Receptor binding kinetics equations: Derivation using the Laplace transform method.

PubMed

Hoare, Sam R J

Measuring unlabeled ligand receptor binding kinetics is valuable in optimizing and understanding drug action. Unfortunately, deriving equations for estimating kinetic parameters is challenging because it involves calculus; integration can be a frustrating barrier to the pharmacologist seeking to measure simple rate parameters. Here, a well-known tool for simplifying the derivation, the Laplace transform, is applied to models of receptor-ligand interaction. The method transforms differential equations to a form in which simple algebra can be applied to solve for the variable of interest, for example the concentration of ligand-bound receptor. The goal is to provide instruction using familiar examples, to enable investigators familiar with handling equilibrium binding equations to derive kinetic equations for receptor-ligand interaction. First, the Laplace transform is used to derive the equations for association and dissociation of labeled ligand binding. Next, its use for unlabeled ligand kinetic equations is exemplified by a full derivation of the kinetics of competitive binding equation. Finally, new unlabeled ligand equations are derived using the Laplace transform. These equations incorporate a pre-incubation step with unlabeled or labeled ligand. Four equations for measuring unlabeled ligand kinetics were compared and the two new equations verified by comparison with numerical solution. Importantly, the equations have not been verified with experimental data because no such experiments are evident in the literature. Equations were formatted for use in the curve-fitting program GraphPad Prism 6.0 and fitted to simulated data. This description of the Laplace transform method will enable pharmacologists to derive kinetic equations for their model or experimental paradigm under study. Application of the transform will expand the set of equations available for the pharmacologist to measure unlabeled ligand binding kinetics, and for other time-dependent pharmacological activities. Copyright © 2017 Elsevier Inc. All rights reserved.

Pedestrian collective motion in competitive room evacuation.

PubMed

Garcimartín, A; Pastor, J M; Martín-Gómez, C; Parisi, D; Zuriguel, I

2017-09-07

When a sizable number of people evacuate a room, if the door is not large enough, an accumulation of pedestrians in front of the exit may take place. This is the cause of emerging collective phenomena where the density is believed to be the key variable determining the pedestrian dynamics. Here, we show that when sustained contact among the individuals exists, density is not enough to describe the evacuation, and propose that at least another variable -such as the kinetic stress- is required. We recorded evacuation drills with different degrees of competitiveness where the individuals are allowed to moderately push each other in their way out. We obtain the density, velocity and kinetic stress fields over time, showing that competitiveness strongly affects them and evidencing patterns which have been never observed in previous (low pressure) evacuation experiments. For the highest competitiveness scenario, we detect the development of sudden collective motions. These movements are related to a notable increase of the kinetic stress and a reduction of the velocity towards the door, but do not depend on the density.

Competitive adsorption/desorption of tetracycline, oxytetracycline and chlortetracycline on two acid soils: Stirred flow chamber experiments.

PubMed

Fernández-Calviño, David; Bermúdez-Couso, Alipio; Arias-Estévez, Manuel; Nóvoa-Muñoz, Juan Carlos; Fernández-Sanjurjo, Maria J; Álvarez-Rodríguez, Esperanza; Núñez-Delgado, Avelino

2015-09-01

The objective of this work was to study the competitive adsorption/desorption of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) on two acid soils. We used the stirred flow chamber technique to obtain experimental data on rapid kinetic processes affecting the retention/release of the antibiotics. Both adsorption and desorption were higher on soil 1 (which showed the highest carbon, clay and Al and Fe oxides content) than on soil 2. Moreover, hysteresis affected the adsorption/desorption processes. Experimental data were fitted to a pseudo-first order equation, resulting qamax (adsorption maximum) values that were higher for soil 1 than for soil 2, and indicating that CTC competed with TC more intensely than OTC in soil 1. Regarding soil 2, the values corresponding to the adsorption kinetics constants (ka) and desorption kinetics constants for fast sites (kd1), followed a trend inverse to qamax and qdmax respectively. In conclusion, competition affected adsorption/desorption kinetics for the three antibiotics assayed, and thus retention/release and subsequent transport processes in soil and water environments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Competition H(D) Kinetic Isotope Effects in the Autoxidation of Hydrocarbons

PubMed Central

Muchalski, Hubert; Levonyak, Alexander J.; Xu, Libin; Ingold, Keith U.; Porter, Ned A.

2016-01-01

Hydrogen atom transfer is central to many important radical chain sequences. We report here a method for determination of both the primary and secondary isotope effects for symmetrical substrates by the use of NMR. Intramolecular competition reactions were carried out on substrates having an increasing number of deuterium atoms at symmetry-related sites. Products that arise from peroxyl radical abstraction at each position of the various substrates reflect the competition rates for H(D) abstraction. The primary KIE for autoxidation of tetralin was determined to be 15.9 ± 1.4, a value that exceeds the maximum predicted by differences in H(D) zero-point energies (~7) and strongly suggests that H atom abstraction by the peroxyl radical occurs with substantial quantum mechanical tunneling. PMID:25533605

Competition H(D) kinetic isotope effects in the autoxidation of hydrocarbons.

PubMed

Muchalski, Hubert; Levonyak, Alexander J; Xu, Libin; Ingold, Keith U; Porter, Ned A

2015-01-14

Hydrogen atom transfer is central to many important radical chain sequences. We report here a method for determination of both the primary and secondary isotope effects for symmetrical substrates by the use of NMR. Intramolecular competition reactions were carried out on substrates having an increasing number of deuterium atoms at symmetry-related sites. Products that arise from peroxyl radical abstraction at each position of the various substrates reflect the competition rates for H(D) abstraction. The primary KIE for autoxidation of tetralin was determined to be 15.9 ± 1.4, a value that exceeds the maximum predicted by differences in H(D) zero-point energies (∼7) and strongly suggests that H atom abstraction by the peroxyl radical occurs with substantial quantum mechanical tunneling.

Photodegradation and ecotoxicology of acyclovir in water under UV254 and UV254/H2O2 processes.

PubMed

Russo, Danilo; Siciliano, Antonietta; Guida, Marco; Galdiero, Emilia; Amoresano, Angela; Andreozzi, Roberto; Reis, Nuno M; Li Puma, Gianluca; Marotta, Raffaele

2017-10-01

The photochemical and ecotoxicological fate of acyclovir (ACY) through UV 254 direct photolysis and in the presence of hydroxyl radicals (UV 254 /H 2 O 2 process) were investigated in a microcapillary film (MCF) array photoreactor, which provided ultrarapid and accurate photochemical reaction kinetics. The UVC phototransformation of ACY was found to be unaffected by pH in the range from 4.5 to 8.0 and resembled an apparent autocatalytic reaction. The proposed mechanism included the formation of a photochemical intermediate (ϕ ACY  = (1.62 ± 0.07)·10 -3  mol ein -1 ) that further reacted with ACY to form by-products (k' = (5.64 ± 0.03)·10 -3  M -1  s -1 ). The photolysis of ACY in the presence of hydrogen peroxide accelerated the removal of ACY as a result of formation of hydroxyl radicals. The kinetic constant for the reaction of OH radicals with ACY (k OH/ACY ) determined with the kinetic modeling method was (1.23 ± 0.07)·10 9  M -1  s -1 and with the competition kinetics method was (2.30 ± 0.11)·10 9  M -1  s -1 with competition kinetics. The acute and chronic effects of the treated aqueous mixtures on different living organisms (Vibrio fischeri, Raphidocelis subcapitata, D. magna) revealed significantly lower toxicity for the samples treated with UV 254 /H 2 O 2 in comparison to those collected during UV 254 treatment. This result suggests that the addition of moderate quantity of hydrogen peroxide (30-150 mg L -1 ) might be a useful strategy to reduce the ecotoxicity of UV 254 based sanitary engineered systems for water reclamation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

NASA Astrophysics Data System (ADS)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

PubMed

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Ankle and knee kinetics between strike patterns at common training speeds in competitive male runners.

PubMed

Kuhman, Daniel; Melcher, Daniel; Paquette, Max R

2016-01-01

The purpose of this study was to investigate the interaction of foot strike and common speeds on sagittal plane ankle and knee joint kinetics in competitive rear foot strike (RFS) runners when running with a RFS pattern and an imposed forefoot strike (FFS) pattern. Sixteen competitive habitual male RFS runners ran at two different speeds (i.e. 8 and 6 min mile(-1)) using their habitual RFS and an imposed FFS pattern. A repeated measures analysis of variance was used to assess a potential interaction between strike pattern and speed for selected ground reaction force (GRF) variables and, sagittal plane ankle and knee kinematic and kinetic variables. No foot strike and speed interaction was observed for any of the kinetic variables. Habitual RFS yielded a greater loading rate of the vertical GRF, peak ankle dorsiflexor moment, peak knee extensor moment, peak knee eccentric extensor power, peak dorsiflexion and sagittal plane knee range of motion compared to imposed FFS. Imposed FFS yielded greater maximum vertical GRF, peak ankle plantarflexor moment, peak ankle eccentric plantarflexor power and sagittal plane ankle ROM compared to habitual RFS. Consistent with previous literature, imposed FFS in habitual RFS reduces eccentric knee extensor and ankle dorsiflexor involvement but produce greater eccentric ankle plantarflexor action compared to RFS. These acute differences between strike patterns were independent of running speeds equivalent to typical easy and hard training runs in competitive male runners. Current findings along with previous literature suggest differences in lower extremity kinetics between habitual RFS and imposed FFS running are consistent among a variety of runner populations.

Generation of radicals and antimalarial activity of dispiro-1,2,4-trioxolanes

NASA Astrophysics Data System (ADS)

Denisov, E. T.; Denisova, T. G.

2013-01-01

The kinetic schemes of the intramolecular oxidation of radicals generated from substituted dispiro-1,2,4-trioxolanes (seven compounds) in the presence of Fe2+ and oxygen were built. Each radical reaction was defined in terms of enthalpy, activation energy, and rate constant. The kinetic characteristics were calculated by the intersecting parabolas method. The competition between the radical reactions was considered. The entry of radicals generated by each compound into the volume was calculated. High antimalarial activity was found for 1,2,4-trioxolanes, which generated hydroxyl radicals. The structural features of trioxolanes responsible for the generation of hydroxyl radicals were determined.

Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments.

PubMed

Eng, Lars; Nygren-Babol, Linnéa; Hanning, Anders

2016-10-01

Surface plasmon resonance (SPR) is a well-established method for studying interactions between small molecules and biomolecules. In particular, SPR is being increasingly applied within fragment-based drug discovery; however, within this application area, the limited sensitivity of SPR may constitute a problem. This problem can be circumvented by the use of label-enhanced SPR that shows a 100-fold higher sensitivity as compared with conventional SPR. Truly label-free interaction data for small molecules can be obtained by applying label-enhanced SPR in a surface competition assay format. The enhanced sensitivity is accompanied by an increased specificity and inertness toward disturbances (e.g., bulk refractive index disturbances). Label-enhanced SPR can be used for fragment screening in a competitive assay format; the competitive format has the added advantage of confirming the specificity of the molecular interaction. In addition, label-enhanced SPR extends the accessible kinetic regime of SPR to the analysis of very fast fragment binding kinetics. In this article, we demonstrate the working principles and benchmark the performance of label-enhanced SPR in a model system-the interaction between carbonic anhydrase II and a number of small-molecule sulfonamide-based inhibitors. Copyright © 2016 Elsevier Inc. All rights reserved.

Studies of the di-iron(VI) Intermediate in ferrate-dependent oxygen evolution from water.

PubMed

Sarma, Rupam; Angeles-Boza, Alfredo M; Brinkley, David W; Roth, Justine P

2012-09-19

Molecular oxygen is produced from water via the following reaction of potassium ferrate (K(2)FeO(4)) in acidic solution: 4[H(3)Fe(VI)O(4)](+) + 8H(3)O(+) → 4Fe(3+) + 3O(2) + 18H(2)O. This study focuses upon the mechanism by which the O-O bond is formed. Stopped-flow kinetics at variable acidities in H(2)O and D(2)O are used to complement the analysis of competitive oxygen-18 kinetic isotope effects ((18)O KIEs) upon consumption of natural abundance water. The derived (18)O KIEs provide insights concerning the identity of the transition state. Water attack (WA) and oxo-coupling (OC) transition states were evaluated for various reactions of monomeric and dimeric ferrates using a calibrated density functional theory protocol. Vibrational frequencies from optimized isotopic structures are used here to predict (18)O KIEs for comparison to experimental values determined using an established competitive isotope-fractionation method. The high level of agreement between experimental and theoretic isotope effects points to an intramolecular OC mechanism within a di-iron(VI) intermediate, consistent with the analysis of the reaction kinetics. Alternative mechanisms are excluded based on insurmountably high free energy barriers and disagreement with calculated (18)O KIEs.

Kinetic mechanism of the dimeric ATP sulfurylase from plants

PubMed Central

Ravilious, Geoffrey E.; Herrmann, Jonathan; Goo Lee, Soon; Westfall, Corey S.; Jez, Joseph M.

2013-01-01

In plants, sulfur must be obtained from the environment and assimilated into usable forms for metabolism. ATP sulfurylase catalyses the thermodynamically unfavourable formation of a mixed phosphosulfate anhydride in APS (adenosine 5′-phosphosulfate) from ATP and sulfate as the first committed step of sulfur assimilation in plants. In contrast to the multi-functional, allosterically regulated ATP sulfurylases from bacteria, fungi and mammals, the plant enzyme functions as a mono-functional, non-allosteric homodimer. Owing to these differences, here we examine the kinetic mechanism of soybean ATP sulfurylase [GmATPS1 (Glycine max (soybean) ATP sulfurylase isoform 1)]. For the forward reaction (APS synthesis), initial velocity methods indicate a single-displacement mechanism. Dead-end inhibition studies with chlorate showed competitive inhibition versus sulfate and non-competitive inhibition versus APS. Initial velocity studies of the reverse reaction (ATP synthesis) demonstrate a sequential mechanism with global fitting analysis suggesting an ordered binding of substrates. ITC (isothermal titration calorimetry) showed tight binding of APS to GmATPS1. In contrast, binding of PPi (pyrophosphate) to GmATPS1 was not detected, although titration of the E•APS complex with PPi in the absence of magnesium displayed ternary complex formation. These results suggest a kinetic mechanism in which ATP and APS are the first substrates bound in the forward and reverse reactions, respectively. PMID:23789618

Kinetics of DSB rejoining and formation of simple chromosome exchange aberrations

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Nikjoo, H.; O'Neill, P.; Goodhead, D. T.

2000-01-01

PURPOSE: To investigate the role of kinetics in the processing of DNA double strand breaks (DSB), and the formation of simple chromosome exchange aberrations following X-ray exposures to mammalian cells based on an enzymatic approach. METHODS: Using computer simulations based on a biochemical approach, rate-equations that describe the processing of DSB through the formation of a DNA-enzyme complex were formulated. A second model that allows for competition between two processing pathways was also formulated. The formation of simple exchange aberrations was modelled as misrepair during the recombination of single DSB with undamaged DNA. Non-linear coupled differential equations corresponding to biochemical pathways were solved numerically by fitting to experimental data. RESULTS: When mediated by a DSB repair enzyme complex, the processing of single DSB showed a complex behaviour that gives the appearance of fast and slow components of rejoining. This is due to the time-delay caused by the action time of enzymes in biomolecular reactions. It is shown that the kinetic- and dose-responses of simple chromosome exchange aberrations are well described by a recombination model of DSB interacting with undamaged DNA when aberration formation increases with linear dose-dependence. Competition between two or more recombination processes is shown to lead to the formation of simple exchange aberrations with a dose-dependence similar to that of a linear quadratic model. CONCLUSIONS: Using a minimal number of assumptions, the kinetics and dose response observed experimentally for DSB rejoining and the formation of simple chromosome exchange aberrations are shown to be consistent with kinetic models based on enzymatic reaction approaches. A non-linear dose response for simple exchange aberrations is possible in a model of recombination of DNA containing a DSB with undamaged DNA when two or more pathways compete for DSB repair.

Competitive Adsorption and Oxidation Behavior of Heavy Metals on nZVI Coated with TEOS.

PubMed

Eglal, Mahmoud M; Ramamurthy, Amruthur S

2015-11-01

Zero valent iron nanoparticle (nanofer ZVI) is a powerful substance due to its coating with tetraethyl orthosilicate (TEOS). Tetraethyl orthosilicate imparts higher reactivity and decreases particle agglomeration. The competitive removal and displacement of multi-metals are influenced by time, pH, and initial concentration, the presence and properties of competing metals ion in the solution. For both the isotherm and kinetic studies performed for multi-metal removal experiments, compared to Pb II and Cd II, Cu II experienced a higher removal rate during the initial 5 minutes. After 120 minutes, all metals achieved removal efficiency in the range of 95 to 99%. The results of single and competitive kinetic tests for all three metals during the initial 5 minutes indicated that the presence of other metals generally reduce removal efficiency of metals. Both kinetic test and electron dispersive spectroscope (EDS) studies found that Cu II gets removed faster than the other metals. Pseudo-second order behavior was noted for the multi-metal removal systems.

Pressure-strain energy redistribution in compressible turbulence: return-to-isotropy versus kinetic-potential energy equipartition

NASA Astrophysics Data System (ADS)

Lee, Kurnchul; Venugopal, Vishnu; Girimaji, Sharath S.

2016-08-01

Return-to-isotropy and kinetic-potential energy equipartition are two fundamental pressure-moderated energy redistributive processes in anisotropic compressible turbulence. Pressure-strain correlation tensor redistributes energy among various Reynolds stress components and pressure-dilatation is responsible for energy reallocation between dilatational kinetic and potential energies. The competition and interplay between these pressure-based processes are investigated in this study. Direct numerical simulations (DNS) of low turbulent Mach number dilatational turbulence are performed employing the hybrid thermal Lattice Boltzman method (HTLBM). It is found that a tendency towards equipartition precedes proclivity for isotropization. An evolution towards equipartition has a collateral but critical effect on return-to-isotropy. The preferential transfer of energy from strong (rather than weak) Reynolds stress components to potential energy accelerates the isotropization of dilatational fluctuations. Understanding of these pressure-based redistributive processes is critical for developing insight into the character of compressible turbulence.

New Editions for the Apple II of the Chelsea Science Simulations.

ERIC Educational Resources Information Center

Pipeline, 1983

1983-01-01

Ten computer simulations for the Apple II are described. Subject areas of programs include: population dynamics, plant competition, enzyme kinetics, evolution and natural selection, genetic mapping, ammonia synthesis, reaction kinetics, wave interference/diffraction, satellite orbits, and particle scattering. (JN)

Regioselective, borinic acid-catalyzed monoacylation, sulfonylation and alkylation of diols and carbohydrates: expansion of substrate scope and mechanistic studies.

PubMed

Lee, Doris; Williamson, Caitlin L; Chan, Lina; Taylor, Mark S

2012-05-16

Synthetic and mechanistic aspects of the diarylborinic acid-catalyzed regioselective monofunctionalization of 1,2- and 1,3-diols are presented. Diarylborinic acid catalysis is shown to be an efficient and general method for monotosylation of pyranoside derivatives bearing three secondary hydroxyl groups (7 examples, 88% average yield). In addition, the scope of the selective acylation, sulfonylation, and alkylation is extended to 1,2- and 1,3-diols not derived from carbohydrates (28 examples); the efficiency, generality, and operational simplicity of this method are competitive with those of state-of-the-art protocols including the broadly applied organotin-catalyzed or -mediated reactions. Mechanistic details of the organoboron-catalyzed processes are explored using competition experiments, kinetics, and catalyst structure-activity relationships. These experiments are consistent with a mechanism in which a tetracoordinate borinate complex reacts with the electrophilic species in the turnover-limiting step of the catalytic cycle.

Ultrasensitive dual phosphorylation dephosphorylation cycle kinetics exhibits canonical competition behavior

NASA Astrophysics Data System (ADS)

Huang, Qingdao; Qian, Hong

2009-09-01

We establish a mathematical model for a cellular biochemical signaling module in terms of a planar differential equation system. The signaling process is carried out by two phosphorylation-dephosphorylation reaction steps that share common kinase and phosphatase with saturated enzyme kinetics. The pair of equations is particularly simple in the present mathematical formulation, but they are singular. A complete mathematical analysis is developed based on an elementary perturbation theory. The dynamics exhibits the canonical competition behavior in addition to bistability. Although widely understood in ecological context, we are not aware of a full range of biochemical competition in a simple signaling network. The competition dynamics has broad implications to cellular processes such as cell differentiation and cancer immunoediting. The concepts of homogeneous and heterogeneous multisite phosphorylation are introduced and their corresponding dynamics are compared: there is no bistability in a heterogeneous dual phosphorylation system. A stochastic interpretation is also provided that further gives intuitive understanding of the bistable behavior inside the cells.

Negative Cooperativity in the Interaction of Prostaglandin H Synthase-1 with the Competitive Inhibitor Naproxen Can Be Described as the Interaction of a Non-competitive Inhibitor with Heterogeneous Enzyme Preparation.

PubMed

Filimonov, I S; Berzova, A P; Barkhatov, V I; Krivoshey, A V; Trushkin, N A; Vrzheshch, P V

2018-02-01

The kinetic mechanism of the interaction of nonsteroidal anti-inflammatory drugs (NSAIDs) with their main pharmacological target, prostaglandin H synthase (PGHS), has not yet been established. We showed that inhibition of PGHS-1 from sheep vesicular glands by naproxen (a representative of NSAIDs) demonstrates a non-competitive character with respect to arachidonic acid and cannot be described within a framework of the commonly used kinetic schemes. However, it can be described by taking into account the negative cooperativity of naproxen binding to the cyclooxygenase active sites of the PGHS-1 homodimer (the first naproxen molecule forms a more stable complex (K 1 = 0.1 µM) with the enzyme than the second naproxen molecule (K 2 = 9.2 µM)). An apparent non-competitive interaction of PGHS-1 with naproxen is due to slow dissociation of the enzyme-inhibitor complexes. The same experimental data could also be described using commonly accepted kinetic schemes, assuming that naproxen interacts was a mixture of two enzyme species with the inhibition constants K α = 0.05 µM and K β = 18.3 µM. Theoretical analysis and numerical calculations show that the phenomenon of kinetic convergence of these two models has a general nature: when K 2 > K 1 , the kinetic patterns (for transient kinetics and equilibrium state) generated by the cooperative model could be described by a scheme assuming the presence of two enzyme forms with the inhibition constants K α = K 1 /2, K β = 2·K 2 . When K 2 < K 1 , the cooperative model can be presented as a scheme with two inhibitor molecules simultaneously binding to the enzyme with the observed inhibition constant K (K = K 1 ·K 2 ). The assumption on the heterogeneity of the enzyme preparation in relation to its affinity to the inhibitor can be used instead of the assumption on the negative cooperativity of the enzyme-inhibitor interactions for convenient and easy practical description of such phenomena in enzymology, biotechnology, pharmacology, and other fields of science.

A hybrid MD-kMC algorithm for folding proteins in explicit solvent.

PubMed

Peter, Emanuel Karl; Shea, Joan-Emma

2014-04-14

We present a novel hybrid MD-kMC algorithm that is capable of efficiently folding proteins in explicit solvent. We apply this algorithm to the folding of a small protein, Trp-Cage. Different kMC move sets that capture different possible rate limiting steps are implemented. The first uses secondary structure formation as a relevant rate event (a combination of dihedral rotations and hydrogen-bonding formation and breakage). The second uses tertiary structure formation events through formation of contacts via translational moves. Both methods fold the protein, but via different mechanisms and with different folding kinetics. The first method leads to folding via a structured helical state, with kinetics fit by a single exponential. The second method leads to folding via a collapsed loop, with kinetics poorly fit by single or double exponentials. In both cases, folding times are faster than experimentally reported values, The secondary and tertiary move sets are integrated in a third MD-kMC implementation, which now leads to folding of the protein via both pathways, with single and double-exponential fits to the rates, and to folding rates in good agreement with experimental values. The competition between secondary and tertiary structure leads to a longer search for the helix-rich intermediate in the case of the first pathway, and to the emergence of a kinetically trapped long-lived molten-globule collapsed state in the case of the second pathway. The algorithm presented not only captures experimentally observed folding intermediates and kinetics, but yields insights into the relative roles of local and global interactions in determining folding mechanisms and rates.

A Hydrogen Exchange Method Using Tritium and Sephadex: Its Application to Ribonuclease*

PubMed Central

Englander, S. Walter

2012-01-01

A new method for measuring the hydrogen exchange of macromolecules in solution is described. The method uses tritium to trace the movement of hydrogen, and utilizes Sephadex columns to effect, in about 2 minutes, a separation between tritiated macromolecule and tritiated solvent great enough to allow the measurement of bound tritium. High sensitivity and freedom from artifact is demonstrated and the possible value of the technique for investigation of other kinds of colloid-small molecule interaction is indicated. Competition experiments involving tritium, hydrogen, and deuterium indicate the absence of any equilibrium isotope effect in the ribonuclease-hydrogen isotope system, though a secondary kinetic isotope effect is apparent when ribonuclease is largely deuterated. Ribonuclease shows four clearly distinguishable kinetic classes of exchangeable hydrogens. Evidence is marshaled to suggest the independently measurable classes II, III, and IV (in order of decreasing rate of exchange) to represent “random-chain” peptides, peptides involved in α-helix, and otherwise shielded side-chain and peptide hydrogens, respectively. PMID:14075117

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.

Study on Synthesis of Thoreau-modified 3, 5-Dimethyl-Thioltoluenediamine Used as Epoxy Resin Curing Agent and Its Performance

NASA Astrophysics Data System (ADS)

Peng, Yongli; Xiao, Wenzheng

2017-06-01

A novel curing agent Thoreau modified 3, 5-Dimethyl-thioltoluenediamine was synthesized and its molecular structure was characterized by FTIR and DSC. The curing kinetics of a high toughness and low volume shrinkage ratio epoxy system (modified DMTDA/DGEBA) was studied by differential scanning calorimetry (DSC) under noni so thermal conditions. The data were fitted to an order model and autocatalytic model respectively. The results indicate that in order model deviates significantly from experimental data. Malik’s method was used to prove that the curing kinetics of the system concerned follow single-step autocatalytic model, and a “single-point model-free” approach was employed to calculate meaningful kinetic parameters. The DSC curves derived from autocatalytic model gave satisfactory agreement with that of experiment in the range 5K/min∼25K/min. As the heating rate increased, the predicted DSC curves deviated from experimental curves, and the total exothermic enthalpy declined owing to the transition of competition relationship between kinetics control and diffusion control.

Role of alkoxyl radicals on the fluorescein-based ORAC (Oxygen Radical Absorbance Capacity) assay.

PubMed

Dorta, E; Atala, E; Aspee, A; Speisky, H; Lissi, E; Lopez-Alarcon, C

2014-10-01

During the last decades the ORAC (Oxygen Radical Absorbance Capacity) assay has been widely employed to evaluate the in vitro antioxidant capacity of polyphenol-rich fruits, vegetables and beverages. The method employs fluorescein (FLH) as target molecule and AAPH (2,2'-azo-bis(2-amidinopropane)dihydrochloride) as the source of peroxyl radicals (ROO•). The protection of FLH, afforded by antioxidants (XH), is often characterized by kinetic profiles with clear lag times (LT), which are directly associated with the stoichiometry (n) of the XH-ROO• reaction. However, even for simple phenolic compounds, the LT measured imply large n values (defined as the number of ROO• moles trapped by each antioxidant molecule) which cannot be explained by a simple reaction mechanism. Nonetheless, they can be explained when considering the formation of alkoxyl radicals (RO•) from the recombination of two AAPH-derived ROO•. In the present work, we provide kinetic data showing that, in the zero order kinetic limit of FLH consumption, there is a low reaction rate incompatible with total trapping of ROO•. Thus, the consumption of FLH should be mostly related to its reaction with RO•. In addition, we present data regarding the assumption that in competitive measurements, the LT is due to efficient trapping of the ROO• by the added phenols, leading to high n values (1.7 to 23) for mono and polyphenols. These values are not in agreement with kinetic studies of the antioxidant consumption mediated by the presence of AAPH carried out by HPLC-DAD technique, which imply a competition by RO•. The results suggest that the use of FLH as probe at low concentrations give, for several antioxidants, ORAC values mainly related to their reaction towards RO• radicals instead of primary ROO•radicals. Copyright © 2014. Published by Elsevier Inc.

New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics.

PubMed

Zeilinger, Markus; Pichler, Florian; Nics, Lukas; Wadsak, Wolfgang; Spreitzer, Helmut; Hacker, Marcus; Mitterhauser, Markus

2017-12-01

Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A 3 R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the K i of eight different A 3 R antagonists, using CHO-K1 cells stably expressing the hA 3 R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants k on and k off , as well as the dedicated K d of the A 3 R agonist [ 125 I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A 3 R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.

The kinetics of crystallization of molten binary and ternary oxide systems and their application to the origination of high modulus glass fibers

NASA Technical Reports Server (NTRS)

Bacon, J. F.

1971-01-01

Emphasis on the consideration of glass formation on a kinetic process made it possible to think of glass compositions different from those normally employed in the manufacture of glass fibers. Approximately 450 new glass compositions were prepared and three dozen of these compositions have values for Young's modulus measured on bulk specimens greater than nineteen million pounds per square inch. Of the new glasses about a hundred could be drawn into fibers by mechanical methods at high speeds. The fiber which has a Young's modulus measured on the fiber of 18.6 million pounds per square inch and has been prepared in quantity as a monofilament (to date more than 150 million lineal feet of 0.2 to 0.4 mil fiber have been produced). This fiber has also been successfully incorporated both in epoxy and polyimide matrices. The epoxy resin composite has shown a modulus forty percent better than that achievable using the most common grade of competitive glass fiber, and twenty percent better than that obtainable with the best available grade of competitive glass fiber. Other glass fibers of even higher modulus have been developed.

Prediction of scuffing failure based on competitive kinetics of oxide formation and removal: Application to lubricated sliding of AISI 52100 steel on steel

NASA Astrophysics Data System (ADS)

Cutiongco, Eric C.; Chung, Yip-Wah

1994-07-01

A method for predicting scuffing failure based on the competitive kinetics of oxide formation and removal has been developed and applied to the sliding of AISI 52100 steel on steel with poly-alpha-olefin as the lubricant. Oxide formation rates were determining using static oxidation tests on coupons of 52100 steel covered with poly-alpha-olefin at temperatures of 140 C to 250 C. Oxide removal rates were determined at different combinations of initial average nominal contact pressures (950 MPa to 1578 MPa) and sliding velocities (0.4 m/s to 1.8 m/s) using a ball-on-disk vacuum tribotester. The nominal asperity flash temperatures generated during the wear tests were calculated and the temperatures corresponding to the intersection of the the Arrhenius plots of oxide formation and removal rates were determined and taken as the critical failure temperatures. The pressure-velocity failure transition diagram was constructed by plotting the critical failure temperatures along isotherms of average nominal asperity flash temperatures calculated at different combinations of contact stress and sliding speed. The predicted failure transition curve agreed well with experimental scuffing data.

A Simulation Game for the Study of Enzyme Kinetics and Inhibition.

ERIC Educational Resources Information Center

Chayoth, Reuben; Cohen, Annette

1996-01-01

Presents a simulation game that facilitates understanding of the concepts of enzyme kinetics and inhibition. The first part of the game deals with the relationship between enzyme activity and substrate concentration while the second part deals with characterization of competitive and noncompetitive inhibition of enzyme activity. (JRH)

Reactivity of superoxide radical anion and hydroperoxyl radical with alpha-phenyl-N-tert-butylnitrone (PBN) derivatives.

PubMed

Durand, Grégory; Choteau, Fanny; Pucci, Bernard; Villamena, Frederick A

2008-12-04

Nitrones have exhibited pharmacological activity against radical-mediated pathophysiological conditions and as analytical reagents for the identification of transient radical species by electron paramagnetic resonance (EPR) spectroscopy. In this work, competitive spin trapping, stopped-flow kinetics, and density functional theory (DFT) were employed to assess and predict the reactivity of O(2)(*-) and HO(2)(*) with various para-substituted alpha-phenyl-N-tert-butylnitrone (PBN) spin traps. Rate constants of O(2)(*-) trapping by nitrones were determined using competitive UV-vis stopped-flow method with phenol red (PR) as probe, while HO(2)(*) trapping rate constants were calculated using competition kinetics with 5,5-dimethylpyrroline N-oxide (DMPO) by employing EPR spectroscopy. The effects of the para substitution on the charge density of the nitronyl-carbon and on the free energies of nitrone reactivity with O(2)(*-) and HO(2)(*) were computationally rationalized at the PCM/B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) level of theory. Theoretical and experimental data show that the rate of O(2)(*-) addition to PBN derivatives is not affected by the polar effect of the substituents. However, the reactivity of HO(2)(*) follows the Hammett equation and is increased as the substituent becomes more electron withdrawing. This supports the conclusion that the nature of HO(2)(*) addition to PBN derivatives is electrophilic, while the addition of O(2)(*-) to PBN-type compounds is only weakly electrophilic.

Genotype-specific relationships among phosphorus use, growth and abundance in Daphnia pulicaria

PubMed Central

Chowdhury, Priyanka Roy; Baker, Kristina D.; Weider, Lawrence J.; Jeyasingh, Punidan D.

2017-01-01

The framework ecological stoichiometry uses elemental composition of species to make predictions about growth and competitive ability in defined elemental supply conditions. Although intraspecific differences in stoichiometry have been observed, we have yet to understand the mechanisms generating and maintaining such variation. We used variation in phosphorus (P) content within a Daphnia species to test the extent to which %P can explain variation in growth and competition. Further, we measured 33P kinetics (acquisition, assimilation, incorporation and retention) to understand the extent to which such variables improved predictions. Genotypes showed significant variation in P content, 33P kinetics and growth rate. P content alone was a poor predictor of growth rate and competitive ability. While most genotypes exhibited the typical growth penalty under P limitation, a few varied little in growth between P diets. These observations indicate that some genotypes can maintain growth under P-limited conditions by altering P use, suggesting that decomposing P content of an individual into physiological components of P kinetics will improve stoichiometric models. More generally, attention to the interplay between nutrient content and nutrient-use is required to make inferences regarding the success of genotypes in defined conditions of nutrient supply. PMID:29308224

Interactions between polyphenols in thinned young apples and porcine pancreatic α-amylase: Inhibition, detailed kinetics and fluorescence quenching.

PubMed

Sun, Lijun; Chen, Weiqi; Meng, Yonghong; Yang, Xingbin; Yuan, Li; Guo, Yurong; Warren, Frederick J; Gidley, Michael J

2016-10-01

Young apple polyphenols (YAP) and nine types of phenolic compounds were investigated regarding the inhibitory activity against porcine pancreatic α-amylase (PPA) in vitro. Tannic acid, chlorogenic acid and caffeic acid in YAP showed relatively high inhibition with the IC50 values of 0.30, 1.96 and 3.69mg/mL, respectively. A detailed kinetics of inhibition study revealed that YAP and tannic acid were competitive inhibitors of PPA, whereas chlorogenic acid and caffeic acid were mixed inhibitors, exhibiting both competitive and uncompetitive characteristics. The fluorescence of PPA could be significantly quenched by YAP and the three polyphenols, and their quenching constants were determined. The results showed that for the polyphenols investigated, the order of the apparent static quenching constants (KFQ) was in agreement with that of the reciprocal competitive inhibition constants (1/Kic) (tannic acid>chlorogenic acid>caffeic acid>epicatechin); both of the parameters were contrary to the order of the IC50 values. Thus, combining detailed kinetics and fluorescence quenching studies can be applied to characterise the interactions between polyphenols in young apples and α-amylase. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploiting Deep Eutectic Solvents and Organolithium Reagent Partnerships: Chemoselective Ultrafast Addition to Imines and Quinolines Under Aerobic Ambient Temperature Conditions.

PubMed

Vidal, Cristian; García-Álvarez, Joaquín; Hernán-Gómez, Alberto; Kennedy, Alan R; Hevia, Eva

2016-12-23

Shattering the long-held dogma that organolithium chemistry needs to be performed under inert atmospheres in toxic organic solvents, chemoselective addition of organolithium reagents to non-activated imines and quinolines has been accomplished in green, biorenewable deep eutectic solvents (DESs) at room temperature and in the presence of air, establishing a novel and sustainable access to amines. Improving on existing methods, this approach proceeds in the absence of additives; occurs without competitive enolization, reduction or coupling processes; and reactions were completed in seconds. Comparing RLi reactivities in DESs with those observed in pure glycerol or THF suggests a kinetic anionic activation of the alkylating reagents occurs, favoring nucleophilic addition over competitive hydrolysis. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a Coping Strategies Questionnaire to Assess Endurance Performance,

DTIC Science & Technology

1987-10-16

Coach. athlete, and the sport psychologist. Human Kinetics Publishers, 1979. Kroll, W. Competitive athletic stress factors in athletes and coaches...Nideffer, R.M. Athlete’s guide to mental training. Human Kinetics Publishers, Champaign, IL., 1985. Posen, K.J., Munro, I., Mitchell, G.W., & Satterth.aite...psychological coping during a 100-mile race. In Sacks, M.H. and M.L. Sacks (Eds.). Psychology of running. Human Kinetics Publishers, Champaign, al

Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

PubMed Central

Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

2009-01-01

The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

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.

Kinetic Post-match Fatigue in Professional and Youth Soccer Players During the Competitive Period

PubMed Central

Djaoui, Leo; Diaz-Cidoncha Garcia, Jorge; Hautier, Christophe; Dellal, Alexandre

2016-01-01

Background No previous research has analysed kinetic fatigue of elite adult players and elite youth players during the competitive period. Objectives The aim of the present study was to analyse kinetic post-match fatigue in professional and youth soccer players during the competitive period. Materials and Methods resting heart rate (HRrest), post-effort recovery heart rate (HRrecovery), rate of perceived exertion fatigue (RPEf), muscle soreness and blood samples with creatine kinase (CK) and resting lactate (La) from nine professional soccer players were measured immediately before, 24 hour and 48 hour after two official French first league matches (Ligue 1) whereas RPEf, HRrest, and 20m speed performance (speed-20 m) were measured in ten U-17 elite players immediately before, 24 hour and 48h after a friendly match. Results for professionals, a soccer match elevated all physiological markers during the next 24 hours (P < 0.05); only HRrecovery remained significantly different 48 hours after the match (P < 0.05) whereas there was no variation of HRrest, RPEf, and speed-20m, which were elevated until 24h and got back to reference values 48 hours after the match (P < 0.05) for the U17 players. Comparing the two groups, HRrest results remained lower all the time for professionals, and RPEf was lower for U-17, 24 hours after the match (P < 0.05). Conclusions Independent of their level, professional soccer players, need 48 hours to recover after an official match. Professionals gain more fatigue than young players after a match, but recover as fast. Thus, they recover more efficiently especially due to a better physical condition and fitness training. It is expected that the results showed in the study help elite soccer and fitness coaches to manage the training load of the team according to the match. PMID:27217927

Characterization and inhibition studies of tissue nonspecific alkaline phosphatase by aminoalkanol derivatives of 1,7-dimethyl-8,9-diphenyl-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5,10-trione, new competitive and non-competitive inhibitors, by capillary electrophoresis.

PubMed

Grodner, Błażej; Napiórkowska, Mariola

2017-09-05

The article describes the inhibitory effect of two new aminoalkanol derivatives on the enzymatic kinetic of tissue non-specific alkaline phosphatase with use of capillary zone electrophoresis to evaluate the inhibitory effect. This technique allows to investigate of the enzymatic kinetic by the measure of the amounts of the substrate and product in the presence of compound (I) or (II) in the reaction mixture. The separation process was conducted using an eCAP fused-silica capillary. The detector was set at 200nm. The best parameters for the analysis were: 25mM sodium dihydrogen phosphate adjusted to pH=2.5, temperature 25°C, and voltage -15kV. Lineweaver-Burk plots were constructed and determined by comparison of the Km, of alkaline phosphatase in the presence of inhibitor (I) or (II) with the Km in a solution without inhibitor. The influence of replacement the propylamine group by the dimethylamine group on tissue non-specific alkaline phosphatase inhibition activity of new derivatives (I) and (II) was investigated. The tested compounds (I) and (II) were found to be tissue non-specific alkaline phosphatase inhibitors. Detailed kinetic studies indicated a competitive mode of inhibition against tissue non-specific alkaline phosphatase for compound (I) and non-competitive mode of inhibition for compound (II). Copyright © 2017 Elsevier B.V. All rights reserved.

Competitive antagonism of recombinant P2X(2/3) receptors by 2', 3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate (TNP-ATP).

PubMed

Burgard, E C; Niforatos, W; van Biesen, T; Lynch, K J; Kage, K L; Touma, E; Kowaluk, E A; Jarvis, M F

2000-12-01

TNP-ATP has become widely recognized as a potent and selective P2X receptor antagonist, and is currently being used to discriminate between subtypes of P2X receptors in a variety of tissues. We have investigated the ability of TNP-ATP to inhibit alpha,beta-methylene ATP (alpha,beta-meATP)-evoked responses in 1321N1 human astrocytoma cells expressing recombinant rat or human P2X(2/3) receptors. Pharmacological responses were measured using electrophysiological and calcium imaging techniques. TNP-ATP was a potent inhibitor of P2X(2/3) receptors, blocking both rat and human receptors with IC(50) values of 3 to 6 nM. In competition studies, 10 to 1000 microM alpha,beta-meATP was able to overcome TNP-ATP inhibition. Schild analysis revealed that TNP-ATP was a competitive antagonist with pA(2) values of -8.7 and -8.2. Inhibition of P2X(2/3) receptors by TNP-ATP was rapid in onset, reversible, and did not display use dependence. Although the onset kinetics of inhibition were concentration-dependent, the TNP-ATP off-kinetics were concentration-independent and relatively slow. Full recovery from TNP-ATP inhibition did not occur until >/=5 s after removal of the antagonist. Because of the slow off-kinetics of TNP-ATP, full competition with alpha,beta-meATP for receptor occupancy could be seen only after both ligands had reached a steady-state condition. It is proposed that the slowly desensitizing P2X(2/3) receptor allowed this competitive interaction to be observed over time, whereas the rapid desensitization of other P2X receptors (P2X(3)) may mask the detection of competitive inhibition by TNP-ATP.

Generic Schemes for Single-Molecule Kinetics. 2: Information Content of the Poisson Indicator.

PubMed

Avila, Thomas R; Piephoff, D Evan; Cao, Jianshu

2017-08-24

Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a normalized measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (i.e., memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics. Based upon fitting to the functional forms of the first two waiting time moments, we show that, to second order, the non-Poissonian kinetics are generally underdetermined but can be specified in certain scenarios. For an enzymatic reaction with an arbitrary intermediate topology, we identify a generic minimum of the Poisson indicator as a function of substrate concentration, which can be used to tune substrate concentration to the stochastic fluctuations and to estimate the largest number of underlying consecutive links in a turnover cycle. We identify a local maximum of the Poisson indicator (with respect to substrate concentration) for a renewal process as a signature of competitive binding, either between a substrate and an inhibitor or between multiple substrates. Our analysis explores the rich connections between Poisson indicator measurements and microscopic kinetic mechanisms.

