence of bulk reactivity between C6H5CH2CN, CH3CH2CN, or (CH3)3CCN and SiF4, nor any significant interaction between (CH3)3CCN and SiF4 in low temperature IR spectra of solid, (CH3)3CCN/SiF4 thin films. Conversely, the interactions in four of the five 1:1, pyridine-SiF4 complexes are generally stronger; binding energies range from 5.7 to 9.6 kcal/mol (23.8-40.2 kJ/mol), and correspondingly the N-Si distances are relatively short (2.12-2.25 Å). The exception is 2,6-C5F2H3N-SiF4, for which the binding energy is only 3.6 kcal/mol (15.1 kJ/mol), and the N-Si distance is quite long (3.12 Å). In addition, both pyridine and 3,5-difluororpyridine were found to form stable reaction products with SiF4; but no analogous product was obtained with 2,6-difluororpyridine and SiF4, nor was any significant interaction indicated in low-temperature IR spectra of 2,6-difluororpyridine/SiF4 films. By contrast, low temperature spectra of pyridine/SiF4 and 3,5-difluororpyridine/SiF4 thin films are consistent with the presence of a distinct 2:1 reaction product. Moreover, the observed frequencies agree reasonably well with those predicted for the cis, octahedral coordination isomers of the 2:1 molecular complexes, in which the N-Si bonds are compressed slightly relative to those in the predicted gas-phase structures.

Monoclonal antibodies to human vitamin D-binding protein.

PubMed Central

Pierce, E A; Dame, M C; Bouillon, R; Van Baelen, H; DeLuca, H F

1985-01-01

Monoclonal antibodies to vitamin D-binding protein isolated from human serum have been produced. The antibodies obtained have been shown to be specific for human vitamin D-binding protein by three independent assays. The antibodies recognize human vitamin D-binding protein specifically in an enzyme-linked immunosorbent assay. Human vitamin D-binding protein is detected specifically in both pure and crude samples by a radiometric immunosorbent assay (RISA) and by an immunoprecipitation assay. The anti-human vitamin D-binding protein antibodies cross-react with monkey and pig vitamin D-binding protein, but not with vitamin D-binding protein from rat, mouse, or chicken, as determined by the RISA and immunoprecipitation assays. Images PMID:3936035

Applications of MASW Method with Different Offsets and Geophone Geometries in Buca District of Izmir City, TURKEY

NASA Astrophysics Data System (ADS)

Pamuk, Eren; Önsen, Funda; Turan, Seçil

2014-05-01

Shear-wave velocity is so critical parameter for evaluating the dynamic behaviour of soil in the subsurface investigations. Multichannel Analysis of Surface Waves (MASW) is a popular method to utilize shear-wave velocity in shallow depth surveys. This method uses the dispersive properties of shear-waves for imaging the subsurface layers. In MASW method, firstly data are acquired multichannel field records (or shot gathers), then dispersion curves are extracted. Finally, these dispersion curves are inverted to obtain one dimension (1D) Vs depth profiles. Reliable and accurate results of evaluating shear wave velocity depends on dispersion curves. Therefore, determination of basic mode dispersion curve is very important. In this study, MASW measurements were carried out different types of spread and various offsets to obtain better results in Ä°zmir, Turkey. The types of spread were selected as pairs geophone group of spread, increase spread and constant interval spread. The data were collected in the Campus of Tinaztepe, Dokuz Eylul University, Izmir (Buca). 24 channel Geometrix Geode seismic instruments, 4.5 Hz low frequency receiver (geophone) and sledge hammer (8kg) as an energy source were used in this study. The data were collected with forward shots. MASW measurements were applied different profiles and their lengths were 24 m. Geophone intervals were selected 1 m in the constant interval spread and offsets were selected respectively 1, 4, 8, 12, 24 m in all spreads. In the first stage of this study, the measurements, which were taken in these offsets, were compared between each other in all spreads. The results show that higher resolution dispersion curves were observed at 1 m, 2 m and 4 m offsets. In the other offsets (8, 12, 24 m), distinguishability between basic and higher modes dispersion curves became difficult. In the second stage of this study, obtained dispersion curves of different spread were compared to all spread type of MASW survey.

Starspots on V711 Tauri /HR 1099/

NASA Astrophysics Data System (ADS)

Dorren, J. D.; Siah, M. J.; Guinan, E. F.; McCook, G. P.

1981-04-01

Hα (λ6563) intermediate- and narrowband light curves of the RS CVn-type binary system V711 Tau (HR 1099) were obtained in 1977-1978 at Biruni Observatory and in 1977-1978 and late 1979 at Villanova Observatory, where a λ7790 light curve was also obtained in 1977-1978. The light curves are quasisinusoidal, with a period approximately equal to the spectroscopic period. A significant change in the λ6585 light curve occurred between the two observing seasons, with an increase in amplitude from 0.075 to 0.125 mag, a change of shape, and an advance in the phases of maximum and minimum light by 0.3 phase. Flaring activity in Hα was observed, on time scales from minutes to days. We fitted our light curves and V-band light curves obtained at the same time using the starspot model of Torres and Ferraz Mello. We the observed light variations are due to the synchronous rotation of spots on the heavier member of the binary system, which has been shown to be the chromospherically active star. The orbital inclination was assumed to be 35°. Radiant fluxes were taken from spectrophotometric tables. Owing to the broad wavelength coverage in 1977-1978, it was possible to determine the spot temperature to be ˜1800 K cooler than the photosphere, and hence to fix the spot area. A simple model with two circular spots of 26° radius at the same latitude, +48°, adequately reproduces the 1977-1978 light curves. The 1979 observations can be reproduced in detail by a model with two slightly larger circular spots of 31°.5 radius at latitude +15°. The spots cover about 14% of the total stellar surface in 1979. The fits also provide an explanation of the presence of an observed phase dependence in the Hα emission in 1979 but not in 1977-1978. There is a strong suggestion that a spot cycle is in progress in V711 Tau.

Kinetic operational models of agonism for G-protein-coupled receptors.

PubMed

Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

2018-06-07

The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Estimation from PET data of transient changes in dopamine concentration induced by alcohol: support for a non-parametric signal estimation method

NASA Astrophysics Data System (ADS)

Constantinescu, C. C.; Yoder, K. K.; Kareken, D. A.; Bouman, C. A.; O'Connor, S. J.; Normandin, M. D.; Morris, E. D.

2008-03-01

We previously developed a model-independent technique (non-parametric ntPET) for extracting the transient changes in neurotransmitter concentration from paired (rest & activation) PET studies with a receptor ligand. To provide support for our method, we introduced three hypotheses of validation based on work by Endres and Carson (1998 J. Cereb. Blood Flow Metab. 18 1196-210) and Yoder et al (2004 J. Nucl. Med. 45 903-11), and tested them on experimental data. All three hypotheses describe relationships between the estimated free (synaptic) dopamine curves (FDA(t)) and the change in binding potential (ΔBP). The veracity of the FDA(t) curves recovered by nonparametric ntPET is supported when the data adhere to the following hypothesized behaviors: (1) ΔBP should decline with increasing DA peak time, (2) ΔBP should increase as the strength of the temporal correlation between FDA(t) and the free raclopride (FRAC(t)) curve increases, (3) ΔBP should decline linearly with the effective weighted availability of the receptor sites. We analyzed regional brain data from 8 healthy subjects who received two [11C]raclopride scans: one at rest, and one during which unanticipated IV alcohol was administered to stimulate dopamine release. For several striatal regions, nonparametric ntPET was applied to recover FDA(t), and binding potential values were determined. Kendall rank-correlation analysis confirmed that the FDA(t) data followed the expected trends for all three validation hypotheses. Our findings lend credence to our model-independent estimates of FDA(t). Application of nonparametric ntPET may yield important insights into how alterations in timing of dopaminergic neurotransmission are involved in the pathologies of addiction and other psychiatric disorders.

Coronal deformity correction in adolescent idiopathic scoliosis patients using the fulcrum-bending radiograph: a prospective comparative analysis of the proximal thoracic, main thoracic, and thoracolumbar/lumbar curves.

PubMed

Li, Jingfeng; Dumonski, Mark L; Samartzis, Dino; Hong, Joseph; He, Shisheng; Zhu, Xiaodong; Wang, Chuanfeng; Vaccaro, Alexander R; Albert, Todd J; Li, Ming

2011-01-01

The aim of the prospective, comparative radiographic analysis was to determine the role of the fulcrum-bending radiograph (FBR) for the assessment of the proximal thoracic (PT), main thoracic (MT), and the thoracolumbar/lumbar (TL/L) curves in patients undergoing posterior spinal pedicle screw fixation and fusion for adolescent idiopathic scoliosis (AIS). The FBR demonstrated statistically better correction than other preoperative methods for the assessment of frontal plane correction of the MT curves. The fulcrum-bending correction index (FBCI) has been considered a superior method than the correction rate for comparing curve correction undergoing posterior spinal fusion because it accounts for the curve flexibility. However, their applicability to assess the PT and TL/L curves in AIS patients remains speculative. The relation between FBR and correction obtained by pedicle screws fixation is still unknown. Thirty-eight consecutive AIS patients who underwent pedicle screw fixation and posterior fusion were included in this study. The assessment of preoperative radiographs included standing posterior-anterior (PA), FBR, supine side-bending, and postoperative standing PA and lateral plain radiographs. The flexibility of the curve, as well as the FBCI, was calculated for all patients. Postoperatively, radiographs were assessed at immediate (i.e. 1 week), 3-month, 6-month, 12-month, and 2-year follow-up. Cobb angles were obtained from the PT, MT, and TL/L curves. The study consisted of 9 PT, 37 MT, and 12 TL/L curves, with a mean age of 15.1 years. The mean FBR flexibility of the PT, MT, and the TL/L curves was 42.6, 61.1, and 66.2%, respectively. The mean operative correction rates in the PT, MT, and TL/L curves were 43.4, 69.3, and 73.9%, respectively, and the mean FBCI was 103.8, 117.0, and 114.8%, respectively. Fulcrum-bending flexibility was positively correlated with the operative correction rate in PT, MT, and TL/L curves. Although the correction rate in MT and TL/L curves was higher than PT curves, the FBCI in PT, MT, and TL/L curves was not significantly different (p < 0.05). The FBR can be used to assist in the assessment of PT, MT, and TL/L curve corrections in AIS patients. When curve flexibility is taken into account by FBR, the ability of pedicle screws to correct PT, MT, and TL/L curves is the same.

Saturation behavior: a general relationship described by a simple second-order differential equation.

PubMed

Kepner, Gordon R

2010-04-13

The numerous natural phenomena that exhibit saturation behavior, e.g., ligand binding and enzyme kinetics, have been approached, to date, via empirical and particular analyses. This paper presents a mechanism-free, and assumption-free, second-order differential equation, designed only to describe a typical relationship between the variables governing these phenomena. It develops a mathematical model for this relation, based solely on the analysis of the typical experimental data plot and its saturation characteristics. Its utility complements the traditional empirical approaches. For the general saturation curve, described in terms of its independent (x) and dependent (y) variables, a second-order differential equation is obtained that applies to any saturation phenomena. It shows that the driving factor for the basic saturation behavior is the probability of the interactive site being free, which is described quantitatively. Solving the equation relates the variables in terms of the two empirical constants common to all these phenomena, the initial slope of the data plot and the limiting value at saturation. A first-order differential equation for the slope emerged that led to the concept of the effective binding rate at the active site and its dependence on the calculable probability the interactive site is free. These results are illustrated using specific cases, including ligand binding and enzyme kinetics. This leads to a revised understanding of how to interpret the empirical constants, in terms of the variables pertinent to the phenomenon under study. The second-order differential equation revealed the basic underlying relations that describe these saturation phenomena, and the basic mathematical properties of the standard experimental data plot. It was shown how to integrate this differential equation, and define the common basic properties of these phenomena. The results regarding the importance of the slope and the new perspectives on the empirical constants governing the behavior of these phenomena led to an alternative perspective on saturation behavior kinetics. Their essential commonality was revealed by this analysis, based on the second-order differential equation.

"Hook"-calibration of GeneChip-microarrays: theory and algorithm.

PubMed

Binder, Hans; Preibisch, Stephan

2008-08-29

: The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationship between the probe intensity and the specific transcript concentration in a complex environment of competing interactions, the estimation of the magnitude these effects and their correction using the intensity information of a given chip and, finally the development of practicable algorithms which judge the quality of a particular hybridization and estimate the expression degree from the intensity values. : We present the so-called hook-calibration method which co-processes the log-difference (delta) and -sum (sigma) of the perfect match (PM) and mismatch (MM) probe-intensities. The MM probes are utilized as an internal reference which is subjected to the same hybridization law as the PM, however with modified characteristics. After sequence-specific affinity correction the method fits the Langmuir-adsorption model to the smoothed delta-versus-sigma plot. The geometrical dimensions of this so-called hook-curve characterize the particular hybridization in terms of simple geometric parameters which provide information about the mean non-specific background intensity, the saturation value, the mean PM/MM-sensitivity gain and the fraction of absent probes. This graphical summary spans a metrics system for expression estimates in natural units such as the mean binding constants and the occupancy of the probe spots. The method is single-chip based, i.e. it separately uses the intensities for each selected chip. : The hook-method corrects the raw intensities for the non-specific background hybridization in a sequence-specific manner, for the potential saturation of the probe-spots with bound transcripts and for the sequence-specific binding of specific transcripts. The obtained chip characteristics in combination with the sensitivity corrected probe-intensity values provide expression estimates scaled in natural units which are given by the binding constants of the particular hybridization.