Concentration-dependent photodegradation kinetics and hydroxyl-radical oxidation of phenicol antibiotics.

PubMed

Li, Kai; Zhang, Peng; Ge, Linke; Ren, Honglei; Yu, Chunyan; Chen, Xiaoyang; Zhao, Yuanfeng

2014-09-01

Thiamphenicol and florfenicol are two phenicol antibiotics widely used in aquaculture and are ubiquitous as micropollutants in surface waters. The present study investigated their photodegradation kinetics, hydroxyl-radical (OH) oxidation reactivities and products. Firstly, the photolytic kinetics of the phenicols in pure water was studied as a function of initial concentrations (C0) under UV-vis irradiation (λ>200nm). It was found that the kinetics was influenced by C0. A linear plot of the pseudo-first-order rate constant vs C0 was observed with a negative slope. Secondly, the reaction between the phenicol antibiotics and OH was examined with a competition kinetic method under simulated solar irradiation (λ>290nm), which quantified their bimolecular reaction rate constants of (2.13±0.02)×10(9)M(-1)s(-1) and (1.82±0.10)×10(9)M(-1)s(-1) for thiamphenicol and florfenicol, respectively. Then the corresponding OH oxidated half-lives in sunlit surface waters were calculated to be 90.5-106.1h. Some main intermediates were formed from the reaction, which suggested that the two phenicols underwent hydroxylation, oxygenation and dehydrogenation when OH existed. These results are of importance to assess the phenicol persistence in wastewater treatment and sunlit surface waters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dewetting kinetics of metallic liquid films: Competition between unbalanced Young's force and dissolutive reaction

NASA Astrophysics Data System (ADS)

Lu, Gui; Lin, Lin; Hui, Sheng; Wang, Shuo-Lin; Wang, Xiao-Dong; Lee, Duu-Jong

2017-11-01

Dewetting kinetics of Al and NiAl metallic liquid films on NiAl (1 0 0) substrates was studied using molecular dynamics simulations. A new dewetting-spreading transitional behavior was observed for high temperature dewetting. The dewetting-spreading transition comes from the competition between unbalanced Young's force and dissolutive reaction. Without dissolutive reaction, liquid films keep dewetting, but immediately turn into spreading when the dissolutive reaction involved. The dissolutive reaction depends on the initial Ni atom contents rather than the contact areas of dewetting films. The far-away-from saturated Ni content is the main mechanism which accelerates the wetting and reverses the dewetting process at high temperatures.

Kinetics of Thermal Decomposition of Ammonium Perchlorate by TG/DSC-MS-FTIR

NASA Astrophysics Data System (ADS)

Zhu, Yan-Li; Huang, Hao; Ren, Hui; Jiao, Qing-Jie

2014-01-01

The method of thermogravimetry/differential scanning calorimetry-mass spectrometry-Fourier transform infrared (TG/DSC-MS-FTIR) simultaneous analysis has been used to study thermal decomposition of ammonium perchlorate (AP). The processing of nonisothermal data at various heating rates was performed using NETZSCH Thermokinetics. The MS-FTIR spectra showed that N2O and NO2 were the main gaseous products of the thermal decomposition of AP, and there was a competition between the formation reaction of N2O and that of NO2 during the process with an iso-concentration point of N2O and NO2. The dependence of the activation energy calculated by Friedman's iso-conversional method on the degree of conversion indicated that the AP decomposition process can be divided into three stages, which are autocatalytic, low-temperature diffusion and high-temperature, stable-phase reaction. The corresponding kinetic parameters were determined by multivariate nonlinear regression and the mechanism of the AP decomposition process was proposed.

Lipase-catalyzed synthesis of palmitanilide: Kinetic model and antimicrobial activity study.

PubMed

Liu, Kuan-Miao; Liu, Kuan-Ju

2016-01-01

Enzymatic syntheses of fatty acid anilides are important owing to their wide range of industrial applications in detergents, shampoo, cosmetics, and surfactant formulations. The amidation reaction of Mucor miehei lipase Lipozyme IM20 was investigated for direct amidation of triacylglycerol in organic solvents. The process parameters (reaction temperature, substrate molar ratio, enzyme amount) were optimized to achieve the highest yield of anilide. The maximum yield of palmitanilide (88.9%) was achieved after 24 h of reaction at 40 °C at an enzyme concentration of 1.4% (70 mg). Kinetics of lipase-catalyzed amidation of aniline with tripalmitin has been investigated. The reaction rate could be described in terms of the Michaelis-Menten equation with a Ping-Pong Bi-Bi mechanism and competitive inhibition by both the substrates. The kinetic constants were estimated by using non-linear regression method using enzyme kinetic modules. The enzyme operational stability study showed that Lipozyme IM20 retained 38.1% of the initial activity for the synthesis of palmitanilide (even after repeated use for 48 h). Palmitanilide, a fatty acid amide, exhibited potent antimicrobial activity toward Bacillus cereus. Copyright © 2015 Elsevier Inc. All rights reserved.

Electro-oxidation of the dye azure B: kinetics, mechanism, and by-products.

PubMed

Olvera-Vargas, Hugo; Oturan, Nihal; Aravindakumar, C T; Paul, M M Sunil; Sharma, Virender K; Oturan, Mehmet A

2014-01-01

In this work, the electrochemical degradation of the dye azure B in aqueous solutions was studied by electrochemical advanced oxidation processes (EAOPs), electro-Fenton, and anodic oxidation processes, using Pt/carbon-felt and boron-doped diamond (BDD)/carbon-felt cells with H₂O₂ electrogeneration. The higher oxidation power of the electro-Fenton (EF) process using BDD anode was demonstrated. The oxidative degradation of azure B by the electrochemically generated hydroxyl radicals ((•)OH) follows a pseudo-first-order kinetics. The apparent rate constants of the oxidation of azure B by (•)OH were measured according to pseudo-first-order kinetic model. The absolute rate constant of azure B hydroxylation reaction was determined by competition kinetics method and found to be 1.19 × 10(9) M(-1) s(-1). It was found that the electrochemical degradation of the dye leads to the formation of aromatic by-products which are then oxidized to aliphatic carboxylic acids before their almost mineralization to CO₂ and inorganic ions (sulfate, nitrate, and ammonium). The evolution of the TOC removal and time course of short-chain carboxylic acids during treatment were also investigated.

[CoCuMnOx Photocatalyzed Oxidation of Multi-component VOCs and Kinetic Analysis].

PubMed

Meng, Hai-long; Bo, Long-li; Liu, Jia-dong; Gao, Bo; Feng, Qi-qi; Tan, Na; Xie, Shuai

2016-05-15

Solar energy absorption coating CoCuMnOx was prepared by co-precipitation method and applied to photodegrade multi- component VOCs including toluene, ethyl acetate and acetone under visible light irradiation. The photocatalytic oxidation performance of toluene, ethyl acetate and acetone was analyzed and reaction kinetics of VOCs were investigated synchronously. The research indicated that removal rates of single-component toluene, ethyl acetate and acetone were 57%, 62% and 58% respectively under conditions of 400 mg · m⁻³ initial concentration, 120 mm illumination distance, 1 g/350 cm² dosage of CoCuMnOx and 6 h of irradiation time by 100 W tungsten halogen lamp. Due to the competition among different VOCs, removal efficiencies in three-component mixture were reduced by 5%-26% as compared with single VOC. Degradation processes of single-component VOC and three-component VOCs both fitted pseudo first order reaction kinetics, and kinetic constants of toluene, ethyl acetate and acetone were 0.002, 0.002 8 and 0.002 33 min⁻¹ respectively under single-component condition. Reaction rates of VOCs in three-component mixture were 0.49-0.88 times of single components.

Kinetic mechanism of ATP-sulphurylase from rat chondrosarcoma.

PubMed Central

Lyle, S; Geller, D H; Ng, K; Westley, J; Schwartz, N B

1994-01-01

ATP-sulphurylase catalyses the production of adenosine 5'-phosphosulphate (APS) from ATP and free sulphate with the release of PPi. APS kinase phosphorylates the APS intermediate to produce adenosine 3'-phosphate 5'-phosphosulphate (PAPS). The kinetic mechanism of rat chondrosarcoma ATP-sulphurylase was investigated by steady-state methods in the physiologically forward direction as well as the reverse direction. The sulphurylase activity was coupled to APS kinase activity in order to overcome the thermodynamic constraints of the sulphurylase reaction in the forward direction. Double-reciprocal initial-velocity plots for the forward sulphurylase intersect to the left of the ordinate for this reaction. KmATP and Kmsulphate were found to be 200 and 97 microM respectively. Chlorate, a competitive inhibitor with respect to sulphate, showed uncompetitive inhibition with respect to ATP with an apparent Ki of 1.97 mM. Steady-state data from experiments in the physiologically reverse direction also yielded double-reciprocal initial-velocity patterns that intersect to the left of the ordinate axis, with a KmAPS of 39 microM and a Kmpyrophosphate of 18 microM. The results of steady-state experiments in which Mg2+ was varied indicated that the true substrate is the MgPPi complex. An analogue of APS, adenosine 5'-[beta-methylene]phosphosulphate, was a linear inhibitor competitive with APS and non-competitive with respect to MgPPi. The simplest formal mechanism that agrees with all the data is an ordered steady-state single displacement with MgATP as the leading substrate in the forward direction and APS as the leading substrate in the reverse direction. PMID:8042976

Low-Concentration Kinetics of Atmospheric CH4 Oxidation in Soil and Mechanism of NH4+ Inhibition

PubMed Central

Gulledge, Jay; Schimel, Joshua P.

1998-01-01

NH4+ inhibition kinetics for CH4 oxidation were examined at near-atmospheric CH4 concentrations in three upland forest soils. Whether NH4+-independent salt effects could be neutralized by adding nonammoniacal salts to control samples in lieu of deionized water was also investigated. Because the levels of exchangeable endogenous NH4+ were very low in the three soils, desorption of endogenous NH4+ was not a significant factor in this study. The Km(app) values for water-treated controls were 9.8, 22, and 57 nM for temperate pine, temperate hardwood, and birch taiga soils, respectively. At CH4 concentrations of ≤15 μl liter−1, oxidation followed first-order kinetics in the fine-textured taiga soil, whereas the coarse-textured temperate soils exhibited Michaelis-Menten kinetics. Compared to water controls, the Km(app) values in the temperate soils increased in the presence of NH4+ salts, whereas the Vmax(app) values decreased substantially, indicating that there was a mixture of competitive and noncompetitive inhibition mechanisms for whole NH4+ salts. Compared to the corresponding K+ salt controls, the Km(app) values for NH4+ salts increased substantially, whereas the Vmax(app) values remained virtually unchanged, indicating that NH4+ acted by competitive inhibition. Nonammoniacal salts caused inhibition to increase with increasing CH4 concentrations in all three soils. In the birch taiga soil, this trend occurred with both NH4+ and K+ salts, and the slope of the increase was not affected by the addition of NH4+. Hence, the increase in inhibition resulted from an NH4+-independent mechanism. These results show that NH4+ inhibition of atmospheric CH4 oxidation resulted from enzymatic substrate competition and that additional inhibition that was not competitive resulted from a general salt effect that was independent of NH4+. PMID:9797279

Kinetics studies with fruit bromelain (Ananas comosus) in the presence of cysteine and divalent ions.

PubMed

Kaur, Tajwinder; Kaur, Amandeep; Grewal, Ravneet K

2015-09-01

The kinetics of cysteine and divalent ion modulation viz. Ca(2+), Cu(2+), Hg(2+) of fruit bromelain (EC 3.4.22.33) have been investigated in the present study. Kinetic studies revealed that at pH 4.5, cysteine induced V-type activation of bromelain catalyzed gelatin hydrolysis. At pH 3.5, Ca(2+) inhibited the enzyme noncompetitively, whereas, both K-and V-type activations of bromelain were observed in the presence of 0.5 mM Ca(2+) at pH 4.5 and 7.5. Bromelain was inhibited competitively at 0.6 mM Cu(2+) ions at pH 3.5, which changed to an uncompetitive inhibition at pH 4.5 and 7.5. An un-competitive inhibition of bromelain catalyzed gelatin hydrolysis was observed in the presence of 0.6 mM Hg(2+) at pH 3.5 and 4.5. These findings suggest that divalent ions modulation of fruit bromelain is pH dependent.

Design of inhibitors of orotidine monophosphate decarboxylase using bioisosteric replacement and determination of inhibition kinetics.

PubMed

Poduch, Ewa; Bello, Angelica M; Tang, Sishi; Fujihashi, Masahiro; Pai, Emil F; Kotra, Lakshmi P

2006-08-10

Inhibitors of orotidine monophosphate decarboxylase (ODCase) have applications in RNA viral, parasitic, and other infectious diseases. ODCase catalyzes the decarboxylation of orotidine monophosphate (OMP), producing uridine monophosphate (UMP). Novel inhibitors 6-amino-UMP and 6-cyano-UMP were designed on the basis of the substructure volumes in the substrate OMP and in an inhibitor of ODCase, barbituric acid monophosphate, BMP. A new enzyme assay method using isothermal titration calorimetry (ITC) was developed to investigate the inhibition kinetics of ODCase. The reaction rates were measured by monitoring the heat generated during the decarboxylation reaction of orotidine monophosphate. Kinetic parameters (k(cat) = 21 s(-1) and KM = 5 microM) and the molar enthalpy (DeltaH(app) = 5 kcal/mol) were determined for the decarboxylation of the substrate by ODCase. Competitive inhibition of the enzyme was observed and the inhibition constants (Ki) were determined to be 12.4 microM and 29 microM for 6-aza-UMP and 6-cyano-UMP, respectively. 6-Amino-UMP was found to be among the potent inhibitors of ODCase, having an inhibition constant of 840 nM. We reveal here the first inhibitors of ODCase designed by the principles of bioisosterism and a novel method of using isothermal calorimetry for enzyme inhibition studies.

Cold Incineration of Chlorophenols in Aqueous Solution by Advanced Electrochemical Process Electro-Fenton. Effect of Number and Position of Chlorine Atoms on the Degradation Kinetics

NASA Astrophysics Data System (ADS)

Oturan, Nihal; Panizza, Marco; Oturan, Mehmet A.

2009-09-01

This study reports the kinetics of the degradation of several chlorophenols (CPs), such as monochlorophenols (2-chlorophenol and 4-chlorophenol), dichlorophenols (2,4-dichlorophenol and 2,6- dichlorophenol), trichlorophenols (2,3,5- trichlorophenol and 2,4,5-trichlorophenol), 2,3,5,6-tetrachlorophenol, and pentachlorophenol, by the electro-Fenton process using a carbon felt cathode and a Pt anode. The effect of number and the position of the chlorine atoms in the aromatic ring on the oxidative degradation rate was evaluated and discussed. The oxidation reaction of all the CPs with hydroxyl radicals evidenced a pseudo-first-order kinetics and the rate constant decreased with increasing the number of chlorine atoms. The absolute rate constant of second-order reaction kinetics between CPs and •OH was determined by the competition kinetics method in the range of (3.56-7.75) × 109 M-1 s-1 and follows the same sequence of the apparent rate constants. The mineralization of several CPs and of a mixture of all CPs under study was monitored by the total organic carbon (TOC) removal and the chlorine release during mineralization was followed by ion chromatography. Our results demonstrated that more chlorinated phenols are more difficult to mineralize; however for all the tested CPs, almost quantitative release of chloride ions was obtained after 6 h of treatment.

Interaction of difluoro-oxaloacetate with aspartate transaminase.

PubMed Central

Briley, P A; Eisenthal, R; Harrison, R; Smith, G D

1977-01-01

Diffluoro-oxaloacetate behaves as a competitive inhibitor of 2-oxoglutarate and as an uncompetitive inhibitor with respect to aspartate in steady-state kinetic experiments with cytoplasmic aspartate transaminase. In the presence of high concentrations of aspartate transaminase, difluoro-oxaloacetate is slowly transaminated to difluoro-aspartate, suggesting its use as a kinetic probe to study the reactions of the aminic form of the enzyme. PMID:849267

Studying of kinetics of rear earth ion (REI) nanoscale complex formation by resonant energy transfer

NASA Astrophysics Data System (ADS)

Ignatova, Tetyana; Pristinski, Denis; Rotkin, Slava V.

2011-03-01

We observed formation of nanoscale complexes between multivalent REIs (Tb and Eu) and negatively charged DNA wrapped SWNTs, ionized in the water solution. Foerster Resonance Energy Transfer (FRET) was found to be an ideal method to confirm the complex formation. Because of its high sensitivity and non-destructive characterization approach FRET can be used to trace the kinetics of the complex formation. Strong dependence of SWNT photoluminescence (PL) on the REI concentration was detected and interpreted as a competition between the REI absorption on the SWNTs and subsequent FRET enhanced PL and the SWNT agglomeration followed by PL quenching. We measured the distance between REI and SWNT which appears to be much shorter than the one from their relative concentration in solution. We speculate that Manning condensation of the REIs on the SWNT/DNA surface happens thereby significantly reducing their spacing and making FRET possible.

Finding Order in Randomness: Single-Molecule Studies Reveal Stochastic RNA Processing | Center for Cancer Research

Cancer.gov

Producing a functional eukaryotic messenger RNA (mRNA) requires the coordinated activity of several large protein complexes to initiate transcription, elongate nascent transcripts, splice together exons, and cleave and polyadenylate the 3’ end. Kinetic competition between these various processes has been proposed to regulate mRNA maturation, but this model could lead to multiple, randomly determined, or stochastic, pathways or outcomes. Regulatory checkpoints have been suggested as a means of ensuring quality control. However, current methods have been unable to tease apart the contributions of these processes at a single gene or on a time scale that could provide mechanistic insight. To begin to investigate the kinetic relationship between transcription and splicing, Daniel Larson, Ph.D., of CCR’s Laboratory of Receptor Biology and Gene Expression, and his colleagues employed a single-molecule RNA imaging approach to monitor production and processing of a human β-globin reporter gene in living cells.

Kinetics and evolved gas analysis for pyrolysis of food processing wastes using TGA/MS/FT-IR.

PubMed

Özsin, Gamzenur; Pütün, Ayşe Eren

2017-06-01

The objective of this study was to identify the pyrolysis of different bio-waste produced by food processing industry in a comprehensible manner. For this purpose, pyrolysis behaviors of chestnut shells (CNS), cherry stones (CS) and grape seeds (GS) were investigated by thermogravimetric analysis (TGA) combined with a Fourier-transform infrared (FT-IR) spectrometer and a mass spectrometer (MS). In order to make available theoretical groundwork for biomass pyrolysis, activation energies were calculated with the help of four different model-free kinetic methods. The results are attributed to the complex reaction schemes which imply parallel, competitive and complex reactions during pyrolysis. During pyrolysis, the evolution of volatiles was also characterized by FT-IR and MS. The main evolved gases were determined as H 2 O, CO 2 and hydrocarbons such as CH 4 and temperature dependent profiles of the species were obtained. Copyright © 2017 Elsevier Ltd. All rights reserved.

Andrographolide sodium bisulphite-induced inactivation of urease: inhibitory potency, kinetics and mechanism.

PubMed

Mo, Zhi-Zhun; Wang, Xiu-Fen; Zhang, Xie; Su, Ji-Yan; Chen, Hai-Ming; Liu, Yu-Hong; Zhang, Zhen-Biao; Xie, Jian-Hui; Su, Zi-Ren

2015-07-16

The inhibitory effect of andrographolide sodium bisulphite (ASB) on jack bean urease (JBU) and Helicobacter pylori urease (HPU) was performed to elucidate the inhibitory potency, kinetics and mechanism of inhibition in 20 mM phosphate buffer, pH 7.0, 2 mM EDTA, 25 °C. The ammonia formations, indicator of urease activity, were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. The inhibitory effect of ASB was characterized with IC50 values. Lineweaver-Burk and Dixon plots for JBU inhibition of ASB was constructed from the kinetic data. SH-blocking reagents and competitive active site Ni2+ binding inhibitors were employed for mechanism study. Molecular docking technique was used to provide some information on binding conformations as well as confirm the inhibition mode. The IC50 of ASB against JBU and HPU was 3.28±0.13 mM and 3.17±0.34 mM, respectively. The inhibition proved to be competitive and concentration- dependent in a slow-binding progress. The rapid formation of initial ASB-JBU complex with an inhibition constant of Ki=2.86×10(-3) mM was followed by a slow isomerization into the final complex with an overall inhibition constant of Ki*=1.33×10(-4) mM. The protective experiment proved that the urease active site is involved in the binding of ASB. Thiol reagents (L-cysteine and dithiothreithol) strongly protect the enzyme from the loss of enzymatic activity, while boric acid and fluoride show weaker protection, indicating that the active-site sulfhydryl group of JBU was potentially involved in the blocking process. Moreover, inhibition of ASB proved to be reversible since ASB-inactivated JBU could be reactivated by dithiothreitol application. Molecular docking assay suggested that ASB made contacts with the important sulfhydryl group Cys-592 residue and restricted the mobility of the active-site flap. ASB was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration-dependently, serving as a promising urease inhibitor for the treatment of urease-related diseases.

A Computational Model for Docking of Noncompetitive Neuraminidase Inhibitors and Probing their Binding Interactions with Neuraminidase of Influenza Virus H5N1.

PubMed

Chintakrindi, Anand S; Martis, Elvis A F; Gohil, Devanshi J; Kothari, Sweta T; Chowdhary, Abhay S; Coutinho, Evans C; Kanyalkar, Meena A

2016-01-01

With cases of emergence of drug resistance to the current competitive inhibitors of neuraminidase (NA) such as oseltamivir and zanamavir, there is a present need for an alternative approach in the treatment of avian influenza. With this in view, some flavones and chalcones were designed based on quercetin, the most active naturally occurring noncompetitive inhibitor. We attempt to understand the binding of quercetin to H5N1-NA, and synthetic analogs of quercetin namely flavones and its precursors the chalcones using computational tools. Molecular docking was done using Libdock. Molecular dynamics (MD) simulations were performed using Amber14. We synthesized the two compounds; their structures were confirmed by infrared spectroscopy, 1H-NMR, and mass spectrometry. These molecules were then tested for H5N1-NA inhibition and kinetics of inhibition. Molecular docking studies yielded two compounds i.e., 4'-methoxyflavone and 2'-hydroxy-4-methoxychalcone, as promising leads which identified them as binders of the 150-cavity of NA. Furthermore, MD simulation studies revealed that quercetin and the two compounds bind and hold the 150 loop in its open conformation, which ultimately perturbs the binding of sialic acid in the catalytic site. Estimation of the free energy of binding by MM-PBSA portrays quercetin as more potent than chalcone and flavone. These molecules were then determined as non-competitive inhibitors from the Lineweaver-Burk plots rendered from the enzyme kinetic studies. We conclude that non-competitive type of inhibition, as shown in this study, can serve as an effective method to block NA and evade the currently seen drug resistance.

Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics

PubMed Central

Skibinski, David O. F.

2018-01-01

Nutrient acquisition is a critical determinant for the competitive advantage for auto- and osmohetero- trophs alike. Nutrient limited growth is commonly described on a whole cell basis through reference to a maximum growth rate (Gmax) and a half-saturation constant (KG). This empirical application of a Michaelis-Menten like description ignores the multiple underlying feedbacks between physiology contributing to growth, cell size, elemental stoichiometry and cell motion. Here we explore these relationships with reference to the kinetics of the nutrient transporter protein, the transporter rate density at the cell surface (TRD; potential transport rate per unit plasma-membrane area), and diffusion gradients. While the half saturation value for the limiting nutrient increases rapidly with cell size, significant mitigation is afforded by cell motion (swimming or sedimentation), and by decreasing the cellular carbon density. There is thus potential for high vacuolation and high sedimentation rates in diatoms to significantly decrease KG and increase species competitive advantage. Our results also suggest that Gmax for larger non-diatom protists may be constrained by rates of nutrient transport. For a given carbon density, cell size and TRD, the value of Gmax/KG remains constant. This implies that species or strains with a lower Gmax might coincidentally have a competitive advantage under nutrient limited conditions as they also express lower values of KG. The ability of cells to modulate the TRD according to their nutritional status, and hence change the instantaneous maximum transport rate, has a very marked effect upon transport and growth kinetics. Analyses and dynamic models that do not consider such modulation will inevitably fail to properly reflect competitive advantage in nutrient acquisition. This has important implications for the accurate representation and predictive capabilities of model applications, in particular in a changing environment. PMID:29702650

Direct Measurement of Equilibrium Constants for High-Affinity Hemoglobins

PubMed Central

Kundu, Suman; Premer, Scott A.; Hoy, Julie A.; Trent, James T.; Hargrove, Mark S.

2003-01-01

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (KD ≪ 1 μM) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and ∼100 μM−1 respectively, indicate that they are not capable of facilitating oxygen transport. PMID:12770899

Effect of nonlinearity in hybrid kinetic Monte Carlo-continuum models.

PubMed

Balter, Ariel; Lin, Guang; Tartakovsky, Alexandre M

2012-01-01

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a kinetic Monte Carlo (KMC) model for a surface to a finite-difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition-dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition-dissolution model including competitive adsorption, which leads to a nonlinear rate, and show that in this case the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.

Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

PubMed Central

Martí-Centelles, Vicente; Burguete, M. Isabel; Luis, Santiago V.

2012-01-01

Several kinetic models for the macrocyclization of a C2 pseudopeptide with a dihalide through a SN2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes. PMID:22666148

Caged Naloxone Reveals Opioid Signaling Deactivation Kinetics

PubMed Central

Banghart, Matthew R.; Shah, Ruchir C.; Lavis, Luke D.

2013-01-01

The spatiotemporal dynamics of opioid signaling in the brain remain poorly defined. Photoactivatable opioid ligands provide a means to quantitatively measure these dynamics and their underlying mechanisms in brain tissue. Although activation kinetics can be assessed using caged agonists, deactivation kinetics are obscured by slow clearance of agonist in tissue. To reveal deactivation kinetics of opioid signaling we developed a caged competitive antagonist that can be quickly photoreleased in sufficient concentrations to render agonist dissociation effectively irreversible. Carboxynitroveratryl-naloxone (CNV-NLX), a caged analog of the competitive opioid antagonist NLX, was readily synthesized from commercially available NLX in good yield and found to be devoid of antagonist activity at heterologously expressed opioid receptors. Photolysis in slices of rat locus coeruleus produced a rapid inhibition of the ionic currents evoked by multiple agonists of the μ-opioid receptor (MOR), but not of α-adrenergic receptors, which activate the same pool of ion channels. Using the high-affinity peptide agonist dermorphin, we established conditions under which light-driven deactivation rates are independent of agonist concentration and thus intrinsic to the agonist-receptor complex. Under these conditions, some MOR agonists yielded deactivation rates that are limited by G protein signaling, whereas others appeared limited by agonist dissociation. Therefore, the choice of agonist determines which feature of receptor signaling is unmasked by CNV-NLX photolysis. PMID:23960100

Kinetics of enzymes with iso-mechanisms: analysis of product inhibition.

PubMed Central

Rebholz, K L; Northrop, D B

1993-01-01

Isomerizations of free enzyme can be detected in kinetic patterns of product inhibition when the isomerization is partially rate-limiting. The kinetic pattern is non-competitive, owing to binding of substrate and product to different forms of free enzyme. This adds an additional term to the rate equation, sometimes represented as KSP. Several kineticists have noted that, as the rate of isomerization becomes high in relation to catalytic turnover, the intercept effect will become small, KSP will approach infinity, and the pattern will look competitive. Britton [(1973) Biochem. J. 133, 255-261] asserted that KSP will also approach infinity when the rate of isomerization becomes low. This second assertion is incorrect and can be traced to the particular model and graphical representation used to examine KSP as a function of relative rate constants. The function portrayed as a parabola with two roots for KSP is, instead, a straight line with one root. The algebraic condition justifying the second root obtains in the limit of zero in the rate of reaction and thus is not experimentally relevant, and the appearance of competitive inhibition, based on KSP alone, is not valid. Using a more general model, new equations are derived and presented which provide direct calculations of the apparent rate constants for free enzyme isomerizations from product-inhibition data when the equilibrium of the isomerization is near 1, and useful limits for the rate constants when greater than or less than 1. PMID:7980736

Soil properties influence kinetics of soil acid phosphatase in response to arsenic toxicity.

PubMed

Wang, Ziquan; Tan, Xiangping; Lu, Guannan; Liu, Yanju; Naidu, Ravi; He, Wenxiang

2018-01-01

Soil phosphatase, which plays an important role in phosphorus cycling, is strongly inhibited by Arsenic (As). However, the inhibition mechanism in kinetics is not adequately investigated. In this study, we investigated the kinetic characteristics of soil acid phosphatase (ACP) in 14 soils with varied properties, and also explored how kinetic properties of soil ACP changed with different spiked As concentrations. The results showed that the Michaelis constant (K m ) and maximum reaction velocity (V max ) values of soil ACP ranged from 1.18 to 3.77mM and 0.025-0.133mMh -1 in uncontaminated soils. The kinetic parameters of soil ACP in different soils changed differently with As contamination. The K m remained unchanged and V max decreased with increase of As concentration in most acid and neutral soils, indicating a noncompetitive inhibition mechanism. However, in alkaline soils, the K m increased linearly and V max decreased with increase of As concentration, indicating a mixed inhibition mechanism that include competitive and noncompetitive. The competitive inhibition constant (K ic ) and noncompetitive inhibition constant (K iu ) varied among soils and ranged from 0.38 to 3.65mM and 0.84-7.43mM respectively. The inhibitory effect of As on soil ACP was mostly affected by soil organic matter and cation exchange capacity. Those factors influenced the combination of As with enzyme, which resulted in a difference of As toxicity to soil ACP. Catalytic efficiency (V max /K m ) of soil ACP was a sensitive kinetic parameter to assess the ecological risks of soil As contamination. Copyright © 2017 Elsevier Inc. All rights reserved.

Modelling biological Cr(VI) reduction in aquifer microcosm column systems.

PubMed

Molokwane, Pulane E; Chirwa, Evans M N

2013-01-01

Several chrome processing facilities in South Africa release hexavalent chromium (Cr(VI)) into groundwater resources. Pump-and-treat remediation processes have been implemented at some of the sites but have not been successful in reducing contamination levels. The current study is aimed at developing an environmentally friendly, cost-effective and self-sustained biological method to curb the spread of chromium at the contaminated sites. An indigenous Cr(VI)-reducing mixed culture of bacteria was demonstrated to reduce high levels of Cr(VI) in laboratory samples. The effect of Cr(VI) on the removal rate was evaluated at concentrations up to 400 mg/L. Following the detailed evaluation of fundamental processes for biological Cr(VI) reduction, a predictive model for Cr(VI) breakthrough through aquifer microcosm reactors was developed. The reaction rate in batch followed non-competitive rate kinetics with a Cr(VI) inhibition threshold concentration of approximately 99 mg/L. This study evaluates the application of the kinetic parameters determined in the batch reactors to the continuous flow process. The model developed from advection-reaction rate kinetics in a porous media fitted best the effluent Cr(VI) concentration. The model was also used to elucidate the logistic nature of biomass growth in the reactor systems.

The effect of oxaloacetic acid on tyrosinase activity and structure: Integration of inhibition kinetics with docking simulation.

PubMed

Gou, Lin; Lee, Jinhyuk; Hao, Hao; Park, Yong-Doo; Zhan, Yi; Lü, Zhi-Rong

2017-08-01

Oxaloacetic acid (OA) is naturally found in organisms and well known as an intermediate of citric acid cycle producing ATP. We evaluated the effects of OA on tyrosinase activity and structure via integrating methods of enzyme kinetics and computational simulations. OA was found to be a reversible inhibitor of tyrosinase and its induced mechanism was the parabolic non-competitive inhibition type (IC 50 =17.5±0.5mM and K i =6.03±1.36mM). Kinetic measurements by real-time interval assay showed that OA induced multi-phasic inactivation process composing with fast (k 1 ) and slow (k 2 ) phases. Spectrofluorimetry studies showed that OA mainly induced regional changes in the active site of tyrosinase accompanying with hydrophobic disruption at high dose. The computational docking simulations further revealed that OA could interact with several residues near the tyrosinase active site pocket such as HIS61, HIS259, HIS263, and VAL283. Our study provides insight into the mechanism by which energy producing intermediate such as OA inhibit tyrosinase and OA is a potential natural anti-pigmentation agent. Copyright © 2017 Elsevier B.V. All rights reserved.

Competitive Inhibition Mechanism of Acetylcholinesterase without Catalytic Active Site Interaction: Study on Functionalized C60 Nanoparticles via in Vitro and in Silico Assays.

PubMed

Liu, Yanyan; Yan, Bing; Winkler, David A; Fu, Jianjie; Zhang, Aiqian

2017-06-07

Acetylcholinesterase (AChE) activity regulation by chemical agents or, potentially, nanomaterials is important for both toxicology and pharmacology. Competitive inhibition via direct catalytic active sites (CAS) binding or noncompetitive inhibition through interference with substrate and product entering and exiting has been recognized previously as an AChE-inhibition mechanism for bespoke nanomaterials. The competitive inhibition by peripheral anionic site (PAS) interaction without CAS binding remains unexplored. Here, we proposed and verified the occurrence of a presumed competitive inhibition of AChE without CAS binding for hydrophobically functionalized C 60 nanoparticles (NPs) by employing both experimental and computational methods. The kinetic inhibition analysis distinguished six competitive inhibitors, probably targeting the PAS, from the pristine and hydrophilically modified C 60 NPs. A simple quantitative nanostructure-activity relationship (QNAR) model relating the pocket accessible length of substituent to inhibition capacity was then established to reveal how the geometry of the surface group decides the NP difference in AChE inhibition. Molecular docking identified the PAS as the potential binding site interacting with the NPs via a T-shaped plug-in mode. Specifically, the fullerene core covered the enzyme gorge as a lid through π-π stacking with Tyr72 and Trp286 in the PAS, while the hydrophobic ligands on the fullerene surface inserted into the AChE active site to provide further stability for the complexes. The modeling predicted that inhibition would be severely compromised by Tyr72 and Trp286 deletions, and the subsequent site-directed mutagenesis experiments proved this prediction. Our results demonstrate AChE competitive inhibition of NPs without CAS participation to gain further understanding of both the neurotoxicity and the curative effect of NPs.

Competitive adsorption of Pb2+, Cu2+, and Cd2+ ions on microporous titanosilicate ETS-10.

PubMed

Lv, Lu; Hor, Mei Peng; Su, Fabing; Zhao, X S

2005-07-01

In the present study, the competitive adsorption characteristics of binary and ternary heavy metal ions Pb2+, Cu2+, and Cd2+ on microporous titanosilicate ETS-10 were investigated in batch systems. Pure microporous titanosilicate ETS-10 was synthesized with P25 as the Ti source and characterized by the techniques of X-ray diffraction (XRD), field emission-scanning electron microscope (FESEM), nitrogen adsorption, and zeta-potential. Equilibrium and kinetic adsorption data showed that ETS-10 displays a high selectivity toward one metal in a two-component or a three-component system with an affinity order of Pb2+ > Cd2+ > Cu2+. The equilibrium behaviors of heavy metals species with stronger affinity toward ETS-10 can be described by the Langmuir equation while the adsorption kinetics of the metals can be well fitted to a pseudo-second-order (PSO) model.

The interaction of the Eco R1 restriction enzyme E.coli with nucleotides

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

Hollis, Donald F.

1979-11-01

The Eco R1 restriction enzyme can be shown to be inhibited by nucleotides which correspond to any part of its known site of phosphodiesterase activity. A series of di-, tetra-, and hexa-nucleotide fragments were synthesized and their effect on the activity of the enzyme upon superhelical Co1 E1 DNA studied. The inhibition caused by the individual mononucleotides were also studied. In general all the nucleotide fragments showed some form of interaction with the enzyme system. Tetranucleotides were stronger inhibitors than dinucleotides, which in turn were stronger inhibitors than the mononucleotides. Within each category of inhibitors, those containing the phosphodiester bondmore » which is acted upon by the enzyme were the strongest inhibitors. Only those fragments which were consistent with the enzymes site of activity showed competitive inhibition kinetics. Nucleotides which do not fit within the site of phosphodiesterase activity show non-competitive inhibition kinetics.« less

Kinetic analysis of competition between aerosol particle removal and generation by ionization air purifiers.

PubMed

Alshawa, Ahmad; Russell, Ashley R; Nizkorodov, Sergey A

2007-04-01

Ionization air purifiers are increasingly used to remove aerosol particles from indoor air. However, certain ionization air purifiers also emit ozone. Reactions between the emitted ozone and unsaturated volatile organic compounds (VOC) commonly found in indoor air produce additional respirable aerosol particles in the ultrafine (<0.1 microm) and fine (<2.5 microm) size domains. A simple kinetic model is used to analyze the competition between the removal and generation of particulate matter by ionization air purifiers under conditions of a typical residential building. This model predicts that certain widely used ionization air purifiers may actually increase the mass concentration of fine and ultrafine particulates in the presence of common unsaturated VOC, such as limonene contained in many household cleaning products. This prediction is supported by an explicit observation of ultrafine particle nucleation events caused by the addition of D-limonene to a ventilated office room equipped with a common ionization air purifier.

Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors.

PubMed

Breitenbach, J; Zhu, C; Sandmann, G

2001-11-01

Cofactor requirement was determined for the heterologous expressed phytoene desaturases from the cyanobacterium Synechococcus and the higher plant Gentiana lutea. The cyanobacterial enzyme is dependent on either NAD(P) or plastoquinone, whereas only quinones such as plastoquinone can function as a cofactor for the phytoene desaturase from G. lutea. Enzyme kinetic studies were carried out to determine a possible competition between the cofactors and the bleaching herbicide norflurazon. For the Synechococcus enzyme, competition between norflurazon and NADP, as well as plastoquinone, could be demonstrated. The K(m) values for these cofactors were 6.6 mM and 0.23 microM, respectively. Inhibition of the phytoene desaturase from G. lutea by norflurazon was also competitive with respect to plastoquinone. The K(m) values of both enzymes for plastoquinone were very close.

Progress in Studying Scintillator Proportionality: Phenomenological Model

NASA Astrophysics Data System (ADS)

Bizarri, G.; Cherepy, N. J.; Choong, W. S.; Hull, G.; Moses, W. W.; Payne, S. A.; Singh, J.; Valentine, J. D.; Vasilev, A. N.; Williams, R. T.

2009-08-01

We present a model to describe the origin of non-proportional dependence of scintillator light yield on the energy of an ionizing particle. The non-proportionality is discussed in terms of energy relaxation channels and their linear and non-linear dependences on the deposited energy. In this approach, the scintillation response is described as a function of the deposited energy deposition and the kinetic rates of each relaxation channel. This mathematical framework allows both a qualitative interpretation and a quantitative fitting representation of scintillation non-proportionality response as function of kinetic rates. This method was successfully applied to thallium doped sodium iodide measured with SLYNCI, a new facility using the Compton coincidence technique. Finally, attention is given to the physical meaning of the dominant relaxation channels, and to the potential causes responsible for the scintillation non-proportionality. We find that thallium doped sodium iodide behaves as if non-proportionality is due to competition between radiative recombinations and non-radiative Auger processes.

Target engagement and drug residence time can be observed in living cells with BRET

PubMed Central

Robers, Matthew B.; Dart, Melanie L.; Woodroofe, Carolyn C.; Zimprich, Chad A.; Kirkland, Thomas A.; Machleidt, Thomas; Kupcho, Kevin R.; Levin, Sergiy; Hartnett, James R.; Zimmerman, Kristopher; Niles, Andrew L.; Ohana, Rachel Friedman; Daniels, Danette L.; Slater, Michael; Wood, Monika G.; Cong, Mei; Cheng, Yi-Qiang; Wood, Keith V.

2015-01-01

The therapeutic action of drugs is predicated on their physical engagement with cellular targets. Here we describe a broadly applicable method using bioluminescence resonance energy transfer (BRET) to reveal the binding characteristics of a drug with selected targets within intact cells. Cell-permeable fluorescent tracers are used in a competitive binding format to quantify drug engagement with the target proteins fused to Nanoluc luciferase. The approach enabled us to profile isozyme-specific engagement and binding kinetics for a panel of histone deacetylase (HDAC) inhibitors. Our analysis was directed particularly to the clinically approved prodrug FK228 (Istodax/Romidepsin) because of its unique and largely unexplained mechanism of sustained intracellular action. Analysis of the binding kinetics by BRET revealed remarkably long intracellular residence times for FK228 at HDAC1, explaining the protracted intracellular behaviour of this prodrug. Our results demonstrate a novel application of BRET for assessing target engagement within the complex milieu of the intracellular environment. PMID:26631872

Low-level laser therapy improves the VO2 kinetics in competitive cyclists.

PubMed

Lanferdini, Fábio J; Krüger, Renata L; Baroni, Bruno M; Lazzari, Caetano; Figueiredo, Pedro; Reischak-Oliveira, Alvaro; Vaz, Marco A

2018-04-01

Some evidence supports that low-level laser therapy (LLLT) reduces neuromuscular fatigue, so incrementing sports performance. A previous randomized controlled trial of our group showed increased exercise tolerance in male competitive cyclists treated with three different LLLT doses (3, 6, and 9 J/diode; or 135, 270, and 405 J/thigh) before time-to-exhaustion cycling tests. Now, the present study was designed to evaluate the effects of these LLLT doses on the VO 2 kinetics of athletes during cycling tests. Twenty male competitive cyclists (29 years) participated in a crossover, randomized, double-blind, and placebo-controlled trial. On the first day, the participants performed an incremental cycling test to exhaustion to determine maximal oxygen uptake (VO 2MAX ) and maximal power output (PO MAX ), as well as a familiarization with the time-to-exhaustion test. In the following days (2 to 5), all participants performed time-to-exhaustion tests at PO MAX . Before the exhaustion test, different doses of LLLT (3, 6, and 9 J/diode; or 135, 270, and 405 J/thigh, respectively) or placebo were applied bilaterally to the quadriceps muscle. All exhaustion tests were monitored online by an open-circuit spirometry system in order to analyze the VO 2 amplitude, VO 2 delay time, time constant (tau), and O 2 deficit. Tau and O 2 deficit were decreased with LLLT applications compared to the placebo condition (p < 0.05). No differences (p > 0.05) were found between the experimental conditions for VO 2 amplitude and VO 2 delay time. In conclusion, LLLT decreases tau and O 2 deficit during time-to-exhaustion tests in competitive cyclists, and these changes in VO 2 kinetics response can be one of the possible mechanisms to explain the ergogenic effect induced by LLLT.

Phase Transition in Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under Static Compression: An Application of the First-Principles Method Specialized for CHNO Solid Explosives.