Structural analysis of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis.

PubMed

Park, Sun Cheol; Song, Wan Seok; Yoon, Sung-il

2014-04-18

S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) methylate diverse biological molecules using a SAM cofactor. The ytqB gene of Bacillus subtilis encodes a putative MTase and its biological function has never been characterized. To reveal the structural features and the cofactor binding mode of YtqB, we have determined the crystal structures of YtqB alone and in complex with its cofactor, SAM, at 1.9 Å and 2.2 Å resolutions, respectively. YtqB folds into a β-sheet sandwiched by two α-helical layers, and assembles into a dimeric form. Each YtqB monomer contains one SAM binding site, which shapes SAM into a slightly curved conformation and exposes the reactive methyl group of SAM potentially to a substrate. Our comparative structural analysis of YtqB and its homologues indicates that YtqB is a SAM-dependent class I MTase, and provides insights into the substrate binding site of YtqB. Copyright © 2014 Elsevier Inc. All rights reserved.

A novel and sensitive radioreceptor assay for serum melatonin levels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tenn, C.; Niles, L.

A simple and sensitive radioreceptor assay (RRA) has been developed to measure melatonin levels in serum. The assay is based on competition between 2-({sup 125}I)iodomelatonin (({sup 125}I)MEL) and melatonin for binding to high-affinity binding sites in chick forebrain. To measure the amount of melatonin present in a serum sample, it was extracted with dichloromethane and added to the assay medium. The percentage inhibition of radioligand binding in the presence of the extracted serum was determined and compared to the percent displacement by known amounts of melatonin in a standard curve. There was little or no cross-reactivity with other structurally relatedmore » compounds. The sensitivity of the assay is {approximately}1.5pg/0.15 mL and the intra- and inter-assay variations are approximately 8%. Since the RRA results are comparable to that of an established radioimmunoassay (RIA), it provides a sensitive and rapid alternative to the more time consuming RIA.« less

Structure-function Analysis of Receptor-binding in Adeno-Associated Virus Serotype 6 (AAV-6)

PubMed Central

Xie, Qing; Lerch, Thomas F.; Meyer, Nancy L.; Chapman, Michael S.

2011-01-01

Crystal structures of the AAV-6 capsid at 3 Å reveal a subunit fold homologous to other parvoviruses with greatest differences in two external loops. The electrostatic potential suggests that receptor-attachment is mediated by four residues: Arg576, Lys493, Lys459 and Lys531, defining a positively charged region curving up from the valley between adjacent spikes. It overlaps only partially with the receptor-binding site of AAV-2, and the residues endowing the electrostatic character are not homologous. Mutational substitution of each residue decreases heparin affinity, particularly Lys531 and Lys459. Neither is conserved among heparin-binding serotypes, indicating that diverse modes of receptor attachment have been selected in different serotypes. Surface topology and charge are also distinct at the shoulder of the spike, where linear epitopes for AAV-2’s neutralizing monoclonal antibody A20 come together. Evolutionarily, selection of changed side-chain charge may have offered a conservative means to evade immune neutralization while preserving other essential functionality. PMID:21917284

Synthesis and binding studies of Alzheimer ligands on solid support.

PubMed

Rzepecki, Petra; Geib, Nina; Peifer, Manuel; Biesemeier, Frank; Schrader, Thomas

2007-05-11

Aminopyrazole derivatives constitute the first class of nonpeptidic rationally designed beta-sheet ligands. Here we describe a double solid-phase protocol for both synthesis and affinity testing. The presented solid-phase synthesis of four types of hybrid compounds relies on the Fmoc strategy and circumvents subsequent HPLC purification by precipitating the final product from organic solution in pure form. Hexa- and octapeptide pendants with internal di- and tetrapeptide bridges are now amenable in high yields to combinatorial synthesis of compound libraries for high-throughput screening purposes. Solid-phase peptide synthesis (SPPS) on an acid-resistant PAM allows us, after PMB deprotection, to subject the free aminopyrazole binding sites in an immobilized state to on-bead assays with fluorescence-labeled peptides. From the fluorescence emission intensity decrease, individual binding constants can be calculated via reference curves by simple application of the law of mass action. Gratifyingly, host/guest complexation can be monitored quantitatively even for those ligands, which are almost insoluble in water.

Kappa2 opioid receptor subtype binding requires the presence of the DOR-1 gene.

PubMed

Ansonoff, Michael A; Wen, Ting; Pintar, John E

2010-01-01

Over the past several years substantial evidence has documented that opioid receptor homo- and heterodimers form in cell lines expressing one or more of the opioid receptors. We used opioid receptor knockout mice to determine whether in vivo pharmacological characteristics of kappa1 and kappa2 opioid receptors changed following knockout of specific opioid receptors. Using displacement of the general opioid ligand diprenorphine, we observed that occupancy or knockout of the DOR-1 gene increases the binding density of kappa1 receptors and eliminates kappa2 receptors in crude membrane preparations while the total density of kappa opioid binding sites is unchanged. Further, the analgesic potency of U69,593 in cumulative dose response curves is enhanced in mice lacking the DOR-1 gene. These results demonstrate that the DOR-1 gene is required for the expression of the kappa2 opioid receptor subtype and are consistent with the possibility that a KOR-1/DOR-1 heterodimer mediates kappa2 pharmacology.

Docking and scoring with ICM: the benchmarking results and strategies for improvement

PubMed Central

Neves, Marco A. C.; Totrov, Maxim; Abagyan, Ruben

2012-01-01

Flexible docking and scoring using the Internal Coordinate Mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The ICM virtual ligand screening was tested against the 40 DUD target benchmarks and 11-target WOMBAT sets. The self-docking accuracy was evaluated for the top 1 and top 3 scoring poses at each ligand binding site with near native conformations below 2 Å RMSD found in 91% and 95% of the predictions, respectively. The virtual ligand screening using single rigid pocket conformations provided the median area under the ROC curves equal to 69.4 with 22.0% true positives recovered at 2% false positive rate. Significant improvements up to ROC AUC= 82.2 and ROC(2%)= 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target. PMID:22569591

Pig liver pyruvate carboxylase. The reaction pathway for the decarboxylation of oxaloacetate

PubMed Central

Warren, Graham B.; Tipton, Keith F.

1974-01-01

1. The reaction pathway for the decarboxylation of oxaloacetate, catalysed by pig liver pyruvate carboxylase, was studied in the presence of saturating concentrations of K+ and acetyl-CoA. 2. Free Mg2+ binds to the enzyme in an equilibrium fashion and remains bound during all further catalytic cycles. MgADP− and Pi bind randomly, at equilibrium, followed by the binding of oxaloacetate. Pyruvate is released before the ordered steay-state release of HCO3− and MgATP2−. 3. These results are entirely consistent with studies on the carboxylation of pyruvate presented in the preceding paper (Warren & Tipton, 1974b) and together they allow a quantitative description of the reaction mechanism of pig liver pyruvate carboxylase. 4. In the absence of other substrates of the back reaction pig liver pyruvate carboxylase will decarboxylate oxaloacetate in a manner that is not inhibited by avidin. 5. Reciprocal plots involving oxaloacetate are non-linear curves, which suggest a negatively co-operative interaction between this substrate and the enzyme. PMID:4447613

The synthetic diazonamide DZ-2384 has distinct effects on microtubule curvature and dynamics without neurotoxicity

PubMed Central

Wieczorek, Michal; Tcherkezian, Joseph; Bernier, Cynthia; Prota, Andrea E.; Chaaban, Sami; Rolland, Yannève; Godbout, Claude; Hancock, Mark A.; Arezzo, Joseph C.; Ocal, Ozhan; Rocha, Cecilia; Olieric, Natacha; Hall, Anita; Ding, Hui; Bramoullé, Alexandre; Annis, Matthew G.; Zogopoulos, George; Harran, Patrick G.; Wilkie, Thomas M.; Brekken, Rolf A.; Siegel, Peter M.; Steinmetz, Michel O.; Shore, Gordon C.; Brouhard, Gary J.; Roulston, Anne

2017-01-01

Microtubule-targeting agents (MTAs) are widely used anticancer agents, but toxicities such as neuropathy limit their clinical use. MTAs bind to and alter the stability of microtubules, causing cell death in mitosis. We describe DZ-2384, a preclinical compound that exhibits potent antitumor activity in models of multiple cancer types. It has an unusually high safety margin and lacks neurotoxicity in rats at effective plasma concentrations. DZ-2384 binds the vinca domain of tubulin in a distinct way, imparting structurally and functionally different effects on microtubule dynamics compared to other vinca-binding compounds. X-ray crystallography and electron microscopy studies demonstrate that DZ-2384 causes straightening of curved protofilaments, an effect proposed to favor polymerization of tubulin. Both DZ-2384 and the vinca alkaloid vinorelbine inhibit microtubule growth rate; however, DZ-2384 increases the rescue frequency and preserves the microtubule network in nonmitotic cells and in primary neurons. This differential modulation of tubulin results in a potent MTA therapeutic with enhanced safety. PMID:27856798

Comparison of two methods to determine fan performance curves using computational fluid dynamics

NASA Astrophysics Data System (ADS)

Onma, Patinya; Chantrasmi, Tonkid

2018-01-01

This work investigates a systematic numerical approach that employs Computational Fluid Dynamics (CFD) to obtain performance curves of a backward-curved centrifugal fan. Generating the performance curves requires a number of three-dimensional simulations with varying system loads at a fixed rotational speed. Two methods were used and their results compared to experimental data. The first method incrementally changes the mass flow late through the inlet boundary condition while the second method utilizes a series of meshes representing the physical damper blade at various angles. The generated performance curves from both methods are compared with an experiment setup in accordance with the AMCA fan performance testing standard.

Light-curve solutions for S Cancri and TT Hydrae with rapid rotation

NASA Technical Reports Server (NTRS)

Van Hamme, W.; Wilson, R. E.

1993-01-01

Physical model light- and velocity-curve solutions for S Cancri and TT Hydrae are obtained, and analyses with incorporation of asynchronous rotation are carried out. A photometric rotation rate for the primary star of TT Hya is determined, and excellent agreement with results from spectral line profiles is found. Both separate light- and velocity-curve solutions and simultaneous light-velocity solutions are listed. The photometric rotation for S Cnc from existing light curves is indeterminate, but is compatible with line profile measures. Evidence for third light from the light curves of S Cnc is found. An explanation for the apparent conflict between the rotational states and mass-transfer activities of the two binaries is suggested.

Axisymmetric indentation of curved elastic membranes by a convex rigid indenter

PubMed Central

Pearce, S.P.; King, J.R.; Holdsworth, M.J.

2011-01-01

Motivated by applications to seed germination, we consider the transverse deflection that results from the axisymmetric indentation of an elastic membrane by a rigid body. The elastic membrane is fixed around its boundary, with or without an initial pre-stretch, and may be initially curved prior to indentation. General indenter shapes are considered, and the load–indentation curves that result for a range of spheroidal tips are obtained for both flat and curved membranes. Wrinkling may occur when the membrane is initially curved, and a relaxed strain-energy function is used to calculate the deformed profile in this case. Applications to experiments designed to measure the mechanical properties of seed endosperms are discussed. PMID:22298913

Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

PubMed

Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

2012-01-01

The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.

A novel specimen-preparing method using epoxy resin as binding material for LIBS analysis of powder samples.

PubMed

Shi, Linli; Lin, Qingyu; Duan, Yixiang

2015-11-01

In view of the inevitable preprocessing of powder samples for LIBS detection, epoxy resin glue was investigated for the first time as a binder of powder samples due to its superior property of improved performance in laser induced breakdown spectroscopy (LIBS) technique as a quantitative analytical tool. For comparative studies of the epoxy resin and traditional polyethylene (PE) pellets in soil, sample detection, the signal intensities of Fe (I) at 404.58 nm, Ca (I) at 443.57 nm, and Cr (I) at 453.52 nm, were studied and subsequently, the calibration curves for these elements were constructed using the standard samples with variable concentrations. The signal intensities of epoxy resin samples were, on average, about 2 times greater than those obtained with the traditional PE pellet samples. Meanwhile, the resin samples showed better R square values of 0.981, 0.985 and 0.979 for curves of Fe (I) 404.58 nm, Ca (I) 443.57 nm, and Cr (I) 453.52 nm, compared to the 0.974, 0.950 and 0.934, of the PE pellet samples. Furthermore, the former represented lower limits of detection (LOD) for Fe, Ca and Cr. These experimental results indicated that this proposed novel method based on epoxy resin can attach samples of properties of high homogeneity, cohesiveness, smoothness and hardness, which are conducive to system stability, testing accuracy and signal enhancement. This method can make LIBS more practical in powder sample analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Space-Based Observation Technology

DTIC Science & Technology

2000-10-01

Conan, V. Michau, and S. Salem . Regularized multiframe myopic deconvolution from wavefront sensing. In Propagation through the Atmosphere III...specified false alarm rate PFA . Proceeding with curving fitting, one obtains a best-fit curve “10.1y14.2 - 0.2” as the detector for the target

7 CFR 42.141 - Obtaining Operating Characteristic (OC) curve information for skip lot sampling and inspection.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., and read the new Percent of Lots Expected to be Accepted, Pas, which results when using these skip lot... point, proceed vertically to the curve and then horizontally to the left to the vertical axis. From this...

7 CFR 42.141 - Obtaining Operating Characteristic (OC) curve information for skip lot sampling and inspection.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., and read the new Percent of Lots Expected to be Accepted, Pas, which results when using these skip lot... point, proceed vertically to the curve and then horizontally to the left to the vertical axis. From this...