PubMed

Zhang, Lei; Jiang, Sheng-Li; Yu, Yi; Long, Yao; Zhao, Han-Yue; Peng, Li-Juan; Chen, Jun

2016-11-10

The first-principles method is challenged by accurate prediction of van der Waals interactions, which are ubiquitous in nature and crucial for determining the structure of molecules and condensed matter. We have contributed to this by constructing a set of pseudopotentials and pseudoatomic orbital basis specialized for molecular systems consisting of C/H/N/O elements. The reliability of the present method is verified from the interaction energies of 45 kinds of complexes (comparing with CCSD(T)) and the crystalline structures of 23 kinds of typical explosive solids (comparing with experiments). Using this method, we have studied the phase transition of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under static compression up to 50 GPa. Kinetically, intramolecular deformation has priority in the competition with intermolecular packing deformation by ∼87%. A possible γ → β phase transition is found at around 2.10 GPa, and the migration of H 2 O has an effect of kinetically pushing this process. We make it clear that no β → δ/ε → δ phase transition occurs at 27 GPa, which has long been a hot debate in experiments. In addition, the P-V relation, bulk modulus, and acoustic velocity are also predicted for α-, δ-, and γ-HMX, which are experimentally unavailable.

Termination of nanoscale zero-valent iron reactivity by addition of bromate as a reducing reactivity competitor

NASA Astrophysics Data System (ADS)

Mines, Paul D.; Kaarsholm, Kamilla M. S.; Droumpali, Ariadni; Andersen, Henrik R.; Lee, Wontae; Hwang, Yuhoon

2017-09-01

Remediation of contaminated groundwater by nanoscale zero-valent iron (nZVI) is widely becoming a leading environmentally friendly solution throughout the globe. Since a wide range of various nZVI-containing materials have been developed for effective remediation, it is necessary to determine an appropriate way to terminate the reactivity of any nZVI-containing material for a practical experimental procedure. In this study, bimetallic Ni/Fe-NPs were prepared to enhance overall reduction kinetics owing to the catalytic reactivity of nickel on the surface of nZVI. We have tested several chemical strategies in order to terminate nZVI reactivity without altering the concentration of volatile compounds in the solution. The strategies include surface passivation in alkaline conditions by addition of carbonate, and consumption of nZVI by a reaction competitor. Four halogenated chemicals, trichloroethylene, 1,1,1-trichloroethane, atrazine, and 4-chlorophenol, were selected and tested as model groundwater contaminants. Addition of carbonate to passivate the nZVI surface was not effective for trichloroethylene. Nitrate and then bromate were applied to competitively consume nZVI by their faster reduction kinetics. Bromate proved to be more effective than nitrate, subsequently terminating nZVI reactivity for all four of the tested halogenated compounds. Furthermore, the suggested termination method using bromate was successfully applied to obtain trichloroethylene reduction kinetics. Herein, we report the simple and effective method to terminate the reactivity of nZVI by addition of a reducing reactivity competitor.

Transient competitive complexation in biological kinetic isotope fractionation explains non-steady isotopic effects: Theory and application to denitrification in soils

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

Maggi, F.M.; Riley, W.J.

2009-06-01

The theoretical formulation of biological kinetic reactions in isotopic applications often assume first-order or Michaelis-Menten-Monod kinetics under the quasi-steady-state assumption to simplify the system kinetics. However, isotopic e ects have the same order of magnitude as the potential error introduced by these simpli cations. Both formulations lead to a constant fractionation factor which may yield incorrect estimations of the isotopic effect and a misleading interpretation of the isotopic signature of a reaction. We have analyzed the isotopic signature of denitri cation in biogeochemical soil systems by Menyailo and Hungate [2006], where high {sup 15}N{sub 2}O enrichment during N{sub 2}O productionmore » and inverse isotope fractionation during N{sub 2}O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with the quasi-steady-state Michaelis-Menten-Monod kinetics. When the quasi-steady-state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observations and aided in interpretation of experimental isotopic signatures. These results may imply a substantial revision in using the Rayleigh equation for interpretation of isotopic signatures and in modeling biological kinetic isotope fractionation with first-order kinetics or quasi-steady-state Michaelis-Menten-Monod kinetics.« less

A study of kinetic friction: The Timoshenko oscillator

NASA Astrophysics Data System (ADS)

Henaff, Robin; Le Doudic, Gabriel; Pilette, Bertrand; Even, Catherine; Fischbach, Jean-Marie; Bouquet, Frédéric; Bobroff, Julien; Monteverde, Miguel; Marrache-Kikuchi, Claire A.

2018-03-01

Friction is a complex phenomenon that is of paramount importance in everyday life. We present an easy-to-build and inexpensive experiment illustrating Coulomb's law of kinetic friction. The so-called friction, or Timoshenko, oscillator consists of a plate set into periodic motion through the competition between gravity and friction on its rotating supports. The period of such an oscillator gives a measurement of the coefficient of kinetic friction μk between the plate and the supports. Our prototype is mainly composed of a motor, LEGO blocks, and a low-cost microcontroller, but despite its simplicity, the results obtained are in good agreement with values of μk found in the literature (enhanced online).

Dependence of erythrocyte vesiculation and hemolysis parameters on the concentration of sodium dodecyl sulfate. Vesicular-competitive hemolysis.

PubMed

Chernitsky, E A; Senkovich, O A; Rozin, V V

2001-07-01

The kinetic and concentration dependences of erythrocyte vesiculation and hemolysis induced by sodium dodecyl sulfate were studied. The similarity of the slopes of the dose dependence of the SDS-induced vesiculation and slow hemolysis rates in the double logarithmic coordinates suggested a close relation between the processes of vesiculation and pore formation for slow hemolysis by the detergent. Further evidence of the competitive nature of the detergent-induced vesiculation and fast hemolysis by sodium dodecyl sulfate was obtained. The phenomenon of partial hemolysis proceeding at a rate comparable to that of cell vesiculation is explained in terms of the competition between hemolysis and vesiculation, without resorting to erythrocyte heterogeneity. New vesicular-competitive hemolysis is described. Based on it, the action of different hemolysis-inducing agents is analysed.

Kinetic evidence for the interactive inhibition of laccase from Trametes versicolor by pH and chloride.

PubMed

Raseda, Nasrin; Hong, Soonho; Kwon, O Yul; Ryu, Keungarp

2014-12-28

The interactive inhibitory effects of pH and chloride on the catalysis of laccase from Trametes versicolor were investigated by studying the alteration of inhibition characteristics of sodium chloride at different pHs for the oxidation of 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid). At pH 3.0, the addition of sodium chloride (50 mM) brought about a 40-fold increase in Km(app) and a 4-fold decrease in Vmax(app). As the pH increased to 7.0, the inhibitory effects of sodium chloride became significantly weakened. The mixed-inhibition mechanism was successfully used to quantitatively estimate the competitive and uncompetitive inhibition strengths by chloride at two different pHs (pH 3.0 and 6.0). At pH 3.0, the competitive inhibition constant, Ki, was 0.35 mM, whereas the uncompetitive inhibition constant, Ki', was 18.1 mM, indicating that the major cause of the laccase inhibition by chloride is due to the competitive inhibition step. At a higher pH of 6.0, where the inhibition of the laccase by hydroxide ions takes effect, the inhibition of the laccase by chloride diminished to a great extent, showing increased values of both the competitive inhibition constant (Ki= 23.7 mM) and uncompetitive inhibition constant (Ki' = 324 mM). These kinetic results evidenced that the hydroxide anion and chloride share a common mechanism to inhibit the laccase activity.

Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time

PubMed Central

Guo, Dong; Mulder-Krieger, Thea; IJzerman, Adriaan P; Heitman, Laura H

2012-01-01

BACKGROUND AND PURPOSE The adenosine A2A receptor belongs to the superfamily of GPCRs and is a promising therapeutic target. Traditionally, the discovery of novel agents for the A2A receptor has been guided by their affinity for the receptor. This parameter is determined under equilibrium conditions, largely ignoring the kinetic aspects of the ligand-receptor interaction. The aim of this study was to assess the binding kinetics of A2A receptor agonists and explore a possible relationship with their functional efficacy. EXPERIMENTAL APPROACH We set up, validated and optimized a kinetic radioligand binding assay (a so-called competition association assay) at the A2A receptor from which the binding kinetics of unlabelled ligands were determined. Subsequently, functional efficacies of A2A receptor agonists were determined in two different assays: a novel label-free impedance-based assay and a more traditional cAMP determination. KEY RESULTS A simplified competition association assay yielded an accurate determination of the association and dissociation rates of unlabelled A2A receptor ligands at their receptor. A correlation was observed between the receptor residence time of A2A receptor agonists and their intrinsic efficacies in both functional assays. The affinity of A2A receptor agonists was not correlated to their functional efficacy. CONCLUSIONS AND IMPLICATIONS This study indicates that the molecular basis of different agonist efficacies at the A2A receptor lies within their different residence times at this receptor. PMID:22324512

[Dynamics of oxygen uptake during a 100 m front crawl event, performed during competition ].

PubMed

Jalab, Chadi; Enea, Carina; Delpech, Nathalie; Bernard, Olivier

2011-04-01

The main purpose of this study is to estimate the dynamics of oxygen uptake (VO2) during a 100 m front crawl event, performed in competition conditions. Eleven trained swimmers participated in 2 separate sessions, in a 25 m swimming pool. Maximal oxygen uptake (VO2max) was determined during a 400 m maximal event. Swimmers also performed a 100 m front crawl in competition conditions, and then, 3 tests (25, 50, and 75 m) following the pacing strategy of the 100 m event. To be free of technical constraints, VO2 was not measured during the tests, but before and just at the end of each test with a 1 min breath-by-breath method. Each post-test VO2 measurement (after 25, 50, 75, and 100 m) allows us to reconstruct the VO2 kinetics of the 100 m performance. Our results differ from previous studies in that VO2 increases faster in the first half of the race (at 50 m, VO2 ≈ 94% VO2max), reaches VO2max at the 75 m mark; then a decrease in VO2 corresponding to 7% of VO2max appears during the last 25 m. These differences are supposed to be mainly the consequences of the adoption of technical elements and a pacing strategy similar to competition conditions. In the future, these observations may lead to different considerations of the bioenergetic contributions.

Kinetically inert Cu in coastal waters.

PubMed

Kogut, Megan B; Voelker, Bettina M

2003-02-01

Many studies have shown that Cu and other metals in natural waters are mostly bound by unidentified compounds interpreted to be strong ligands reversibly complexing a given metal. However, commonly applied analytical techniques are not capable of distinguishing strongly but reversibly complexed metal from metal bound in kinetically inert compounds. In this work, we use a modified competitive ligand exchange adsorptive cathodic stripping voltammetry method combined with size fractionation to show that most if not all of the apparently very strongly (log K > or = 13) bound Cu in samples from five New England coastal waters (1-18 nM, 10-60% of total Cu) is actually present as kinetically inert compounds. In three of the five samples examined by ultrafiltration, a significant portion of the 0.2-microm-filtrable inert Cu was retained by a 0.02-microm-pore size filter, suggesting that at least some of the Cu was kinetically inert because it was physically sequestered in colloidal material. The rest of the ambient Cu, and Cu added in titrations, were reversibly bound in complexes that could be modeled as having conditional stability constants of 10(10)-10(13). The Cu-binding ability of these complexes was equivalent to that of seawater containing reasonable concentrations of humic substances from terrestrial sources, approximately 0.15-0.45 mg of C/L. Both the inert compounds and the reversible ligands were important for determining [Cu2+] at ambient Cu levels in our samples.

Competition between isoprene emission and pigment synthesis during leaf development in aspen

PubMed Central

Rasulov, Bahtijor; Bichele, Irina; Laisk, Agu; Niinemets, Ülo

2014-01-01

In growing leaves, lack of isoprene synthase is considered responsible for delayed isoprene emission, but competition for dimethylallyl diphosphate (DMADP), the substrate for both isoprene synthesis and prenyltransferase reactions in photosynthetic pigment and phytohormone synthesis, can also play a role. We used a kinetic approach based on postillumination isoprene decay and modeling DMADP consumption to estimate in vivo kinetic characteristics of isoprene synthase and prenyltransferase reactions, and determine the share of DMADP use by different processes through leaf development in Populus tremula. Pigment synthesis rate was also estimated from pigment accumulation data, and distribution of DMADP use from isoprene emission changes due to alendronate, a selective inhibitor of prenyltransferases. Development of photosynthetic activity and pigment synthesis occurred with the greatest rate in 1-5 days old leaves when isoprene emission was absent. Isoprene emission commenced on days 5-6 and increased simultaneously with slowing down of pigment synthesis. In vivo Michaelis-Menten constant (Km) values obtained were 265 nmol m−2 (20 μM) for DMADP-consuming prenyltransferase reactions and 2560 nmol m−2 (190 μM) for isoprene synthase. Thus, despite decelerating pigment synthesis reactions in maturing leaves, isoprene emission in young leaves was limited by both isoprene synthase activity and competition for DMADP by prenyltransferase reactions. PMID:24033429

Evaluation of cryogenine on rat paw thermal oedema and rat isolated uterus

PubMed Central

Malone, M. H.; Trottier, R. W.

1973-01-01

1. Significant inhibition of oedema formation caused by thermal injury was observed for calcium carbaspirin, phenylbutazone, hydrocortisone, cryogenine and indomethacin when given daily beginning 2 days prior to thermal exposure and afterwards. Several anti-inflammatory drugs, including cryogenine, failed to reduce thermal oedema significantly when given as single doses 1 h prior to the thermal injury. 2. Kinetic experiments on the rat isolated uterus demonstrated that cryogenine, chlorpromazine, and flufenamic acid were, in part, competitive inhibitors of synthetic bradykinin, while indomethacin and tetrabenazine showed only non-competitive antagonism. PMID:4733728

Reaction kinetics and inhibition of adenosine kinase from Leishmania donovani.

PubMed

Bhaumik, D; Datta, A K

1988-04-01

The reaction kinetics and the inhibitor specificity of adenosine kinase (ATP:adenosine 5'-phosphotransferase, EC 2.7.1.20) from Leishmania donovani, have been analysed using homogeneous preparation of the enzyme. The reaction proceeds with equimolar stoichiometry of each reactant. Double reciprocal plots of initial velocity studies in the absence of products yielded intersecting lines for both adenosine and Mg2+-ATP. AMP is a competitive inhibitor of the enzyme with respect to adenosine and noncompetitive inhibitor with respect to ATP. In contrast, ADP was a noncompetitive inhibitor with respect to both adenosine and ATP, with inhibition by ADP becoming uncompetitive at very high concentration of ATP. Parallel equilibrium dialysis experiments against [3H]adenosine and [gamma-32P]ATP resulted in binding of adenosine to fre enzyme. Tubercidin (7-deazaadenosine) and 6-methyl-mercaptopurine riboside acted as substrates for the enzyme and were found to inhibit adenosine phosphorylation competitively in vitro. 'Substrate efficiency (Vmax/Km)' and 'turnover numbers (Kcat)' of the enzyme with respect to specific analogs were determined. Taken together the results suggest that (a) the kinetic mechanism of adenosine kinase is sequential Bi-Bi, (b) AMP and ADP may regulate enzyme activity in vivo and (c) tubercidin and 6-methylmercaptopurine riboside are monophosphorylated by the parasite enzyme.

Mechanism of di-tert-butylsilylene transfer from a silacyclopropane to an alkene.

PubMed

Driver, Tom G; Woerpel, K A

2003-09-03

Kinetic and thermodynamic studies of the reactions of cyclohexene silacyclopropane 1 and monosubstituted alkenes suggested a possible mechanism for di-tert-butylsilylene transfer. The kinetic order in cyclohexene silacyclopropane 1 and cyclohexene were determined to be 1 and -1, respectively. Saturation kinetic behavior in monosubstituted alkene concentration was observed. Competition experiments between substituted styrenes and a deficient amount of di-tert-butylsilylene from 1 correlated well with the Hammett equation and provided a rho value of -0.666 +/- 0.008, using sigma(p) constants. These data supported a two-step mechanism involving reversible di-tert-butylsilylene extrusion from 1, followed by irreversible concerted electrophilic attack of the silylene on the monosubstituted alkene. Eyring activation parameters were found to be DeltaH++ = 22.1 +/- 0.9 kcal.mol(-1) and DeltaS++ = -15 +/- 2 eu. Competition experiments between cycloalkenes and allylbenzene determined cycloalkenes to be more efficient silylene traps (k(rel) =1.3, DeltaDeltaG++ = 0.200 kcal.mol(-1)). A summary of the data resulted in a postulated reaction coordinate diagram. The mechanistic studies enabled rational modification of reaction conditions that improved the synthetic utility of silylene transfer. Removal of the volatile cyclohexene from the reaction mixture into an evacuated headspace led to the formation of previously inaccessible cyclohexene-derived silacyclopropanes.

Physiological pattern changes in response to a simulated competition in elite women artistic gymnasts.

PubMed

Isacco, Laurie; Ennequin, Gaël; Cassirame, Johan; Tordi, Nicolas

2017-08-04

The outstanding progress in women's artistic gymnastics in recent decades has led to increased technical and physiological demands. The aim of this study was to investigate i) the physiological demands of elite French gymnasts and ii) the impact of a competitive routine on physiological pattern changes. Fourteen French elite female gymnasts performed anthropometric measurements, physical fitness tests and a simulated four event competition. Heart rate (HR) was continuously recorded throughout the duration of the simulated competition. Blood lactate concentrations were assessed at rest, before the beginning and at 2, 4 and 10 min after completion of the routine on each apparatus. Isometric handgrip strength and anaerobic endurance and power were assessed during the simulated competition. The highest values of HR and blood lactate concentrations were reached during the floor and uneven bar exercises. Blood lactate concentrations and HR kinetics were apparatus dependent and values remained significantly increased at 10 min of recovery compared with resting data. Anaerobic endurance and power decreased significantly as the competition progressed (P <0.001). The present results show specifically cardiorespiratory and anaerobic apparatus- dependent responses throughout a simulated competition. Recovery approaches appear relevant to prevent and/or minimize fatigue and optimize performance in these athletes.

An Overview on Aerospatiale Magnetic Bearing Products for Spacecraft Attitude Control and for Industry

NASA Technical Reports Server (NTRS)

Samuel, Alain; Lechable, Bernard

1996-01-01

Aerospatiale magnetic bearings are based on the use of permanent magnets and on the control of the rotor around a zero force equilibrium point. The present developments of magnetic bearing wheels for space applications focus on the versatility of a basic design which leads to a family of reaction and momentum wheels with tailored torque and kinetic momentum, leading to competitive mass and cost. The present industrial applications concern kinetic energy accumulators, medical x-ray rotating devices, avionics equipment, cryotechnic compressors and vacuum pumps.

Inhibition of tyrosinase by 4H-chromene analogs: Synthesis, kinetic studies, and computational analysis.

PubMed

Brasil, Edikarlos M; Canavieira, Luciana M; Cardoso, Érica T C; Silva, Edilene O; Lameira, Jerônimo; Nascimento, José L M; Eifler-Lima, Vera L; Macchi, Barbarella M; Sriram, Dharmarajan; Bernhardt, Paul V; Silva, José Rogério Araújo; Williams, Craig M; Alves, Cláudio N

2017-11-01

Inhibition of mushroom tyrosinase was observed with synthetic dihydropyrano[3,2-b]chromenediones. Among them, DHPC04 displayed the most potent tyrosinase inhibitory activity with a K i value of 4 μm, comparable to the reference standard inhibitor kojic acid. A kinetic study suggested that these synthetic heterocyclic compounds behave as competitive inhibitors for the L-DOPA binding site of the enzyme. Furthermore, molecular modeling provided important insight into the mechanism of binding interactions with the tyrosinase copper active site. © 2017 John Wiley & Sons A/S.

Resolving DNA-ligand intercalation in the entropic stretching regime

NASA Astrophysics Data System (ADS)

Almaqwashi, Ali A.

Single molecule studies of DNA intercalation are typically conducted by applying stretching forces to obtain force-dependent DNA elongation measurements. The zero-force properties of DNA intercalation are determined by equilibrium and kinetic force-analysis. However, the applied stretching forces that are above the entropic regime (>5 pN) prevent DNA-DNA contact which may eliminate competitive DNA-ligand interactions. In particular, it is noted that cationic mono-intercalators investigated by single molecule force spectroscopy are mostly found to intercalate DNA with single rate, while bulk studies reported additional slower rates. Here, a proposed framework quantifies DNA intercalation by cationic ligands in competition with relatively rapid kinetic DNA-ligand aggregation. At a constant applied force in the entropic stretching regime, the analysis illustrates that DNA intercalation would be measurably optimized only within a narrow range of low ligand concentrations. As DNA intercalators are considered for potential DNA-targeted therapeutics, this analysis provides insights in tuning ligand concertation to maximize therapeutics efficiency.

Upper limb joint kinetic analysis during tennis serve: Assessment of competitive level on efficiency and injury risks.

PubMed

Martin, C; Bideau, B; Ropars, M; Delamarche, P; Kulpa, R

2014-08-01

The aim of this work was to compare the joint kinetics and stroke production efficiency for the shoulder, elbow, and wrist during the serve between professionals and advanced tennis players and to discuss their potential relationship with given overuse injuries. Eleven professional and seven advanced tennis players were studied with an optoelectronic motion analysis system while performing serves. Normalized peak kinetic values of the shoulder, elbow, and wrist joints were calculated using inverse dynamics. To measure serve efficiency, all normalized peak kinetic values were divided by ball velocity. t-tests were used to determine significant differences between the resultant joint kinetics and efficiency values in both groups (advanced vs professional). Shoulder inferior force, shoulder anterior force, shoulder horizontal abduction torque, and elbow medial force were significantly higher in advanced players. Professional players were more efficient than advanced players, as they maximize ball velocity with lower joint kinetics. Since advanced players are subjected to higher joint kinetics, the results suggest that they appeared more susceptible to high risk of shoulder and elbow injuries than professionals, especially during the cocking and deceleration phases of the serve. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Mechanism and Kinetics of Ethanol Coupling to Butanol over Hydroxyapatite

DOE PAGES

Ho, Christopher R.; Shylesh, Sankaranarayanapillai; Bell, Alexis T.

2015-12-23

The mechanism and kinetics for ethanol coupling to n-butanol over hydroxyapatite (HAP) were investigated at 573-613 K. In situ titration experiments show that the active sites for acetaldehyde and butanol formation are different. In combination with FTIR studies, it was found that ethanol dehydrogenation is catalyzed by Ca-O sites, whereas condensation of acetaldehyde is catalyzed by CaO/PO 4 3- pairs. Measurements of the reaction kinetics at various ethanol (3.5-9.4 kPa) and acetaldehyde (0.055-0.12 kPa) partial pressures reveal that direct condensation involving two ethanol molecules does not play a significant role in butanol formation; instead, n-butanol is formed via a Guerbetmore » pathway. At a constant acetaldehyde pressure, enolate formation is rate-limiting, and ethanol inhibits acetaldehyde condensation rates by competitive adsorption. A model of the reaction kinetics consistent with all experimental observations is developed.« less

Mechanism of silver-mediated di-tert-butylsilylene transfer from a silacyclopropane to an alkene.

PubMed

Driver, Tom G; Woerpel, K A

2004-08-18

Kinetic studies of the reactions of cyclohexene silacyclopropane 1 and monosubstituted alkenes in the presence of 5 mol % of (Ph3P)2AgOTf suggested a possible mechanism for silver-mediated di-tert-butylsilylene transfer. The kinetic order in cyclohexene silacyclopropane 1 was determined to be one. Inverse kinetic saturation behavior (rate inhibition) was observed in monosubstituted alkene and cyclohexene concentrations. Saturation kinetic behavior in catalyst concentration was observed. A reactive intermediate, a silylsilver complex, was observed using low temperature 29Si NMR spectroscopy. Competition experiments between substituted styrenes and a deficient amount of 1 correlated well with the Hammett equation and provided a rho value of -0.62 +/- 0.02 using sigmap constants. These data support a mechanism involving reversible silver-promoted di-tert-butylsilylene extrusion from 1 followed by irreversible concerted electrophilic attack of the silylsilver intermediate on the alkene.

Morphomechanics of bacterial biofilms undergoing anisotropic differential growth

NASA Astrophysics Data System (ADS)

Zhang, Cheng; Li, Bo; Huang, Xiao; Ni, Yong; Feng, Xi-Qiao

2016-10-01

Growing bacterial biofilms exhibit a number of surface morphologies, e.g., concentric wrinkles, radial ridges, and labyrinthine networks, depending on their physiological status and nutrient access. We explore the mechanisms underlying the emergence of these greatly different morphologies. Ginzburg-Landau kinetic method and Fourier spectral method are integrated to simulate the morphological evolution of bacterial biofilms. It is shown that the morphological instability of biofilms is triggered by the stresses induced by anisotropic and heterogeneous bacterial expansion, and involves the competition between membrane energy and bending energy. Local interfacial delamination further enriches the morphologies of biofilms. Phase diagrams are established to reveal how the anisotropy and spatial heterogeneity of growth modulate the surface patterns. The mechanics of three-dimensional microbial morphogenesis may also underpin self-organization in other development systems and provide a potential strategy for engineering microscopic structures from bacterial aggregates.

Proteome-level interplay between folding and aggregation propensities of proteins.

PubMed

Tartaglia, Gian Gaetano; Vendruscolo, Michele

2010-10-08

With the advent of proteomics, there is an increasing need of tools for predicting the properties of large numbers of proteins by using the information provided by their amino acid sequences, even in the absence of the knowledge of their structures. One of the most important types of predictions concerns whether proteins will fold or aggregate. Here, we study the competition between these two processes by analyzing the relationship between the folding and aggregation propensity profiles for the human and Escherichia coli proteomes. These profiles are calculated, respectively, using the CamFold method, which we introduce in this work, and the Zyggregator method. Our results indicate that the kinetic behavior of proteins is, to a large extent, determined by the interplay between regions of low folding and high aggregation propensities. Copyright © 2010. Published by Elsevier Ltd.

Label-Free, LC-MS-Based Assays to Quantitate Small-Molecule Antagonist Binding to the Mammalian BLT1 Receptor.

PubMed

Chen, Xun; Stout, Steven; Mueller, Uwe; Boykow, George; Visconti, Richard; Siliphaivanh, Phieng; Spencer, Kerrie; Presland, Jeremy; Kavana, Michael; Basso, Andrea D; McLaren, David G; Myers, Robert W

2017-08-01

We have developed and validated label-free, liquid chromatography-mass spectrometry (LC-MS)-based equilibrium direct and competition binding assays to quantitate small-molecule antagonist binding to recombinant human and mouse BLT1 receptors expressed in HEK 293 cell membranes. Procedurally, these binding assays involve (1) equilibration of the BLT1 receptor and probe ligand, with or without a competitor; (2) vacuum filtration through cationic glass fiber filters to separate receptor-bound from free probe ligand; and (3) LC-MS analysis in selected reaction monitoring mode for bound probe ligand quantitation. Two novel, optimized probe ligands, compounds 1 and 2, were identified by screening 20 unlabeled BLT1 antagonists for direct binding. Saturation direct binding studies confirmed the high affinity, and dissociation studies established the rapid binding kinetics of probe ligands 1 and 2. Competition binding assays were established using both probe ligands, and the affinities of structurally diverse BLT1 antagonists were measured. Both binding assay formats can be executed with high specificity and sensitivity and moderate throughput (96-well plate format) using these approaches. This highly versatile, label-free method for studying ligand binding to membrane-associated receptors should find broad application as an alternative to traditional methods using labeled ligands.

Competition kinetics using the UV/H2O2 process: a structure reactivity correlation for the rate constants of hydroxyl radicals toward nitroaromatic compounds.

PubMed

García Einschlag, Fernando S; Carlos, Luciano; Capparelli, Alberto L

2003-10-01

The rate constants for hydroxyl radical reaction toward a set of nitroaromatic substrates kS, have been measured at 25 degrees C using competition experiments in the UV/H2O2 process. For a given pair of substrates S1 and S2, the relative reactivity beta (defined as kS1/kS2) was calculated from the slope of the corresponding double logarithmic plot, i.e., of ln[S1] vs. ln[S2]. This method is more accurate and remained linear for larger conversions in comparison with the plots of ln[S1] and ln[S2] against time. The rate constants measured ranged from 0.33 to 8.6 x 10(9) M(-1)s(-1). A quantitative structure-reactivity relationship was found using the Hammett equation. Assuming sigma values to be additive, a value of -0.60 was obtained for the reaction constant rho. This value agrees with the high reactivity and the electrophilic nature of HO* radical.

Modeling the Mousetrap Car

ERIC Educational Resources Information Center

Jumper, William D.

2012-01-01

Many high school and introductory college physics courses make use of mousetrap car projects and competitions as a way of providing an engaging hands-on learning experience incorporating Newton's laws, conversion of potential to kinetic energy, dissipative forces, and rotational mechanics. Presented here is a simple analytical and finite element…

Removal of artificial sweetener aspartame from aqueous media by electrochemical advanced oxidation processes.

PubMed

Lin, Heng; Oturan, Nihal; Wu, Jie; Sharma, Virender K; Zhang, Hui; Oturan, Mehmet A

2017-01-01

The degradation and mineralization of aspartame (ASP) in aqueous solution were investigated, for the first time, by electrochemical advanced oxidation processes (EAOPs) in which hydroxyl radicals were formed concomitantly in the bulk from Fenton reaction via in situ electrogenerated Fenton's reagent and at the anode surface from the water oxidation. Experiments were performed in an undivided cylindrical glass cell with a carbon-felt cathode and a Pt or boron-doped diamond (BDD) anode. The effect of Fe 2+ concentration and applied current on the degradation and mineralization kinetics of ASP was evaluated. The absolute rate constant for the reaction between ASP and OH was determined as (5.23 ± 0.02) × 10 9  M -1  s -1 by using the competition kinetic method. Almost complete mineralization of ASP was achieved with BDD anode at 200 mA constant current electrolysis. The formation and generation of the formed carboxylic acids (as ultimate end products before complete mineralization) and released inorganic ion were monitored by ion-exclusion high performance liquid chromatography (HPLC) and ion chromatography techniques, respectively. The global toxicity of the treated ASP solution during treatment was assessed by the Microtox ® method using V. fischeri bacteria luminescence inhibition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical oxidation of a malodorous compound, indole, using iron entrapped in calcium alginate beads.

PubMed

Ben Hammouda, Samia; Adhoum, Nafaâ; Monser, Lotfi

2016-01-15

Iron-alginate beads (Fe-ABs) were successfully prepared by the ion-gelation method, and applied as heterogeneous Fenton catalysts for the removal of a malodorous compound 'indole'. Similarly, copper-enriched alginate beads (Cu-ABs) were synthesized and tested as like-Fenton catalyst, however, their application proved not to be effective for this purpose. Fe-ABs catalysts were characterized by FTIR, SEM, EDS and AAS spectroscopy. Results pointed out that the parameters affecting Fenton catalysis must be carefully chosen to avoid excessive iron release. Under optimal conditions, complete indole removal and considerably high reduction of TOC, without significant leaching was achieved. Indole decay followed a pseudo-first-order kinetics. The absolute rate constant for indole hydroxylation was 3.59×10(9) M(-1) s(-1), as determined by the competition kinetics method. Four reaction intermediates (Isatin, Dioxindole, Oxindole and Anthralinic acid) were identified by ULC/MS/MS analysis. Short-chain aliphatic carboxylic acids like formic, acetic, oxalic, maleic, oxamic and pyruvic acids were identified by ion exclusion chromatography and as end-products. Based on the identified by-products, a plausible mineralization pathway was proposed. Moreover, the catalyst was recovered quantitatively by simple filtration and reused for several times without significant loss of activity. Copyright © 2015 Elsevier B.V. All rights reserved.

Catalytic efficiency is a better predictor of arsenic toxicity to soil alkaline phosphatase.

PubMed

Wang, Ziquan; Tian, Haixia; Lu, Guannan; Zhao, Yiming; Yang, Rui; Megharaj, Mallavarapu; He, Wenxiang

2018-02-01

Arsenic (As) is an inhibitor of phosphatase, however, in the complex soil system, the substrate concentration effect and the mechanism of As inhibition of soil alkaline phosphatase (ALP) and its kinetics has not been adequately studied. In this work, we investigated soil ALP activity in response to As pollution at different substrate concentrations in various types of soils and explored the inhibition mechanism using the enzyme kinetics. The results showed that As inhibition of soil ALP activity was substrate concentration-dependent. Increasing substrate concentration decreased inhibition rate, suggesting reduced toxicity. This dependency was due to the competitive inhibition mechanism of As to soil ALP. The kinetic parameters, maximum reaction velocity (V max ) and Michaelis constant (K m ) in unpolluted soils were 0.012-0.267mMh -1 and 1.34-3.79mM respectively. The competitive inhibition constant (K ic ) was 0.17-0.70mM, which was lower than K m , suggesting higher enzyme affinity for As than for substrate. The ecological doses, ED 10 and ED 50 (concentration of As that results in 10% and 50% inhibition on enzyme parameter) for inhibition of catalytic efficiency (V max /K m ) were lower than those for inhibition of enzyme activity at different substrate concentrations. This suggests that the integrated kinetic parameter, catalytic efficiency is substrate concentration independent and more sensitive to As than ALP activity. Thus, catalytic efficiency was proposed as a more reliable indicator than ALP activity for risk assessment of As pollution. Copyright © 2017 Elsevier Inc. All rights reserved.

Substrate-Induced Facilitated Dissociation of the Competitive Inhibitor from the Active Site of O-Acetyl Serine Sulfhydrylase Reveals a Competitive-Allostery Mechanism.

PubMed

Singh, Appu Kumar; Ekka, Mary Krishna; Kaushik, Abhishek; Pandya, Vaibhav; Singh, Ravi P; Banerjee, Shrijita; Mittal, Monica; Singh, Vijay; Kumaran, S

2017-09-19

By classical competitive antagonism, a substrate and competitive inhibitor must bind mutually exclusively to the active site. The competitive inhibition of O-acetyl serine sulfhydrylase (OASS) by the C-terminus of serine acetyltransferase (SAT) presents a paradox, because the C-terminus of SAT binds to the active site of OASS with an affinity that is 4-6 log-fold (10 4 -10 6 ) greater than that of the substrate. Therefore, we employed multiple approaches to understand how the substrate gains access to the OASS active site under physiological conditions. Single-molecule and ensemble approaches showed that the active site-bound high-affinity competitive inhibitor is actively dissociated by the substrate, which is not consistent with classical views of competitive antagonism. We employed fast-flow kinetic approaches to demonstrate that substrate-mediated dissociation of full length SAT-OASS (cysteine regulatory complex) follows a noncanonical "facilitated dissociation" mechanism. To understand the mechanism by which the substrate induces inhibitor dissociation, we resolved the crystal structures of enzyme·inhibitor·substrate ternary complexes. Crystal structures reveal a competitive allosteric binding mechanism in which the substrate intrudes into the inhibitor-bound active site and disengages the inhibitor before occupying the site vacated by the inhibitor. In summary, here we reveal a new type of competitive allosteric binding mechanism by which one of the competitive antagonists facilitates the dissociation of the other. Together, our results indicate that "competitive allostery" is the general feature of noncanonical "facilitated/accelerated dissociation" mechanisms. Further understanding of the mechanistic framework of "competitive allosteric" mechanism may allow us to design a new family of "competitive allosteric drugs/small molecules" that will have improved selectivity and specificity as compared to their competitive and allosteric counterparts.

Effect of Temperature on the Prevalence of Saccharomyces Non cerevisiae Species against a S. cerevisiae Wine Strain in Wine Fermentation: Competition, Physiological Fitness, and Influence in Final Wine Composition.

PubMed

Alonso-Del-Real, Javier; Lairón-Peris, María; Barrio, Eladio; Querol, Amparo

2017-01-01

Saccharomyces cerevisiae is the main microorganism responsible for the fermentation of wine. Nevertheless, in the last years wineries are facing new challenges due to current market demands and climate change effects on the wine quality. New yeast starters formed by non-conventional Saccharomyces species (such as S. uvarum or S. kudriavzevii ) or their hybrids ( S. cerevisiae x S. uvarum and S. cerevisiae x S. kudriavzevii ) can contribute to solve some of these challenges. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts. However, S . cerevisiae can competitively displace other yeast species from wine fermentations, therefore the use of these new starters requires an analysis of their behavior during competition with S. cerevisiae during wine fermentation. In the present study we analyzed the survival capacity of non- cerevisiae strains in competition with S. cerevisiae during fermentation of synthetic wine must at different temperatures. First, we developed a new method, based on QPCR, to quantify the proportion of different Saccharomyces yeasts in mixed cultures. This method was used to assess the effect of competition on the growth fitness. In addition, fermentation kinetics parameters and final wine compositions were also analyzed. We observed that some cryotolerant Saccharomyces yeasts, particularly S. uvarum , seriously compromised S. cerevisiae fitness during competences at lower temperatures, which explains why S. uvarum can replace S. cerevisiae during wine fermentations in European regions with oceanic and continental climates. From an enological point of view, mixed co-cultures between S. cerevisiae and S. paradoxus or S. eubayanus , deteriorated fermentation parameters and the final product composition compared to single S. cerevisiae inoculation. However, in co-inoculated synthetic must in which S. kudriavzevii or S. uvarum coexisted with S. cerevisiae , there were fermentation performance improvements and the final wines contained less ethanol and higher amounts of glycerol. Finally, it is interesting to note that in co-inoculated fermentations, wine strains of S. cerevisiae and S. uvarum performed better than non-wine strains of the same species.

Effect of Temperature on the Prevalence of Saccharomyces Non cerevisiae Species against a S. cerevisiae Wine Strain in Wine Fermentation: Competition, Physiological Fitness, and Influence in Final Wine Composition

PubMed Central

Alonso-del-Real, Javier; Lairón-Peris, María; Barrio, Eladio; Querol, Amparo

2017-01-01

Saccharomyces cerevisiae is the main microorganism responsible for the fermentation of wine. Nevertheless, in the last years wineries are facing new challenges due to current market demands and climate change effects on the wine quality. New yeast starters formed by non-conventional Saccharomyces species (such as S. uvarum or S. kudriavzevii) or their hybrids (S. cerevisiae x S. uvarum and S. cerevisiae x S. kudriavzevii) can contribute to solve some of these challenges. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts. However, S. cerevisiae can competitively displace other yeast species from wine fermentations, therefore the use of these new starters requires an analysis of their behavior during competition with S. cerevisiae during wine fermentation. In the present study we analyzed the survival capacity of non-cerevisiae strains in competition with S. cerevisiae during fermentation of synthetic wine must at different temperatures. First, we developed a new method, based on QPCR, to quantify the proportion of different Saccharomyces yeasts in mixed cultures. This method was used to assess the effect of competition on the growth fitness. In addition, fermentation kinetics parameters and final wine compositions were also analyzed. We observed that some cryotolerant Saccharomyces yeasts, particularly S. uvarum, seriously compromised S. cerevisiae fitness during competences at lower temperatures, which explains why S. uvarum can replace S. cerevisiae during wine fermentations in European regions with oceanic and continental climates. From an enological point of view, mixed co-cultures between S. cerevisiae and S. paradoxus or S. eubayanus, deteriorated fermentation parameters and the final product composition compared to single S. cerevisiae inoculation. However, in co-inoculated synthetic must in which S. kudriavzevii or S. uvarum coexisted with S. cerevisiae, there were fermentation performance improvements and the final wines contained less ethanol and higher amounts of glycerol. Finally, it is interesting to note that in co-inoculated fermentations, wine strains of S. cerevisiae and S. uvarum performed better than non-wine strains of the same species. PMID:28223968

Coordination responsive tellurium-containing multilayer film for controlled delivery.

PubMed

Cao, Wei; Wang, Lu; Xu, Huaping

2015-03-28

A coordination-responsive tellurium containing film was fabricated for controlled release. The coordination chemistry between telluride molecules and cisplatin was utilized for the loading of cisplatin, while competitive ligands were used for triggered release. This work could enrich the coordination responsive system and further tune the release kinetics of cisplatin.

INFLUENCE OF BISOLUTE COMPETITION ON THE DESORPTION KINETICS OF POLYCYCLIC AROMATIC HYDROCARBONS IN SOIL. (R825959)

EPA Science Inventory

The dual-mode (partition/hole-filling) model of soil organic matter (SOM) as
a heterogeneous polymerlike sorbent of hydrophobic compounds predicts that a
competing solute will accelerate diffusion of the primary solute by blocking the
holes, allowing the principal ...

Excess zinc ions are a competitive inhibitor for carboxypeptidase A

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

Hirose, J.; Ando, S.; Kidani, Y.

The mechanism for inhibition of enzyme activity by excess zinc ions has been studied by kinetic and equilibrium dialysis methods at pH 8.2, I = 0.5 M. With carboxypeptidase A (bovine pancreas), peptide (carbobenzoxyglycyl-L-phenylalanine and hippuryl-L-phenylalanine) and ester (hippuryl-L-phenyl lactate) substrates were inhibited competitively by excess zinc ions. The K/sub i/ values for excess zinc ions with carboxypeptidase A at pH 8.2 are all similar. The apparent constant for dissociation of excess zinc ions from carboxypeptidase A was also obtained by equilibrium dialysis at pH 8.2 and was 2.4 x 10/sup -5/ M, very close to the K/sub i/ valuesmore » above. With arsanilazotyrosine-248 carboxypeptidase A ((Azo-CPD)Zn)), hippuryl-L-phenylalanine, carbobenzoxyglycyl-L-phenylalanine, and hippuryl-L-phenyl lactate were also inhibited with a competitive pattern by excess zinc ions, and the K/sub i/ values were (3.0-3.5) x 10/sup -5/ M. The apparent constant for dissociation of excess zinc ions from arsanilazotyrosine-248 carboxypeptidase A, which was obtained from absorption changes at 510 nm, was 3.2 x 10/sup -5/ M and is similar to the K/sub i/ values for ((Azo-CPD)Zn). The apparent dissociation and inhibition constants, which were obtained by inhibition of enzyme activity and spectrophotometric and equilibrium dialysis methods with native carboxypeptidase A and arsanilazotyrosine-248 carboxypeptidase A, were almost the same. This agreement between the apparent dissociation and inhibition constants indicates that the zinc binding to the enzymes directly relates to the inhibition of enzyme activity by excess zinc ions. Excess zinc ions were competitive inhibitors for both peptide and ester substrates. This behavior is believed to arise by the excess zinc ions fixing the enzyme in a conformation to which the substrates cannot bind.« less

Examination of the Mechanism of Rh2(II)-Catalyzed Carbazole Formation Using Intramolecular Competition Experiments

PubMed Central

Stokes, Benjamin J.; Richert, Kathleen J.; Driver, Tom G.

2009-01-01

The use of a rhodium(II) carboxylate catalyst enables the mild and stereoselective formation of carbazoles from biaryl azides. Intramolecular competition experiments of triaryl azides suggested the source of the selectivity. A primary intramolecular kinetic isotope effect was not observed and correlation of the product ratios with Hammett σ+-values produced a plot with two intersecting lines with opposite ρ-values. These data suggest that electronic donation by the biaryl π-system accelerates the formation of rhodium nitrenoid and that C–N bond formation occurs through a 4π-electron-5-atom electrocyclization. PMID:19663433

Competitive adsorption from mixed hen egg-white lysozyme/surfactant solutions at the air-water interface studied by tensiometry, ellipsometry, and surface dilational rheology.

PubMed

Alahverdjieva, V S; Grigoriev, D O; Fainerman, V B; Aksenenko, E V; Miller, R; Möhwald, H

2008-02-21

The competitive adsorption at the air-water interface from mixed adsorption layers of hen egg-white lysozyme with a non-ionic surfactant (C10DMPO) was studied and compared to the mixture with an ionic surfactant (SDS) using bubble and drop shape analysis tensiometry, ellipsometry, and surface dilational rheology. The set of equilibrium and kinetic data of the mixed solutions is described by a thermodynamic model developed recently. The theoretical description of the mixed system is based on the model parameters for the individual components.