The top view for analysis of scoliosis progression

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Smet, A.A.; Tarlton, M.A.; Cook, L.T.

1983-05-01

Using computerized spinal analysis, a new top view was developed that displays the spine as if the observer were above and looking down on the patient. Serial top views were obtained of 12 patients with idiopathic scoliosis. In five patients with clinically stable curves, the top views showed no change. One patient with an enlaring rib hump was seen on the top view to have progressive kyphosis but stable scoliosis. Six patients with progressive scoliosis all demonstrated collapse of the thoracic curve in the anteroposterior direction. Five of these six patients had associated lumbar curves. Three lumbar curves demonstrated collapsemore » in the anteroposterior direction similar to the collapse of the thoracic curves, and the other two curves appeared elongated in the anteroposterior direction.« less

Properties of the redback millisecond pulsar binary 3FGL J0212.1+5320

NASA Astrophysics Data System (ADS)

Shahbaz, T.; Linares, M.; Breton, R. P.

2017-12-01

Linares et al. obtained quasi-simultaneous g΄-, r΄- and i΄-band light curves and an absorption-line radial velocity curve of the secondary star in the redback system 3FGL J0212.1+5320. The light curves showed two maxima and minima primarily due to the secondary star's ellipsoidal modulation, but with unequal maxima and minima. We fit these light curves and radial velocities with our X-ray binary model including either a dark solar-type star spot or a hotspot due to off-centre heating from an intrabinary shock to account for the unequal maxima. Both models give a radial velocity semi-amplitude and rotational broadening that agree with the observations. The observed secondary star's effective temperature is best matched with the value obtained using the hotspot model, which gives a neutron star and secondary star mass of M1 = 1.85 ^{+0.32}_{-0.26} M⊙ and M2 = 0.50 ^{+0.22}_{-0.19} M⊙, respectively.

The 124Sb activity standardization by gamma spectrometry for medical applications

NASA Astrophysics Data System (ADS)

de Almeida, M. C. M.; Iwahara, A.; Delgado, J. U.; Poledna, R.; da Silva, R. L.

2010-07-01

This work describes a metrological activity determination of 124Sb, which can be used as radiotracer, applying gamma spectrometry methods with hyper pure germanium detector and efficiency curves. This isotope with good activity and high radionuclidic purity is employed in the form of meglumine antimoniate (Glucantime) or sodium stibogluconate (Pentostam) to treat leishmaniasis. 124Sb is also applied in animal organ distribution studies to solve some questions in pharmacology. 124Sb decays by β-emission and it produces several photons (X and gamma rays) with energy varying from 27 to 2700 keV. Efficiency curves to measure point 124Sb solid sources were obtained from a 166mHo standard that is a multi-gamma reference source. These curves depend on radiation energy, sample geometry, photon attenuation, dead time and sample-detector position. Results for activity determination of 124Sb samples using efficiency curves and a high purity coaxial germanium detector were consistent in different counting geometries. Also uncertainties of about 2% ( k=2) were obtained.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

PubMed Central

Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

/sup 125/I interstitial implants in the RIF-1 murine flank tumor: an animal model for brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernstein, M.; Gutin, P.H.; Weaver, D.A.

1982-09-01

The development of a model for interstitial brachytherapy that uses high-activity, removable /sup 125/I sources in the RIF-1 murine flank tumor is reported. Experimental end points are clonogenic cell and tumor regrowth delay assays. For the clonogenic cell assay, interestitial radiation is delivered at total doses of 500-10,000 rad at dose rates of 0.9-2.7 rad/min to cells in annuli of tissue in the tumor. Dose-survival curves are characterized by an initial shoulder followed by a straight (exponential) portion, with D/sub 0/ similar to that of the curve obtained by external irradiation of the RIF-1 tumor in a self-contained cesium irradiatormore » at similar dose rates. Tumor regrowth curves have been obtained for minimum tumor doses of 500-5000 rad; marked tumor regression has been observed with minimum tumor doses as low as 2000 rad, but results are not as reproducible as the results obtained with the clonogenic cell assay.« less

Aerodynamic shape optimization of Airfoils in 2-D incompressible flow

NASA Astrophysics Data System (ADS)

Rangasamy, Srinivethan; Upadhyay, Harshal; Somasekaran, Sandeep; Raghunath, Sreekanth

2010-11-01

An optimization framework was developed for maximizing the region of 2-D airfoil immersed in laminar flow with enhanced aerodynamic performance. It uses genetic algorithm over a population of 125, across 1000 generations, to optimize the airfoil. On a stand-alone computer, a run takes about an hour to obtain a converged solution. The airfoil geometry was generated using two Bezier curves; one to represent the thickness and the other the camber of the airfoil. The airfoil profile was generated by adding and subtracting the thickness curve from the camber curve. The coefficient of lift and drag was computed using potential velocity distribution obtained from panel code, and boundary layer transition prediction code was used to predict the location of onset of transition. The objective function of a particular design is evaluated as the weighted-average of aerodynamic characteristics at various angles of attacks. Optimization was carried out for several objective functions and the airfoil designs obtained were analyzed.

Aging curve of neuromotor function by pronation and supination of forearms using three-dimensional wireless acceleration and angular velocity sensors.

PubMed

Kaneko, M; Okui, H; Hirakawa, G; Ishinishi, H; Katayama, Y; Iramina, K

2012-01-01

We have developed an evaluation system for pronation and supination of forearms. The motion of pronation and supination of the forearm is used as a diagnosis method of developmental disability, etc. However, this diagnosis method has a demerit in which diagnosis results between doctors are not consistent. It is hoped that a more quantitative and simple evaluation method is established. Moreover it is hoped a diagnostic criteria obtained from healthy subjects can be established to diagnose developmental disorder patients. We developed a simple and portable evaluation system for pronation and supination of forearms. Three-dimensional wireless acceleration and angular velocity sensors are used for this system. In this study, pronation and supination of forearms of 570 subjects (subjects aged 6-12, 21-100) were examined. We could obtain aging curves in the neuromotor function of pronation and supination. These aging curves obtained by our developed system, has the potential to become diagnostic criteria for a developmental disability, etc.

Evaluation of iron-binding activity of collagen peptides prepared from the scales of four cultivated fishes in Taiwan.

PubMed

Huang, Chun-Yung; Wu, Chien-Hui; Yang, Jing-Iong; Li, Ying-Han; Kuo, Jen-Min

2015-12-01

Iron deficiency is one of the most concerning deficiency problems in the world. It may generate several adverse effects such as iron deficiency anemia (IDA) and reduced physical and intellectual working capacity. The aim of this study is to evaluate the Fe(II)-binding activity of collagen peptides from fishery by-products. Lates calcarifer, Mugil cephalus, Chanos chanos, and Oreochromis spp are four major cultivated fishes in Taiwan; thousands of scales of these fish are wasted without valuable utilization. In this study, scales of these fish were hydrolyzed by papain plus flavourzyme. Collagen peptides were obtained and compared for their Fe(II)-binding activity. Collagen peptides from Chanos chanos showed the highest Fe(II)-binding activity, followed by those from Lates calcarifer and Mugil cephalus; that from Oreochromis spp exhibited the lowest one. Fe(II)-binding activity of collagen peptides from fish scales was also confirmed with a dialysis method. Molecular weight (MW) distributions of the collagen peptides from scales of four fish are all < 10 kDa, and averaged 1.3 kDa. Hydrolysates of fish scales were further partially purified with ion exchange chromatography. Fractions having Fe(II)-binding activity were obtained and their activity compared. Data obtained showed that collagen peptides from fish scales did have Fe(II)-binding activity. This is the first observation elucidating fish scale collagen possessing this functionality. The results from this study also indicated that collagen peptides from fish scales could be applied in industry as a bioresource. Copyright © 2014. Published by Elsevier B.V.

Computational approach to compact Riemann surfaces

NASA Astrophysics Data System (ADS)

Frauendiener, Jörg; Klein, Christian

2017-01-01

A purely numerical approach to compact Riemann surfaces starting from plane algebraic curves is presented. The critical points of the algebraic curve are computed via a two-dimensional Newton iteration. The starting values for this iteration are obtained from the resultants with respect to both coordinates of the algebraic curve and a suitable pairing of their zeros. A set of generators of the fundamental group for the complement of these critical points in the complex plane is constructed from circles around these points and connecting lines obtained from a minimal spanning tree. The monodromies are computed by solving the defining equation of the algebraic curve on collocation points along these contours and by analytically continuing the roots. The collocation points are chosen to correspond to Chebychev collocation points for an ensuing Clenshaw-Curtis integration of the holomorphic differentials which gives the periods of the Riemann surface with spectral accuracy. At the singularities of the algebraic curve, Puiseux expansions computed by contour integration on the circles around the singularities are used to identify the holomorphic differentials. The Abel map is also computed with the Clenshaw-Curtis algorithm and contour integrals. As an application of the code, solutions to the Kadomtsev-Petviashvili equation are computed on non-hyperelliptic Riemann surfaces.

Temporal Evolution of the Gamma-ray Burst Afterglow Spectrum for an Observer: GeV–TeV Synchrotron Self-Compton Light Curve

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukushima, Takuma; Fujita, Yutaka; To, Sho

We numerically simulate the gamma-ray burst (GRB) afterglow emission with a one-zone time-dependent code. The temporal evolutions of the decelerating shocked shell and energy distributions of electrons and photons are consistently calculated. The photon spectrum and light curves for an observer are obtained taking into account the relativistic propagation of the shocked shell and the curvature of the emission surface. We find that the onset time of the afterglow is significantly earlier than the previous analytical estimate. The analytical formulae of the shock propagation and light curve for the radiative case are also different from our results. Our results showmore » that even if the emission mechanism is switching from synchrotron to synchrotron self-Compton, the gamma-ray light curves can be a smooth power law, which agrees with the observed light curve and the late detection of a 32 GeV photon in GRB 130427A. The uncertainty of the model parameters obtained with the analytical formula is discussed, especially in connection with the closure relation between spectral index and decay index.« less

Principal curve detection in complicated graph images

NASA Astrophysics Data System (ADS)

Liu, Yuncai; Huang, Thomas S.

2001-09-01

Finding principal curves in an image is an important low level processing in computer vision and pattern recognition. Principal curves are those curves in an image that represent boundaries or contours of objects of interest. In general, a principal curve should be smooth with certain length constraint and allow either smooth or sharp turning. In this paper, we present a method that can efficiently detect principal curves in complicated map images. For a given feature image, obtained from edge detection of an intensity image or thinning operation of a pictorial map image, the feature image is first converted to a graph representation. In graph image domain, the operation of principal curve detection is performed to identify useful image features. The shortest path and directional deviation schemes are used in our algorithm os principal verve detection, which is proven to be very efficient working with real graph images.

Alpha-amylase inhibitor, CS-1036 binds to serum amylase in a concentration-dependent and saturable manner.

PubMed

Honda, Tomohiro; Kaneno-Urasaki, Yoko; Ito, Takashi; Kimura, Takako; Matsushima, Nobuko; Okabe, Hiromi; Yamasaki, Atsushi; Izumi, Takashi

2014-03-01

(2R,3R,4R)-4-hydroxy-2-(hydroxymethyl)pyrrolidin-3-yl 4-O-(6-deoxy-β-D-glucopyranosyl)-α-D-glucopyranoside (CS-1036), which is an α-amylase inhibitor, exhibited biphasic and sustained elimination with a long t1/2 (18.4-30.0 hours) in rats and monkeys, but exhibited a short t1/2 (3.7-7.9 hours) in humans. To clarify the species differences in the t1/2, the plasma protein binding of CS-1036 was evaluated by ultrafiltration. A concentration-dependent and saturable plasma protein binding of CS-1036 was observed in rats and monkeys with the dissociation rate constant (KD) of 8.95 and 27.2 nM, and maximal binding capacity (Bmax) of 52.8 and 22.1 nM, respectively. By the assessments of the recombinant amylase and immunoprecipitation, the major binding protein of CS-1036 in rats was identified as salivary amylase (KD 5.64 nM). CS-1036 also showed concentration-dependent and saturable binding to human salivary and pancreatic amylase, with similar binding affinity in rats. However, the protein binding of CS-1036 was constant in human plasma (≤10.2%) due to the lower serum amylase level compared with rats and monkeys. From the calculation of the unbound fraction (fu) in plasma based on in vitro KD and Bmax, the dose-dependent increase in fu after oral administration is speculated to lead to a dose-dependent increase in total body clearance and a high area under the curve/dose at lower doses, such as 0.3 mg/kg in rats.

Lipid Microarray Biosensor for Biotoxin Detection.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.

2006-05-01

We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates bymore » TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4« less

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

PubMed Central

Hine, Nicholas D. M.; Mostofi, Arash A.; Yarovsky, Irene

2013-01-01

Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth. PMID:24339760

iDBPs: a web server for the identification of DNA binding proteins.

PubMed

Nimrod, Guy; Schushan, Maya; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2010-03-01

The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies. http://idbps.tau.ac.il/

Interpretation of OAO-2 ultraviolet light curves of beta Doradus

NASA Technical Reports Server (NTRS)

Hutchinson, J. L.; Lillie, C. F.; Hill, S. J.

1975-01-01

Middle-ultraviolet light curves of beta Doradus, obtained by OAO-2, are presented along with other evidence indicating that the small additional bumps observed on the rising branches of these curves have their origin in shock-wave phenomena in the upper atmosphere of this classical Cepheid. A simple piston-driven spherical hydrodynamic model of the atmosphere is developed to explain the bumps, and the calculations are compared with observations. The model is found to be consistent with the shapes of the light curves as well as with measurements of the H-alpha radial velocities.