Biological evaluation and molecular docking of baicalin and scutellarin as Helicobacter pylori urease inhibitors.

PubMed

Yu, Xiao-Dan; Zheng, Rong-Bo; Xie, Jian-Hui; Su, Ji-Yan; Huang, Xiao-Qi; Wang, Yong-Hong; Zheng, Yi-Feng; Mo, Zhi-Zhun; Wu, Xiao-Li; Wu, Dian-Wei; Liang, Ye-er; Zeng, Hui-Fang; Su, Zi-Ren; Huang, Ping

2015-03-13

Baicalin and scutellarin are the principal bioactive components of Scutellaria baicalensis Georgi which has extensively been incorporated into heat-clearing and detoxification formulas for the treatment of Helicobacter pylori-related gastrointestinal disorders in traditional Chinese medicine. However, the mechanism of action remained to be defined. To explore the inhibitory effect, kinetics and mechanism of Helicobacter pylori urease (the vital pathogenetic factor for Helicobacter pylori infection) inhibition by baicalin and scutellarin, for their therapeutic potential. The ammonia formations, indicator of urease activity, were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. The inhibitory effect of baicalin and scutellarin was characterized with IC50 values, compared to acetohydroxamic acid (AHA), a well known Helicobacter pylori urease inhibitor. Lineweaver-Burk and Dixon plots for the Helicobacter pylori urease inhibition of baicalin and scutellarin was constructed from the kinetic data. SH-blocking reagents and competitive active site Ni(2+) binding inhibitors were employed for mechanism study. Molecular docking technique was used to provide some information on binding conformations as well as confirm the inhibition mode. Moreover, cytotoxicity experiment using Gastric Epithelial Cells (GES-1) was evaluated. Baicalin and scutellarin effectively suppressed Helicobacter pylori urease in dose-dependent and time-independent manner with IC50 of 0.82±0.07 mM and 0.47±0.04 mM, respectively, compared to AHA (IC50=0.14±0.05 mM). Structure-activity relationship disclosed 4'-hydroxyl gave flavones an advantage to binding with Helicobacter pylori urease. Kinetic analysis revealed that the types of inhibition were non-competitive and reversible with inhibition constant Ki of 0.14±0.01 mM and 0.18±0.02 mM for baicalin and scutellarin, respectively. The mechanism of urease inhibition was considered to be blockage of the SH groups of Helicobacter pylori urease, since thiol reagents (L,D-dithiothreitol, L-cysteine and glutathione) abolished the inhibitory action and competitive active site Ni(2+) binding inhibitors (boric acid and sodium fluoride) carried invalid effect. Molecular docking study further supported the structure-activity analysis and indicated that baicalin and scutellarin interacted with the key residues Cys321 located on the mobile flap through S-H·π interaction, but did not interact with active site Ni(2+). Moreover, Baicalin (at 0.59-1.05 mM concentrations) and scutellarin (at 0.23-0.71 mM concentrations) did not exhibit significant cytotoxicity to GES-1. Baicalin and scutellarin were non-competitive inhibitors targeting sulfhydryl groups especially Cys321 around the active site of Helicobacter pylori urease, representing potential to be good candidate for future research as urease inhibitor for treatment of Helicobacter pylori infection. Furthermore, our work gave additional scientific support to the use of Scutellaria baicalensis in traditional Chinese medicine (TCM) to treat gastrointestinal disorders. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Esterification of fatty acids using nylon-immobilized lipase in n-hexane: kinetic parameters and chain-length effects.

PubMed

Zaidi, A; Gainer, J L; Carta, G; Mrani, A; Kadiri, T; Belarbi, Y; Mir, A

2002-02-28

The esterification of long-chain fatty acids in n-hexane catalyzed by nylon-immobilized lipase from Candida rugosa has been investigated. Butyl oleate (22 carbon atoms), oleyl butyrate (22 carbon atoms) and oleyl oleate (36 carbon atoms) were produced at maximum reaction rates of approximately equal to 60 mmol h(-1) g(-1) immobilized enzyme when the substrates were present in equimolar proportions at an initial concentration of 0.6 mol l(-1). The observed kinetic behavior of all the esterification reactions is found to follow a ping-pong bi-bi mechanism with competitive inhibition by both substrates. The effect of the chain-length of the fatty acids and the alcohols could be correlated to some mechanistic models, in accordance with the calculated kinetic parameters.

Kinetic Analysis of Competitive Electrocatalytic Pathways: New Insights into Hydrogen Production with Nickel Electrocatalysts

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

Wiedner, Eric S.; Brown, Houston J.; Helm, Monte L.

2016-01-20

The hydrogen production electrocatalyst Ni(PPh2NPh2)22+ (1) is capable of traversing multiple electrocatalytic pathways. When using dimethylformamidium, DMF(H)+, the mechanism of formation of H2 catalyzed by 1 changes from an ECEC to an EECC mechanism as the potential approaches the Ni(I/0) couple. Two recent electrochemical methods, current-potential analysis and foot-of-the-wave analysis (FOWA), were performed on 1 to measure the detailed chemical kinetics of the competing ECEC and EECC pathways. A sensitivity analysis was performed on the electrochemical methods using digital simulations to gain a better understanding of their strengths and limitations. Notably, chemical rate constants were significantly underestimated when not accountingmore » for electron transfer kinetics, even when electron transfer was fast enough to afford a reversible non-catalytic wave. The EECC pathway of 1 was found to be faster than the ECEC pathway under all conditions studied. Using buffered DMF: DMF(H)+ mixtures led to an increase in the catalytic rate constant (kobs) of the EECC pathway, but kobs for the ECEC pathway did not change when using buffered acid. Further kinetic analysis of the ECEC path revealed that added base increases the rate of isomerization of the exo-protonated Ni(0) isomers to the catalytically active endo-isomers, but decreases the net rate of protonation of Ni(I). FOWA on 1 did not provide accurate rate constants due to incomplete reduction of the exo-protonated Ni(I) intermediate at the foot of the wave, but FOWA could be used to estimate the reduction potential of this previously undetected intermediate. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Nitroxyl (HNO) Reacts with Molecular Oxygen and Forms Peroxynitrite at Physiological pH

PubMed Central

Smulik, Renata; Dębski, Dawid; Zielonka, Jacek; Michałowski, Bartosz; Adamus, Jan; Marcinek, Andrzej; Kalyanaraman, Balaraman; Sikora, Adam

2014-01-01

Nitroxyl (HNO), the protonated one-electron reduction product of NO, remains an enigmatic reactive nitrogen species. Its chemical reactivity and biological activity are still not completely understood. HNO donors show biological effects different from NO donors. Although HNO reactivity with molecular oxygen is described in the literature, the product of this reaction has not yet been unambiguously identified. Here we report that the decomposition of HNO donors under aerobic conditions in aqueous solutions at physiological pH leads to the formation of peroxynitrite (ONOO−) as a major intermediate. We have specifically detected and quantified ONOO− with the aid of boronate probes, e.g. coumarin-7-boronic acid or 4-boronobenzyl derivative of fluorescein methyl ester. In addition to the major phenolic products, peroxynitrite-specific minor products of oxidation of boronate probes were detected under these conditions. Using the competition kinetics method and a set of HNO scavengers, the value of the second order rate constant of the HNO reaction with oxygen (k = 1.8 × 104 m−1 s−1) was determined. The rate constant (k = 2 × 104 m−1 s−1) was also determined using kinetic simulations. The kinetic parameters of the reactions of HNO with selected thiols, including cysteine, dithiothreitol, N-acetylcysteine, captopril, bovine and human serum albumins, and hydrogen sulfide, are reported. Biological and cardiovascular implications of nitroxyl reactions are discussed. PMID:25378389

Differences in pedalling technique between road cyclists of different competitive levels.

PubMed

García-López, Juan; Díez-Leal, Sergio; Ogueta-Alday, Ana; Larrazabal, Josu; Rodríguez-Marroyo, José A

2016-09-01

The purpose of this study was to compare the pedalling technique in road cyclists of different competitive levels. Eleven professional, thirteen elite and fourteen club cyclists were assessed at the beginning of their competition season. Cyclists' anthropometric characteristics and bike measurements were recorded. Three sets of pedalling (200, 250 and 300 W) on a cycle ergometer that simulated their habitual cycling posture were performed at a constant cadence (~90 rpm), while kinetic and kinematic variables were registered. The results showed no differences on the main anthropometric variables and bike measurements. Professional cyclists obtained higher positive impulse proportion (1.5-3.3% and P < 0.05), mainly due to a lower resistive torque during the upstroke (15.4-28.7% and P < 0.05). They also showed a higher ankle range of movement (ROM, 1.1-4.0° and P < 0.05). Significant correlations (P < 0.05) were found between the cyclists' body mass and the kinetic variables of pedalling: positive impulse proportion (r = -0.59 to -0.61), minimum (r = -0.59 to -0.63) and maximum torques (r = 0.35-0.47). In conclusion, professional cyclists had better pedalling technique than elite and club cyclists, because they opted for enhancing pulling force at the recovery phase to sustain the same power output. This technique depended on cycling experience and level of expertise.

Competition between isoprene emission and pigment synthesis during leaf development in aspen.

PubMed

Rasulov, Bahtijor; Bichele, Irina; Laisk, Agu; Niinemets, Ülo

2014-03-01

In growing leaves, lack of isoprene synthase (IspS) is considered responsible for delayed isoprene emission, but competition for dimethylallyl diphosphate (DMADP), the substrate for both isoprene synthesis and prenyltransferase reactions in photosynthetic pigment and phytohormone synthesis, can also play a role. We used a kinetic approach based on post-illumination isoprene decay and modelling DMADP consumption to estimate in vivo kinetic characteristics of IspS and prenyltransferase reactions, and to determine the share of DMADP use by different processes through leaf development in Populus tremula. Pigment synthesis rate was also estimated from pigment accumulation data and distribution of DMADP use from isoprene emission changes due to alendronate, a selective inhibitor of prenyltransferases. Development of photosynthetic activity and pigment synthesis occurred with the greatest rate in 1- to 5-day-old leaves when isoprene emission was absent. Isoprene emission commenced on days 5 and 6 and increased simultaneously with slowing down of pigment synthesis. In vivo Michaelis-Menten constant (Km ) values obtained were 265 nmol m(-2) (20 μm) for DMADP-consuming prenyltransferase reactions and 2560 nmol m(-2) (190 μm) for IspS. Thus, despite decelerating pigment synthesis reactions in maturing leaves, isoprene emission in young leaves was limited by both IspS activity and competition for DMADP by prenyltransferase reactions. © 2013 John Wiley & Sons Ltd.

Growth of InAs Quantum Dots on GaAs (511)A Substrates: The Competition between Thermal Dynamics and Kinetics.

PubMed

Wen, Lei; Gao, Fangliang; Zhang, Shuguang; Li, Guoqiang

2016-08-01

The growth process of InAs quantum dots grown on GaAs (511)A substrates has been studied by atomic force microscopy. According to the atomic force microscopy studies for quantum dots grown with varying InAs coverage, a noncoherent nucleation of quantum dots is observed. Moreover, due to the long migration length of In atoms, the Ostwald ripening process is aggravated, resulting in the bad uniformity of InAs quantum dots on GaAs (511)A. In order to improve the uniformity of nucleation, the growth rate is increased. By studying the effects of increased growth rates on the growth of InAs quantum dots, it is found that the uniformity of InAs quantum dots is greatly improved as the growth rates increase to 0.14 ML s(-1) . However, as the growth rates increase further, the uniformity of InAs quantum dots becomes dual-mode, which can be attributed to the competition between Ostwald ripening and strain relaxation processes. The results in this work provide insights regarding the competition between thermal dynamical barriers and the growth kinetics in the growth of InAs quantum dots, and give guidance to improve the size uniformity of InAs quantum dots on (N11)A substrates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multisubstrate biodegradation kinetics of naphthalene, phenanthrene, and pyrene mixtures

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

Guha, S.; Peters, C.A.; Jaffe, P.R.

Biodegradation kinetics of naphthalene, phenanthrene and pyrene were studied in sole-substrate systems, and in binary and ternary mixtures to examine substrate interactions. The experiments were conducted in aerobic batch aqueous systems inoculated with a mixed culture that had been isolated from soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Monod kinetic parameters and yield coefficients for the individual parameters and yield coefficients for the individual compounds were estimated from substrate depletion and CO{sub 2} evolution rate data in sole-substrate experiments. In all three binary mixture experiments, biodegradation kinetics were comparable to the sole-substrate kinetics. In the ternary mixture, biodegradation of naphthalenemore » was inhibited and the biodegradation rates of phenanthrene and pyrene were enhanced. A multisubstrate form of the Monod kinetic model was found to adequately predict substrate interactions in the binary and ternary mixtures using only the parameters derived from sole-substrate experiments. Numerical simulations of biomass growth kinetics explain the observed range of behaviors in PAH mixtures. In general, the biodegradation rates of the more degradable and abundant compounds are reduced due to competitive inhibition, but enhanced biodegradation of the more recalcitrant PAHs occurs due to simultaneous biomass growth on multiple substrates. In PAH-contaminated environments, substrate interactions may be very large due to additive effects from the large number of compounds present.« less

Biphasic Kinetic Behavior of E. coli WrbA, an FMN-Dependent NAD(P)H:Quinone Oxidoreductase

PubMed Central

Kishko, Iryna; Harish, Balasubramanian; Zayats, Vasilina; Reha, David; Tenner, Brian; Beri, Dhananjay; Gustavsson, Tobias; Ettrich, Rüdiger; Carey, Jannette

2012-01-01

The E. coli protein WrbA is an FMN-dependent NAD(P)H:quinone oxidoreductase that has been implicated in oxidative defense. Three subunits of the tetrameric enzyme contribute to each of four identical, cavernous active sites that appear to accommodate NAD(P)H or various quinones, but not simultaneously, suggesting an obligate tetramer with a ping-pong mechanism in which NAD departs before oxidized quinone binds. The present work was undertaken to evaluate these suggestions and to characterize the kinetic behavior of WrbA. Steady-state kinetics results reveal that WrbA conforms to a ping-pong mechanism with respect to the constancy of the apparent Vmax to Km ratio with substrate concentration. However, the competitive/non-competitive patterns of product inhibition, though consistent with the general class of bi-substrate reactions, do not exclude a minor contribution from additional forms of the enzyme. NMR results support the presence of additional enzyme forms. Docking and energy calculations find that electron-transfer-competent binding sites for NADH and benzoquinone present severe steric overlap, consistent with the ping-pong mechanism. Unexpectedly, plots of initial velocity as a function of either NADH or benzoquinone concentration present one or two Michaelis-Menten phases depending on the temperature at which the enzyme is held prior to assay. The effect of temperature is reversible, suggesting an intramolecular conformational process. WrbA shares these and other details of its kinetic behavior with mammalian DT-diaphorase, an FAD-dependent NAD(P)H:quinone oxidoreductase. An extensive literature review reveals several other enzymes with two-plateau kinetic plots, but in no case has a molecular explanation been elucidated. Preliminary sedimentation velocity analysis of WrbA indicates a large shift in size of the multimer with temperature, suggesting that subunit assembly coupled to substrate binding may underlie the two-plateau behavior. An additional aim of this report is to bring under wider attention the apparently widespread phenomenon of two-plateau Michaelis-Menten plots. PMID:22952804

Quantum Chemical Examination of the Sequential Halogen Incorporation Scheme for the Modeling of Speciation of I/Br/Cl-Containing Trihalomethanes.

PubMed

Zhang, Chenyang; Li, Maodong; Han, Xuze; Yan, Mingquan

2018-02-20

The recently developed three-step ternary halogenation model interprets the incorporation of chlorine, bromine, and iodine ions into natural organic matter (NOM) and formation of iodine-, bromine-, and chlorine-containing trihalomethanes (THMs) based on the competition of iodine, bromine, and chlorine species at each node of the halogenation sequence. This competition is accounted for using the dimensionless ratios (denoted as γ) of kinetic rates of reactions of the initial attack sites or halogenated intermediates with chlorine, bromine, and iodine ions. However, correlations between the model predictions made and mechanistic aspects of the incorporation of halogen species need to be ascertained in more detail. In this study, quantum chemistry calculations were first used to probe the formation mechanism of 10 species of Cl-/Br-/I- THMs. The HOMO energy (E HOMO ) of each mono-, bi-, or trihalomethanes were calculated by B3LYP method in Gaussian 09 software. Linear correlations were found to exist between the logarithms of experimentally determined kinetic preference coefficients γ reported in prior research and, on the other hand, differences of E HOMO values between brominated/iodinated and chlorinated halomethanes. One notable exception from this trend was that observed for the incorporation of iodine into mono- and di-iodinated intermediates. These observations confirm the three-step halogen incorporation sequence and the factor γ in the statistical model. The combined use of quantum chemistry calculations and the ternary sequential halogenation model provides a new insight into the microscopic nature of NOM-halogen interactions and the trends seen in the behavior of γ factors incorporated in the THM speciation models.

Characterization of inhibitory effects of the potential therapeutic inhibitors, benzoic acid and pyridine derivatives, on the monophenolase and diphenolase activities of tyrosinase

PubMed Central

Gheibi, Nematollah; Taherkhani, Negar; Ahmadi, Abolfazl; Haghbeen, Kamahldin; Ilghari, Dariush

2015-01-01

Objective(s): Involvement of tyrosinase in the synthesis of melanin and cell signaling pathway has made it an attractive target in the search for therapeutic inhibitors for treatment of different skin hyperpigmentation disorders and melanoma cancers. Materials and Methods: In the present study, we conducted a comprehensive kinetic analysis to understand the mechanisms of inhibition imposed by 2-amino benzoic acid, 4-amino benzoic acid, nicotinic acid, and picolinic acid on the monophenolase and diphenolase activities of the mushroom tyrosinase, and then MTT assay was exploited to evaluate their toxicity on the melanoma cells. Results: Kinetic analysis revealed that nicotinic acid and picolinic acid competitively restricted the monophenolase activity with inhibition constants (Ki) of 1.21 mM and 1.97 mM and the diphenolase activity with Kis of 2.4 mM and 2.93 mM, respectively. 2-aminobenzoic acid and 4-aminobenzoic acid inhibited the monophenolase activity in a non-competitive fashion with Kis of 5.15 µM and 3.8 µM and the diphenolase activity with Kis of 4.72 µM and 20 µM, respectively. Conclusion: Our cell-based data revealed that only the pyridine derivatives imposed cytotoxicity in melanoma cells. Importantly, the concentrations of the inhibitors leading to 50% decrease in the cell density (IC50) were comparable to those causing 50% drop in the enzyme activity, implying that the observed cytotoxicity is highly likely due to the tyrosinase inhibition. Moreover, our cell-based data exhibited that the pyridine derivatives acted as anti-proliferative agents, perhaps inducing cytotoxicity in the melanoma cells through inhibition of the tyrosinase activities. PMID:25810885

Kinetically Defined Mechanisms and Positions of Action of Two New Modulators of Glucocorticoid Receptor-regulated Gene Induction*

PubMed Central

Pradhan, Madhumita A.; Blackford, John A.; Devaiah, Ballachanda N.; Thompson, Petria S.; Chow, Carson C.; Singer, Dinah S.; Simons, S. Stoney

2016-01-01

Most of the steps in, and many of the factors contributing to, glucocorticoid receptor (GR)-regulated gene induction are currently unknown. A competition assay, based on a validated chemical kinetic model of steroid hormone action, is now used to identify two new factors (BRD4 and negative elongation factor (NELF)-E) and to define their sites and mechanisms of action. BRD4 is a kinase involved in numerous initial steps of gene induction. Consistent with its complicated biochemistry, BRD4 is shown to alter both the maximal activity (Amax) and the steroid concentration required for half-maximal induction (EC50) of GR-mediated gene expression by acting at a minimum of three different kinetically defined steps. The action at two of these steps is dependent on BRD4 concentration, whereas the third step requires the association of BRD4 with P-TEFb. BRD4 is also found to bind to NELF-E, a component of the NELF complex. Unexpectedly, NELF-E modifies GR induction in a manner that is independent of the NELF complex. Several of the kinetically defined steps of BRD4 in this study are proposed to be related to its known biochemical actions. However, novel actions of BRD4 and of NELF-E in GR-controlled gene induction have been uncovered. The model-based competition assay is also unique in being able to order, for the first time, the sites of action of the various reaction components: GR < Cdk9 < BRD4 ≤ induced gene < NELF-E. This ability to order factor actions will assist efforts to reduce the side effects of steroid treatments. PMID:26504077

Kinetics of the utilization of dietary arginine for nitric oxide and urea synthesis: insight into the arginine-nitric oxide metabolic system in humans.

PubMed

Mariotti, François; Petzke, Klaus J; Bonnet, Damien; Szezepanski, Isabelle; Bos, Cécile; Huneau, Jean-François; Fouillet, Hélène

2013-05-01

The systemic availability of oral/dietary arginine and its utilization for nitric oxide (NO) synthesis remains unknown and may be related to a competitive hydrolysis of arginine into urea in the splanchnic area and systemic circulation. We investigated the kinetics and dose-dependency of dietary arginine utilization for NO compared with urea synthesis and studied the characteristics of the arginine-NO metabolic system in healthy humans. We traced the metabolic fate and analyzed the utilization dynamics of dietary arginine after its ingestion at 2 nutritional amounts in healthy humans (n = 9) in a crossover design by using [(15)N-(15)N-(guanido)]-arginine, isotope ratio mass spectrometry techniques, and data analysis with a compartmental modeling approach. Whatever the amount of dietary arginine, 60 ± 3% (±SEM) was converted to urea, with kinetics indicative of a first-pass splanchnic phenomenon. Despite this dramatic extraction, intact dietary arginine made a major contribution to the postprandial increase in plasma arginine. However, the model identified that the plasma compartment was a very minor (~2%) precursor for the conversion of dietary arginine into NO, which, in any case, was small (<0.1% of the dose). The whole-body and plasma kinetics of arginine metabolism were consistent with the suggested competitive metabolism by the arginase and NO synthase pathways. The conversion of oral/dietary arginine into NO is not limited by the systemic availability of arginine but by a tight metabolic compartmentation at the systemic level. We propose an organization of the arginine metabolic system that explains the daily maintenance of NO homeostasis in healthy humans.

Lightweight Materials for Vehicles: Needs, Goals, and Future Technologies

DTIC Science & Technology

2010-08-01

during heating, cooling, and deformation - Developing an improved understanding of the kinetics and mechanisms for tranisition Friction Stir Welding ...technology worthiness - Identify new gaps and opportunities Pre- competitive Research Solicitations and Demonstrations - Identify technology gaps...or processing . Key Technology Gaps Active Research . Gap: Microstructural damage during welding limits potential usefulness - Many

QUANTITATIVE STRUCTURE—PROPERTY RELATIONSHIPS FOR ENHANCING PREDICTIONS OF SYNTHETIC ORGANIC CHEMICAL REMOVAL FROM DRINKING WATER BY GRANULAR ACTIVATED CARBON

EPA Science Inventory

A number of mathematical models have been developed to predict activated carbon column performance using single-solute isotherm data as inputs. Many assumptions are built into these models to account for kinetics of adsorption and competition for adsorption sites. This work...

CCND1–CDK4–mediated cell cycle progression provides a competitive advantage for human hematopoietic stem cells in vivo

PubMed Central

Mende, Nicole; Kuchen, Erika E.; Lesche, Mathias; Grinenko, Tatyana; Kokkaliaris, Konstantinos D.; Hanenberg, Helmut; Lindemann, Dirk; Dahl, Andreas; Platz, Alexander; Höfer, Thomas; Calegari, Federico

2015-01-01

Maintenance of stem cell properties is associated with reduced proliferation. However, in mouse hematopoietic stem cells (HSCs), loss of quiescence results in a wide range of phenotypes, ranging from functional failure to extensive self-renewal. It remains unknown whether the function of human HSCs is controlled by the kinetics of cell cycle progression. Using human HSCs and human progenitor cells (HSPCs), we report here that elevated levels of CCND1–CDK4 complexes promoted the transit from G0 to G1 and shortened the G1 cell cycle phase, resulting in protection from differentiation-inducing signals in vitro and increasing human leukocyte engraftment in vivo. Further, CCND1–CDK4 overexpression conferred a competitive advantage without impacting HSPC numbers. In contrast, accelerated cell cycle progression mediated by elevated levels of CCNE1–CDK2 led to the loss of functional HSPCs in vivo. Collectively, these data suggest that the transition kinetics through the early cell cycle phases are key regulators of human HSPC function and important for lifelong hematopoiesis. PMID:26150472

CCND1-CDK4-mediated cell cycle progression provides a competitive advantage for human hematopoietic stem cells in vivo.

PubMed

Mende, Nicole; Kuchen, Erika E; Lesche, Mathias; Grinenko, Tatyana; Kokkaliaris, Konstantinos D; Hanenberg, Helmut; Lindemann, Dirk; Dahl, Andreas; Platz, Alexander; Höfer, Thomas; Calegari, Federico; Waskow, Claudia

2015-07-27

Maintenance of stem cell properties is associated with reduced proliferation. However, in mouse hematopoietic stem cells (HSCs), loss of quiescence results in a wide range of phenotypes, ranging from functional failure to extensive self-renewal. It remains unknown whether the function of human HSCs is controlled by the kinetics of cell cycle progression. Using human HSCs and human progenitor cells (HSPCs), we report here that elevated levels of CCND1-CDK4 complexes promoted the transit from G0 to G1 and shortened the G1 cell cycle phase, resulting in protection from differentiation-inducing signals in vitro and increasing human leukocyte engraftment in vivo. Further, CCND1-CDK4 overexpression conferred a competitive advantage without impacting HSPC numbers. In contrast, accelerated cell cycle progression mediated by elevated levels of CCNE1-CDK2 led to the loss of functional HSPCs in vivo. Collectively, these data suggest that the transition kinetics through the early cell cycle phases are key regulators of human HSPC function and important for lifelong hematopoiesis. © 2015 Mende et al.

Extensional Flow-Induced Dynamic Phase Transitions in Isotactic Polypropylene.

PubMed

Ju, Jianzhu; Wang, Zhen; Su, Fengmei; Ji, Youxin; Yang, Haoran; Chang, Jiarui; Ali, Sarmad; Li, Xiangyang; Li, Liangbin

2016-09-01

With a combination of fast extension rheometer and in situ synchrotron radiation ultra-fast small- and wide-angle X-ray scattering, flow-induced crystallization (FIC) of isotactic polypropylene (iPP) is studied at temperatures below and above the melting point of α crystals (Tmα). A flow phase diagram of iPP is constructed in strain rate-temperature space, composing of melt, non-crystalline shish, α and α&β coexistence regions, based on which the kinetic and dynamic competitions among these four phases are discussed. Above Tmα , imposing strong flow reverses thermodynamic stabilities of the disordered melt and the ordered phases, leading to the occurrence of FIC of β and α crystals as a dynamic phase transition. Either increasing temperature or stain rate favors the competiveness of the metastable β over the stable α crystals, which is attributed to kinetic rate rather than thermodynamic stability. The violent competitions among four phases near the boundary of crystal-melt may frustrate crystallization and result in the non-crystalline shish winning out. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DICER-ARGONAUTE2 Complex in Continuous Fluorogenic Assays of RNA Interference Enzymes

PubMed Central

Bernard, Mark A.; Wang, Leyu; Tachado, Souvenir D.

2015-01-01

Mechanistic studies of RNA processing in the RNA-Induced Silencing Complex (RISC) have been hindered by lack of methods for continuous monitoring of enzymatic activity. “Quencherless” fluorogenic substrates of RNAi enzymes enable continuous monitoring of enzymatic reactions for detailed kinetics studies. Recombinant RISC enzymes cleave the fluorogenic substrates targeting human thymidylate synthase (TYMS) and hypoxia-inducible factor 1-α subunit (HIF1A). Using fluorogenic dsRNA DICER substrates and fluorogenic siRNA, DICER+ARGONAUTE2 mixtures exhibit synergistic enzymatic activity relative to either enzyme alone, and addition of TRBP does not enhance the apparent activity. Titration of AGO2 and DICER in enzyme assays suggests that AGO2 and DICER form a functional high-affinity complex in equimolar ratio. DICER and DICER+AGO2 exhibit Michaelis-Menten kinetics with DICER substrates. However, AGO2 cannot process the fluorogenic siRNA without DICER enzyme, suggesting that AGO2 cannot self-load siRNA into its active site. The DICER+AGO2 combination processes the fluorogenic siRNA substrate (K m=74 nM) with substrate inhibition kinetics (K i=105 nM), demonstrating experimentally that siRNA binds two different sites that affect Dicing and AGO2-loading reactions in RISC. This result suggests that siRNA (product of DICER) bound in the active site of DICER may undergo direct transfer (as AGO2 substrate) to the active site of AGO2 in the DICER+AGO2 complex. Competitive substrate assays indicate that DICER+AGO2 cleavage of fluorogenic siRNA is specific, since unlabeled siRNA and DICER substrates serve as competing substrates that cause a concentration-dependent decrease in fluorescent rates. Competitive substrate assays of a series of DICER substrates in vitro were correlated with cell-based assays of HIF1A mRNA knockdown (log-log slope=0.29), suggesting that improved DICER substrate designs with 10-fold greater processing by the DICER+AGO2 complex can provide a strong (~2800-fold) improvement in potency for mRNA knockdown. This study lays the foundation of a systematic biochemical approach to optimize nucleic acid-based therapeutics for Dicing and ARGONAUTE2-loading for improving efficacy. PMID:25793518

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

Suryanarayana, Phanish, E-mail: phanish.suryanarayana@ce.gatech.edu; Phanish, Deepa

We present an Augmented Lagrangian formulation and its real-space implementation for non-periodic Orbital-Free Density Functional Theory (OF-DFT) calculations. In particular, we rewrite the constrained minimization problem of OF-DFT as a sequence of minimization problems without any constraint, thereby making it amenable to powerful unconstrained optimization algorithms. Further, we develop a parallel implementation of this approach for the Thomas–Fermi–von Weizsacker (TFW) kinetic energy functional in the framework of higher-order finite-differences and the conjugate gradient method. With this implementation, we establish that the Augmented Lagrangian approach is highly competitive compared to the penalty and Lagrange multiplier methods. Additionally, we show that higher-ordermore » finite-differences represent a computationally efficient discretization for performing OF-DFT simulations. Overall, we demonstrate that the proposed formulation and implementation are both efficient and robust by studying selected examples, including systems consisting of thousands of atoms. We validate the accuracy of the computed energies and forces by comparing them with those obtained by existing plane-wave methods.« less

Optimization of High-Throughput Sequencing Kinetics for determining enzymatic rate constants of thousands of RNA substrates

PubMed Central

Niland, Courtney N.; Jankowsky, Eckhard; Harris, Michael E.

2016-01-01

Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High Throughput Sequencing Kinetics (HTS-Kin) uses high throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigate the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we find that high-throughput sequencing, and experimental reproducibility contribute their own sources of error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed. PMID:27296633

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

NASA Astrophysics Data System (ADS)

Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; van Houten, Bennett; He, Chuan; Ansari, Anjum; Min, Jung-Hyun

2015-01-01

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

DOE PAGES

Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; ...

2015-01-06

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivitymore » arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Lastly, kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.« less

Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex.

PubMed

Zhao, Yong; Kan, Zhong-yuan; Zeng, Zhi-xiong; Hao, Yu-hua; Chen, Hua; Tan, Zheng

2004-10-20

Nucleic acid molecules may fold into secondary structures, and the formation of such structures is involved in many biological processes and technical applications. The folding and unfolding rate constants define the kinetics of conformation interconversion and the stability of these structures and is important in realizing their functions. We developed a method to determine these kinetic parameters using an optical biosensor based on surface plasmon resonance. The folding and unfolding of a nucleic acid is coupled with a hybridization reaction by immobilization of the target nucleic acid on a sensor chip surface and injection of a complementary probe nucleic acid over the sensor chip surface. By monitoring the time course of duplex formation, both the folding and unfolding rate constants for the target nucleic acid and the association and dissociation rate constants for the target-probe duplex can all be derived from the same measurement. We applied this method to determine the folding and unfolding rate constants of the G-quadruplex of human telomere sequence (TTAGGG)(4) and its association and dissociation rate constants with the complementary strand (CCCTAA)(4). The results show that both the folding and unfolding occur on the time scale of minutes at physiological concentration of K(+). We speculate that this property might be important for telomere elongation. A complete set of the kinetic parameters for both of the structures allows us to study the competition between the formation of the quadruplex and the duplex. Calculations indicate that the formation of both the quadruplex and the duplex is strand concentration-dependent, and the quadruplex can be efficiently formed at low strand concentration. This property may provide the basis for the formation of the quadruplex in vivo in the presence of a complementary strand.

Competitive adsorption of furfural and phenolic compounds onto activated carbon in fixed bed column.

PubMed

Sulaymon, Abbas H; Ahmed, Kawther W

2008-01-15

For a multicomponent competitive adsorption of furfural and phenolic compounds, a mathematical model was builtto describe the mass transfer kinetics in a fixed bed column with activated carbon. The effects of competitive adsorption equilibrium constant, axial dispersion, external mass transfer, and intraparticle diffusion resistance on the breakthrough curve were studied for weakly adsorbed compound (furfural) and strongly adsorbed compounds (parachlorophenol and phenol). Experiments were carried out to remove the furfural and phenolic compound from aqueous solution. The equilibrium data and intraparticle diffusion coefficients obtained from separate experiments in a batch adsorber, by fitting the experimental data with theoretical model. The results show that the mathematical model includes external mass transfer and pore diffusion using nonlinear isotherms and provides a good description of the adsorption process for furfural and phenolic compounds in a fixed bed adsorber.

Kinetics of the addition of olefins to Si-centered radicals: the critical role of dispersion interactions revealed by theory and experiment.

PubMed

Johnson, Erin R; Clarkin, Owen J; Dale, Stephen G; DiLabio, Gino A

2015-06-04

Solution-phase rate constants for the addition of selected olefins to the triethylsilyl and tris(trimethylsilyl)silyl radicals are measured using laser-flash photolysis and competition kinetics. The results are compared with predictions from density functional theory (DFT) calculations, both with and without dispersion corrections obtained from the exchange-hole dipole moment (XDM) model. Without a dispersion correction, the rate constants are consistently underestimated; the errors increase with system size, up to 10(6) s(-1) for the largest system considered. Dispersion interactions preferentially stabilize the transition states relative to the separated reactants and bring the DFT-calculated rate constants into excellent agreement with experiment. Thus, dispersion interactions are found to play a key role in determining the kinetics for addition reactions, particularly those involving sterically bulky functional groups.

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

Cuskey, S.M.; Schamhart, D.H.J.; Chase, T. Jr.

A simple technique, using an esculin-ferric salt visualization system, for selective isolation of mutants of Trichoderma reesei was employed. The ..beta..-glucosidase crude enzyme complexes of the 17 mutants isolated from some 66,000 colonies screened were characterized. Type of inhibition (competitive, noncompetitive) by glucose, and kinetic parameters K/sub m/ (mM pNPG), V/sub max/ (units/mg extracellular protein), and K/sub i/ slopes (mM glucose) were determined for the mutants using p-nitrophenyl ..beta..-D-glucoside (pNPG) as substrate. All the isolates were inhibited competitively by glucose, but certain of them were less sensitive than parent and wild-type to inhibition by glucose. 5 figures, 1 table.

The role of fluid pressure on frictional behavior at the base of the seismogenic zone

USGS Publications Warehouse

Hirth, Greg; Beeler, Nicholas M.

2015-01-01

To characterize stress and deformation style at the base of the seismogenic zone, we investigate how the mechanical properties of fluid-rock systems respond to variations in temperature and strain rate. The role of fluids on the processes responsible for the brittle-ductile transition in quartz-rich rocks has not been explored at experimental conditions where the kinetic competition between microcracking and viscous flow is similar to that expected in the Earth. Our initial analysis of this competition suggests that the effective stress law for sliding friction should not work as efficiently near the brittle-ductile transition as it does at shallow conditions

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.

PubMed

Zhang, Hua; Zhang, Tuo; Gao, Jianzhao; Ruan, Jishou; Shen, Shiyi; Kurgan, Lukasz

2012-01-01

Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.

Degradation of anti-inflammatory drug ketoprofen by electro-oxidation: comparison of electro-Fenton and anodic oxidation processes.

PubMed

Feng, Ling; Oturan, Nihal; van Hullebusch, Eric D; Esposito, Giovanni; Oturan, Mehmet A

2014-01-01

The electrochemical degradation of the nonsteroidal anti-inflammatory drug ketoprofen in tap water has been studied using electro-Fenton (EF) and anodic oxidation (AO) processes with platinium (Pt) and boron-doped diamond (BDD) anodes and carbon felt cathode. Fast degradation of the parent drug molecule and its degradation intermediates leading to complete mineralization was achieved by BDD/carbon felt, Pt/carbon felt, and AO with BDD anode. The obtained results showed that oxidative degradation rate of ketoprofen and mineralization of its aqueous solution increased by increasing applied current. Degradation kinetics fitted well to a pseudo-first-order reaction. Absolute rate constant of the oxidation of ketoprofen by electrochemically generated hydroxyl radicals was determined to be (2.8 ± 0.1) × 10(9) M(-1) s(-1) by using competition kinetic method. Several reaction intermediates such as 3-hydroxybenzoic acid, pyrogallol, catechol, benzophenone, benzoic acid, and hydroquinone were identified by high-performance liquid chromatography (HPLC) analyses. The formation, identification, and evolution of short-chain aliphatic carboxylic acids like formic, acetic, oxalic, glycolic, and glyoxylic acids were monitored with ion exclusion chromatography. Based on the identified aromatic/cyclic intermediates and carboxylic acids as end products before mineralization, a plausible mineralization pathway was proposed. The evolution of the toxicity during treatments was also monitored using Microtox method, showing a faster detoxification with higher applied current values.

Levofloxacin oxidation by ozone and hydroxyl radicals: kinetic study, transformation products and toxicity.

PubMed

Hamdi El Najjar, Nasma; Touffet, Arnaud; Deborde, Marie; Journel, Romain; Leitner, Nathalie Karpel Vel

2013-10-01

This work was carried out to investigate the fate of the antibiotic levofloxacin upon oxidation with ozone and hydroxyl radicals. A kinetic study was conducted at 20 °C for each oxidant. Ozonation experiments were performed using a competitive kinetic method with carbamazepin as competitor. Significant levofloxacin removal was observed during ozonation and a rate constant value of 6.0×10(4) M(-1) s(-1) was obtained at pH 7.2. An H2O2/UV system was used for the formation of hydroxyl radicals HO. The rate constant of HO was determined in the presence of a high H2O2 concentration. The kinetic expressions yielded a [Formula: see text] value of 4.5×10(9) M(-1) s(-1) at pH 6.0 and 5.2×10(9) M(-1) s(-1) at pH 7.2. These results were used to develop a model to predict the efficacy of the ozonation process and pharmaceutical removal was estimated under different ozonation conditions (i.e. oxidant concentrations and contact times). The results showed that levofloxacin was completely degraded by molecular ozone during ozonation of water and that hydroxyl radicals had no effect in real waters conditions. Moreover, LC/MS/MS and toxicity assays using Lumistox test were performed to identify ozonation transformation products. Under these conditions, four transformation products were observed and their chemical structures were proposed. The results showed an increase in toxicity during ozonation, even after degradation of all of the observed transformation products. The formation of other transformation products not identified under our experimental conditions could be responsible for the observed toxicity. These products might be ozone-resistant and more toxic to Vibrio fisheri than levofloxacin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Human disease mortality kinetics are explored through a chain model embodying principles of extreme value theory and competing risks.

PubMed

Juckett, D A; Rosenberg, B

1992-04-21

The distributions for human disease-specific mortality exhibit two striking characteristics: survivorship curves that intersect near the longevity limit; and, the clustering of best-fitting Weibull shape parameter values into groups centered on integers. Correspondingly, we have hypothesized that the distribution intersections result from either competitive processes or population partitioning and the integral clustering in the shape parameter results from the occurrence of a small number of rare, rate-limiting events in disease progression. In this report we initiate a theoretical examination of these questions by exploring serial chain model dynamics and parameteric competing risks theory. The links in our chain models are composed of more than one bond, where the number of bonds in a link are denoted the link size and are the number of events necessary to break the link and, hence, the chain. We explored chains with all links of the same size or with segments of the chain composed of different size links (competition). Simulations showed that chain breakage dynamics depended on the weakest-link principle and followed kinetics of extreme-values which were very similar to human mortality kinetics. In particular, failure distributions for simple chains were Weibull-type extreme-value distributions with shape parameter values that were identifiable with the integral link size in the limit of infinite chain length. Furthermore, for chains composed of several segments of differing link size, the survival distributions for the various segments converged at a point in the S(t) tails indistinguishable from human data. This was also predicted by parameteric competing risks theory using Weibull underlying distributions. In both the competitive chain simulations and the parametric competing risks theory, however, the shape values for the intersecting distributions deviated from the integer values typical of human data. We conclude that rare events can be the source of integral shapes in human mortality, that convergence is a salient feature of multiple endpoints, but that pure competition may not be the best explanation for the exact type of convergence observable in human mortality. Finally, while the chain models were not motivated by any specific biological structures, interesting biological correlates to them may be useful in gerontological research.

Kinetics of natural oxidant demand by permanganate in aquifer solids.

PubMed

Urynowicz, Michael A; Balu, Balamurali; Udayasankar, Umamaheshwari

2008-02-19

During in situ chemical oxidation with permanganate, natural organic matter and other reduced species in the subsurface compete with the target compounds for the available oxidant and can exert a significant natural oxidant demand. This competition between target and nontarget compounds can have a significant impact on the permeation, dispersal, and persistence of permanganate in the subsurface. The kinetics of natural oxidant demand by permanganate was investigated using a composite sample made up of aquifer material collected from three different sites. The study found that although the depletion of organic carbon increased with increased permanganate dosage and increased reaction period, the mass ratio of MnO(4)(-):OC (wt/wt) was relatively constant over time (11.4+/-0.9). The reaction order and rate with respect to permanganate were found to decrease with time suggesting a continuum of reactions with the slower reactions becoming more controlling with time. However, the data also suggests that this continuum of reactions can be simplified into short- and long-term kinetic expressions representing fast and slow reactions. An independent first-order kinetic model with separate fast and slow reaction rate constants was used to successfully describe the complete kinetic expression of natural oxidant demand. The kinetic parameters used in the model are easily determined and can be used to better understand the complex kinetics of natural oxidant demand.