Signal processing system for electrotherapy applications

NASA Astrophysics Data System (ADS)

Płaza, Mirosław; Szcześniak, Zbigniew

2017-08-01

The system of signal processing for electrotherapeutic applications is proposed in the paper. The system makes it possible to model the curve of threshold human sensitivity to current (Dalziel's curve) in full medium frequency range (1kHz-100kHz). The tests based on the proposed solution were conducted and their results were compared with those obtained according to the assumptions of High Tone Power Therapy method and referred to optimum values. Proposed system has high dynamics and precision of mapping the curve of threshold human sensitivity to current and can be used in all methods where threshold curves are modelled.

Characteristic overpressure-impulse-distance curves for vapour cloud explosions using the TNO Multi-Energy model.

PubMed

Díaz Alonso, Fernando; González Ferradás, Enrique; Sánchez Pérez, Juan Francisco; Miñana Aznar, Agustín; Ruiz Gimeno, José; Martínez Alonso, Jesús

2006-09-21

A number of models have been proposed to calculate overpressure and impulse from accidental industrial explosions. When the blast is produced by ignition of a vapour cloud, the TNO Multi-Energy model is widely used. From the curves given by this model, data are fitted to obtain equations showing the relationship between overpressure, impulse and distance. These equations, referred herein as characteristic curves, can be fitted by means of power equations, which depend on explosion energy and charge strength. Characteristic curves allow the determination of overpressure and impulse at each distance.

On the reconstruction of the surface structure of the spotted stars

NASA Astrophysics Data System (ADS)

Kolbin, A. I.; Shimansky, V. V.; Sakhibullin, N. A.

2013-07-01

We have developed and tested a light-curve inversion technique for photometric mapping of spotted stars. The surface of a spotted star is partitioned into small area elements, over which a search is carried out for the intensity distribution providing the best agreement between the observed and model light curves within a specified uncertainty. We have tested mapping techniques based on the use of both a single light curve and several light curves obtained in different photometric bands. Surface reconstruction artifacts due to the ill-posed nature of the problem have been identified.

Microstructure based simulations for prediction of flow curves and selection of process parameters for inter-critical annealing in DP steel

NASA Astrophysics Data System (ADS)

Deepu, M. J.; Farivar, H.; Prahl, U.; Phanikumar, G.

2017-04-01

Dual phase steels are versatile advanced high strength steels that are being used for sheet metal applications in automotive industry. It also has the potential for application in bulk components like gear. The inter-critical annealing in dual phase steels is one of the crucial steps that determine the mechanical properties of the material. Selection of the process parameters for inter-critical annealing, in particular, the inter-critical annealing temperature and time is important as it plays a major role in determining the volume fractions of ferrite and martensite, which in turn determines the mechanical properties. Selection of these process parameters to obtain a particular required mechanical property requires large number of experimental trials. Simulation of microstructure evolution and virtual compression/tensile testing can help in reducing the number of such experimental trials. In the present work, phase field modeling implemented in the commercial software Micress® is used to predict the microstructure evolution during inter-critical annealing. Virtual compression tests are performed on the simulated microstructure using finite element method implemented in the commercial software, to obtain the effective flow curve of the macroscopic material. The flow curves obtained by simulation are experimentally validated with physical simulation in Gleeble® and compared with that obtained using linear rule of mixture. The methodology could be used in determining the inter-critical annealing process parameters required for achieving a particular flow curve.

M-wave, H- and V-reflex recruitment curves during maximal voluntary contraction.

PubMed

Racinais, Sebastien; Maffiuletti, Nicola A; Girard, Olivier

2013-08-01

To investigate whether the H reflex-M wave recruitment curves obtained during maximal voluntary contraction (MVC) differ from rest and to determine the stimulation intensities allowing to record stable reflex responses. Full recruitment curves (precision, 2 mA) were obtained from the soleus muscle in 14 volunteers at rest and during plantar flexion MVCs. Maximal M-wave reached significantly larger amplitude during MVC (+2.2 [0.4; 3.9] mV) for a higher stimulation intensity (+7.9 [-0.4; 16] mA). Similarly, maximal H-reflex reached significantly larger amplitude during MVC than at rest (+3.2 [0.9; 5.5] mV) for a much higher stimulation intensity (+17.7 [9.7; 25.7] mA). V-wave amplitude plateaued only when M-wave during MVC plateaued, that is, at higher intensity than M-wave at rest. V-wave was correlated to the maximal H-reflex during MVC (r = 0.79, P < 0.05). Electrically evoked potentials showed a specific recruitment curve during MVC with higher maximal values attained for higher stimulation intensities. Thus, recording reflex responses during MVC based on intensities determined at rest or as a percentage of M-wave may yield inaccurate results. V-wave presented a plateau for stimulation intensity of 1.5 times the onset of the resting M-wave plateau. Evoked potentials obtained during actual contractions should be normalized to M-waves obtained during contractions of the same force level.

Method of non-destructively inspecting a curved wall portion

DOEpatents

Fong, James T.

1996-01-01

A method of non-destructively inspecting a curved wall portion of a large and thick walled vessel for a defect by computed tomography is provided. A collimated source of radiation is placed adjacent one side of the wall portion and an array of detectors for the radiation is placed on the other side adjacent the source. The radiation from the source passing through the wall portion is then detected with the detectors over a limited angle, dependent upon the curvature of the wall of the vessel, to obtain a dataset. The source and array are then coordinately moved relative to the wall portion in steps and a further dataset is obtained at each step. The plurality of datasets obtained over the limited angle is then processed to produce a tomogram of the wall portion to determine the presence of a defect therein. In a preferred embodiment, the curved wall portion has a center of curvature so that the source and the array are positioned at each step along a respective arc curved about the center. If desired, the detector array and source can be reoriented relative to a new wall portion and an inspection of the new wall portion can be easily obtained. Further, the source and detector array can be indexed in a direction perpendicular to a plane including the limited angle in a plurality of steps so that by repeating the detecting and moving steps at each index step, a three dimensional image can be created of the wall portion.

The application of statistical parametric mapping to 123I-FP-CIT SPECT in dementia with Lewy bodies, Alzheimer's disease and Parkinson's disease.

PubMed

Colloby, Sean J; O'Brien, John T; Fenwick, John D; Firbank, Michael J; Burn, David J; McKeith, Ian G; Williams, E David

2004-11-01

Dopaminergic loss can be visualised using (123)I-FP-CIT single photon emission computed tomography (SPECT) in several disorders including Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Most previous SPECT studies have adopted region of interest (ROI) methods for analysis, which are subjective and operator-dependent. The purpose of this study was to investigate differences in striatal binding of (123)I-FP-CIT SPECT using the automated technique of statistical parametric mapping (SPM99) in subjects with DLB, Alzheimer's disease (AD), PD and healthy age-matched controls. This involved spatial normalisation of each subject's image to a customised template, followed by smoothing and intensity normalisation of each image to its corresponding mean occipital count per voxel. Group differences were assessed using a two-sample t test. Applying a height threshold of P

Concentration-dependent interactions of the organophosphates chlorpyrifos oxon and methyl paraoxon with human recombinant acetylcholinesterase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaushik, R.; Rosenfeld, Clint A.; Sultatos, L.G.

2007-06-01

For many decades it has been thought that oxygen analogs (oxons) of organophosphorus insecticides phosphorylate the catalytic site of acetylcholinesterase by a mechanism that follows simple Michaelis-Menten kinetics. More recently, the interactions of at least some oxons have been shown to be far more complex and likely involve binding of oxons to a second site on acetylcholinesterase that modulates the inhibitory capacity of other oxon molecules at the catalytic site. The current study has investigated the interactions of chlorpyrifos oxon and methyl paraoxon with human recombinant acetylcholinesterase. Both chlorpyrifos oxon and methyl paraoxon were found to have k {sub i}'smore » that change as a function of oxon concentration. Furthermore, 10 nM chlorpyrifos oxon resulted in a transient increase in acetylthiocholine hydrolysis, followed by inhibition. Moreover, in the presence of 100 nM chlorpyrifos oxon, acetylthiocholine was found to influence both the K {sub d} (binding affinity) and k {sub 2} (phosphorylation constant) of this oxon. Collectively, these results demonstrate that the interactions of chlorpyrifos oxon and methyl paraoxon with acetylcholinesterase cannot be described by simple Michaelis-Menten kinetics but instead support the hypothesis that these oxons bind to a secondary site on acetylcholinesterase, leading to activation/inhibition of the catalytic site, depending on the nature of the substrate and inhibitor. Additionally, these data raise questions regarding the adequacy of estimating risk of low levels of insecticide exposure from direct extrapolation of insecticide dose-response curves since the capacity of individual oxon molecules at low oxon levels could be greater than individual oxon molecules in vivo associated with the dose-response curve.« less

An analytical approach to obtaining JWL parameters from cylinder tests

NASA Astrophysics Data System (ADS)

Sutton, B. D.; Ferguson, J. W.; Hodgson, A. N.

2017-01-01

An analytical method for determining parameters for the JWL Equation of State from cylinder test data is described. This method is applied to four datasets obtained from two 20.3 mm diameter EDC37 cylinder tests. The calculated pressure-relative volume (p-Vr) curves agree with those produced by hydro-code modelling. The average calculated Chapman-Jouguet (CJ) pressure is 38.6 GPa, compared to the model value of 38.3 GPa; the CJ relative volume is 0.729 for both. The analytical pressure-relative volume curves produced agree with the one used in the model out to the commonly reported expansion of 7 relative volumes, as do the predicted energies generated by integrating under the p-Vr curve. The calculated energy is within 1.6% of that predicted by the model.

Bootstrap rolling window estimation approach to analysis of the Environment Kuznets Curve hypothesis: evidence from the USA.

PubMed

Aslan, Alper; Destek, Mehmet Akif; Okumus, Ilyas

2018-01-01

This study aims to examine the validity of inverted U-shaped Environmental Kuznets Curve by investigating the relationship between economic growth and environmental pollution for the period from 1966 to 2013 in the USA. Previous studies based on the assumption of parameter stability and obtained parameters do not change over the full sample. This study uses bootstrap rolling window estimation method to detect the possible changes in causal relations and also obtain the parameters for sub-sample periods. The results show that the parameter of economic growth has increasing trend in 1982-1996 sub-sample periods, and it has decreasing trend in 1996-2013 sub-sample periods. Therefore, the existence of inverted U-shaped Environmental Kuznets Curve is confirmed in the USA.

New well testing applications of the pressure derivative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onur, M.

1989-01-01

This work presents new derivative type curves based on a new derivative group which is equal to the dimensionless pressure group divided by its logarithmic derivative with respect to dimensionless time group. One major advantage of these type curves is that the type-curve match of field pressure/pressure-derivative data with the new derivative type curves is accomplished by moving the field data plot in only the horizontal direction. This type-curve match fixes time match-point values. The pressure change versus time data is then matched with the dimensionless pressure solution to determine match-point values. Well/reservoir parameters can then be estimated in themore » standard way. This two step type-curve matching procedure increases the likelihood of obtaining a unique match. Moreover, the unique correspondence between the ordinate of the field data plot and the new derivative type curves should prove useful in determining whether given field data actually represents the well/reservoir model assumed by a selected type curve solution. It is also shown that the basic idea used in construction the type curves can be used to ensure that proper semilog straight lines are chosen when analyzing pressure data by semilog methods. Analysis of both drawdown and buildup data is considered and actual field cases are analyzed using the new derivative type curves and the semilog identification method. This work also presents new methods based on the pressure derivative to analyze buildup data obtained at a well (fracture or unfractured) produced to pseudosteady-state prior to shut-in. By using a method of analysis based on the pressure derivative, it is shown that a well's drainage area at the instant of shut-in and the flow capacity can be computed directly from buildup data even in cases where conventional semilog straight lines are not well-defined.« less

A comparative study for Hydrogen storage in metal decorated graphyne nanotubes and graphyne monolayers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Jinlian; Guo, Yanhua; Zhang, Yun

A comparative study for hydrogen storage in metal decorated graphyne nanotubes and graphyne monolayers has been investigated within the framework of first-principle calculations. Our results show that the binding energies of Li, Ca, Sc, Ti on graphyne nanotubes are stronger than that on graphyne monolayers. Such strong binding would prevent the formation of metal clusters on graphyne nanotubes. From the charge transfer and partial density of states, it is found that the curvature effect of nanotubes plays an important role for the strong binding strength of metal on graphyne nanotubes. And the hydrogen storage capacity is 4.82 wt%, 5.08 wt%,more » 4.88 wt%, 4.76 wt% for Li, Ca, Sc, Ti decorated graphyne nanotubes that promise a potential material for storing hydrogen. - Graphical abstract: Metal atoms (Li, Ca, Sc and Ti) can strongly bind to graphyne nanotubes to avoid the formation of metal clusters, and a capacity of Ca@graphyne nanotube is 5.08 wt% which is close to the requirement of DOE in 2015. Twenty-four hydrogen molecules absorb to Ti-decorated graphyne nanotube. - Highlights: • The binding strength for metal on graphyne nanotubes is much stronger than that on γ-graphyne monolayer. • Metal atoms can strongly bind to the curving triangle acetylenes rings to avoid the formation of metal clusters. • A capacity of Ca@graphyne nanotube is 5.08 wt% which is close to the requirement of DOE in 2015.« less