Genome-scale modeling of the evolutionary path to C4 photosynthesis

NASA Astrophysics Data System (ADS)

Myers, Christopher R.; Bogart, Eli

In C4 photosynthesis, plants maintain a high carbon dioxide level in specialized bundle sheath cells surrounding leaf veins and restrict CO2 assimilation to those cells, favoring CO2 over O2 in competition for Rubisco active sites. In C3 plants, which do not possess such a carbon concentrating mechanism, CO2 fixation is reduced due to this competition. Despite the complexity of the C4 system, it has evolved convergently from more than 60 independent origins in diverse families of plants around the world over the last 30 million years. We study the evolution of the C4 system in a genome-scale model of plant metabolism that describes interacting mesophyll and bundle sheath cells and enforces key nonlinear kinetic relationships. Adapting the zero-temperature string method for simulating transition paths in physics and chemistry, we find the highest-fitness paths connecting C3 and C4 positions in the model's high-dimensional parameter space, and show that they reproduce known aspects of the C3-C4 transition while making additional predictions about metabolic changes along the path. We explore the relationship between evolutionary history and C4 biochemical subtype, and the effects of atmospheric carbon dioxide levels.

Tyrosinase-catalyzed oxidation of fluorophenols.

PubMed

Battaini, Giuseppe; Monzani, Enrico; Casella, Luigi; Lonardi, Emanuela; Tepper, Armand W J W; Canters, Gerard W; Bubacco, Luigi

2002-11-22

The activity of the type 3 copper enzyme tyrosinase toward 2-, 3-, and 4-fluorophenol was studied by kinetic methods and (1)H and (19)F NMR spectroscopy. Whereas 3- and 4-fluorophenol react with tyrosinase to give products that undergo a rapid polymerization process, 2-fluorophenol is not reactive and actually acts as a competitive inhibitor in the enzymatic oxidation of 3,4-dihydroxyphenylalanine (L-dopa). The tyrosinase-mediated polymerization of 3- and 4-fluorophenols has been studied in detail. It proceeds through a phenolic coupling pathway in which the common reactive fluoroquinone, produced stereospecifically by tyrosinase, eliminates an inorganic fluorine ion. The enzymatic reaction studied as a function of substrate concentration shows a prominent lag that is completely depleted in the presence of L-dopa. The kinetic parameters of the reactions can be correlated to the electronic and steric effects of the fluorine substituent position. Whereas the fluorine electron withdrawing effect appears to control the binding of the substrates (K(m) for 3- and 4-fluorophenols and K(I) for 2-fluorophenol), the k(cat) parameters do not follow the expected trend, indicating that in the transition state some additional steric effect rules the reactivity.

Kinetics and Mechanism Study of Competitive Inhibition of Jack-Bean Urease by Baicalin

PubMed Central

Tan, Lirong; Su, Jiyan; Wu, Dianwei; Yu, Xiaodan; Su, Zuqing; Wu, Xiaoli; Kong, Songzhi; Lai, Xiaoping; Lin, Ji; Su, Ziren

2013-01-01

Baicalin (BA) is the principal component of Radix Scutellariae responsible for its pharmacological activity. In this study, kinetics and mechanism of inhibition by BA against jack-bean urease were investigated for its therapeutic potential. It was revealed that the IC50 of BA against jack-bean urease was 2.74 ± 0.51 mM, which was proved to be a competitive and concentration-dependent inhibition with slow-binding progress curves. The rapid formation of initial BA-urease complex with an inhibition constant of K i = 3.89 × 10−3 mM was followed by a slow isomerization into the final complex with an overall inhibition constant of K i* = 1.47 × 10−4 mM. High effectiveness of thiol protectors against BA inhibition indicated that the strategic role of the active-site sulfhydryl group of the urease was involved in the blocking process. Moreover, the inhibition of BA was proved to be reversible due to the fact that urease could be reactivated by dithiothreitol but not reactant dilution. Molecular docking assay suggested that BA made contacts with the important activating sulfhydryl group Cys-592 residues and restricted the mobility of the active-site flap. Taken together, it could be deduced that BA was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration-dependently, serving as a promising urease inhibitor for treatments on urease-related diseases. PMID:24198731

Perfluorooctane sulfonate adsorption on powder activated carbon: Effect of phosphate (P) competition, pH, and temperature.

PubMed

Qian, Jin; Shen, Mengmeng; Wang, Peifang; Wang, Chao; Li, Kun; Liu, Jingjing; Lu, Bianhe; Tian, Xin

2017-09-01

Powdered activated carbon (PAC), as an adsorbent, was applied to remove perfluorooctane sulfonate (PFOS) from aqueous solution. Laboratory batch experiments were performed to investigate the influences of phosphate (P) competition, temperature, and pH for PFOS adsorption onto PAC. The results showed that higher temperature favored PFOS adsorption in single and binary systems. The kinetic data fitted very well to the pseudo second-order kinetic model. Thermodynamically, the endothermic enthalpy of the PFOS adsorption in single and binary systems were 125.07 and 21.25 kJ mol -1 , respectively. The entropy of the PFOS adsorption in single and binary systems were 0.479 and 0.092 kJ mol -1  K -1 , respectively. And the Gibbs constants were negative. These results indicated that the adsorption processes were spontaneous. The adsorption isotherms of PFOS agreed well with the Langmuir model. In the single system, PFOS adsorption decreased with increased pH value. The difference in the amount of PFOS adsorption between the single and binary systems increased at higher pH. Frustrated total internal reflection (FTIR) demonstrated that P competition increased the hydrophilicity of the PAC and the electrostatic repulsion between PFOS and PAC, then the PFOS adsorption amount decreased. It also demonstrated that, at higher temperature, increased PFOS adsorption was mainly due to the higher diffusion rate of PFOS molecules and greater number of active sites opened on the PAC surface. Copyright © 2017 Elsevier Ltd. All rights reserved.

ARSENATE AND ARSENITE REMOVAL BY ZERO-VALENT IRON: EFFECTS OF PHOSPHATE, SILICATE, CARBONATE, BORATE, SULFATE, CHROMATE, MOLYBDATE, AND NITRATE, RELATIVE TO CHLORIDE

EPA Science Inventory

Batch tests were performed to evaluate the effects of inorganic anion competition on the kinetics of arsenate (As(V)) and arsenite (As(III)) removal by zerovalent iron (Peerless Fe0) in aqueous solution. The oxyanions underwent either sorption-dominated reactions (phosphate, sil...

Aquantis Ocean Current Turbine Development Project Report

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

Fleming, Alex J.

2014-08-23

The Aquantis® Current Plane (“C-Plane”) technology developed by Dehlsen Associates, LLC (DA) and Aquantis, Inc. is an ocean current turbine designed to extract kinetic energy from ocean currents. The technology is capable of achieving competitively priced base-load, continuous, and reliable power generation from a source of renewable energy not before possible in this scale or form.

Decavanadate, a P2X receptor antagonist, and its use to study ligand interactions with P2X7 receptors.

PubMed

Michel, Anton D; Xing, Mengle; Thompson, Kyla M; Jones, Clare A; Humphrey, Patrick P A

2006-03-18

In this study we have studied decavanadate effects at P2X receptors. Decavanadate competitively blocked 2'- and 3'-O-(4benzoylbenzoyl) ATP (BzATP) stimulated ethidium accumulation in HEK293 cells expressing human recombinant P2X7 receptors (pK(B) 7.5). The effects of decavanadate were rapid (minutes) in both onset and offset and contrasted with the much slower kinetics of pyridoxal 5-phosphate (P5P), Coomassie brilliant blue (CBB) and 1-[N,O-bis(5-isoquinolinesulfonyl)-N-methyl-L-tyrosyl]-4-phenylpiperazine (KN62). Decavanadate competitively blocked the slowly reversible, or irreversible, blockade of the P2X7 receptor produced by P5P and oxidised ATP suggesting competition for a common binding site. However, the interaction between decavanadate and KN62 was non-competitive. Decavanadate also blocked P2X2 and P2X4 receptors but with slightly lower potency. These data demonstrate that decavanadate is the first reversible and competitive antagonist of the P2X7 receptor and is a useful tool for studying the mechanism of interaction of ligands with the P2X7 receptor.

Kinetics of Competitive Adsorption between Lysozyme and Lactoferrin on Silicone Hydrogel Contact Lenses and the Effect on Lysozyme Activity.

PubMed

Hall, Brad; Jones, Lyndon; Forrest, James A

2015-05-01

To determine the effect of competitive adsorption between lysozyme and lactoferrin on silicone hydrogel contact lenses and the effect on lysozyme activity. Three commercially available silicone hydrogel contact lens materials (senofilcon A, lotrafilcon B and balafilcon A) were examined, for time points ranging from 10 s to 2 h. Total protein deposition was determined by I(125) radiolabeling of lysozyme and lactoferrin, while the activity of lysozyme was determined by a micrococcal activity assay. Senofilcon A and balafilcon A did not show any relevant competitive adsorption between lysozyme and lactoferrin. Lotrafilcon B showed reduced protein deposition due to competitive adsorption for lactoferrin at all time points and lysozyme after 7.5 min. Co-adsorption of lactoferrin and lysozyme decreased the activity of lysozyme in solution for senofilcon A and lotrafilcon B, but co-adsorption had no effect on the surface activity of lysozyme for all lens types investigated. Competition between lysozyme and lactoferrin is material specific. Co-adsorption of lysozyme and lactoferrin does not affect the activity of surface-bound lysozyme but can reduce the activity of subsequently desorbed lysozyme.

Competition between Primary Nucleation and Autocatalysis in Amyloid Fibril Self-Assembly

PubMed Central

Eden, Kym; Morris, Ryan; Gillam, Jay; MacPhee, Cait E.; Allen, Rosalind J.

2015-01-01

Kinetic measurements of the self-assembly of proteins into amyloid fibrils are often used to make inferences about molecular mechanisms. In particular, the lag time—the quiescent period before aggregates are detected—is often found to scale with the protein concentration as a power law, whose exponent has been used to infer the presence or absence of autocatalytic growth processes such as fibril fragmentation. Here we show that experimental data for lag time versus protein concentration can show signs of kinks: clear changes in scaling exponent, indicating changes in the dominant molecular mechanism determining the lag time. Classical models for the kinetics of fibril assembly suggest that at least two mechanisms are at play during the lag time: primary nucleation and autocatalytic growth. Using computer simulations and theoretical calculations, we investigate whether the competition between these two processes can account for the kinks which we observe in our and others’ experimental data. We derive theoretical conditions for the crossover between nucleation-dominated and growth-dominated regimes, and analyze their dependence on system volume and autocatalysis mechanism. Comparing these predictions to the data, we find that the experimentally observed kinks cannot be explained by a simple crossover between nucleation-dominated and autocatalytic growth regimes. Our results show that existing kinetic models fail to explain detailed features of lag time versus concentration curves, suggesting that new mechanistic understanding is needed. More broadly, our work demonstrates that care is needed in interpreting lag-time scaling exponents from protein assembly data. PMID:25650930

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.

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

Ho, Christopher R.; Shylesh, Sankaranarayanapillai; Bell, Alexis T.

The mechanism and kinetics for ethanol coupling to n-butanol over hydroxyapatite (HAP) were investigated at 573-613 K. In situ titration experiments show that the active sites for acetaldehyde and butanol formation are different. In combination with FTIR studies, it was found that ethanol dehydrogenation is catalyzed by Ca-O sites, whereas condensation of acetaldehyde is catalyzed by CaO/PO 4 3- pairs. Measurements of the reaction kinetics at various ethanol (3.5-9.4 kPa) and acetaldehyde (0.055-0.12 kPa) partial pressures reveal that direct condensation involving two ethanol molecules does not play a significant role in butanol formation; instead, n-butanol is formed via a Guerbetmore » pathway. At a constant acetaldehyde pressure, enolate formation is rate-limiting, and ethanol inhibits acetaldehyde condensation rates by competitive adsorption. A model of the reaction kinetics consistent with all experimental observations is developed.« less

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

Kinetic studies of the inhibition of a human liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase isozyme by bile acids and anti-inflammatory drugs.

PubMed

Miyabe, Y; Amano, T; Deyashiki, Y; Hara, A; Tsukada, F

1995-01-01

We have investigated the steady-state kinetics for a cytosolic 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase isozyme of human liver and its inhibition by several bile acids and anti-inflammatory drugs such as indomethacin, flufemanic acid and naproxen. Initial velocity and product inhibition studies performed in the NADP(+)-linked (S)-1-indanol oxidation at pH 7.4 were consistent with a sequential ordered mechanism in which NADP+ binds first and leaves last. The bile acids and drugs, competitive inhibitors with respect to the alcohol substrate, exhibited uncompetitive inhibition with respect to the coenzyme, with Ki values less than 1 microM, whereas indomethacin exhibited noncompetitive inhibition (Ki < 24 microM). The kinetics of the inhibition by a mixture of the two inhibitors suggests that bile acids and drugs, except indomethacin, bind to overlapping sites at the active center of the enzyme-coenzyme binary complex.

Second-order kinetic model for the sorption of cadmium onto tree fern: a comparison of linear and non-linear methods.

PubMed

Ho, Yuh-Shan

2006-01-01

A comparison was made of the linear least-squares method and a trial-and-error non-linear method of the widely used pseudo-second-order kinetic model for the sorption of cadmium onto ground-up tree fern. Four pseudo-second-order kinetic linear equations are discussed. Kinetic parameters obtained from the four kinetic linear equations using the linear method differed but they were the same when using the non-linear method. A type 1 pseudo-second-order linear kinetic model has the highest coefficient of determination. Results show that the non-linear method may be a better way to obtain the desired parameters.

Adsorption, Desorption, and Displacement Kinetics of H2O and CO2 on Forsterite, Mg2SiO4(011)

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

Smith, R. Scott; Li, Zhenjun; Dohnalek, Zdenek

We have examined the adsorbate-substrate interaction kinetics of CO2 and H2O on a natural forsterite crystal surface, Mg2SiO4(011), with 10-15% of substitutional Fe2+. We use temperature programmed desorption (TPD) and molecular beam techniques to determine the adsorption, desorption, and displacement kinetics for H2O and CO2. Neither CO2 nor H2O has distinct sub-monolayer desorption peaks but instead both have a broad continuous desorption feature that evolve smoothly into multilayer desorption. Inversion of the monolayer coverage spectra for both molecules reveals that the corresponding binding energies for H2O are greater than that for CO2 on all sites. The relative strength of thesemore » interactions is the dominant factor in the competitive adsorption/displacement kinetics. In experiments where the two adsorbates are co-dosed, H2O always binds to the highest energy binding sites available and displaces CO2. The onset of CO2 displacement by H2O occurs between 65 and 75 K.« less

Direct determination of GSK-3β activity and inhibition by UHPLC-UV-vis diode arrays detector (DAD).

PubMed

D'Urzo, Annalisa; De Simone, Angela; Fiori, Jessica; Naldi, Marina; Milelli, Andrea; Andrisano, Vincenza

2016-05-30

Altered GSK-3β activity can contribute to a number of pathological processes including Alzheimer's disease (AD). Indeed, GSK-3β catalyzes the hyperphosphorylation of tau protein by transferring a phosphate moiety from ATP to the protein substrate serine residue causing the formation of the toxic insoluble neurofibrillary tangles; for this reason it represents a key target for the development of new therapeutic agents for AD treatment. Herein we describe a new selective UHPLC methodology developed for the direct characterization of GSK-3β kinase activity and for the determination of its inhibition, which could be crucial in AD drug discovery. The UHPLC-UV (DAD) based method was validated for the very fast determination of ATP as reactant and ADP as product, and applied for the analysis of the enzymatic reaction between a phosphate primed peptide substrate (GSM), resembling tau protein sequence, ATP and GSK-3β, with/without inhibitors. Analysis time was ten times improved, when compared with previously published chromatographic methods. The method was also validated by determining enzyme reaction kinetic constants (KM and vmax) for GSM and ATP and by analyzing well known GSK-3β inhibitors. Inhibition potency (IC50) values for SB-415286 (81 ± 6 nM) and for Tideglusib (251 ± 17 nM), found by the newly developed UHPLC method, were in good agreement with the luminescence method taken as independent reference method. Further on, the UHPLC method was applied to the elucidation of Tideglusib mechanism of action by determining its inhibition constants (Ki). In agreement with literature data, Tideglusib resulted a GSM competitive inhibitor, whereas SB-415286 was found inhibiting GSK-3β in an ATP competitive manner. This method was applied to the determination of the potency of a new lead compound and was found potentially scalable to inhibitor screening of large compounds collections. Copyright © 2016 Elsevier B.V. All rights reserved.

Finding Order in Randomness: Single-Molecule Studies Reveal Stochastic RNA Processing | Center for Cancer Research

Cancer.gov

Producing a functional eukaryotic messenger RNA (mRNA) requires the coordinated activity of several large protein complexes to initiate transcription, elongate nascent transcripts, splice together exons, and cleave and polyadenylate the 3’ end. Kinetic competition between these various processes has been proposed to regulate mRNA maturation, but this model could lead to

Field Flight Dynamics of Hummingbirds during Territory Encroachment and Defense

PubMed Central

Sholtis, Katherine M.; Shelton, Ryan M.; Hedrick, Tyson L.

2015-01-01

Hummingbirds are known to defend food resources such as nectar sources from encroachment by competitors (including conspecifics). These competitive intraspecific interactions provide an opportunity to quantify the biomechanics of hummingbird flight performance during ecologically relevant natural behavior. We recorded the three-dimensional flight trajectories of Ruby-throated Hummingbirds defending, being chased from and freely departing from a feeder. These trajectories allowed us to compare natural flight performance to earlier laboratory measurements of maximum flight speed, aerodynamic force generation and power estimates. During field observation, hummingbirds rarely approached the maximal flight speeds previously reported from wind tunnel tests and never did so during level flight. However, the accelerations and rates of change in kinetic and potential energy we recorded indicate that these hummingbirds likely operated near the maximum of their flight force and metabolic power capabilities during these competitive interactions. Furthermore, although birds departing from the feeder while chased did so faster than freely-departing birds, these speed gains were accomplished by modulating kinetic and potential energy gains (or losses) rather than increasing overall power output, essentially trading altitude for speed during their evasive maneuver. Finally, the trajectories of defending birds were directed toward the position of the encroaching bird rather than the feeder. PMID:26039101

Nitrate transport in the cyanobacterium Anacystis nidulans R2. Kinetic and energetic aspects.

PubMed Central

Rodríguez, R; Lara, C; Guerrero, M G

1992-01-01

Nitrate transport has been studied in the cyanobacterium Anacystis nidulans R2 by monitoring intracellular nitrate accumulation in intact cells of the mutant strain FM6, which lacks nitrate reductase activity and is therefore unable to reduce the transported nitrate. Kinetic analysis of nitrate transport as a function of external nitrate concentration revealed apparent substrate inhibition, with a peak velocity at 20-25 microM-nitrate. A Ks (NO3-) of 1 microM was calculated. Nitrate transport exhibited a stringent requirement for Na+. Neither Li+ nor K+ could substitute for Na+. Monensin depressed nitrate transport in a concentration-dependent manner, inhibition being more than 60% at 2 microM, indicating that the Na(+)-dependence of active nitrate transport relies on the maintenance of a Na+ electrochemical gradient. The operation of an Na+/NO3- symport system is suggested. Nitrite behaved as an effective competitive inhibitor of nitrate transport, with a Ki (NO2-) of 3 microM. The time course of nitrite inhibition of nitrate transport was consistent with competitive inhibition by mixed alternative substrates. Nitrate and nitrite might be transported by the same carrier. PMID:1554347

Field Flight Dynamics of Hummingbirds during Territory Encroachment and Defense.

PubMed

Sholtis, Katherine M; Shelton, Ryan M; Hedrick, Tyson L

2015-01-01

Hummingbirds are known to defend food resources such as nectar sources from encroachment by competitors (including conspecifics). These competitive intraspecific interactions provide an opportunity to quantify the biomechanics of hummingbird flight performance during ecologically relevant natural behavior. We recorded the three-dimensional flight trajectories of Ruby-throated Hummingbirds defending, being chased from and freely departing from a feeder. These trajectories allowed us to compare natural flight performance to earlier laboratory measurements of maximum flight speed, aerodynamic force generation and power estimates. During field observation, hummingbirds rarely approached the maximal flight speeds previously reported from wind tunnel tests and never did so during level flight. However, the accelerations and rates of change in kinetic and potential energy we recorded indicate that these hummingbirds likely operated near the maximum of their flight force and metabolic power capabilities during these competitive interactions. Furthermore, although birds departing from the feeder while chased did so faster than freely-departing birds, these speed gains were accomplished by modulating kinetic and potential energy gains (or losses) rather than increasing overall power output, essentially trading altitude for speed during their evasive maneuver. Finally, the trajectories of defending birds were directed toward the position of the encroaching bird rather than the feeder.

Characterization of an LED based photoreactor to degrade 4-chlorophenol in an aqueous medium using coumarin (C-343) sensitized TiO2.

PubMed

Ghosh, Jyoti P; Langford, Cooper H; Achari, Gopal

2008-10-16

A detailed performance evaluation of a simple high intensity LED based photoreactor exploiting a narrow wavelength range of the LED to match the spectrum of a dye in a photocatalysis system is reported. A dye sensitized (coumarin-343, lambda max = 446 nm) TiO 2 photocatalyst was used for the degradation of 4-chlorophenol (4-CP) in an aqueous medium using the 436 nm LED based photoreactor. The LED reactor performed competitively with a conventional multilamp reactor and sunlight in the degradation of 4-CP. Light intensities entering the reaction vessel were measured by conventional ferrioxalate actinometry. The results can be fitted by approximate first order kinetic behavior in this system. Hydroxyl radicals were detected by spin trapping EPR, and effects of OH radical quenchers on kinetics suggest that the reaction is initiated by these radicals or their equivalents. LEDs operating at competitive intensities offer a number of advantages to the photochemist or the environmental engineer via long life, efficient current to light conversion, narrow bandwidth, forward directed output, and direct current power for remote operation. Matching light source spectrum to chromophore is a key.

An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes.

PubMed

Chen, Sherry Xi; Seelig, Georg

2016-04-20

Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology.

Spatial Competition: Roughening of an Experimental Interface.

PubMed

Allstadt, Andrew J; Newman, Jonathan A; Walter, Jonathan A; Korniss, G; Caraco, Thomas

2016-07-28

Limited dispersal distance generates spatial aggregation. Intraspecific interactions are then concentrated within clusters, and between-species interactions occur near cluster boundaries. Spread of a locally dispersing invader can become motion of an interface between the invading and resident species, and spatial competition will produce variation in the extent of invasive advance along the interface. Kinetic roughening theory offers a framework for quantifying the development of these fluctuations, which may structure the interface as a self-affine fractal, and so induce a series of temporal and spatial scaling relationships. For most clonal plants, advance should become spatially correlated along the interface, and width of the interface (where invader and resident compete directly) should increase as a power function of time. Once roughening equilibrates, interface width and the relative location of the most advanced invader should each scale with interface length. We tested these predictions by letting white clover (Trifolium repens) invade ryegrass (Lolium perenne). The spatial correlation of clover growth developed as anticipated by kinetic roughening theory, and both interface width and the most advanced invader's lead scaled with front length. However, the scaling exponents differed from those predicted by recent simulation studies, likely due to clover's growth morphology.

Spatial Competition: Roughening of an Experimental Interface

PubMed Central

Allstadt, Andrew J.; Newman, Jonathan A.; Walter, Jonathan A.; Korniss, G.; Caraco, Thomas

2016-01-01

Limited dispersal distance generates spatial aggregation. Intraspecific interactions are then concentrated within clusters, and between-species interactions occur near cluster boundaries. Spread of a locally dispersing invader can become motion of an interface between the invading and resident species, and spatial competition will produce variation in the extent of invasive advance along the interface. Kinetic roughening theory offers a framework for quantifying the development of these fluctuations, which may structure the interface as a self-affine fractal, and so induce a series of temporal and spatial scaling relationships. For most clonal plants, advance should become spatially correlated along the interface, and width of the interface (where invader and resident compete directly) should increase as a power function of time. Once roughening equilibrates, interface width and the relative location of the most advanced invader should each scale with interface length. We tested these predictions by letting white clover (Trifolium repens) invade ryegrass (Lolium perenne). The spatial correlation of clover growth developed as anticipated by kinetic roughening theory, and both interface width and the most advanced invader’s lead scaled with front length. However, the scaling exponents differed from those predicted by recent simulation studies, likely due to clover’s growth morphology. PMID:27465518

Adsorption of Methyl Tertiary Butyl Ether on Granular Zeolites: Batch and Column Studies

PubMed Central

Abu-Lail, Laila; Bergendahl, John A.; Thompson, Robert W.

2010-01-01

Methyl tertiary butyl ether (MTBE) has been shown to be readily removed from water with powdered zeolites, but the passage of water through fixed beds of very small powdered zeolites produces high friction losses not encountered in flow through larger sized granular materials. In this study, equilibrium and kinetic adsorption of MTBE onto granular zeolites, a coconut shell granular activated carbon (CS-1240), and a commercial carbon adsorbent (CCA) sample was evaluated. In addition, the effect of natural organic matter (NOM) on MTBE adsorption was evaluated. Batch adsorption experiments determined that ZSM-5 was the most effective granular zeolite for MTBE adsorption. Further equilibrium and kinetic experiments verified that granular ZSM-5 is superior to CS-1240 and CCA in removing MTBE from water. No competitive-adsorption effects between NOM and MTBE were observed for adsorption to granular ZSM-5 or CS-1240, however there was competition between NOM and MTBE for adsorption onto the CCA granules. Fixed-bed adsorption experiments for longer run times were performed using granular ZSM-5. The bed depth service time model (BDST) was used to analyze the breakthrough data. PMID:20153106

Simultaneous saccharification and co-fermentation of paper sludge to ethanol by Saccharomyces cerevisiae RWB222--Part I: kinetic modeling and parameters.

PubMed

Zhang, Jiayi; Shao, Xiongjun; Townsend, Oliver V; Lynd, Lee R

2009-12-01

A kinetic model was developed to predict batch simultaneous saccharification and co-fermentation (SSCF) of paper sludge by the xylose-utilizing yeast Saccharomyces cerevisiae RWB222 and the commercial cellulase preparation Spezyme CP. The model accounts for cellulose and xylan enzymatic hydrolysis and competitive uptake of glucose and xylose. Experimental results show that glucan and xylan enzymatic hydrolysis are highly correlated, and that the low concentrations of xylose encountered during SSCF do not have a significant inhibitory effect on enzymatic hydrolysis. Ethanol is found to not only inhibit the specific growth rate, but also to accelerate cell death. Glucose and xylose uptake rates were found to be competitively inhibitory, but this did not have a large impact during SSCF because the sugar concentrations are low. The model was used to evaluate which constants had the greatest impact on ethanol titer for a fixed substrate loading, enzyme loading, and fermentation time. The cellulose adsorption capacity and cellulose hydrolysis rate constants were found to have the greatest impact among enzymatic hydrolysis related constants, and ethanol yield and maximum ethanol tolerance had the greatest impact among fermentation related constants.

Changes in Energy Cost and Total External Work of Muscles in Elite Race Walkers Walking at Different Speeds

PubMed Central

Chwała, Wiesław; Klimek, Andrzej; Mirek, Wacław

2014-01-01

The aim of the study was to assess energy cost and total external work (total energy) depending on the speed of race walking. Another objective was to determine the contribution of external work to total energy cost of walking at technical, threshold and racing speed in elite competitive race walkers. The study involved 12 competitive race walkers aged 24.9 4.10 years with 6 to 20 years of experience, who achieved a national or international sports level. Their aerobic endurance was determined by means of a direct method involving an incremental exercise test on the treadmill. The participants performed three tests walking each time with one of the three speeds according to the same protocol: an 8-minute walk with at steady speed was followed by a recovery phase until the oxygen debt was repaid. To measure exercise energy cost, an indirect method based on the volume of oxygen uptake was employed. The gait of the participants was recorded using the 3D Vicon opto-electronic motion capture system. Values of changes in potential energy and total kinetic energy in a gate cycle were determined based on vertical displacements of the centre of mass. Changes in mechanical energy amounted to the value of total external work of muscles needed to accelerate and lift the centre of mass during a normalised gait cycle. The values of average energy cost and of total external work standardised to body mass and distance covered calculated for technical speed, threshold and racing speeds turned out to be statistically significant (p 0.001). The total energy cost ranged from 51.2 kJ.m-1 during walking at technical speed to 78.3 kJ.m-1 during walking at a racing speed. Regardless of the type of speed, the total external work of muscles accounted for around 25% of total energy cost in race walking. Total external work mainly increased because of changes in the resultant kinetic energy of the centre of mass movement. PMID:25713673

A kinetic study of hypoxanthine oxidation by milk xanthine oxidase.

PubMed Central

Escribano, J; Garcia-Canovas, F; Garcia-Carmona, F

1988-01-01

The course of the reaction sequence hypoxanthine----xanthine----uric acid catalysed by xanthine:oxygen oxidoreductase from milk was investigated on the basis of u.v. spectra taken during the course of hypoxanthine and xanthine oxidations. It was found that xanthine accumulated in the reaction mixture when hypoxanthine was used as a substrate. The time course of the concentrations of hypoxanthine, xanthine intermediate and uric acid product was simulated numerically. The mathematical model takes into account the competition of substrate, intermediate and product and the accumulation of the intermediate at the enzyme. This type of analysis permits the kinetic parameters of the enzyme for hypoxanthine and xanthine to be obtained. PMID:3196295

A Century of Enzyme Kinetic Analysis, 1913 to 2013

PubMed Central

Johnson, Kenneth A.

2013-01-01

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. PMID:23850893

Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms

NASA Astrophysics Data System (ADS)

Druschel, Gregory K.; Emerson, David; Sutka, R.; Suchecki, P.; Luther, George W., III

2008-07-01

Neutrophilic iron oxidizing bacteria (FeOB) must actively compete with rapid abiotic processes governing Fe(II) oxidation and as a result have adapted to primarily inhabit low-O 2 environments where they can more successfully compete with abiotic Fe(II) oxidation. The spatial distribution of these microorganisms can be observed through the chemical gradients they affect, as measured using in situ voltammetric analysis for dissolved Fe(II), Fe(III), O 2, and FeS (aq). Field and laboratory determination of the chemical environments inhabited by the FeOB were coupled with detailed kinetic competition studies for abiotic and biotic oxidation processes using a pure culture of FeOB to quantify the geochemical niche these organisms inhabit. In gradient culture tubes, the maximum oxygen levels, which were associated with growth bands of Sideroxydans lithotrophicus (ES-1, a novel FeOB), were 15-50 μM. Kinetic measurements made on S. lithotrophicus compared biotic/abiotic (killed control) Fe oxidation rates. The biotic rate can be a significant and measurable fraction of the total Fe oxidation rate below O 2 concentrations of approximately 50 μM, but biotic Fe(II) oxidation (via the biotic/abiotic rate comparison) becomes difficult to detect at higher O 2 levels. These results are further supported by observations of conditions supporting FeOB communities in field settings. Variablity in cell densities and cellular activity as well as variations in hydrous ferrous oxide mineral quantities significantly affect the laboratory kinetic rates. The microbial habitat (or geochemical niche) where FeOB are active is thus largely controlled by the competition between abiotic and biotic kinetics, which are dependent on Fe(II) concentration, P O2, temperature and pH in addition to the surface area of hydrous ferric oxide minerals and the cell density/activity of FeOB. Additional field and lab culture observations suggest a potentially important role for the iron-sulfide aqueous molecular cluster, FeS (aq), in the overall cycling of iron associated with the environments these microorganisms inhabit.

Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists

PubMed Central

McCully, Alexandra L.; LaSarre, Breah

2017-01-01

ABSTRACT Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer’s waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris. In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris. In return, R. palustris cross-feeds E. coli ammonium (NH4+), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH4+ in each species. The model predicted that interpartner competition for NH4+ could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH4+ transporters in both NH4+ competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH4+ to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. PMID:29184014

Linear and non-linear regression analysis for the sorption kinetics of methylene blue onto activated carbon.

PubMed

Kumar, K Vasanth

2006-10-11

Batch kinetic experiments were carried out for the sorption of methylene blue onto activated carbon. The experimental kinetics were fitted to the pseudo first-order and pseudo second-order kinetics by linear and a non-linear method. The five different types of Ho pseudo second-order expression have been discussed. A comparison of linear least-squares method and a trial and error non-linear method of estimating the pseudo second-order rate kinetic parameters were examined. The sorption process was found to follow a both pseudo first-order kinetic and pseudo second-order kinetic model. Present investigation showed that it is inappropriate to use a type 1 and type pseudo second-order expressions as proposed by Ho and Blanachard et al. respectively for predicting the kinetic rate constants and the initial sorption rate for the studied system. Three correct possible alternate linear expressions (type 2 to type 4) to better predict the initial sorption rate and kinetic rate constants for the studied system (methylene blue/activated carbon) was proposed. Linear method was found to check only the hypothesis instead of verifying the kinetic model. Non-linear regression method was found to be the more appropriate method to determine the rate kinetic parameters.

Experimental Study and Mathematical Modeling of Self-Sustained Kinetic Oscillations in Catalytic Oxidation of Methane over Nickel.

PubMed

Lashina, Elena A; Kaichev, Vasily V; Saraev, Andrey A; Vinokurov, Zakhar S; Chumakova, Nataliya A; Chumakov, Gennadii A; Bukhtiyarov, Valerii I

2017-09-21

The self-sustained kinetic oscillations in the oxidation of CH 4 over Ni foil have been studied at atmospheric pressure using an X-ray diffraction technique and mass spectrometry. It has been shown that the regular oscillations appear under oxygen-deficient conditions; CO, CO 2 , H 2 , and H 2 O are detected as the products. According to in situ X-ray diffraction measurements, nickel periodically oxidizes to NiO initiating the reaction-rate oscillations. To describe the oscillations, we have proposed a five-stage mechanism of the partial oxidation of methane over Ni and a corresponding three-variable kinetic model. The mechanism considers catalytic methane decomposition, dissociative adsorption of oxygen, transformation of chemisorbed oxygen to surface nickel oxide, and reaction of adsorbed carbon and oxygen species to form CO. Analysis of the kinetic model indicates that the competition of two processes, i.e., the oxidation and the carbonization of the catalyst surface, is the driving force of the self-sustained oscillations in the oxidation of methane. We have compared this mechanism with the detailed 18-stage mechanism described previously by Lashina et al. (Kinetics and Catalysis 2012, 53, 374-383). It has been shown that both kinetic mechanisms coupled with a continuous stirred-tank reactor model describe well the oscillatory behavior in the oxidation of methane under non-isothermal conditions.

Pulse radiolysis study of the reactions of catechins with nitrogen dioxide

NASA Astrophysics Data System (ADS)

Gebicki, Jerzy L.; Meisner, Piotr; Stawowska, Katarzyna; Gebicka, Lidia

2012-12-01

Nitrogen dioxide (•NO2), one of the oxidizing radicals formed in vivo is suspected to play a role in various pathophysiological processes. The reactions of •NO2 with dietary catechins, the group of flavonoids present in high amounts in green tea and red wine, have been investigated by pulse radiolysis method. The kinetics of the reaction of •NO2 with gallic acid have been also studied for comparison. The spectra of transient intermediates are presented. The rate constants of the reaction of •NO2 with catechin, epigallocatechin, epigallocatechin gallate and gallic acid determined by the competition method with 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonate) at pH 7.0 and room temperature have been found to be 0.9, 1.0, 2.3 and 0.5×108 M-1 s-1, respectively. The values for catechins are among the highest reported for the reactions of •NO2 with non-radical compounds.

Competitive Degradation of Steroid Estrogens by Potassium Permanganate Combined with Ultrasound

PubMed Central

Deng, Jing; Tang, Kai; Zhu, Shijun; Ma, Xiaoyan; Zhang, Kejia; Song, Yali; Li, Xueyan; Li, Qingsong; Liu, Zhenhua; Zhou, Kejin

2015-01-01

The occurrence of natural estrogens including estrone (E1), 17β-estradiol (E2), and synthetic 17α-ethinylestradiol (EE2), which can be excreted by both humans and animals, and can enter the aqueous environment along with the discharge of domestic sewage, is a major concern since this may represent a serious health risk to humans even at extremely trace levels (ng·L−1). Simultaneous degradation of three coexisting steroid estrogens (SEs) in aqueous solutions by coupled ultrasound and KMnO4 systems (KMnO4/ultrasound) were investigated to find out whether there is a competitive degradation of multiple contaminants or not. Results indicate that the degradation ratios of target SEs were all more than 50% after 120 min reaction contact, greatly enhanced when compared with the single KMnO4 (2 mg·L−1) oxidation of E2 (37.0%), EE2 (34.4%), and E1 (34.0%), and the single sonochemical oxidation of E2 (37.1%), EE2 (31.1%), and E1 (29.7%). In the adopted processes, the degradations of SEs fit the first-order kinetic reaction, with different reaction rates. Kinetic parameters revealed there was little difference between coexisting SEs, which means there was almost no competitive degradation. The removal efficiency and degradation rate of SEs in natural water was higher than those in pure water, which suggested that the coupled KMnO4/ultrasound technology had prospective applications in the removal of complex contaminants in actual drinking water treatment. PMID:26690185

Growth of non-Saccharomyces yeasts affects nutrient availability for Saccharomyces cerevisiae during wine fermentation.

PubMed

Medina, Karina; Boido, Eduardo; Dellacassa, Eduardo; Carrau, Francisco

2012-07-02

Yeast produces numerous secondary metabolites during fermentation that impact final wine quality. Although it is widely recognized that growth of diverse non-Saccharomyces (NS) yeast can positively affect flavor complexity during Saccharomyces cerevisiae wine fermentation, the inability to control spontaneous or co-fermentation processes by NS yeast has restricted their use in winemaking. We selected two NS yeasts from our Uruguayan native collection to study NS-S. cerevisiae interactions during wine fermentation. The selected strains of Hanseniaspora vineae and Metschnikowia pulcherrima had different yeast assimilable nitrogen consumption profiles and had different effects on S. cerevisiae fermentation and growth kinetics. Studies in which we varied inoculum size and using either simultaneous or sequential inoculation of NS yeast and S. cerevisiae suggested that competition for nutrients had a significant effect on fermentation kinetics. Sluggish fermentations were more pronounced when S. cerevisiae was inoculated 24h after the initial stage of fermentation with a NS strain compared to co-inoculation. Monitoring strain populations using differential WL nutrient agar medium and fermentation kinetics of mixed cultures allowed for a better understanding of strain interactions and nutrient addition effects. Limitation of nutrient availability for S. cerevisiae was shown to result in stuck fermentations as well as to reduce sensory desirability of the resulting wine. Addition of diammonium phosphate (DAP) and a vitamin mix to a defined medium allowed for a comparison of nutrient competition between strains. Addition of DAP and the vitamin mix was most effective in preventing stuck fermentations. Copyright © 2012 Elsevier B.V. All rights reserved.

Substrate specificity of the aspartate:alanine antiporter (AspT) of Tetragenococcus halophilus in reconstituted liposomes.

PubMed

Sasahara, Ayako; Nanatani, Kei; Enomoto, Masaru; Kuwahara, Shigefumi; Abe, Keietsu

2011-08-19

The aspartate:alanine antiporter (AspT) of the lactic acid bacterium Tetragenococcus halophilus is a member of the aspartate:alanine exchanger (AAEx) transporter family. T. halophilus AspT catalyzes the electrogenic exchange of L-aspartate(1-) with L-alanine(0). Although physiological functions of AspT were well studied, L-aspartate(1-):L-alanine(0) antiport mechanisms are still unsolved. Here we report that the binding sites of L-aspartate and L-alanine are independently present in AspT by means of the kinetic studies. We purified His(6)-tagged T. halophilus AspT and characterized its kinetic properties when reconstituted in liposomes (K(m) = 0.35 ± 0.03 mm for L-aspartate, K(m) = 0.098 ± 0 mm for D-aspartate, K(m) = 26 ± 2 mm for L-alanine, K(m) = 3.3 ± 0.2 mm for D-alanine). Competitive inhibition by various amino acids of L-aspartate or L-alanine in self-exchange reactions revealed that L-cysteine selectively inhibited L-aspartate self-exchange but only weakly inhibited L-alanine self-exchange. Additionally, L-serine selectively inhibited L-alanine self-exchange but barely inhibited L-aspartate self-exchange. The aspartate analogs L-cysteine sulfinic acid, L-cysteic acid, and D-cysteic acid competitively and strongly inhibited L-aspartate self-exchange compared with L-alanine self-exchange. Taken together, these kinetic data suggest that the putative binding sites of L-aspartate and L-alanine are independently located in the substrate translocation pathway of AspT.

Kinematics and Kinetics of Squats, Drop Jumps and Imitation Jumps of Ski Jumpers

PubMed Central

Pauli, Carole A.; Keller, Melanie; Ammann, Fabian; Hübner, Klaus; Lindorfer, Julia; Taylor, William R.

2016-01-01

Abstract Pauli, CA, Keller, M, Ammann, F, Hübner, K, Lindorfer, J, Taylor, WR, and Lorenzetti, S. Kinematics and kinetics of squats, drop jumps and imitation jumps of ski jumpers. J Strength Cond Res 30(3): 643–652, 2016—Squats, drop jumps, and imitation jumps are commonly used training exercises in ski jumping to enhance maximum force, explosive force, and sport-specific skills. The purpose of this study was to evaluate the kinetics and kinematics of training exercises in ski jumping and to find objective parameters in training exercises that most correlate with the competition performance of ski jumpers. To this end, barbell squats, drop jumps, and imitation jumps were measured in a laboratory environment for 10 elite ski jumpers. Force and motion data were captured, and the influence of maximum vertical force, force difference, vertical take-off velocity, knee moments, knee joint power, and a knee valgus/varus index was evaluated and correlated with their season jump performance. The results indicate that, especially for the imitation jumps, a good correlation exists between the vertical take-off velocity and the personal jump performance on the hill (R = 0.718). Importantly, however, the more the athletes tended toward a valgus knee alignment during the measured movements, the worse their performance (R = 0.729 imitation jumps; R = 0.685 squats). Although an evaluation of the athletes' lower limb alignment during competitive jumping on the hill is still required, these preliminary data suggest that performance training should additionally concentrate on improving knee alignment to increase ski jumping performance. PMID:26418370

Experimental evaluation of the power balance model of speed skating.

PubMed

de Koning, Jos J; Foster, Carl; Lampen, Joanne; Hettinga, Floor; Bobbert, Maarten F

2005-01-01

Prediction of speed skating performance with a power balance model requires assumptions about the kinetics of energy production, skating efficiency, and skating technique. The purpose of this study was to evaluate these parameters during competitive imitations for the purpose of improving model predictions. Elite speed skaters (n = 8) performed races and submaximal efficiency tests. External power output (P(o)) was calculated from movement analysis and aerodynamic models and ice friction measurements. Aerobic kinetics was calculated from breath-by-breath oxygen uptake (Vo(2)). Aerobic power (P(aer)) was calculated from measured skating efficiency. Anaerobic power (P(an)) kinetics was determined by subtracting P(aer) from P(o). We found gross skating efficiency to be 15.8% (1.8%). In the 1,500-m event, the kinetics of P(an) was characterized by a first-order system as P(an) = 88 + 556e(-0.0494t) (in W, where t is time). The rate constant for the increase in P(aer) was -0.153 s(-1), the time delay was 8.7 s, and the peak P(aer) was 234 W; P(aer) was equal to 234[1 - e(-0.153(t-8.7))] (in W). Skating position changed with preextension knee angle increasing and trunk angle decreasing throughout the event. We concluded the pattern of P(aer) to be quite similar to that reported during other competitive imitations, with the exception that the increase in P(aer) was more rapid. The pattern of P(an) does not appear to fit an "all-out" pattern, with near zero values during the last portion of the event, as assumed in our previous model (De Koning JJ, de Groot G, and van Ingen Schenau GJ. J Biomech 25: 573-580, 1992). Skating position changed in ways different from those assumed in our previous model. In addition to allowing improved predictions, the results demonstrate the importance of observations in unique subjects to the process of model construction.

Low-concentration kinetics of atmospheric CH{sub 4} oxidation in soil and mechanism of NH{sub 4}{sup +} inhibition

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

Gulledge, J.; Schimel, J.P.

1998-11-01

NH{sub 4}{sup +} inhibition kinetics for CH{sub 4} oxidation were examined at near-atmospheric CH{sub 4} concentrations in three upland forest soils. Whether NH{sub 4}{sup +}-independent salt effects could be neutralized by adding nonammoniacal salts to control samples in lieu of deionized water was also investigated. Because the levels of exchangeable endogenous NH{sub 4}{sup +} were very low in the three soils, desorption of endogenous NH{sub 4}{sup +} was not a significant factor in this study. The K{sub m(app)} values for water-treated controls were 9.8, 22, and 57 nM for temperate pine, temperate hardwood, and birch taiga soils, respectively. At CH{submore » 4} concentrations of {le}15 {micro}l liter{sup {minus}1}, oxidation followed first-order kinetics in the fine-textured taiga soil, whereas the coarse-textured temperate soils exhibited Michaelis-Menten kinetics. Compared to water controls, the K{sub m(app)} values in the temperate soils increased in the presence of NH{sub 4}{sup +} salts, whereas the V{sub max(app)} values decreased substantially, indicating that there was a mixture of competitive and noncompetitive inhibition mechanisms for whole NH{sub 4}{sup +} salts. Compared to the corresponding K{sup +} salt controls, the K{sub m(app)} values for NH{sub 4}{sup +} salts increased substantially, whereas the V{sub max(app)} values remained virtually unchanged, indicating that NH{sub 4}{sup +} acted by competitive inhibition. Nonammoniacal salts caused inhibition to increase with increasing CH{sub 4} concentrations in all three soils. In the birch taiga soil, this trend occurred with both NH{sub 4}{sup +} and K{sup +} salts, and the slope of the increase was not affected by the addition of NH{sub 4}{sup +}. Hence, the increase in inhibition resulted from an NH{sub 4}{sup +}-independent mechanism.« less

Kinetic memory based on the enzyme-limited competition.

PubMed

Hatakeyama, Tetsuhiro S; Kaneko, Kunihiko

2014-08-01

Cellular memory, which allows cells to retain information from their environment, is important for a variety of cellular functions, such as adaptation to external stimuli, cell differentiation, and synaptic plasticity. Although posttranslational modifications have received much attention as a source of cellular memory, the mechanisms directing such alterations have not been fully uncovered. It may be possible to embed memory in multiple stable states in dynamical systems governing modifications. However, several experiments on modifications of proteins suggest long-term relaxation depending on experienced external conditions, without explicit switches over multi-stable states. As an alternative to a multistability memory scheme, we propose "kinetic memory" for epigenetic cellular memory, in which memory is stored as a slow-relaxation process far from a stable fixed state. Information from previous environmental exposure is retained as the long-term maintenance of a cellular state, rather than switches over fixed states. To demonstrate this kinetic memory, we study several models in which multimeric proteins undergo catalytic modifications (e.g., phosphorylation and methylation), and find that a slow relaxation process of the modification state, logarithmic in time, appears when the concentration of a catalyst (enzyme) involved in the modification reactions is lower than that of the substrates. Sharp transitions from a normal fast-relaxation phase into this slow-relaxation phase are revealed, and explained by enzyme-limited competition among modification reactions. The slow-relaxation process is confirmed by simulations of several models of catalytic reactions of protein modifications, and it enables the memorization of external stimuli, as its time course depends crucially on the history of the stimuli. This kinetic memory provides novel insight into a broad class of cellular memory and functions. In particular, applications for long-term potentiation are discussed, including dynamic modifications of calcium-calmodulin kinase II and cAMP-response element-binding protein essential for synaptic plasticity.

Continuum kinetic methods for analyzing wave physics and distribution function dynamics in the turbulence dissipation challenge

NASA Astrophysics Data System (ADS)

Juno, J.; Hakim, A.; TenBarge, J.; Dorland, W.

2015-12-01

We present for the first time results for the turbulence dissipation challenge, with specific focus on the linear wave portion of the challenge, using a variety of continuum kinetic models: hybrid Vlasov-Maxwell, gyrokinetic, and full Vlasov-Maxwell. As one of the goals of the wave problem as it is outlined is to identify how well various models capture linear physics, we compare our results to linear Vlasov and gyrokinetic theory. Preliminary gyrokinetic results match linear theory extremely well due to the geometry of the problem, which eliminates the dominant nonlinearity. With the non-reduced models, we explore how the subdominant nonlinearities manifest and affect the evolution of the turbulence and the energy budget. We also take advantage of employing continuum methods to study the dynamics of the distribution function, with particular emphasis on the full Vlasov results where a basic collision operator has been implemented. As the community prepares for the next stage of the turbulence dissipation challenge, where we hope to do large 3D simulations to inform the next generation of observational missions such as THOR (Turbulence Heating ObserveR), we argue for the consideration of hybrid Vlasov and full Vlasov as candidate models for these critical simulations. With the use of modern numerical algorithms, we demonstrate the competitiveness of our code with traditional particle-in-cell algorithms, with a clear plan for continued improvements and optimizations to further strengthen the code's viability as an option for the next stage of the challenge.

Influencing factors and kinetic studies of imidacloprid degradation by ozonation.

PubMed

Chen, Shi; Deng, Jing; Deng, Yang; Gao, Naiyun

2018-03-02

Batch kinetic tests in ozonation of imidacloprid from water were performed in this study. The pseudo-first-order rate constant of imidacloprid degradation was increased from 0.079 to 0.326 min -1 with the increasing pH from 6.02 to 8.64 at an average ozone dose of 1.149 mg L -1 . When the alkalinity was increased from 0 to 250 mg L -1 NaHCO 3 , the pseudo-first-order rate constants decreased from 0.121 to 0.034 min -1 . These results suggested that the predominant oxidant gradually switched from ozone to hydroxyl radicals ([Formula: see text]) with the increase in solution pH. The secondary rate constant [Formula: see text] (10.92 ± 0.12 M -1 s -1 ) for the reaction of imidacloprid and molecular ozone was determined at pH 2.0 and in the presence of 50 mM ter-butyl alcohol (p-chlorobenzoic acid, pCBA), respectively. An indirect competition method was used to determine the secondary rate constant for [Formula: see text] oxidation of imidacloprid in the presence of pCBA as the reference compound. The rate constants [Formula: see text] were estimated to range 2.65-3.79 M -1 s -1 at pH 6.02-8.64. Results obtained from this study demonstrate that ozonation appears to be an effective method to remove imidacloprid from water.

Experimental and theoretical study using DFT method for the competitive adsorption of two cationic dyes from wastewaters

NASA Astrophysics Data System (ADS)

Regti, Abdelmajid; Ayouchia, Hicham Ben El; Laamari, My Rachid; Stiriba, Salah Eddine; Anane, Hafid; Haddad, Mohammadine El

2016-12-01

The adsorption of cationic dyes, Basic Yellow (BY28) and Methylene Blue (MB) on a new activated carbon from medlar species were studied in both single and binary system. Some experimental parameters, namely, pH, amount of adsorbent and contact time are studied. Quantum chemical results indicate that the adsorption efficiency was directly related to the dye electrophilicity power. Some theorical parameters were calculated and proved that MB is more electrophilic than BY28, than greatest interaction with surface sites. Kinetic study showed that the adsorption follows the pseudo-second-order model and Freundlich was the best model to describe the phenomenon in the single and binary system. According to the local reactivity results using Parr functions, the sulphur and nitrogen atoms will be the main adsorption sites.

Advantages and limitations of common testing methods for antioxidants.

PubMed

Amorati, R; Valgimigli, L

2015-05-01

Owing to the importance of antioxidants in the protection of both natural and man-made materials, a large variety of testing methods have been proposed and applied. These include methods based on inhibited autoxidation studies, which are better followed by monitoring the kinetics of oxygen consumption or of the formation of hydroperoxides, the primary oxidation products. Analytical determination of secondary oxidation products (e.g. carbonyl compounds) has also been used. The majority of testing methods, however, do not involve substrate autoxidation. They are based on the competitive bleaching of a probe (e.g. ORAC assay, β-carotene, crocin bleaching assays, and luminol assay), on reaction with a different probe (e.g. spin-trapping and TOSC assay), or they are indirect methods based on the reduction of persistent radicals (e.g. galvinoxyl, DPPH and TEAC assays), or of inorganic oxidizing species (e.g. FRAP, CUPRAC and Folin-Ciocalteu assays). Yet other methods are specific for preventive antioxidants. The relevance, advantages, and limitations of these methods are critically discussed, with respect to their chemistry and the mechanisms of antioxidant activity. A variety of cell-based assays have also been proposed, to investigate the biological activity of antioxidants. Their importance and critical aspects are discussed, along with arguments for the selection of the appropriate testing methods according to the different needs.

Mathematical model for internal pH control in immobilized enzyme particles

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

Liou, J.K.; Rousseau, I.

A mathematical model has been developed for the internal pH control in immobilized enzyme particles. This model describes the kinetics of a coupled system of two enzymes, immobilized in particles of either planar, cylindrical, or spherical shape. The enzyme kinetics are assumed to be of a mixed type, including Michaelis-Menten kinetics, uncompetitive substrate inhibition, and competitive and noncompetitive product inhibition. In a case study we have considered the enzyme combination urease and penicillin acylase, whose kinetics are coupled through the pH dependence of the kinetic parameters. The hydrolysis of urea by urease yields ammonia and carbon dioxide, whereas benzylpenicillin (Pen-G)more » is converted to 6-animo penicillanic acid and phenyl acetic acid by penicillin acylase. The production of acids by the latter enzyme will cause a decrease in pH. Because of the presence of the ammonia-carbon dioxide system, however, the pH may be kept under control. In order to obtain information about the optimum performance of this enzymatic pH controller, we have computed the effectiveness factor and the conversion in a CSTR at different enzyme loadings. The results of the computer simulations indicate that a high conversion of Pen-G may be achieved (80-90%) at bulk pH values of about 7.5 - 8. 27 references.« less

Inhibition of thrombin by functionalized C60 nanoparticles revealed via in vitro assays and in silico studies.

PubMed

Liu, Yanyan; Fu, Jianjie; Pan, Wenxiao; Xue, Qiao; Liu, Xian; Zhang, Aiqian

2018-01-01

The studies on the human toxicity of nanoparticles (NPs) are far behind the rapid development of engineered functionalized NPs. Fullerene has been widely used as drug carrier skeleton due to its reported low risk. However, different from other kinds of NPs, fullerene-based NPs (C 60 NPs) have been found to have an anticoagulation effect, although the potential target is still unknown. In the study, both experimental and computational methods were adopted to gain mechanistic insight into the modulation of thrombin activity by nine kinds of C 60 NPs with diverse surface chemistry properties. In vitro enzyme activity assays showed that all tested surface-modified C 60 NPs exhibited thrombin inhibition ability. Kinetic studies coupled with competitive testing using 3 known inhibitors indicated that six of the C 60 NPs, of greater hydrophobicity and hydrogen bond (HB) donor acidity or acceptor basicity, acted as competitive inhibitors of thrombin by directly interacting with the active site of thrombin. A simple quantitative nanostructure-activity relationship model relating the surface substituent properties to the inhibition potential was then established for the six competitive inhibitors. Molecular docking analysis revealed that the intermolecular HB interactions were important for the specific binding of C 60 NPs to the active site canyon, while the additional stability provided by the surface groups through van der Waals interaction also play a key role in the thrombin binding affinity of the NPs. Our results suggest that thrombin is a possible target of the surface-functionalized C 60 NPs relevant to their anticoagulation effect. Copyright © 2017. Published by Elsevier B.V.

A century of enzyme kinetic analysis, 1913 to 2013.

PubMed

Johnson, Kenneth A

2013-09-02

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

The Backstroke Swimming Start: State of the Art

PubMed Central

de Jesus, Karla; de Jesus, Kelly; Fernandes, Ricardo J.; Vilas-Boas, João Paulo; Sanders, Ross

2014-01-01

As sprint swimming events can be decided by margins as small as .01 s, thus, an effective start is essential. This study reviews and discusses the ‘state of the art’ literature regarding backstroke start biomechanics from 23 documents. These included two swimming specific publications, eight peer-reviewed journal articles, three from the Biomechanics and Medicine in Swimming Congress series, eight from the International Society of Biomechanics in Sports Conference Proceedings, one from a Biomechanics Congress and one academic (PhD) thesis. The studies had diverse aims, including swimmers’ proficiency levels and data collection settings. There was no single consensus for defining phase descriptions; and kinematics, kinetics and EMG approaches were implemented in laboratory settings. However, researchers face great challenges in improving methods of quantifying valid, reliable and accurate data between laboratory and competition conditions. For example, starting time was defined from the starting signal to distances as disparate as ∼5 m to 22.86 m in several studies. Due to recent rule changes, some of the research outcomes now refer to obsolete backstroke start techniques, and only a few studies considered the actual international rules. This literature review indicated that further research is required, in both laboratory and competition settings focusing on the combined influences of the current rules and block configuration on backstroke starting performances. PMID:25414737

The reliability of an instrumented start block analysis system.

PubMed

Tor, Elaine; Pease, David L; Ball, Kevin A

2015-02-01

The swimming start is highly influential to overall competition performance. Therefore, it is paramount to develop reliable methods to perform accurate biomechanical analysis of start performance for training and research. The Wetplate Analysis System is a custom-made force plate system developed by the Australian Institute of Sport--Aquatic Testing, Training and Research Unit (AIS ATTRU). This sophisticated system combines both force data and 2D digitization to measure a number of kinetic and kinematic parameter values in an attempt to evaluate start performance. Fourteen elite swimmers performed two maximal effort dives (performance was defined as time from start signal to 15 m) over two separate testing sessions. Intraclass correlation coefficients (ICC) were used to determine each parameter's reliability. The kinetic parameters all had ICC greater than 0.9 except the time of peak vertical force (0.742). This may have been due to variations in movement initiation after the starting signal between trials. The kinematic and time parameters also had ICC greater than 0.9 apart from for the time of maximum depth (0.719). This parameter was lower due to the swimmers varying their depth between trials. Based on the high ICC scores for all parameters, the Wetplate Analysis System is suitable for biomechanical analysis of swimming starts.

Intrinsic Compressive Stress in Polycrystalline Films is Localized at Edges of the Grain Boundaries.

PubMed

Vasco, Enrique; Polop, Celia

2017-12-22

The intrinsic compression that arises in polycrystalline thin films under high atomic mobility conditions has been attributed to the insertion or trapping of adatoms inside grain boundaries. This compression is a consequence of the stress field resulting from imperfections in the solid and causes the thermomechanical fatigue that is estimated to be responsible for 90% of mechanical failures in current devices. We directly measure the local distribution of residual intrinsic stress in polycrystalline thin films on nanometer scales, using a pioneering method based on atomic force microscopy. Our results demonstrate that, at odds with expectations, compression is not generated inside grain boundaries but at the edges of gaps where the boundaries intercept the surface. We describe a model wherein this compressive stress is caused by Mullins-type surface diffusion towards the boundaries, generating a kinetic surface profile different from the mechanical equilibrium profile by the Laplace-Young equation. Where the curvatures of both profiles differ, an intrinsic stress is generated in the form of Laplace pressure. The Srolovitz-type surface diffusion that results from the stress counters the Mullins-type diffusion and stabilizes the kinetic surface profile, giving rise to a steady compression regime. The proposed mechanism of competition between surface diffusions would explain the flux and time dependency of compressive stress in polycrystalline thin films.

Intrinsic Compressive Stress in Polycrystalline Films is Localized at Edges of the Grain Boundaries

NASA Astrophysics Data System (ADS)

Vasco, Enrique; Polop, Celia

2017-12-01

The intrinsic compression that arises in polycrystalline thin films under high atomic mobility conditions has been attributed to the insertion or trapping of adatoms inside grain boundaries. This compression is a consequence of the stress field resulting from imperfections in the solid and causes the thermomechanical fatigue that is estimated to be responsible for 90% of mechanical failures in current devices. We directly measure the local distribution of residual intrinsic stress in polycrystalline thin films on nanometer scales, using a pioneering method based on atomic force microscopy. Our results demonstrate that, at odds with expectations, compression is not generated inside grain boundaries but at the edges of gaps where the boundaries intercept the surface. We describe a model wherein this compressive stress is caused by Mullins-type surface diffusion towards the boundaries, generating a kinetic surface profile different from the mechanical equilibrium profile by the Laplace-Young equation. Where the curvatures of both profiles differ, an intrinsic stress is generated in the form of Laplace pressure. The Srolovitz-type surface diffusion that results from the stress counters the Mullins-type diffusion and stabilizes the kinetic surface profile, giving rise to a steady compression regime. The proposed mechanism of competition between surface diffusions would explain the flux and time dependency of compressive stress in polycrystalline thin films.

Miming the cancer-immune system competition by kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Bianca, Carlo; Lemarchand, Annie

2016-10-01

In order to mimic the interactions between cancer and the immune system at cell scale, we propose a minimal model of cell interactions that is similar to a chemical mechanism including autocatalytic steps. The cells are supposed to bear a quantity called activity that may increase during the interactions. The fluctuations of cell activity are controlled by a so-called thermostat. We develop a kinetic Monte Carlo algorithm to simulate the cell interactions and thermalization of cell activity. The model is able to reproduce the well-known behavior of tumors treated by immunotherapy: the first apparent elimination of the tumor by the immune system is followed by a long equilibrium period and the final escape of cancer from immunosurveillance.

Mound-Interface Kinetics in Dictyostelium Aggregation

NASA Astrophysics Data System (ADS)

Tutu, Hiroki

2002-09-01

The mound development of the cellular slime mold amoebae Dictyostelium discoideum is studied with an interface kinetic model for the height of cell layers. As a competitive role for the chemotaxis, we compare two types of curvature relaxations; the surface relaxation induced by cell-substrate affinity (model A), and that comes from a cell-cell adhesive effect (model B). It is found that both models are characterized by the growth law for the maximum mound height. Based on a self-similarity scaling hypothesis for the spatial structure of streaming pattern, we suggest a scaling law for the growth of mound-height hmax ˜ t1-1/α+β/α with α = 2 (4) for the model A (B) and a number 0 ≤ β < 1.

Substrate-induced inactivation of the OXA2 beta-lactamase.

PubMed Central

Ledent, P; Frère, J M

1993-01-01

The hydrolysis time courses of 22 beta-lactam antibiotics by the class D OXA2 beta-lactamase were studied. Among these, only three appeared to correspond to the integrated Henri-Michaelis equation. 'Burst' kinetics, implying branched pathways, were observed with most penicillins, cephalosporins and with flomoxef and imipenem. Kinetic parameters characteristic of the different phases of the hydrolysis were determined for some substrates. Mechanisms generally accepted to explain such reversible partial inactivations involving branches at either the free enzyme or the acyl-enzyme were inadequate to explain the enzyme behaviour. The hydrolysis of imipenem was characterized by the occurrence of two 'bursts', and that of nitrocefin by a partial substrate-induced inactivation complicated by a competitive inhibition by the hydrolysis product. PMID:8240304

Prostaglandin E2 enhances long-term repopulation but does not permanently alter inherent stem cell competitiveness.

PubMed

Hoggatt, Jonathan; Mohammad, Khalid S; Singh, Pratibha; Pelus, Louis M

2013-10-24

Hematopoietic stem cell (HSC) transplantation is a lifesaving therapy for malignant and nonmalignant hematologic diseases and metabolic disorders. Although successful, hematopoietic transplantation can be hindered by inadequate stem cell number or poor engrafting efficiency. To overcome these deficits, we and others have previously reported the HSC-enhancing ability of a short-term exposure of prostaglandin E2 (PGE2); this strategy has now progressed to phase 1 clinical trials in double cord blood transplantation. To further analyze the short- and long-term effects of HSC exposure to PGE2, we followed the repopulation kinetics of PGE2-treated hematopoietic grafts through 5 serial transplantations and compared inherent long-term competitiveness in a HSC head-to-head secondary transplantation model. Treatment with PGE2 did not result in a long-term increase in HSC competitiveness, lineage bias, or enhanced proliferative potential, demonstrating that pulse exposure to PGE2 results in transient increases in HSC homing and engraftment potential.

Competition between Hydrogen Bonding and Proton Transfer during Specific Anion Recognition by Dihomooxacalix[4]arene Bidentate Ureas.

PubMed

Martínez-González, Eduardo; González, Felipe J; Ascenso, José R; Marcos, Paula M; Frontana, Carlos

2016-08-05

Competition between hydrogen bonding and proton transfer reactions was studied for systems composed of electrogenerated dianionic species from dinitrobenzene isomers and substituted dihomooxacalix[4]arene bidentate urea derivatives. To analyze this competition, a second-order ErCrCi mechanism was considered where the binding process is succeeded by proton transfer and the voltammetric responses depend on two dimensionless parameters: the first related to hydrogen bonding reactions, and the second one to proton transfer processes. Experimental results indicated that, upon an increase in the concentration of phenyl-substituted dihomooxacalix[4]arene bidentate urea, voltammetric responses evolve from diffusion-controlled waves (where the binding process is at chemical equilibrium) into irreversible kinetic responses associated with proton transfer. In particular, the 1,3-dinitrobenzene isomer showed a higher proton transfer rate constant (∼25 M(-1) s(-1)) compared to that of the 1,2-dinitrobenzene (∼5 M(-1) s(-1)), whereas the 1,4-dinitrobenzene did not show any proton transfer effect in the experimental conditions employed.

Mechanisms Underlying Early Rapid Increases in Creatinine in Paraquat Poisoning

PubMed Central

Mohamed, Fahim; Endre, Zoltan; Jayamanne, Shaluka; Pianta, Timothy; Peake, Philip; Palangasinghe, Chathura; Chathuranga, Umesh; Jayasekera, Kithsiri; Wunnapuk, Klintean; Shihana, Fathima; Shahmy, Seyed; Buckley, Nicholas

2015-01-01

Background Acute kidney injury (AKI) is common after severe paraquat poisoning and usually heralds a fatal outcome. The rapid large increases in serum creatinine (Cr) exceed that which can be explained by creatinine kinetics based on loss of glomerular filtration rate (GFR). Methods and Findings This prospective multi-centre study compared the kinetics of two surrogate markers of GFR, serum creatinine and serum cystatin C (CysC), following paraquat poisoning to understand and assess renal functional loss after paraquat poisoning. Sixty-six acute paraquat poisoning patients admitted to medical units of five hospitals were included. Relative changes in creatinine and CysC were monitored in serial blood and urine samples, and influences of non-renal factors were also studied. Results Forty-eight of 66 patients developed AKI (AKIN criteria), with 37 (56%) developing moderate to severe AKI (AKIN stage 2 or 3). The 37 patients showed rapid increases in creatinine of >100% within 24 hours, >200% within 48 hours and >300% by 72 hours and 17 of the 37 died. CysC concentration increased by 50% at 24 hours in the same 37 patients and then remained constant. The creatinine/CysC ratio increased 8 fold over 72 hours. There was a modest fall in urinary creatinine and serum/urine creatinine ratios and a moderate increase in urinary paraquat during first three days. Conclusion Loss of renal function contributes modestly to the large increases in creatinine following paraquat poisoning. The rapid rise in serum creatinine most probably represents increased production of creatine and creatinine to meet the energy demand following severe oxidative stress. Minor contributions include increased cyclisation of creatine to creatinine because of acidosis and competitive or non-competitive inhibition of creatinine secretion. Creatinine is not a good marker of renal functional loss after paraquat poisoning and renal injury should be evaluated using more specific biomarkers of renal injury. PMID:25815837

Quantitatively and Kinetically Identifying Binding Motifs of Amelogenin Proteins to Mineral Crystals Through Biochemical and Spectroscopic Assays

PubMed Central

Zhu, Li; Hwang, Peter; Witkowska, H. Ewa; Liu, Haichuan; Li, Wu

2014-01-01

Tooth enamel is the hardest tissue in vertebrate animals. Consisting of millions of carbonated hydroxyapatite crystals, this highly mineralized tissue develops from a protein matrix in which amelogenin is the predominant component. The enamel matrix proteins are eventually and completely degraded and removed by proteinases to form mineral-enriched tooth enamel. Identification of the apatite-binding motifs in amelogenin is critical for understanding the amelogenin–crystal interactions and amelogenin–proteinases interactions during tooth enamel biomineralization. A stepwise strategy is introduced to kinetically and quantitatively identify the crystal-binding motifs in amelogenin, including a peptide screening assay, a competitive adsorption assay, and a kinetic-binding assay using amelogenin and gene-engineered amelogenin mutants. A modified enzyme-linked immunosorbent assay on crystal surfaces is also applied to compare binding amounts of amelogenin and its mutants on different planes of apatite crystals. We describe the detailed protocols for these assays and provide the considerations for these experiments in this chapter. PMID:24188774

Kinetics and inhibition of cyclomaltodextrinase from alkalophilic Bacillus sp. I-5.

PubMed

Kim, M J; Park, W S; Lee, H S; Kim, T J; Shin, J H; Yoo, S H; Cheong, T K; Ryu, S; Kim, J C; Kim, J W; Moon, T W; Robyt, J F; Park, K H

2000-01-01

The cyclomaltodextrinase from alkalophilic Bacillus sp. I-5 (CDase I-5) was expressed in Escherichia coli and the purified enzyme was used for characterization of the enzyme action. The hydrolysis products were monitored by both HPLC and high-performance ion chromatography analysis that enable the kinetic analysis of the cyclomaltodextrin (CD)-degrading reaction. Analysis of the kinetics of cyclomaltodextrin hydrolysis by CDase I-5 indicated that ring-opening of the cyclomaltodextrin was the major limiting step and that CDase I-5 preferentially degraded the linear maltodextrin chain by removing the maltose unit. The substrate binding affinity of the enzyme was almost same for those of cyclomaltodextrins while the rate of ring-opening was the fastest for cyclomaltoheptaose. Acarbose and methyl 6-amino-6-deoxy-alpha-d-glucopyranoside were relatively strong competitive inhibitors with K(i) values of 1.24 x 10(-3) and 8.44 x 10(-1) mM, respectively. Both inhibitors are likely to inhibit the ring-opening step of the CD degradation reaction. Copyright 2000 Academic Press.

Modified ADM1 disintegration/hydrolysis structures for modeling batch thermophilic anaerobic digestion of thermally pretreated waste activated sludge.

PubMed

Ramirez, Ivan; Mottet, Alexis; Carrère, Hélène; Déléris, Stéphane; Vedrenne, Fabien; Steyer, Jean-Philippe

2009-08-01

Anaerobic digestion disintegration and hydrolysis have been traditionally modeled according to first-order kinetics assuming that their rates do not depend on disintegration/hydrolytic biomass concentrations. However, the typical sigmoid-shape increase in time of the disintegration/hydrolysis rates cannot be described with first-order models. For complex substrates, first-order kinetics should thus be modified to account for slowly degradable material. In this study, a slightly modified IWA ADM1 model is presented to simulate thermophilic anaerobic digestion of thermally pretreated waste activated sludge. Contois model is first included for disintegration and hydrolysis steps instead of first-order kinetics and Hill function is then used to model ammonia inhibition of aceticlastic methanogens instead of a non-competitive function. One batch experimental data set of anaerobic degradation of a raw waste activated sludge is used to calibrate the proposed model and three additional data sets from similar sludge thermally pretreated at three different temperatures are used to validate the parameters values.

Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1

NASA Astrophysics Data System (ADS)

Park, Hwangseo; Lee, Hye Seon; Ku, Bonsu; Lee, Sang-Rae; Kim, Seung Jun

2017-08-01

Despite a wealth of persuasive evidence for the involvement of human small C-terminal domain phosphatase 1 (Scp1) in the impairment of neuronal differentiation and in Huntington's disease, small-molecule inhibitors of Scp1 have been rarely reported so far. This study aims to the discovery of both competitive and allosteric Scp1 inhibitors through the two-track virtual screening procedure. By virtue of the improvement of the scoring function by implementing a new molecular solvation energy term and by reoptimizing the atomic charges for the active-site Mg2+ ion cluster, we have been able to identify three allosteric and five competitive Scp1 inhibitors with low-micromolar inhibitory activity. Consistent with the results of kinetic studies on the inhibitory mechanisms, the allosteric inhibitors appear to be accommodated in the peripheral binding pocket through the hydrophobic interactions with the nonpolar residues whereas the competitive ones bind tightly in the active site with a direct coordination to the central Mg2+ ion. Some structural modifications to improve the biochemical potency of the newly identified inhibitors are proposed based on the binding modes estimated with docking simulations.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Solvable Catalyzed Birth-Death-Exchange Competition Model of Three Species

NASA Astrophysics Data System (ADS)

Wang, Hai-Feng; Lin, Zhen-Quan; Gao, Yan; Zhang, Heng

2009-10-01

A competition model of three species in exchange-driven aggregation growth is proposed. In the model, three distinct aggregates grow by exchange of monomers and in parallel, birth of species A is catalyzed by species B and death of species A is catalyzed by species C. The rates for both catalysis processes are proportional to kjν and kjω respectively, where ν(Ω) is a parameter reflecting the dependence of the catalysis reaction rate of birth (death) on the catalyst aggregate's size. The kinetic evolution behaviors of the three species are investigated by the rate equation approach based on the mean-field theory. The form of the aggregate size distribution of A-species ak(t) is found to be dependent crucially on the two catalysis rate kernel parameters. The results show that (i) in case of μ <= 0, the form of ak(t) mainly depends on the competition between self-exchange of species A and species-C-catalyzed death of species A; (ii) in case of ν > 0, the form of ak(t) mainly depends on the competition between species-B-catalyzed birth of species A and species-C-catalyzed death of species A.

Anoxic denitrification of BTEX: Biodegradation kinetics and pollutant interactions.

PubMed

Carvajal, Andrea; Akmirza, Ilker; Navia, Daniel; Pérez, Rebeca; Muñoz, Raúl; Lebrero, Raquel

2018-05-15

Anoxic mineralization of BTEX represents a promising alternative for their abatement from O 2 -deprived emissions. However, the kinetics of anoxic BTEX biodegradation and the interactions underlying the treatment of BTEX mixtures are still unknown. An activated sludge inoculum was used for the anoxic abatement of single, dual and quaternary BTEX mixtures, being acclimated prior performing the biodegradation kinetic tests. The Monod model and a Modified Gompertz model were then used for the estimation of the biodegradation kinetic parameters. Results showed that both toluene and ethylbenzene are readily biodegradable under anoxic conditions, whereas the accumulation of toxic metabolites resulted in partial xylene and benzene degradation when present both as single components or in mixtures. Moreover, the supplementation of an additional pollutant always resulted in an inhibitory competition, with xylene inducing the highest degree of inhibition. The Modified Gompertz model provided an accurate fitting for the experimental data for single and dual substrate experiments, satisfactorily representing the antagonistic pollutant interactions. Finally, microbial analysis suggested that the degradation of the most biodegradable compounds required a lower microbial specialization and diversity, while the presence of the recalcitrant compounds resulted in the selection of a specific group of microorganisms. Copyright © 2018 Elsevier Ltd. All rights reserved.

Kinetic controls on the complexation between mercury and dissolved organic matter in a contaminated environment.

PubMed

Miller, Carrie L; Southworth, George; Brooks, Scott; Liang, Liyuan; Gu, Baohua

2009-11-15

The interaction of mercury (Hg) with dissolved natural organic matter (NOM) under equilibrium conditions is the focus of many studies but the kinetic controls on Hg-NOM complexation in aquatic systems have often been overlooked. We examined the rates of Hg-NOM complexation both in a contaminated Upper East Fork Poplar Creek (UEFPC) in Oak Ridge, Tennessee, and in controlled laboratory experiments using reducible Hg (Hg(R)) measurements and C(18) solid phase extraction techniques. Of the filterable Hg at the headwaters of UEFPC, >90% was present as Hg(R) and this fraction decreased downstream but remained >29% of the filterable Hg at all sites. The presence of higher Hg(R) concentrations than would be predicted under equilibrium conditions in UEFPC and in experiments with a NOM isolate suggests that kinetic reactions are controlling the complexation between Hg and NOM. The slow formation of Hg-NOM complexes is attributed to competitive ligand exchange among various moieties and functional groups in NOM with a range of binding strengths and configurations. This study demonstrates the need to consider the effects of Hg-NOM complexation kinetics on processes such as Hg methylation and solid phase partitioning.

Acute effects of different dynamic exercises on hamstring strain risk factors.

PubMed

Chen, Che Hsiu; Xin, Ye; Lee, Kuang Wu; Lin, Ming Ju; Lin, Jiu Jenq

2018-01-01

The purpose of the study was to examine the acute effects of different dynamic exercise interventions on hamstring muscle performance. Thirty-six young men with poor hamstring flexibility were randomly assigned to three intervention groups: jogging combined with dynamic open kinetic chain stretching (DS), jogging combined with dynamic closed kinetic chain stretching (lunge with eccentric hamstring windmills, LEC), and jogging only (CON) groups. Hamstring flexibility, muscle stiffness (area under the curve, AUC), joint position sense (JPS), maximal eccentric strength (ECC), and angle of peak torque (APT) were recorded before and immediately after the exercise interventions. The results showed that the hamstring flexibility increased in DS (p < 0.001); muscle stiffness decreased in DS and was lower than jogging (p < 0.001). Moreover, ECC increased in LEC and was higher than jogging and DS (p < 0.001). APT was different among 3 groups (p < 0.001). Decreased accuracy of JPS was found in DS and jogging (p < 0.001). In conclusion, the dynamic closed kinetic chain stretching (LEC) as compared to open kinetic chain stretching (DS) or jogging group, may be an effective technique to enhance muscle performance during the pre-competition warm-up routine.

Acute effects of different dynamic exercises on hamstring strain risk factors

PubMed Central

Xin, Ye; Lee, Kuang Wu; Lin, Ming Ju

2018-01-01

The purpose of the study was to examine the acute effects of different dynamic exercise interventions on hamstring muscle performance. Thirty-six young men with poor hamstring flexibility were randomly assigned to three intervention groups: jogging combined with dynamic open kinetic chain stretching (DS), jogging combined with dynamic closed kinetic chain stretching (lunge with eccentric hamstring windmills, LEC), and jogging only (CON) groups. Hamstring flexibility, muscle stiffness (area under the curve, AUC), joint position sense (JPS), maximal eccentric strength (ECC), and angle of peak torque (APT) were recorded before and immediately after the exercise interventions. The results showed that the hamstring flexibility increased in DS (p < 0.001); muscle stiffness decreased in DS and was lower than jogging (p < 0.001). Moreover, ECC increased in LEC and was higher than jogging and DS (p < 0.001). APT was different among 3 groups (p < 0.001). Decreased accuracy of JPS was found in DS and jogging (p < 0.001). In conclusion, the dynamic closed kinetic chain stretching (LEC) as compared to open kinetic chain stretching (DS) or jogging group, may be an effective technique to enhance muscle performance during the pre-competition warm-up routine. PMID:29390001

Mechanics of competition walking.

PubMed

Cavagna, G A; Franzetti, P

1981-06-01

1. The work done at each step to lift and accelerate the centre of mass of the body has been measured in competition walkers during locomotion from 2 to 20 km/hr. 2. Three distinct phases characterize the mechanics of walking. From 2 to 6 km/hr the vertical displacement during each step, Sv, increases to a maximum (3.5 vs. 6 cm in normal walking) due to an increase in the amplitude of the rotation over the supporting leg. 3. The transfer, R, between potential energy of vertical displacement and kinetic energy of forward motion during this rotation, reaches a maximum at 4-5 km/hr (R = 65%). From 6 to 10 km/hr R decreases more steeply than in normal walking, indicating a smaller utilization of the pendulum-like mechanism characteristic of walking. 4. Above 10 km/hr potential and kinetic energies vary during each step because both are simultaneously taken up and released by the muscles with almost no transfer between them (R = 2-10%). Above 13-14 km/hr an aerial phase (25-60 msec) takes place during the step. 5. Speeds considerably greater than in normal walking are attained thanks to a greater efficiency of doing positive work. This is made possible by a mechanism of locomotion allowing an important storage and recovery of mechanical energy by the muscles.

Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems

PubMed Central

Sleutels, Tom H. J. A.; Molenaar, Sam D.; Heijne, Annemiek Ter; Buisman, Cees J. N.

2016-01-01

A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future. PMID:27681899

The effects of iron(II) on the kinetics of arsenic oxidation and sorption on manganese oxides.

PubMed

Wu, Yun; Li, Wei; Sparks, Donald L

2015-11-01

In this study, As(III) oxidation kinetics by a poorly-crystalline phyllomanganate (δ-MnO2) in the presence and absence of dissolved Fe(II) was investigated using stirred-flow and batch experiments. Chemically synthetic δ-MnO2 was reacted with four influent solutions, containing the same As(III) concentration but different Fe(II) concentrations, at pH 6. The results show an initial rapid As(III) oxidation by δ-MnO2, which is followed by an appreciably slow reaction after 8h. In the presence of Fe(II), As(III) oxidation is inhibited due to the competitive oxidation of Fe(II) as well as the formation of Fe(III)-(hydr)oxides on the δ-MnO2 surface. However, the sorption of As(III), As(V) and Mn(II) are increased, for the newly formed Fe(III)-(hydr)oxides provide additional sorption sites. This study suggests that the competitive oxidation of Fe(II) and consequently the precipitation of Fe(III) compounds on the δ-MnO2 surface play an important role in As(III) oxidation and As sequestration. Understanding these processes would be helpful in developing in situ strategies for remediation of As-contaminated waters and soils. Copyright © 2015 Elsevier Inc. All rights reserved.

Kinematics and Kinetics of Squats, Drop Jumps and Imitation Jumps of Ski Jumpers.

PubMed

Pauli, Carole A; Keller, Melanie; Ammann, Fabian; Hübner, Klaus; Lindorfer, Julia; Taylor, William R; Lorenzetti, Silvio

2016-03-01

Squats, drop jumps, and imitation jumps are commonly used training exercises in ski jumping to enhance maximum force, explosive force, and sport-specific skills. The purpose of this study was to evaluate the kinetics and kinematics of training exercises in ski jumping and to find objective parameters in training exercises that most correlate with the competition performance of ski jumpers. To this end, barbell squats, drop jumps, and imitation jumps were measured in a laboratory environment for 10 elite ski jumpers. Force and motion data were captured, and the influence of maximum vertical force, force difference, vertical take-off velocity, knee moments, knee joint power, and a knee valgus/varus index was evaluated and correlated with their season jump performance. The results indicate that, especially for the imitation jumps, a good correlation exists between the vertical take-off velocity and the personal jump performance on the hill (R = 0.718). Importantly, however, the more the athletes tended toward a valgus knee alignment during the measured movements, the worse their performance (R = 0.729 imitation jumps; R = 0.685 squats). Although an evaluation of the athletes' lower limb alignment during competitive jumping on the hill is still required, these preliminary data suggest that performance training should additionally concentrate on improving knee alignment to increase ski jumping performance.

User’s Guide for Biodegradation Reactions in TMVOCBio

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

Jung, Yoojin; Battistelli, Alfredo

TMVOCBio is an extended version of the TMVOC numerical reservoir simulator, with the capability of simulating multiple biodegradation reactions mediated by different microbial populations or based on different redox reactions, thus involving different electron acceptors. This modeling feature is implemented within the existing TMVOC module in iTOUGH2. TMVOCBio, originally developed by Battistelli (2003; 2004), uses a general modified form of the Monod kinetic rate equation to simulate biodegradation reactions, which effectively simulates the uptake of a substrate while accounting for various limiting factors (i.e., the limitation by substrate, electron acceptor, or nutrients). Two approaches are included: 1) a multiple Monodmore » kinetic rate equation, which assumes all the limiting factors simultaneously affect the substrate uptake rate, and 2) a minimum Monod model, which assumes that the substrate uptake rate is controlled by the most limiting factor among those acting for the specific substrate. As the limiting factors, biomass growth inhibition, toxicity effects, as well as competitive and non-competitive inhibition effects are included. The temperature and moisture dependence of biodegradation reactions is also considered. This report provides mathematical formulations and assumptions used for modeling the biodegradation reactions, and describes additional modeling capabilities. Detailed description of input format for biodegradation reactions is presented along with sample problems.« less

Low Substrate Loading Limits Methanogenesis and Leads to High Coulombic Efficiency in Bioelectrochemical Systems.

PubMed

Sleutels, Tom H J A; Molenaar, Sam D; Heijne, Annemiek Ter; Buisman, Cees J N

2016-01-05

A crucial aspect for the application of bioelectrochemical systems (BESs) as a wastewater treatment technology is the efficient oxidation of complex substrates by the bioanode, which is reflected in high Coulombic efficiency (CE). To achieve high CE, it is essential to give a competitive advantage to electrogens over methanogens. Factors that affect CE in bioanodes are, amongst others, the type of wastewater, anode potential, substrate concentration and pH. In this paper, we focus on acetate as a substrate and analyze the competition between methanogens and electrogens from a thermodynamic and kinetic point of view. We reviewed experimental data from earlier studies and propose that low substrate loading in combination with a sufficiently high anode overpotential plays a key-role in achieving high CE. Low substrate loading is a proven strategy against methanogenic activity in large-scale reactors for sulfate reduction. The combination of low substrate loading with sufficiently high overpotential is essential because it results in favorable growth kinetics of electrogens compared to methanogens. To achieve high current density in combination with low substrate concentrations, it is essential to have a high specific anode surface area. New reactor designs with these features are essential for BESs to be successful in wastewater treatment in the future.

Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease.

PubMed

Mazzei, Luca; Cianci, Michele; Benini, Stefano; Bertini, Leonardo; Musiani, Francesco; Ciurli, Stefano

2016-01-01

Urease is the most efficient enzyme known to date, and catalyzes the hydrolysis of urea using two Ni(II) ions in the active site. Urease is a virulence factor in several human pathogens, while causing severe environmental and agronomic problems. Sporosarcina pasteurii urease has been used extensively in the structural characterization of the enzyme. Sodium sulfite has been widely used as a preservative in urease solutions to prevent oxygen-induced oxidation, but its role as an inhibitor has also been suggested. In the present study, isothermal titration microcalorimetry was used to establish sulfite as a competitive inhibitor for S. pasteurii urease, with an inhibition constant of 0.19mM at pH7. The structure of the urease-sulfite complex, determined at 1.65Å resolution, shows the inhibitor bound to the dinuclear Ni(II) center of urease in a tridentate mode involving bonds between the two Ni(II) ions in the active site and all three oxygen atoms of the inhibitor, supporting the observed competitive inhibition kinetics. This coordination mode of sulfite has never been observed, either in proteins or in small molecule complexes, and could inspire synthetic coordination chemists as well as biochemists to develop urease inhibitors based on this chemical moiety. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantitative In Vivo Fluorescence Cross-Correlation Analyses Highlight the Importance of Competitive Effects in the Regulation of Protein-Protein Interactions

PubMed Central

Sadaie, Wakako; Harada, Yoshie; Matsuda, Michiyuki

2014-01-01

Computer-assisted simulation is a promising approach for clarifying complicated signaling networks. However, this approach is currently limited by a deficiency of kinetic parameters determined in living cells. To overcome this problem, we applied fluorescence cross-correlation spectrometry (FCCS) to measure dissociation constant (Kd) values of signaling molecule complexes in living cells (in vivo Kd). Among the pairs of fluorescent molecules tested, that of monomerized enhanced green fluorescent protein (mEGFP) and HaloTag-tetramethylrhodamine was most suitable for the measurement of in vivo Kd by FCCS. Using this pair, we determined 22 in vivo Kd values of signaling molecule complexes comprising the epidermal growth factor receptor (EGFR)–Ras–extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway. With these parameters, we developed a kinetic simulation model of the EGFR-Ras-ERK MAP kinase pathway and uncovered a potential role played by stoichiometry in Shc binding to EGFR during the peak activations of Ras, MEK, and ERK. Intriguingly, most of the in vivo Kd values determined in this study were higher than the in vitro Kd values reported previously, suggesting the significance of competitive bindings inside cells. These in vivo Kd values will provide a sound basis for the quantitative understanding of signal transduction. PMID:24958104

A Method to Determine 18O Kinetic Isotope Effects in the Hydrolysis of Nucleotide Triphosphates

PubMed Central

Du, Xinlin; Ferguson, Kurt; Sprang, Stephen R.

2007-01-01

A method to determine 18O kinetic isotope effects (KIE) in the hydrolysis of GTP is described that is generally applicable to reactions involving other nucleotide triphosphates. Internal competition, wherein the substrate of the reaction is a mixture of 18O-labeled and unlabeled nucleotides, is employed and the change in relative abundance of the two species in the course of the reaction is used to calculate KIE. The nucleotide labeled with 18O at sites of mechanistic interest also contains 13C at all carbon positions, while the 16O-nucleotide is depleted of 13C. The relative abundance of the labeled and unlabeled substrates or products is reflected in the carbon isotope ratio (13C/12C) in GTP or GDP, which is determined by use of a liquid chromatography-coupled isotope ratio mass spectrometer (LC-coupled IRMS). The LC is coupled to the IRMS by an Isolink™ interface (ThermoFinnigan). Carbon isotope ratios can be determined with accuracy and precision greater than 0.04%, and are consistent over an order of magnitude in sample amount. KIE values for Ras/NF1333-catalyzed hydrolysis of [β18O3,13C]GTP were determined by change in the isotope ratio of GTP or GDP or the ratio of the isotope ratio of GDP to that of GTP. KIE values computed in the three ways agree within 0.1%, although the method using the ratio of isotope ratios of GDP and GTP gives superior precision (< 0.1%). A single KIE measurement can be conducted in 25 minutes with less than 5 μg nucleotide reaction product. PMID:17963711

Native UCP1 displays simple competitive kinetics between the regulators purine nucleotides and fatty acids.

PubMed

Shabalina, Irina G; Jacobsson, Anders; Cannon, Barbara; Nedergaard, Jan

2004-09-10

Elucidation of the regulation of uncoupling protein 1 (UCP1) activity in its native environment, i.e. the inner membrane of brown-fat mitochondria, has been hampered by the presence of UCP1-independent, quantitatively unresolved effects of investigated regulators on the brown-fat mitochondria themselves. Here we have utilized the availability of UCP1-ablated mice to dissect UCP1-dependent and UCP1-independent effects of regulators. Using a complex-I-linked substrate (pyruvate), we found that UCP1 can mediate a 4-fold increase in thermogenesis when stimulated with the classical positive regulator fatty acids (oleate). After demonstrating that the fatty acids act in their free form, we found that UCP1 increased fatty acid sensitivity approximately 30-fold (as compared with the 1.5-fold increase reported earlier based on nominal fatty acid values). By identifying the UCP1-mediated fraction of the response, we could conclude that the interaction between purine nucleotides (GDP) and fatty acids (oleate) unexpectedly displayed simple competitive kinetics. In GDP-inhibited mitochondria, oleate apparently acted as an activator. However, only a model in which UCP1 is inherently active (i.e."activating" fatty acids cannot be included in the model), where GDP functions as an inhibitor with a K(m) of 0.05 mm, and where oleate functions as a competitive antagonist for the GDP effect (with a K(i) of 5 nm) can fit all of the experimental data. We conclude that, when examined in its native environment, UCP1 functions as a proton (equivalent) carrier in the absence of exogenous or endogenous fatty acids.

Influence of Familiarization and Competitive Level on the Reliability of Countermovement Vertical Jump Kinetic and Kinematic Variables.

PubMed

Nibali, Maria L; Tombleson, Tom; Brady, Philip H; Wagner, Phillip

2015-10-01

Understanding typical variation of vertical jump (VJ) performance and confounding sources of its typical variability (i.e., familiarization and competitive level) is pertinent in the routine monitoring of athletes. We evaluated the presence of systematic error (learning effect) and nonuniformity of error (heteroscedasticity) across VJ performances of athletes that differ in competitive level and quantified the reliability of VJ kinetic and kinematic variables relative to the smallest worthwhile change (SWC). One hundred thirteen high school athletes, 30 college athletes, and 35 professional athletes completed repeat VJ trials. Average eccentric rate of force development (RFD), average concentric (CON) force, CON impulse, and jump height measurements were obtained from vertical ground reaction force (VGRF) data. Systematic error was assessed by evaluating changes in the mean of repeat trials. Heteroscedasticity was evaluated by plotting the difference score (trial 2 - trial 1) against the mean of the trials. Variability of jump variables was calculated as the typical error (TE) and coefficient of variation (%CV). No substantial systematic error (effect size range: -0.07 to 0.11) or heteroscedasticity was present for any of the VJ variables. Vertical jump can be performed without the need for familiarization trials, and the variability can be conveyed as either the raw TE or the %CV. Assessment of VGRF variables is an effective and reliable means of assessing VJ performance. Average CON force and CON impulse are highly reliable (%CV: 2.7% ×/÷ 1.10), although jump height was the only variable to display a %CV ≤SWC. Eccentric RFD is highly variable yet should not be discounted from VJ assessments on this factor alone because it may be sensitive to changes in response to training or fatigue that exceed the TE.

The Parkinson Disease-linked LRRK2 Protein Mutation I2020T Stabilizes an Active State Conformation Leading to Increased Kinase Activity*

PubMed Central

Ray, Soumya; Bender, Samantha; Kang, Stephanie; Lin, Regina; Glicksman, Marcie A.; Liu, Min

2014-01-01

The effect of leucine-rich repeat kinase 2 (LRRK2) mutation I2020T on its kinase activity has been controversial, with both increased and decreased effects being reported. We conducted steady-state and pre-steady-state kinetic studies on LRRKtide and its analog LRRKtideS. Their phosphorylation differs by the rate-limiting steps: product release is rate-limiting for LRRKtide and phosphoryl transfer is rate-limiting for LRRKtideS. As a result, we observed that the I2020T mutant is more active than wild type (WT) LRRK2 for LRRKtideS phosphorylation, whereas it is less active than WT for LRRKtide phosphorylation. Our pre-steady-state kinetic data suggest that (i) the I2020T mutant accelerates the rates of phosphoryl transfer of both reactions by 3–7-fold; (ii) this increase is masked by a rate-limiting product release step for LRRKtide phosphorylation; and (iii) the observed lower activity of the mutant for LRRKtide phosphorylation is a consequence of its instability: the concentration of the active form of the mutant is 3-fold lower than WT. The I2020T mutant has a dramatically low KATP and therefore leads to resistance to ATP competitive inhibitors. Two well known DFG-out or type II inhibitors are also weaker toward the mutant because they inhibit the mutant in an unexpected ATP competitive mechanism. The I2020 residue lies next to the DYG motif of the activation loop of the LRRK2 kinase domain. Our modeling and metadynamic simulations suggest that the I2020T mutant stabilizes the DYG-in active conformation and creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP competitive fashion. PMID:24695735

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.

Competition between conjugation and M13 phage infection in Escherichia coli in the absence of selection pressure: a kinetic study.

PubMed

Wan, Zhenmao; Goddard, Noel L

2012-10-01

Inter- and intraspecies horizontal gene transfer enabled by bacterial secretion systems is a powerful mechanism for bacterial genome plasticity. The type IV secretion system of Escherichia coli, encoded by the F plasmid, enables cell-to-cell contact and subsequent DNA transfer known as conjugation. Conjugation is compromised by phage infection that specifically targets the secretion machinery. Hence, the use of phages to regulate the spread of genes, such as acquired antibiotic resistance or as general biosanitation agents, has gained interest. To predict the potential efficacy, the competition kinetics must first be understood. Using quantitative PCR to enumerate genomic loci in a resource-limited batch culture, we quantify the infection kinetics of the nonlytic phage M13 and its impact on conjugation in the absence of selection pressure (isogenic set). Modeling the resulting experimental data reveals the cellular growth rate to be reduced to 60% upon phage infection. We also find a maximum phage infection rate of 3×10(-11) mL phage(-1) min(-1) which is only 1 order of magnitude slower than the maximum conjugation rate (3×10(-10) mL cell(-1) min(-1)), suggesting phages must be in significant abundance to be effective antagonists to horizontal gene transfer. In the regime where the number of susceptible cells (F(+)) and phages are equal upon initial infection, we observe the spread of the conjugative plasmid throughout the cell population despite phage infection, but only at 10% of the uninfected rate. This has interesting evolutionary implications, as even in the absence of selection pressure, cells maintain the ability to conjugate despite phage vulnerability and the associated growth consequences.

Uptake of dissolved inorganic and organic nitrogen by the benthic toxic dinoflagellate Ostreopsis cf. ovata.

PubMed

Jauzein, Cécile; Couet, Douglas; Blasco, Thierry; Lemée, Rodolphe

2017-05-01

Environmental factors that shape dynamics of benthic toxic blooms are largely unknown. In particular, for the toxic dinoflagellate Ostreopsis cf. ovata, the importance of the availability of nutrients and the contribution of the inorganic and organic pools to growth need to be quantified in marine coastal environments. The present study aimed at characterizing N-uptake of dissolved inorganic and organic sources by O. cf. ovata cells, using the 15 N-labelling technique. Experiments were conducted taking into account potential interactions between nutrient uptake systems as well as variations with the diel cycle. Uptake abilities of O. cf. ovata were parameterized for ammonium (NH 4 + ), nitrate (NO 3 - ) and N-urea, from the estimation of kinetic and inhibition parameters. In the range of 0 to 10μmolNL -1 , kinetic curves showed a clear preference pattern following the ranking NH 4 + >NO 3 - >N-urea, where the preferential uptake of NH 4 + relative to NO 3 - was accentuated by an inhibitory effect of NH 4 + concentration on NO 3 - uptake capabilities. Conversely, under high nutrient concentrations, the preference for NH 4 + relative to NO 3 - was largely reduced, probably because of the existence of a low-affinity high capacity inducible NO 3 - uptake system. Ability to take up nutrients in darkness could not be defined as a competitive advantage for O. cf. ovata. Species competitiveness can also be defined from nutrient uptake kinetic parameters. A strong affinity for NH 4 + was observed for O. cf. ovata cells that may partly explain the success of this toxic species during the summer season in the Bay of Villefranche-sur-mer (France). Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative assessment of hematopoietic chimerism by quantitative real-time polymerase chain reaction of sequence polymorphism systems after hematopoietic stem cell transplantation.

PubMed

Qin, Xiao-ying; Li, Guo-xuan; Qin, Ya-zhen; Wang, Yu; Wang, Feng-rong; Liu, Dai-hong; Xu, Lan-ping; Chen, Huan; Han, Wei; Wang, Jing-zhi; Zhang, Xiao-hui; Li, Jin-lan; Li, Ling-di; Liu, Kai-yan; Huang, Xiao-jun

2011-08-01

Analysis of changes in recipient and donor hematopoietic cell origin is extremely useful to monitor the effect of hematopoietic stem cell transplantation (HSCT) and sequential adoptive immunotherapy by donor lymphocyte infusions. We developed a sensitive, reliable and rapid real-time PCR method based on sequence polymorphism systems to quantitatively assess the hematopoietic chimerism after HSCT. A panel of 29 selected sequence polymorphism (SP) markers was screened by real-time PCR in 101 HSCT patients with leukemia and other hematological diseases. The chimerism kinetics of bone marrow samples of 8 HSCT patients in remission and relapse situations were followed longitudinally. Recipient genotype discrimination was possible in 97.0% (98 of 101) with a mean number of 2.5 (1-7) informative markers per recipient/donor pair. Using serial dilutions of plasmids containing specific SP markers, the linear correlation (r) of 0.99, the slope between -3.2 and -3.7 and the sensitivity of 0.1% were proved reproducible. By this method, it was possible to very accurately detect autologous signals in the range from 0.1% to 30%. The accuracy of the method in the very important range of autologous signals below 5% was extraordinarily high (standard deviation <1.85%), which might significantly improve detection accuracy of changes in autologous signals early in the post-transplantation course of follow-up. The main advantage of the real-time PCR method over short tandem repeat PCR chimerism assays is the absence of PCR competition and plateau biases, with demonstrated greater sensitivity and linearity. Finally, we prospectively analyzed bone marrow samples of 8 patients who received allografts and presented the chimerism kinetics of remission and relapse situations that illustrated the sensitivity level and the promising clinical application of this method. This SP-based real-time PCR assay provides a rapid, sensitive, and accurate quantitative assessment of mixed chimerism that can be useful in predicting graft rejection and early relapse.

Kinetic and thermodynamic studies of AISI 4130 steel alloy corrosion in ethylene glycol-water mixture in presence of inhibitors

NASA Astrophysics Data System (ADS)

Khomami, M. Niknejad; Danaee, I.; Attar, A. A.; Peykari, M.

2013-05-01

The electrochemical behavior of steel alloy in ethylene glycol-water mixture was investigated by electrochemical methods. The results obtained showed that corrosion rate was decreased with increasing ethylene glycol concentration. The effect of inorganic inhibitors including NO3 -, NO2 -, Cr2O7 2- and CrO4 2- were studied using electrochemical techniques where the highest inhibition efficiency was obtained for CrO4 2-. In the presence of chromate the inhibitor efficiency increased with its concentration. The inhibiting effect of the chromate was explained on the basis of the competitive adsorption between the inorganic anions and the aggressive Cl- ions, and the adsorption isotherm basically obeys the Langmuir adsorption isotherm. Thermodynamic parameters for steel corrosion and inhibitor adsorption were determined and reveal that the adsorption process is spontaneous. Also, a phenomenon of both physical and chemical adsorption is proposed.

Removal of dissolved textile dyes from wastewater by a compost sorbent

USGS Publications Warehouse

Tsui, L.S.; Roy, W.R.; Cole, M.A.

2003-01-01

The objective of this study was to evaluate the potential for treating dye-contaminated waste streams by sorption using compost as a low-cost sorbent. A mature, thermophilic compost sample was used to sorb CI Acid Black 24, CI Acid Orange 74, CI Basic Blue 9, CI Basic Green 4, CI Direct Blue 71, CI Direct Orange 39, CI Reactive Orange 16 and CI Reactive Red 2 from solution using a batch-sorption method. With the exception of the two reactive dyes, the sorption kinetics were favourable for a continuous-flow treatment process with the compost-dye mixtures reaching a steady state within 3-5 h. Based on limited comparisons, the affinity of the compost for each dye appeared to be competitive with other non-activated carbon sorbents. The results suggest that additional research on using compost as a sorbent for dye-contaminated solutions is warranted.

Environmental controls on denitrifying communities and denitrification rates--Insights from molecular methods

USGS Publications Warehouse

Wallenstein, Matthew D.; Myrold, David D.; Firestone, Mary; Voytek, Mary

2006-01-01

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3− pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

Scavenging and recombination kinetics in a radiation spur: The successive ordered scavenging events

NASA Astrophysics Data System (ADS)

Al-Samra, Eyad H.; Green, Nicholas J. B.

2018-03-01

This study describes stochastic models to investigate the successive ordered scavenging events in a spur of four radicals, a model system based on a radiation spur. Three simulation models have been developed to obtain the probabilities of the ordered scavenging events: (i) a Monte Carlo random flight (RF) model, (ii) hybrid simulations in which the reaction rate coefficient is used to generate scavenging times for the radicals and (iii) the independent reaction times (IRT) method. The results of these simulations are found to be in agreement with one another. In addition, a detailed master equation treatment is also presented, and used to extract simulated rate coefficients of the ordered scavenging reactions from the RF simulations. These rate coefficients are transient, the rate coefficients obtained for subsequent reactions are effectively equal, and in reasonable agreement with the simple correction for competition effects that has recently been proposed.

A barrier-free atomic radical-molecule reaction: N (2D) NO2 (2A1) mechanistic study

NASA Astrophysics Data System (ADS)

Zuo, Ming-Hui; Liu, Hui-Ling; Huang, Xu-Ri; Zhan, Jin-Hui; Sun, Chia-Chung

The reaction of N (2D) radical with NO2 molecule has been studied theoretically using density functional theory and ab initio quantum chemistry method. Singlet electronic state [N2O2] potential energy surfaces (PES) are calculated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311+G(d) + ZPE and G3B3 levels of theory. All the involved transition states for generation of (2NO) and (O2 + N2) lie much lower than the reactants. Thus, the novel reaction N + NO2 can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction.

Self-assembled ultrathin nanotubes on diamond (100) surface

NASA Astrophysics Data System (ADS)

Lu, Shaohua; Wang, Yanchao; Liu, Hanyu; Miao, Mao-Sheng; Ma, Yanming

2014-04-01

Surfaces of semiconductors are crucially important for electronics, especially when the devices are reduced to the nanoscale. However, surface structures are often elusive, impeding greatly the engineering of devices. Here we develop an efficient method that can automatically explore the surface structures using structure swarm intelligence. Its application to a simple diamond (100) surface reveals an unexpected surface reconstruction featuring self-assembled carbon nanotubes arrays. Such a surface is energetically competitive with the known dimer structure under normal conditions, but it becomes more favourable under a small compressive strain or at high temperatures. The intriguing covalent bonding between neighbouring tubes creates a unique feature of carrier kinetics (that is, one dimensionality of hole states, while two dimensionality of electron states) that could lead to novel design of superior electronics. Our findings highlight that the surface plays vital roles in the fabrication of nanodevices by being a functional part of them.

A Springloaded Metal-Ligand Mesocate Allows Access to Trapped Intermediates of Self-Assembly.

PubMed

Bogie, Paul M; Holloway, Lauren R; Lyon, Yana; Onishi, Nicole C; Beran, Gregory J O; Julian, Ryan R; Hooley, Richard J

2018-04-02

A strained, "springloaded" Fe 2 L 3 iminopyridine mesocate shows highly variable reactivity upon postassembly reaction with competitive diamines. The strained assembly is reactive toward transimination in minutes at ambient temperature and allows observation of kinetically trapped intermediates in the self-assembly pathway. When diamines are used that can only form less favored cage products upon full equilibration, trapped ML 3 fragments with pendant, "hanging" NH 2 groups are selectively formed instead. Slight variations in diamine structure have large effects on the product outcome: less rigid diamines convert the mesocate to more favored self-assembled cage complexes under mild conditions and allow observation of heterocomplex intermediates in the displacement pathway. The mesocate allows control of equilibrium processes and direction of product outcomes via small, iterative changes in added subcomponent structure and provides a method of accessing metal-ligand cage structures not normally observed in multicomponent Fe-iminopyridine self-assembly.

A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation.

PubMed

Jesus, Catarina S H; Almeida, Zaida L; Vaz, Daniela C; Faria, Tiago Q; Brito, Rui M M

2016-08-31

Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer's and Parkinson's. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo.

A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation

PubMed Central

Jesus, Catarina S. H.; Almeida, Zaida L.; Vaz, Daniela C.; Faria, Tiago Q.; Brito, Rui M. M.

2016-01-01

Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer’s and Parkinson’s. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo. PMID:27589730

A Sensitive and Robust Enzyme Kinetic Experiment Using Microplates and Fluorogenic Ester Substrates

ERIC Educational Resources Information Center

Johnson, R. Jeremy; Hoops, Geoffrey C.; Savas, Christopher J.; Kartje, Zachary; Lavis, Luke D.

2015-01-01

Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein…

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method

NASA Astrophysics Data System (ADS)

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-01

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method.

PubMed

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-21

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Moller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol(-1). Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Existence, Uniqueness and Asymptotic Stability of Time Periodic Traveling Waves for a Periodic Lotka-Volterra Competition System with Diffusion

PubMed Central

Zhao, Guangyu; Ruan, Shigui

2011-01-01

We study the existence, uniqueness, and asymptotic stability of time periodic traveling wave solutions to a periodic diffusive Lotka-Volterra competition system. Under certain conditions, we prove that there exists a maximal wave speed c* such that for each wave speed c ≤ c*, there is a time periodic traveling wave connecting two semi-trivial periodic solutions of the corresponding kinetic system. It is shown that such a traveling wave is unique modulo translation and is monotone with respect to its co-moving frame coordinate. We also show that the traveling wave solutions with wave speed c < c* are asymptotically stable in certain sense. In addition, we establish the nonexistence of time periodic traveling waves for nonzero speed c > c*. PMID:21572575

Substrate specificity and kinetic properties of alpha-galactosidases from Vicia faba.

PubMed

Dey, P M; Pridham, J B

1969-10-01

1. The hydrolysis of a variety of galactosides and other glycosides by alpha-galactosidases I and II of Vicia faba was studied. 2. The effect of temperature on kinetic parameters was also examined. 3. Both enzymes are inhibited by excess of substrate (p-nitrophenyl alpha-d-galactoside); with enzyme I this is competitive and is caused by the galactosyl moiety. 4. Enzyme I is inhibited by oligosaccharides possessing terminal non-reducing galactose residues and to a smaller extent by l-arabinose and d-fucose. 5. The effect of pH on K(m) and V(max.) values suggests that carboxyl and imidazole groups are involved in the catalytic activity of enzyme I. 6. Photo-oxidation experiments with enzyme I also suggest that an imidazole group is present at the active site.

Evaluation of the effectiveness factor along immobilized enzyme fixed-bed reactors: design of a reactor with naringinase covalently immobilized into glycophase-coated porous glass

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

Manjon, A.; Iborra, J.L.; Gomez, J.L.

A design equation is presented for packed-bed reactors containing immobilized enzymes in spherical porous particles with internal diffusion effects and obeying reversible one-intermediate Michaelis-Menten kinetics. The equation is also able to explain irreversible and competitive product inhibition kinetics. It allows the axial substrate profiles to be calculated and the dependence of the effectiveness factor along the reactor length to be continuously evaluated. The design equation was applied to explain the behavior of naringinase immobilized in Glycophase-coated porous glass operating in a packed-bed reactor and hydrolyzing both p-nitrophenyl-alpha-L-rhamnoside and naringin. The theoretically predicted results were found to fit well with experimentallymore » measured values. (Refs. 28).« less

Combustor kinetic energy efficiency analysis of the hypersonic research engine data

NASA Astrophysics Data System (ADS)

Hoose, K. V.

1993-11-01

A one-dimensional method for measuring combustor performance is needed to facilitate design and development scramjet engines. A one-dimensional kinetic energy efficiency method is used for measuring inlet and nozzle performance. The objective of this investigation was to assess the use of kinetic energy efficiency as an indicator for scramjet combustor performance. A combustor kinetic energy efficiency analysis was performed on the Hypersonic Research Engine (HRE) data. The HRE data was chosen for this analysis due to its thorough documentation and availability. The combustor, inlet, and nozzle kinetic energy efficiency values were utilized to determine an overall engine kinetic energy efficiency. Finally, a kinetic energy effectiveness method was developed to eliminate thermochemical losses from the combustion of fuel and air. All calculated values exhibit consistency over the flight speed range. Effects from fuel injection, altitude, angle of attack, subsonic-supersonic combustion transition, and inlet spike position are shown and discussed. The results of analyzing the HRE data indicate that the kinetic energy efficiency method is effective as a measure of scramjet combustor performance.

On the relationship between competitive flow and FFT analysis of the flow waves in the left internal mammary artery graft in the process of CABG.

PubMed

Mao, Boyan; Wang, Wenxin; Zhao, Zhou; Zhao, Xi; Li, Lanlan; Zhang, Huixia; Liu, Youjun

2016-12-28

During coronary artery bypass grafting (CABG), the ratio of powers of the fundamental frequency and its first harmonic (F0/H1) in fast Fourier transformation (FFT) analysis of the graft's flow waves has been used in the field of evaluation of the patency in anastomosis. But there is no report about using the FFT method to evaluate the magnitude of competitive flow. This study is aiming at exploring the relationship between competitive flow and FFT analysis of the flow waves in left internal mammary artery (LIMA) graft, and finding a new method to evaluate the magnitude of competitive flow. At first, establishing the CABG multiscale models of different stenosis in left anterior descending artery (LAD) to get different magnitude of competitive flows. Then, calculating the models by ANSYS-CFX and getting the flow waves in LIMA. Finally, analyzing the flow waves by FFT method and comparing the FFT results with the magnitude of competitive flow. There is no relationship between competitive flow and F0/H1. As for F0/H2 and F0/H3, they both increase with the reduction of the stenosis in LAD. But the increase of F0/H3 is not obviously enough and it can't identify the significant competitive flow clearly, so it can't be used as the evaluation index. It is found that F0/H2 increases obviously with the increase of the competitive flow and can identify the significant competitive flow. The FFT method can be used in the evaluation of competitive flow and the F0/H2 is the ideal index. High F0/H2 refers to the significant competitive flow. This method can be used during CABG to avoid the risk of competitive flow.

Competition of Escherichia coli O157 with a drinking water bacterial community at low nutrient concentrations.

PubMed

Vital, Marius; Hammes, Frederik; Egli, Thomas

2012-12-01

In contrast to studies on (long-term) survival of enteric pathogens in the environment, investigations on the principles of their growth and competition with autochthonous aquatic bacteria are rare and unexplored. Hence, improved basic knowledge is crucial for an adequate risk assessment and for understanding (and avoiding) the spreading of waterborne diseases. Therefore, the pathogen Escherichia coli O157 was grown in competition with a drinking water bacterial community on natural assimilable organic carbon (AOC) originating from diluted wastewater, in both batch and continuous culture. Growth was monitored by flow cytometry enabling enumeration of total cell concentration as well as specific E. coli O157 detection using fluorescently-labelled antibodies. An enhanced competitive fitness of E. coli O157 with higher AOC concentrations, higher temperatures and increased dilution rates (continuous culture) was observed. A classical "opportunist" versus "gleaner" relationship, where E. coli O157 is the "opportunist", specialised for growth at high nutrient concentrations (μ(max): 0.87 h(-1) and K(s): 489 μg consumed DOC L(-1)), and the bacterial community is the "gleaner" adapted to nutrient-poor environments (μ(max): 0.33 h(-1) and K(s): 7.4 μg consumed DOC L(-1)) was found. The obtained competition results can be explained by the growth properties of the two competitors determined in pure cultures and it was possible to model many of the observed dynamics based on Monod kinetics. The study provides new insights into the principles governing competition of an enteric pathogen with autochthonous aquatic bacteria. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Relational Approach to Measuring Competition Among Hospitals

PubMed Central

Sohn, Min-Woong

2002-01-01

Objective To present a new, relational approach to measuring competition in hospital markets and to compare this relational approach with alternative methods of measuring competition. Data Sources The California Office of Statewide Health Planning and Development patient discharge abstracts and financial disclosure files for 1991. Study Design Patient discharge abstracts for an entire year were used to derive patient flows, which were combined to calculate the extent of overlap in patient pools for each pair of hospitals. This produces a cross-sectional measure of market competition among hospitals. Principal Findings The relational approach produces measures of competition between each and every pair of hospitals in the study sample, allowing us to examine a much more “local” as well as dyadic effect of competition. Preliminary analyses show the following: (1) Hospital markets are smaller than thought. (2) For-profit hospitals received considerably more competition from their neighbors than either nonprofit or government hospitals. (3) The size of a hospital does not matter in the amount of competition received, but the larger hospitals generated significantly more competition than smaller ones. Comparisons of this method to the other methods show considerable differences in identifying competitors, indicating that these methods are not as comparable as previously thought. Conclusion The relational approach measures competition in a more detailed way and allows researchers to conduct more fine-grained analyses of market competition. This approach allows one to model market structure in a manner that goes far beyond the traditional categories of monopoly, oligopoly, and perfect competition. It also opens up an entirely new range of analytic possibilities in examining the effect of competition on hospital performance, price of medical care, changes in the market, technology acquisition, and many other phenomena in the health care field. PMID:12036003

Product competitiveness analysis for e-commerce platform of special agricultural products

NASA Astrophysics Data System (ADS)

Wan, Fucheng; Ma, Ning; Yang, Dongwei; Xiong, Zhangyuan

2017-09-01

On the basis of analyzing the influence factors of the product competitiveness of the e-commerce platform of the special agricultural products and the characteristics of the analytical methods for the competitiveness of the special agricultural products, the price, the sales volume, the postage included service, the store reputation, the popularity, etc. were selected in this paper as the dimensionality for analyzing the competitiveness of the agricultural products, and the principal component factor analysis was taken as the competitiveness analysis method. Specifically, the web crawler was adopted to capture the information of various special agricultural products in the e-commerce platform ---- chi.taobao.com. Then, the original data captured thereby were preprocessed and MYSQL database was adopted to establish the information library for the special agricultural products. Then, the principal component factor analysis method was adopted to establish the analysis model for the competitiveness of the special agricultural products, and SPSS was adopted in the principal component factor analysis process to obtain the competitiveness evaluation factor system (support degree factor, price factor, service factor and evaluation factor) of the special agricultural products. Then, the linear regression method was adopted to establish the competitiveness index equation of the special agricultural products for estimating the competitiveness of the special agricultural products.

Automated Transition State Theory Calculations for High-Throughput Kinetics.

PubMed

Bhoorasingh, Pierre L; Slakman, Belinda L; Seyedzadeh Khanshan, Fariba; Cain, Jason Y; West, Richard H

2017-09-21

A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

Radio frequency heating: a potential method for post-harvest pest control in nuts and dry products

PubMed Central

Wang, Shao-jin; Tang, Ju-ming

2004-01-01

The multi-billion dollar US tree nut industries rely heavily on methyl bromide fumigation for postharvest insect control and are facing a major challenge with the mandated cessation by 2005 of its use for most applications. There is an urgent need to develop effective and economically viable alternative treatments to replace current phytosanitary and quarantine practices in order to maintain the competitiveness of US agriculture in domestic and international markets. With the reliable heating block system, the thermal death kinetics for fifth-instar codling moth, Indianmeal moth, and navel orangeworm were determined at a heating rate of 18 °C/min. A practical process protocol was developed to control the most heat resistant insect pest, fifth-instar navel orangeworm, in in-shell walnuts using a 27 MHz pilot scale radio frequency (RF) system. RF heating to 55 °C and holding in hot air for at least 5 min resulted in 100% mortality of the fifth-instar navel orangeworm. Rancidity, sensory qualities and shell characteristics were not affected by the treatments. If this method can be economically integrated into the handling process, it should have excellent potential as a disinfestation method for in-shell walnuts. PMID:15362185

Comparative kinetic analysis on thermal degradation of some cephalosporins using TG and DSC data

PubMed Central

2013-01-01

Background The thermal decomposition of cephalexine, cefadroxil and cefoperazone under non-isothermal conditions using the TG, respectively DSC methods, was studied. In case of TG, a hyphenated technique, including EGA, was used. Results The kinetic analysis was performed using the TG and DSC data in air for the first step of cephalosporin’s decomposition at four heating rates. The both TG and DSC data were processed according to an appropriate strategy to the following kinetic methods: Kissinger-Akahira-Sunose, Friedman, and NPK, in order to obtain realistic kinetic parameters, even if the decomposition process is a complex one. The EGA data offer some valuable indications about a possible decomposition mechanism. The obtained data indicate a rather good agreement between the activation energy’s values obtained by different methods, whereas the EGA data and the chemical structures give a possible explanation of the observed differences on the thermal stability. A complete kinetic analysis needs a data processing strategy using two or more methods, but the kinetic methods must also be applied to the different types of experimental data (TG and DSC). Conclusion The simultaneous use of DSC and TG data for the kinetic analysis coupled with evolved gas analysis (EGA) provided us a more complete picture of the degradation of the three cephalosporins. It was possible to estimate kinetic parameters by using three different kinetic methods and this allowed us to compare the Ea values obtained from different experimental data, TG and DSC. The thermodegradation being a complex process, the both differential and integral methods based on the single step hypothesis are inadequate for obtaining believable kinetic parameters. Only the modified NPK method allowed an objective separation of the temperature, respective conversion influence on the reaction rate and in the same time to ascertain the existence of two simultaneous steps. PMID:23594763

Inhibition of Cell Wall-Associated Enzymes in Vitro and in Vivo with Sugar Analogs

PubMed Central

Nagahashi, Gerald; Tu, Shu-I; Fleet, George; Namgoong, Sun K.

1990-01-01

Sugar analogs were used to study the inhibition of cell wall-associated glycosidases in vitro and in vivo. For in vitro characterization, cell walls were highly purified from corn (Zea mays L.) root cortical cells and methods were developed to assay enzyme activity in situ. Inhibitor dependence curves, mode of inhibition, and specificity were determined for three sugar analogs. At low concentrations of castanospermine (CAS), 2-acetamido-1,5-imino-1,2,5-trideoxy-d-glucitol, and swainsonine, these inhibitors showed competitive inhibition kinetics with β-glucosidase, β-GIcNAcase, and α-mannosidase, respectively. Swainsonine specifically inhibited α-mannosidase activity, and 2-acetamido-1,5-imino-1,2,5-trideoxy-d-glucitol specifically inhibited β-N-acetyl-hexosamindase activity. However, CAS inhibited a broad spectrum of cell wall-associated enzymes. When the sugar analogs were applied to 2 day old corn seedlings, only CAS caused considerable changes in root growth and development. To ensure that the concentration of inhibitors used in vitro also inhibited enzyme activity in vivo, an in vivo method for measuring cell wall-associated activity was devised. PMID:16667291

Effect of Nonlinearity in Hybrid Kinetic Monte Carlo-Continuum Models

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

Balter, Ariel I.; Lin, Guang; Tartakovsky, Alexandre M.

2012-04-23

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a KMC model for a surface to a finite difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and also show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition/dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition/dissolution model including competitive adsorption, which leadsmore » to a nonlinear rate, and show that, in this case, the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.« less

Competition: how hypnosis can help women to hold their own in the workplace.

PubMed

Hornyak, Lynne M

2004-07-01

This paper takes the perspective that competitive strivings in self and others have been an area of difficulty for women and that gender socialization has played a significant role. The author discusses elements of competition that seem toxic for women and proposes descriptors of healthy competition. It is proposed that hypnosis provides a suitable method for neutralizing negative elements and promoting adaptive responses in competitive situations. Five applications of hypnotic methods are illustrated through two case examples.

Atomistic to Continuum Multiscale and Multiphysics Simulation of NiTi Shape Memory Alloy

NASA Astrophysics Data System (ADS)

Gur, Sourav

Shape memory alloys (SMAs) are materials that show reversible, thermo-elastic, diffusionless, displacive (solid to solid) phase transformation, due to the application of temperature and/ or stress (/strain). Among different SMAs, NiTi is a popular one. NiTi shows reversible phase transformation, the shape memory effect (SME), where irreversible deformations are recovered upon heating, and superelasticity (SE), where large strains imposed at high enough temperatures are fully recovered. Phase transformation process in NiTi SMA is a very complex process that involves the competition between developed internal strain and phonon dispersion instability. In NiTi SMA, phase transformation occurs over a wide range of temperature and/ or stress (strain) which involves, evolution of different crystalline phases (cubic austenite i.e. B2, different monoclinic variant of martensite i.e. B19', and orthorhombic B19 or BCO structures). Further, it is observed from experimental and computational studies that the evolution kinetics and growth rate of different phases in NiTi SMA vary significantly over a wide spectrum of spatio-temporal scales, especially with length scales. At nano-meter length scale, phase transformation temperatures, critical transformation stress (or strain) and phase fraction evolution change significantly with sample or simulation cell size and grain size. Even, below a critical length scale, the phase transformation process stops. All these aspects make NiTi SMA very interesting to the science and engineering research community and in this context, the present focuses on the following aspects. At first this study address the stability, evolution and growth kinetics of different phases (B2 and variants of B19'), at different length scales, starting from the atomic level and ending at the continuum macroscopic level. The effects of simulation cell size, grain size, and presence of free surface and grain boundary on the phase transformation process (transformation temperature, phase fraction evolution kinetics due to temperature) are also demonstrated herein. Next, to couple and transfer the statistical information of length scale dependent phase transformation process, multiscale/ multiphysics methods are used. Here, the computational difficulty from the fact that the representative governing equations (i.e. different sub-methods such as molecular dynamics simulations, phase field simulations and continuum level constitutive/ material models) are only valid or can be implemented over a range of spatiotemporal scales. Therefore, in the present study, a wavelet based multiscale coupling method is used, where simulation results (phase fraction evolution kinetics) from different sub-methods are linked via concurrent multiscale coupling fashion. Finally, these multiscale/ multiphysics simulation results are used to develop/ modify the macro/ continuum scale thermo-mechanical constitutive relations for NiTi SMA. Finally, the improved material model is used to model new devices, such as thermal diodes and smart dampers.

Competitive folding of RNA structures at a termination–antitermination site

PubMed Central

Ait-Bara, Soraya; Clerté, Caroline; Declerck, Nathalie; Margeat, Emmanuel

2017-01-01

Antitermination is a regulatory process based on the competitive folding of terminator–antiterminator structures that can form in the leader region of nascent transcripts. In the case of the Bacillus subtilis licS gene involved in β-glucosides utilization, the binding of the antitermination protein LicT to a short RNA hairpin (RAT) prevents the formation of an overlapping terminator and thereby allows transcription to proceed. Here, we monitored in vitro the competition between termination and antitermination by combining bulk and single-molecule fluorescence-based assays using labeled RNA oligonucleotide constructs of increasing length that mimic the progressive transcription of the terminator invading the antiterminator hairpin. Although high affinity binding is abolished as soon as the antiterminator basal stem is disrupted by the invading terminator, LicT can still bind and promote closing of the partially unfolded RAT hairpin. However, binding no longer occurs once the antiterminator structure has been disrupted by the full-length terminator. Based on these findings, we propose a kinetic competition model for the sequential events taking place at the termination–antitermination site, where LicT needs to capture its RAT target before completion of the terminator to remain tightly bound during RNAP pausing, before finally dissociating irreversibly from the elongated licS transcript. PMID:28235843

Kinetics of the phosphotransferase reaction of the catalytic subunit of the tick salivary gland cAMP-dependent protein kinase

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

Mane, S.D.; Essenberg, R.C.; Sauer, J.R.

1986-05-01

The catalytic subunit of the cAMP dependent protein kinase was purified 100-fold from tick salivary glands. The enzyme mechanism of the phosphotransferase reaction catalyzed by this subunit was investigated. Highly purified enzyme did not show ATP-ase activity in the absence of protein substrates. Initial velocities were measured using histone H-1 or a synthetic heptapeptide, Kemptide, as P/sub i/ acceptors and (..gamma..-/sup 32/P) ATP as a phosphodonor. Patterns were consistent with a sequential, but not a ping pong mechanism. At high concentration (>2Km), histone showed substrate inhibition which was noncompetitive versus ATP. Product inhibition by Mg.ADP was competitive versus ATP andmore » noncompetitive with respect to H-1. Phosphohistone on the other hand was noncompetitive with respect to H-1, but gave parabolic competitive inhibition against ATP. Dead-end inhibition by AMP-PNP, an analogue of ATP, was competitive and noncompetitive against ATP and H-1, respectively. The inhibitory of cAMP dependent protein kinase was noncompetitive with ATP and competitive with histone. These studies strongly suggest that the tick salivary gland protein kinase has a sequential mechanism with primarily ordered addition of ATP followed by protein substrate and ordered release of phosphoprotein and ADP, but some random character.« less

Measuring the Indonesian provinces competitiveness by using PCA technique

NASA Astrophysics Data System (ADS)

Runita, Ditha; Fajriyah, Rohmatul

2017-12-01

Indonesia is a country which has vast teritoty. It has 34 provinces. Building local competitiveness is critical to enhance the long-term national competitiveness especially for a country as diverse as Indonesia. A competitive local government can attract and maintain successful firms and increase living standards for its inhabitants, because investment and skilled workers gravitate from uncompetitive regions to more competitive ones. Altough there are other methods to measuring competitiveness, but here we have demonstrated a simple method using principal component analysis (PCA). It can directly be applied to correlated, multivariate data. The analysis on Indonesian provinces provides 3 clusters based on the competitiveness measurement and the clusters are Bad, Good and Best perform provinces.

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

DeTuri, V.F.; Ervin, K.M.

Energy-resolved competitive collision-induced dissociation methods are used to measure the gas-phase acidities of a series of alcohols (methanol, ethanol, 2-propanol, and 2-methyl-2-propanol). The competitive dissociation reactions of fluoride-alcohol, [F{sup {minus}}{center{underscore}dot}HOR], alkoxide-water, [RO{sup {minus}}{center{underscore}dot}HOH], and alkoxide-methanol [RO{+-}{center{underscore}dot}HOCH{sub 3}] proton-bound complexes are studied using a guided ion beam tandem mass spectrometer. The reaction cross sections and product branching fractions to the two proton transfer channels are measured as a function of collision energy. The enthalpy difference between the two product channels is found by modeling the reaction cross sections near threshold using RRKM theory to account for the energy-dependent product branching ratiomore » and kinetic shift. From the enthalpy difference, the alcohol gas-phase acidities are determined relative to the well-known values of HF and H{sub 2}O. The measured gas-phase acidities are {Delta}{sub acid}H{sub 298}(CH{sub 3}OH) = 1599 {+-} 3 kJ/mol, {Delta}{sub acid}H{sub 298}(CH{sub 3}CH{sub 2}OH) = 1586 {+-} 5 kJ/mol, {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 2}CHOH) = 1576 {+-} 4 kJ/mol, and {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 3}COH) = 1573 {+-} 3 kJ/mol.« less

Consistency of kinematic and kinetic patterns during a prolonged spell of cricket fast bowling: an exploratory laboratory study.

PubMed

Schaefer, Andrew; O'dwyer, Nicholas; Ferdinands, René E D; Edwards, Suzi

2018-03-01

Due to the high incidence of lumbar spine injury in fast bowlers, international cricket organisations advocate limits on workload for bowlers under 19 years of age in training/matches. The purpose of this study was to determine whether significant changes in either fast bowling technique or movement variability could be detected throughout a 10-over bowling spell that exceeded the recommended limit. Twenty-five junior male fast bowlers bowled at competition pace while three-dimensional kinematic and kinetic data were collected for the leading leg, trunk and bowling arm. Separate analyses for the mean and within-participant standard deviation of each variable were performed using repeated measures factorial analyses of variance and computation of effect sizes. No substantial changes were observed in mean values or variability of any kinematic, kinetic or performance variables, which instead revealed a high degree of consistency in kinematic and kinetic patterns. Therefore, the suggestion that exceeding the workload limit per spell causes technique- and loading-related changes associated with lumbar injury risk is not valid and cannot be used to justify the restriction of bowling workload. For injury prevention, the focus instead should be on the long-term effect of repeated spells and on the fast bowling technique itself.

Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle▿

PubMed Central

Bourne, Christina; Lee, Sejin; Venkataiah, Bollu; Lee, Angela; Korba, Brent; Finn, M. G.; Zlotnick, Adam

2008-01-01

The relationship between the physical chemistry and biology of self-assembly is poorly understood, but it will be critical to quantitatively understand infection and for the design of antivirals that target virus genesis. Here we take advantage of heteroaryldihydropyrimidines (HAPs), which affect hepatitis B virus (HBV) assembly, to gain insight and correlate in vitro assembly with HBV replication in culture. Based on a low-resolution crystal structure of a capsid-HAP complex, a closely related series of HAPs were designed and synthesized. These differentially strengthen the association between neighboring capsid proteins, alter the kinetics of assembly, and give rise to aberrant structures incompatible with a functional capsid. The chemical nature of the HAP variants correlated well with the structure of the HAP binding pocket. The thermodynamics and kinetics of in vitro assembly had strong and predictable effects on product morphology. However, only the kinetics of in vitro assembly had a strong correlation with inhibition of HBV replication in HepG2.2.15 cells; there was at best a weak correlation between assembly thermodynamics and replication. The correlation between assembly kinetics and virus suppression implies a competition between successful assembly and misassembly, small molecule induced or otherwise. This is a predictive and testable model for the mechanism of action of assembly effectors. PMID:18684823

Ranking nano-enabled hybrid media for simultaneous removal of contaminants with different chemistries: Pseudo-equilibrium sorption tests versus column tests.

PubMed

Custodio, Tomas; Garcia, Jose; Markovski, Jasmina; McKay Gifford, James; Hristovski, Kiril D; Olson, Larry W

2017-12-15

The underlying hypothesis of this study was that pseudo-equilibrium and column testing conditions would provide the same sorbent ranking trends although the values of sorbents' performance descriptors (e.g. sorption capacity) may vary because of different kinetics and competition effects induced by the two testing approaches. To address this hypothesis, nano-enabled hybrid media were fabricated and its removal performances were assessed for two model contaminants under multi-point batch pseudo-equilibrium and continuous-flow conditions. Calculation of simultaneous removal capacity indices (SRC) demonstrated that the more resource demanding continuous-flow tests are able to generate the same performance rankings as the ones obtained by conducing the simpler pseudo-equilibrium tests. Furthermore, continuous overlap between the 98% confidence boundaries for each SRC index trend, not only validated the hypothesis that both testing conditions provide the same ranking trends, but also pointed that SRC indices are statistically the same for each media, regardless of employed method. In scenarios where rapid screening of new media is required to obtain the best performing synthesis formulation, use of pseudo-equilibrium tests proved to be reliable. Considering that kinetics induced effects on sorption capacity must not be neglected, more resource demanding column test could be conducted only with the top performing media that exhibit the highest sorption capacity. Copyright © 2017 Elsevier B.V. All rights reserved.

Direct Measurements of Gas/Particle Partitioning and Mass Accommodation Coefficients in Environmental Chambers.

PubMed

Krechmer, Jordan E; Day, Douglas A; Ziemann, Paul J; Jimenez, Jose L

2017-10-17

Secondary organic aerosols (SOA) are a major contributor to fine particulate mass and wield substantial influences on the Earth's climate and human health. Despite extensive research in recent years, many of the fundamental processes of SOA formation and evolution remain poorly understood. Most atmospheric aerosol models use gas/particle equilibrium partitioning theory as a default treatment of gas-aerosol transfer, despite questions about potentially large kinetic effects. We have conducted fundamental SOA formation experiments in a Teflon environmental chamber using a novel method. A simple chemical system produces a very fast burst of low-volatility gas-phase products, which are competitively taken up by liquid organic seed particles and Teflon chamber walls. Clear changes in the species time evolution with differing amounts of seed allow us to quantify the particle uptake processes. We reproduce gas- and aerosol-phase observations using a kinetic box model, from which we quantify the aerosol mass accommodation coefficient (α) as 0.7 on average, with values near unity especially for low volatility species. α appears to decrease as volatility increases. α has historically been a very difficult parameter to measure with reported values varying over 3 orders of magnitude. We use the experimentally constrained model to evaluate the correction factor (Φ) needed for chamber SOA mass yields due to losses of vapors to walls as a function of species volatility and particle condensational sink. Φ ranges from 1-4.

Cholecystokinin octa- and tetrapeptide degradation by synaptic membranes. I. Evidence for competition with enkephalins for in vitro common degradation pathways.

PubMed

Deschodt-Lanckman, M; Bui, N D

1981-01-01

Degradation of CCK-4 and -8 by purified synaptic membranes was followed by measuring the fluorescence of tryptophan released from the peptides after separation of degradation products by HPLC. For enkephalins and related fragments, the release of tyrosine was monitored using the same method. Kinetics of hydrolysis of CCK-like peptides indicated a rapid processing of CCK-4 and a slower breakdown of CCK-8 (with a greater resistance of the sulfated form of CCK-8 as compared to the unsulfated peptide). Leu- and met-enkephalins were degraded at the same rate while their N-terminal tri- and dipeptides were hydrolysed more slowly. When CCK-4 or CCK-8 were incubated in the presence of leu-enkephalin, a dose-dependent inhibition of the release of tryptophan was observed. Enkaphalin fragments do not modify the kinetics of degradation of CCK-4. The degradation of leu-enkephalin was inhibited in a dose-dependent manner by the presence of CCK-related peptides in the medium. After solubilization of membrane-bound enzymes by Triton X-100 followed by chromatography on DEAE cellulose, five peaks of CCK-4 degrading activity were detected (two minor and three major peaks). With enkephalin as substrate, five peaks were also observed; the three major activities were the same as those detected for CCK-4.

Towards ultra-fast solvent evaporation, the development of a computer controlled solvent vapor annealing chamber

NASA Astrophysics Data System (ADS)

Nelson, Gunnar; Wong, J.; Drapes, C.; Grant, M.; Baruth, A.

Despite the promise of cheap and fast nanoscale ordering of block polymer thin films via solvent vapor annealing, a standardized, scalable production scheme remains elusive. Solvent vapor annealing exposes a nano-thin film to the vapors of one or more solvents with the goal of forming a swollen and mobile state to direct the self-assembly process by tuning surface energies and mediating unfavorable chain interactions. We have shown that optimized annealing conditions, where kinetic and thermal properties for crystal growth are extremely fast (<1s), exist at solvent concentrations just below the order-disorder transition of the film. However, when investigating the propagation of a given morphology into the bulk of a film during drying, the role of solvent evaporation comes under great scrutiny. During this process, the film undergoes a competition between two fronts; phase separation and kinetic trapping. Recent results in both theory and experiment point toward this critical element in controlling the resultant morphologies; however, no current method includes a controllable solvent evaporation rate at ultra-fast time scales. We report on a computer-controlled, pneumatically actuated chamber that provides control over solvent evaporation down to 15 ms. Furthermore, in situ spectral reflectance monitors solvent concentration with 10 ms temporal resolution and reveals several possible evaporation trajectories, ranging from linear to exponential to logarithmic. Funded by Dr. Randolph Ferlic Summer Research Scholarship and NASA Nebraska Space Grant.

Analysis of oxidative stress biomarkers using a simultaneous competitive/non-competitive micromosaic immunoassay.

PubMed

Murphy, Brian M; Dandy, David S; Henry, Charles S

2009-04-27

Immunoassays represent a core workhorse methodology for many applications ranging from clinical diagnostics to environmental monitoring. In traditional formats such as the enzyme linked immunosorbent assay (ELISA), analytes are measured singly or in small sets. As more biomarkers are identified for disease states, there is a need to develop methods that can measure multiple markers simultaneously. Immunoaffinity arrays are one such chemistry that can achieve multi-marker screening. Most arrays are performed in either competitive or non-competitive formats, where the former are used predominantly for small molecules and the later for macromolecules. To date, ELISA and immunoaffinity array methods have relied exclusively on one of these formats and not the other. Here an immunoaffinity array method capable of performing simultaneous competitive and non-competitive analysis generated using micromosaic immunoassay techniques is introduced for the analysis of metabolites and proteins. In this report, three markers of oxidative stress were used as a model system. The method described here demonstrates the simultaneous analysis of 3-nitrotyrosine, by indirect competitive immunoassay while the enzymes catalase and superoxide dismutase are analyzed by non-competitive sandwich immunoassay. The method requires less than 1 microL sample and 45 min for completion. Logistic curve fits and LOD (limits of detection) statistical analysis of the binding results are presented and show good agreement with published data for these antibody-antigen systems.

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.

Mixing effects on the kinetics and the dynamics of two-phase enzymatic hydrolysis of hemicellulose for biofuel production.

PubMed

Dutta, Sajal Kanti; Chakraborty, Saikat

2018-07-01

This work uses a coupled experimental and modeling approach to explore the effects of macro- and micro-mixing on the kinetics and the dynamics of two-phase enzymatic hydrolysis of hemicellulose. Reactor mixing does not alter the non-competitive nature of product inhibition in hemicellulose hydrolysis by endoxylanase, but produces stronger inhibition that reduces the soluble sugar yield by 8-14.5%, as the mixing speed increases from 0 to 200 rpm. The kinetic constants (K m , V max , K x ) assume mass-transfer disguised values at 0-200 rpm. An optimal mixing strategy, comprising of 55-70 min of initial rapid convective macromixing followed by diffusive micromixing (without any macromixing) for the rest of the hydrolysis, increases xylose and reducing sugar yields by 6.3-8% and 13-20%, respectively, over continuous mixing at 200 rpm, for 1-5 mg/ml substrate loading at an optimum enzyme to substrate ratio of 1:20, with an energy saving of 94-96% over 24 h. Copyright © 2018 Elsevier Ltd. All rights reserved.

Exploring between the extremes: conversion-dependent kinetics of phosphite-modified hydroformylation catalysis.

PubMed

Kubis, Christoph; Selent, Detlef; Sawall, Mathias; Ludwig, Ralf; Neymeyr, Klaus; Baumann, Wolfgang; Franke, Robert; Börner, Armin

2012-07-09

The kinetics of the hydroformylation of 3,3-dimethyl-1-butene with a rhodium monophosphite catalyst has been studied in detail. Time-dependent concentration profiles covering the entire olefin conversion range were derived from in situ high-pressure FTIR spectroscopic data for both, pure organic components and catalytic intermediates. These profiles fit to Michaelis-Menten-type kinetics with competitive and uncompetitive side reactions involved. The characteristics found for the influence of the hydrogen concentration verify that the pre-equilibrium towards the catalyst substrate complex is not established. It has been proven experimentally that the hydrogenolysis of the intermediate acyl complex remains rate limiting even at high conversions when the rhodium hydride is the predominant resting state and the reaction is nearly of first order with respect to the olefin. Results from in situ FTIR and high-pressure (HP) NMR spectroscopy and from DFT calculations support the coordination of only one phosphite ligand in the dominating intermediates and a preferred axial position of the phosphite in the electronically saturated, trigonal bipyramidal (tbp)-structured acyl rhodium complex. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An expedient synthesis of N-(1-(5-mercapto-4-((substituted benzylidene)amino)-4H-1,2,4-triazol-3-yl)-2-phenylethyl)benzamides as jack bean urease inhibitors and free radical scavengers: Kinetic mechanism and molecular docking studies.

PubMed

Saeed, Aamer; Larik, Fayaz Ali; Channar, Pervaiz Ali; Mehfooz, Haroon; Ashraf, Mohammad Haseeb; Abbas, Qamar; Hassan, Mubashir; Seo, Sung-Yum

2017-11-01

In this study, some new azomethine-triazole hybrids 5a-5l derived from N-benzoyl-L-phenylalanine were synthesized and characterized. The synthesized compounds showed first-rate, urease inhibition, and compounds 5c and 5e were found to be most effective inhibitors with 0.0137 ± 0.00082 μm and 0.0183 ± 0.00068 μm, respectively (thiourea 15.151 ± 1.27 μm). The kinetic mechanism of urease inhibition revealed the compounds 5c and 5e to be non-competitive inhibitors, whereas compounds 5d and 5j were found to be of mixed-type inhibitors. Docking studies also indicated better interaction patterns with urease enzyme. The results of enzyme inhibition, kinetic mechanism and molecular docking suggest that these compounds can serve as lead compounds in the design of more effective urease inhibitors. © 2017 John Wiley & Sons A/S.

Discussion of the Investigation Method on the Reaction Kinetics of Metallurgical Reaction Engineering

NASA Astrophysics Data System (ADS)

Du, Ruiling; Wu, Keng; Zhang, Jiazhi; Zhao, Yong

Reaction kinetics of metallurgical physical chemistry which was successfully applied in metallurgy (as ferrous metallurgy, non-ferrous metallurgy) became an important theoretical foundation for subject system of traditional metallurgy. Not only the research methods were very perfect, but also the independent structures and systems of it had been formed. One of the important tasks of metallurgical reaction engineering was the simulation of metallurgical process. And then, the mechanism of reaction process and the conversion time points of different control links should be obtained accurately. Therefore, the research methods and results of reaction kinetics in metallurgical physical chemistry were not very suitable for metallurgical reaction engineering. In order to provide the definite conditions of transmission, reaction kinetics parameters and the conversion time points of different control links for solving the transmission and reaction equations in metallurgical reaction engineering, a new method for researching kinetics mechanisms in metallurgical reaction engineering was proposed, which was named stepwise attempt method. Then the comparison of results between the two methods and the further development of stepwise attempt method were discussed in this paper. As a new research method for reaction kinetics in metallurgical reaction engineering, stepwise attempt method could not only satisfy the development of metallurgical reaction engineering, but also provide necessary guarantees for establishing its independent subject system.

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance

NASA Astrophysics Data System (ADS)

Kuzyakov, Yakov; Xu, Xingliang

2014-05-01

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 15N-labelling studies that investigated 15N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on Km (Michaelis constant) and Vmax (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower Km values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (Vmax) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms.

Long-term competition between sulfate reducing and methanogenic bacteria in UASB reactors treating volatile fatty acids.

PubMed

Omil, F; Lens, P; Visser, A; Hulshoff Pol, L W; Lettinga, G

1998-03-20

The competition between acetate utilizing methane-producing bacteria (MB) and sulfate-reducing bacteria (SRB) was studied in mesophilic (30 degrees C) upflow anaerobic sludge bed (UASB) reactors (upward velocity 1 m h-1; pH 8) treating volatile fatty acids and sulfate. The UASB reactors treated a VFA mixture (with an acetate:propionate:butyrate ratio of 5:3:2 on COD basis) or acetate as the sole substrate at different COD:sulfate ratios. The outcome of the competition was evaluated in terms of conversion rates and specific methanogenic and sulfidogenic activities. The COD:sulfate ratio was a key factor in the partitioning of acetate utilization between MB and SRB. In excess of sulfate (COD:sulfate ratio lower than 0.67), SRB became predominant over MB after prolonged reactor operation: 250 and 400 days were required to increase the amount of acetate used by SRB from 50 to 90% in the reactor treating, respectively, the VFA mixture or acetate as the sole substrate. The competition for acetate was further studied by dynamic simulations using a mathematical model based on the Monod kinetic parameters of acetate utilizing SRB and MB. The simulations confirmed the long term nature of the competition between these acetotrophs. A high reactor pH (+/-8), a short solid retention time (<150 days), and the presence of a substantial SRB population in the inoculum may considerably reduce the time required for acetate-utilising SRB to outcompete MB. Copyright 1998 John Wiley & Sons, Inc.

A gas-kinetic BGK scheme for the compressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Xu, Kun

2000-01-01

This paper presents an improved gas-kinetic scheme based on the Bhatnagar-Gross-Krook (BGK) model for the compressible Navier-Stokes equations. The current method extends the previous gas-kinetic Navier-Stokes solver developed by Xu and Prendergast by implementing a general nonequilibrium state to represent the gas distribution function at the beginning of each time step. As a result, the requirement in the previous scheme, such as the particle collision time being less than the time step for the validity of the BGK Navier-Stokes solution, is removed. Therefore, the applicable regime of the current method is much enlarged and the Navier-Stokes solution can be obtained accurately regardless of the ratio between the collision time and the time step. The gas-kinetic Navier-Stokes solver developed by Chou and Baganoff is the limiting case of the current method, and it is valid only under such a limiting condition. Also, in this paper, the appropriate implementation of boundary condition for the kinetic scheme, different kinetic limiting cases, and the Prandtl number fix are presented. The connection among artificial dissipative central schemes, Godunov-type schemes, and the gas-kinetic BGK method is discussed. Many numerical tests are included to validate the current method.

Self-Consistent Kinetic Theory of Stochasticity.

DTIC Science & Technology

1979-08-01

induced contractions. The results indicated that there is a minor contaminant in yel l ow HC— 3 other than deanol which was a potent inhibitor of...pectively (Fi g. 2). Also , the wh i te HC-3 was a competitive inhibitor of AChE (Fig. 3), whereas the yellow HC-3 was a mixed—type inhibitor. Deanol ...by yellow HC-3 recrystallized one time from boiling methanol fell in between the white and yellow commercial samples (Fig. 1). Deanol has been

Development of Bicarbonate-Activated Peroxide as a Chemical and Biological Warfare Agent Decontaminant

DTIC Science & Technology

2006-06-30

may operate for certain substrates. The reaction of equation 1 proceeds with the intermediacy of CO2 as shown in Figure 1. Although it is well...competition between paths 5 and 6 will depend on the conditions and the nature of the substrate S. Note that figures, equations , etc. in the...1 shows the complete reaction scheme used to model the equilibration reaction at low temperature. Table 1 Kinetic equations and their

Individual and competitive adsorption of phenol and nickel onto multiwalled carbon nanotubes

PubMed Central

Abdel-Ghani, Nour T.; El-Chaghaby, Ghadir A.; Helal, Farag S.

2014-01-01

Individual and competitive adsorption studies were carried out to investigate the removal of phenol and nickel ions by adsorption onto multiwalled carbon nanotubes (MWCNTs). The carbon nanotubes were characterized by different techniques such as X-ray diffraction, scanning electron microscopy, thermal analysis and Fourier transformation infrared spectroscopy. The different experimental conditions affecting the adsorption process were investigated. Kinetics and equilibrium models were tested for fitting the adsorption experimental data. The characterization experimental results proved that the studied adsorbent possess different surface functional groups as well as typical morphological features. The batch experiments revealed that 300 min of contact time was enough to achieve equilibrium for the adsorption of both phenol and nickel at an initial adsorbate concentration of 25 mg/l, an adsorbent dosage of 5 g/l, and a solution pH of 7. The adsorption of phenol and nickel by MWCNTs followed the pseudo-second order kinetic model and the intraparticle diffusion model was quite good in describing the adsorption mechanism. The Langmuir equilibrium model fitted well the experimental data indicating the homogeneity of the adsorbent surface sites. The maximum Langmuir adsorption capacities were found to be 32.23 and 6.09 mg/g, for phenol and Ni ions, respectively. The removal efficiency of MWCNTs for nickel ions or phenol in real wastewater samples at the optimum conditions reached up to 60% and 70%, respectively. PMID:26257938

Effect of herbicide resistance endowing Ile-1781-Leu and Asp-2078-Gly ACCase gene mutations on ACCase kinetics and growth traits in Lolium rigidum

PubMed Central

Vila-Aiub, Martin M.; Yu, Qin; Han, Heping; Powles, Stephen B.

2015-01-01

The rate of herbicide resistance evolution in plants depends on fitness traits endowed by alleles in both the presence and absence (resistance cost) of herbicide selection. The effect of two Lolium rigidum spontaneous homozygous target-site resistance-endowing mutations (Ile-1781-Leu, Asp-2078-Gly) on both ACCase activity and various plant growth traits have been investigated here. Relative growth rate (RGR) and components (net assimilation rate, leaf area ratio), resource allocation to different organs, and growth responses in competition with a wheat crop were assessed. Unlike plants carrying the Ile-1781-Leu resistance mutation, plants homozygous for the Asp-2078-Gly mutation exhibited a significantly lower RGR (30%), which translated into lower allocation of biomass to roots, shoots, and leaves, and poor responses to plant competition. Both the negligible and significant growth reductions associated, respectively, with the Ile-1781-Leu and Asp-2078-Gly resistance mutations correlated with their impact on ACCase activity. Whereas the Ile-1781-Leu mutation showed no pleiotropic effects on ACCase kinetics, the Asp-2078-Gly mutation led to a significant reduction in ACCase activity. The impaired growth traits are discussed in the context of resistance costs and the effects of each resistance allele on ACCase activity. Similar effects of these two particular ACCase mutations on the ACCase activity of Alopecurus myosuroides were also confirmed. PMID:26019257

Quantitative in vivo fluorescence cross-correlation analyses highlight the importance of competitive effects in the regulation of protein-protein interactions.

PubMed

Sadaie, Wakako; Harada, Yoshie; Matsuda, Michiyuki; Aoki, Kazuhiro

2014-09-01

Computer-assisted simulation is a promising approach for clarifying complicated signaling networks. However, this approach is currently limited by a deficiency of kinetic parameters determined in living cells. To overcome this problem, we applied fluorescence cross-correlation spectrometry (FCCS) to measure dissociation constant (Kd) values of signaling molecule complexes in living cells (in vivo Kd). Among the pairs of fluorescent molecules tested, that of monomerized enhanced green fluorescent protein (mEGFP) and HaloTag-tetramethylrhodamine was most suitable for the measurement of in vivo Kd by FCCS. Using this pair, we determined 22 in vivo Kd values of signaling molecule complexes comprising the epidermal growth factor receptor (EGFR)-Ras-extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway. With these parameters, we developed a kinetic simulation model of the EGFR-Ras-ERK MAP kinase pathway and uncovered a potential role played by stoichiometry in Shc binding to EGFR during the peak activations of Ras, MEK, and ERK. Intriguingly, most of the in vivo Kd values determined in this study were higher than the in vitro Kd values reported previously, suggesting the significance of competitive bindings inside cells. These in vivo Kd values will provide a sound basis for the quantitative understanding of signal transduction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

A Novel Selective Inverse Agonist of the CB2 Receptor as a Radiolabeled Tool Compound for Kinetic Binding Studies.

PubMed

Martella, Andrea; Sijben, Huub; Rufer, Arne C; Grether, Uwe; Fingerle, Juergen; Ullmer, Christoph; Hartung, Thomas; IJzerman, Adriaan P; van der Stelt, Mario; Heitman, Laura H

2017-10-01

The endocannabinoid system, and in particular the cannabinoid type 2 receptor (CB2R), raised the interest of many medicinal chemistry programs for its therapeutic relevance in several (patho)physiologic processes. However, the physico-chemical properties of tool compounds for CB2R (e.g., the radioligand [ 3 H]CP55,940) are not optimal, despite the research efforts in developing effective drugs to target this system. At the same time, the importance of drug-target binding kinetics is growing since the kinetic binding profile of a ligand may provide important insights for the resulting in vivo efficacy. In this context we synthesized and characterized [ 3 H]RO6957022, a highly selective CB2R inverse agonist, as a radiolabeled tool compound. In equilibrium and kinetic binding experiments [ 3 H]RO6957022 showed high affinity for human CB2R with fast association ( k on ) and moderate dissociation ( k off ) kinetics. To demonstrate the robustness of [ 3 H]RO6957022 binding, affinity studies were carried out for a wide range of CB2R reference ligands, spanning the range of full, partial, and inverse agonists. Finally, we used [ 3 H]RO6957022 to study the kinetic binding profiles (i.e., k on and k off values) of selected synthetic and endogenous (i.e., 2-arachidonoylglycerol, anandamide, and noladin ether) CB2R ligands by competition association experiments. All tested ligands, and in particular the endocannabinoids, displayed distinct kinetic profiles, shedding more light on their mechanism of action and the importance of association rates in the determination of CB2R affinity. Altogether, this study shows that the use of a novel tool compound, i.e., [ 3 H]RO6957022, can support the development of novel ligands with a repertoire of kinetic binding profiles for CB2R. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Local anesthetics QX 572 and benzocaine act at separate sites on the batrachotoxin-activated sodium channel

PubMed Central

1981-01-01

We have studied the effect of local anesthetics QX 572, which is permanently charged, and benzocaine, which is neutral, on batrachotoxin- activated sodium channels in mouse neuroblastoma N18 cells. The dose- response curves for each drug suggest that QX 752 and benzocaine each act on a single class of binding sites. The dissociation constants are 3.15 X 10(-5) M for QX 572 and 2.65 X 10(-4) M for benzocaine. Equilibrium and kinetic experiments indicate that both drugs are competitive inhibitors of batrachotoxin. When benzocaine and QX 572 are present with batrachotoxin, they are much more effective at inhibiting Na+ flux than would be predicted by a one-site model. Our results indicate that QX 572 and benzocaine bind to separate sites, each of which interacts competitively with batrachotoxin. PMID:6267160

Competition between monomeric and dimeric crystals in schematic models for globular proteins.

PubMed

Fusco, Diana; Charbonneau, Patrick

2014-07-17

Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. However, they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why (nearly) identical crystallization conditions can sometimes result in the formation of different crystal forms. Here, we develop a patchy particle model with competing sets of patches that provides a microscopic explanation of this phenomenon. We identify different regimes in which one or two crystal forms can coexist with a low-density fluid. Using analytical approximations, we extend our findings to different crystal phases, providing a general framework for treating protein crystallization when multiple crystal forms compete. Our results also suggest different experimental routes for targeting a specific crystal form, and for reducing the dynamical competition between the two forms, thus facilitating protein crystal assembly.

Non-equilibrium plasma kinetics of reacting CO: an improved state to state approach

NASA Astrophysics Data System (ADS)

Pietanza, L. D.; Colonna, G.; Capitelli, M.

2017-12-01

Non-equilibrium plasma kinetics of reacting CO for conditions typically met in microwave discharges have been developed based on the coupling of excited state kinetics and the Boltzmann equation for the electron energy distribution function (EEDF). Particular attention is given to the insertion in the vibrational kinetics of a complete set of electron molecule resonant processes linking the whole vibrational ladder of the CO molecule, as well as to the role of Boudouard reaction, i.e. the process of forming CO2 by two vibrationally excited CO molecules, in shaping the vibrational distribution of CO and promoting reaction channels assisted by vibrational excitation (pure vibrational mechanisms, PVM). PVM mechanisms can become competitive with electron impact dissociation processes (DEM) in the activation of CO. A case study reproducing the conditions of a microwave discharge has been considered following the coupled kinetics also in the post discharge conditions. Results include the evolution of EEDF in discharge and post discharge conditions highlighting the role of superelastic vibrational and electronic collisions in shaping the EEDF. Moreover, PVM rate coefficients and DEM ones are studied as a function of gas temperature, showing a non-Arrhenius behavior, i.e. the rate coefficients increase with decreasing gas temperature as a result of a vibrational-vibrational (V-V) pumping up mechanism able to form plateaux in the vibrational distribution function. The accuracy of the results is discussed in particular in connection to the present knowledge of the activation energy of the Boudouard process.

A Competitive Kinetics Study of the Reaction of Cl with CS2 in Air at 298 K

NASA Technical Reports Server (NTRS)

Wallington, Timothy J.; Andino, Jean M.; Potts, Alan R.; Wine, Paul H.

1997-01-01

The relative rate technique has been used to investigate the kinetics of the reaction of Cl atoms with carbon disulfide, CS2, at 700 Torr total pressure of air at 298 K. The decay rate of CS2 was measured relative to CH4, CH3Cl and CHF2CL. For experiments using CH4 and CH3Cl references, the decay rate of CS2 was dependent on the ratio of the concentration of the reference to that of CS2. We ascribe this behavior to the generation of OH radicals in the system leading to complicated secondary chemistry. From experiments using CHF2Cl we are able to assign an upper limit of 4 x 10(exp -15) cu cm/(molecule s) for the overall reaction, Cl + CS2 yields products.

Ozonation of the pharmaceutical compound ranitidine: reactivity and kinetic aspects.

PubMed

Rivas, Javier; Gimeno, Olga; Encinas, Angel; Beltrán, Fernando

2009-07-01

Ranitidine has been ozonated under different operating conditions of pH, applied ozone dose, initial ranitidine concentration and presence or absence of free radical inhibitors. Results of ranitidine evolution with time indicate a high reactivity of this compound with molecular ozone. Mineralization levels achieved in the order of 20-25% suggest that the (CH3)2-N-CH2- moiety bonded to the furan ring could be separated from the rest of the ranitidine structure and further mineralized. Only alkaline conditions (pH=11) are capable of increasing TOC conversion up to values close to 70%. Determination of the direct ozonation rate constant for ranitidine by means of competitive kinetics reveals an unacceptable dependence of the aforementioned constant with the reference compound reactivity. It is hypothesised that only reference compounds with reactivity similar to the target species should be used.

Calculation of ground state rotational populations for kinetic gas homonuclear diatomic molecules including electron-impact excitation and wall collisions.

PubMed

Farley, David R

2010-09-07

A model has been developed to calculate the ground state rotational populations of homonuclear diatomic molecules in kinetic gases, including the effects of electron-impact excitation, wall collisions, and gas feed rate. The equations are exact within the accuracy of the cross sections used and of the assumed equilibrating effect of wall collisions. It is found that the inflow of feed gas and equilibrating wall collisions can significantly affect the rotational distribution in competition with nonequilibrating electron-impact effects. The resulting steady-state rotational distributions are generally Boltzmann for N≥3, with a rotational temperature between the wall and feed gas temperatures. The N=0,1,2 rotational level populations depend sensitively on the relative rates of electron-impact excitation versus wall collision and gas feed rates.

Redefining the utility of the three-isotope method

NASA Astrophysics Data System (ADS)

Cao, Xiaobin; Bao, Huiming

2017-09-01

The equilibrium isotope fractionation factor αeq is a fundamental parameter in the study of stable isotope effects. Experimentally, it has been difficult to establish that a system has attained equilibrium. The three-isotope method, using the initial trajectory of changing isotope ratios (e.g. 16O, 17O, and 18O) to deduce the final equilibrium point of isotope exchange, has long been hailed as the most rigorous experimental approach. However, over the years some researchers have cautioned on the limitations of this method, but the foundation of three-isotope method has not been properly examined and the method is still widely used in calibrating αeq for both traditional and increasingly non-traditional isotope systems today. Here, using water-water and dissolved CO2-water oxygen exchange as model systems, we conduct an isotopologues-specific kinetic analysis of the exchange processes and explore the underlying assumptions and validity of the three-isotope method. We demonstrate that without knowing the detailed exchange kinetics a priori the three-isotope method cannot lead to a reliable αeq. For a two-reservoir exchanging system, α determined by this method may be αeq, kinetic isotope effect, or apparent kinetic isotope effect, which can all bear different values. When multiple reservoirs exist during exchange, the evolving trajectory can be complex and hard to predict. Instead of being a tool for αeq determination, three-isotope method should be used as a tool for studying kinetic isotope effect, apparent kinetic isotope effect, and detailed exchange kinetics in diverse systems.

Prediction of free turbulent mixing using a turbulent kinetic energy method

NASA Technical Reports Server (NTRS)

Harsha, P. T.

1973-01-01

Free turbulent mixing of two-dimensional and axisymmetric one- and two-stream flows is analyzed by a relatively simple turbulent kinetic energy method. This method incorporates a linear relationship between the turbulent shear and the turbulent kinetic energy and an algebraic relationship for the length scale appearing in the turbulent kinetic energy equation. Good results are obtained for a wide variety of flows. The technique is shown to be especially applicable to flows with heat and mass transfer, for which nonunity Prandtl and Schmidt numbers may be assumed.

Iron oxide nanoparticle-based magnetic resonance method to monitor release kinetics from polymeric particles with high resolution.

PubMed

Chan, Minnie; Schopf, Eric; Sankaranarayanan, Jagadis; Almutairi, Adah

2012-09-18

A new method to precisely monitor rapid release kinetics from polymeric particles using super paramagnetic iron oxide nanoparticles, specifically by measuring spin-spin relaxation time (T(2)), is reported. Previously, we have published the formulation of logic gate particles from an acid-sensitive poly-β-aminoester ketal-2 polymer. Here, a series of poly-β-aminoester ketal-2 polymers with varying hydrophobicities were synthesized and used to formulate particles. We attempted to measure fluorescence of released Nile red to determine whether the structural adjustments could finely tune the release kinetics in the range of minutes to hours; however, this standard technique did not differentiate each release rate of our series. Thus, a new method based on encapsulation of iron oxide nanoparticles was developed, which enabled us to resolve the release kinetics of our particles. Moreover, the kinetics matched the relative hydrophobicity order determined by octanol-water partition coefficients. To the best of our knowledge, this method provides the highest resolution of release kinetics to date.

Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

PubMed

Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

2017-01-25

This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

Generalized fluid theory including non-Maxwellian kinetic effects

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

Izacard, Olivier

The results obtained by the plasma physics community for the validation and the prediction of turbulence and transport in magnetized plasmas come mainly from the use of very central processing unit (CPU)-consuming particle-in-cell or (gyro)kinetic codes which naturally include non-Maxwellian kinetic effects. To date, fluid codes are not considered to be relevant for the description of these kinetic effects. Here, after revisiting the limitations of the current fluid theory developed in the 19th century, we generalize the fluid theory including kinetic effects such as non-Maxwellian super-thermal tails with as few fluid equations as possible. The collisionless and collisional fluid closuresmore » from the nonlinear Landau Fokker–Planck collision operator are shown for an arbitrary collisionality. Indeed, the first fluid models associated with two examples of collisionless fluid closures are obtained by assuming an analytic non-Maxwellian distribution function. One of the main differences with the literature is our analytic representation of the distribution function in the velocity phase space with as few hidden variables as possible thanks to the use of non-orthogonal basis sets. These new non-Maxwellian fluid equations could initiate the next generation of fluid codes including kinetic effects and can be expanded to other scientific disciplines such as astrophysics, condensed matter or hydrodynamics. As a validation test, we perform a numerical simulation based on a minimal reduced INMDF fluid model. The result of this test is the discovery of the origin of particle and heat diffusion. The diffusion is due to the competition between a growing INMDF on short time scales due to spatial gradients and the thermalization on longer time scales. Here, the results shown here could provide the insights to break some of the unsolved puzzles of turbulence.« less

Generalized fluid theory including non-Maxwellian kinetic effects

DOE PAGES

Izacard, Olivier

2017-03-29

The results obtained by the plasma physics community for the validation and the prediction of turbulence and transport in magnetized plasmas come mainly from the use of very central processing unit (CPU)-consuming particle-in-cell or (gyro)kinetic codes which naturally include non-Maxwellian kinetic effects. To date, fluid codes are not considered to be relevant for the description of these kinetic effects. Here, after revisiting the limitations of the current fluid theory developed in the 19th century, we generalize the fluid theory including kinetic effects such as non-Maxwellian super-thermal tails with as few fluid equations as possible. The collisionless and collisional fluid closuresmore » from the nonlinear Landau Fokker–Planck collision operator are shown for an arbitrary collisionality. Indeed, the first fluid models associated with two examples of collisionless fluid closures are obtained by assuming an analytic non-Maxwellian distribution function. One of the main differences with the literature is our analytic representation of the distribution function in the velocity phase space with as few hidden variables as possible thanks to the use of non-orthogonal basis sets. These new non-Maxwellian fluid equations could initiate the next generation of fluid codes including kinetic effects and can be expanded to other scientific disciplines such as astrophysics, condensed matter or hydrodynamics. As a validation test, we perform a numerical simulation based on a minimal reduced INMDF fluid model. The result of this test is the discovery of the origin of particle and heat diffusion. The diffusion is due to the competition between a growing INMDF on short time scales due to spatial gradients and the thermalization on longer time scales. Here, the results shown here could provide the insights to break some of the unsolved puzzles of turbulence.« less

Quantification of metabotropic glutamate subtype 5 receptors in the brain by an equilibrium method using 18F-SP203.

PubMed

Kimura, Yasuyuki; Siméon, Fabrice G; Zoghbi, Sami S; Zhang, Yi; Hatazawa, Jun; Pike, Victor W; Innis, Robert B; Fujita, Masahiro

2012-02-01

A new PET ligand, 3-fluoro-5-(2-(2-(18)F-(fluoromethyl)-thiazol-4-yl)ethynyl)benzonitrile (18F-SP203) can quantify metabotropic glutamate subtype 5 receptors (mGluR5) in human brain by a bolus injection and kinetic modeling. As an alternative approach to a bolus injection, binding can simply be measured as a ratio of tissue to metabolite-corrected plasma at a single time point under equilibrium conditions achieved by administering the radioligand with a bolus injection followed by a constant infusion. The purpose of this study was to validate the equilibrium method as an alternative to the standard kinetic method for measuring 18F-SP203 binding in the brain. Nine healthy subjects were injected with 18F-SP203 using a bolus plus constant infusion for 300 min. A single ratio of bolus-to-constant infusion (the activity of bolus equaled to that of infusion over 219 min) was applied to all subjects to achieve equilibrium in approximately 120 min. As a measure of ligand binding, we compared total distribution volume (VT) calculated by the equilibrium and kinetic methods in each scan. The equilibrium method calculated VT by the ratio of radioactivity in the brain to the concentration of 18F-SP203 in arterial plasma at 120 min, and the kinetic method calculated VT by a two-tissue compartment model using brain and plasma dynamic data from 0 to 120 min. VT obtained via the equilibrium method was highly correlated with VT obtained via kinetic modeling. Inter-subject variability of VT obtained via the equilibrium method was slightly smaller than VT obtained via the kinetic method. VT obtained via the equilibrium method was ~10% higher than VT obtained via the kinetic method, indicating a small difference between the measurements. Taken together, the results of this study show that using the equilibrium method is an acceptable alternative to the standard kinetic method when using 18F-SP203 to measure mGluR5. Although small differences in the measurements obtained via the equilibrium and kinetic methods exist, both methods consistently measured mGluR5 as indicated by the highly correlated VT values; the equilibrium method was slightly more precise, as indirectly measured by the smaller coefficient of variability across subjects. In addition, when using 18F-SP203, the equilibrium method is more efficient because it requires much less data. Copyright © 2011. Published by Elsevier Inc.

Cross-Diffusion Driven Instability for a Lotka-Volterra Competitive Reaction-Diffusion System

NASA Astrophysics Data System (ADS)

Gambino, G.; Lombardo, M. C.; Sammartino, M.

2008-04-01

In this work we investigate the possibility of the pattern formation for a reaction-diffusion system with nonlinear diffusion terms. Through a linear stability analysis we find the conditions which allow a homogeneous steady state (stable for the kinetics) to become unstable through a Turing mechanism. In particular, we show how cross-diffusion effects are responsible for the initiation of spatial patterns. Finally, we find a Fisher amplitude equation which describes the weakly nonlinear dynamics of the system near the marginal stability.

Prediction of competitive diffusion on complex networks

NASA Astrophysics Data System (ADS)

Zhao, Jiuhua; Liu, Qipeng; Wang, Lin; Wang, Xiaofan

2018-10-01

In this paper, we study the prediction problem of diffusion process on complex networks in competitive circumstances. With this problem solved, the competitors could timely intervene the diffusion process if needed such that an expected outcome might be obtained. We consider a model with two groups of competitors spreading opposite opinions on a network. A prediction method based on the mutual influences among the agents is proposed, called Influence Matrix (IM for short), and simulations on real-world networks show that the proposed IM method has quite high accuracy on predicting both the preference of any normal agent and the final competition result. For comparison purpose, classic centrality measures are also used to predict the competition result. It is shown that PageRank, Degree, Katz Centrality, and the IM method are suitable for predicting the competition result. More precisely, in undirected networks, the IM method performs better than these centrality measures when the competing group contains more than one agent; in directed networks, the IM method performs only second to PageRank.

Electrochemical advanced oxidation for cold incineration of the pharmaceutical ranitidine: mineralization pathway and toxicity evolution.

PubMed

Olvera-Vargas, Hugo; Oturan, Nihal; Brillas, Enric; Buisson, Didier; Esposito, Giovanni; Oturan, Mehmet A

2014-12-01

Ranitidine (RNTD) is a widely prescribed histamine H2-receptor antagonist whose unambiguous presence in water sources appointed it as an emerging pollutant. Here, the degradation of 0.1 mM of this drug in aqueous medium was studied by electrochemical advanced oxidation processes (EAOPs) like anodic oxidation with electrogenerated H2O2 and electro-Fenton using Pt/carbon-felt, BDD/carbon-felt and DSA-Ti/RuO2–IrO2/carbon-felt cells. The higher oxidation power of the electro-Fenton process using a BDD anode was demonstrated. The oxidative degradation of RNTD by the electrochemically generated OH radicals obeyed a pseudo-first order kinetics. The absolute rate constant for its hydroxylation reaction was 3.39 × 109 M−1 s−1 as determined by the competition kinetics method. Almost complete mineralization of the RNTN solution was reached by using a BDD anode in both anodic oxidation with electrogenerated H2O2 and electro-Fenton processes. Up to 11 cyclic intermediates with furan moiety were detected from the degradation of RNTD, which were afterwards oxidized to short-chain carboxylic acids before their mineralization to CO2 and inorganic ions such as NH4+, NO3− and SO42−. Based on identified products, a plausible reaction pathway was proposed for RNTD mineralization. Toxicity assessment by the Microtox® method revealed that some cyclic intermediates are more toxic than the parent molecule. Toxicity was quickly removed following the almost total mineralization of the treated solution. Overall results confirm the effectiveness of EAOPs for the efficient removal of RNTD and its oxidation by-products from water.

Effective removal of cesium from wastewater solutions using an innovative low-cost adsorbent developed from sewage sludge molten slag.

PubMed

Khandaker, Shahjalal; Toyohara, Yusaku; Kamida, Seiya; Kuba, Takahiro

2018-06-01

This study investigates the effective removal of cesium (Cs) from aqueous solution using sewage sludge molten (SSM) slag that has undergone the surface modification with alkali (NaOH) hydrothermal treatment. The raw and modified slags were characterised systematically using the BET method, the FESEM, the XRF, the XRD spectroscopy and the CEC analysis to understand the physicochemical changes of the materials, and its sensitivity to Cs ions adsorption. Batch adsorption experiments were carried out to investigate the effects of adsorbent dose, contact time, solution pH, different initial Cs concentrations, temperature and the effect of competitive ions on Cs adsorption. The adsorption isotherm, kinetic and thermodynamic studies were also evaluated based on the experimental results. A higher Cs removal efficiency of almost 100% (for 20-100 mg/L of initial concentration) was achieved by the modified SSM slag, and the maximum adsorption capacity was found to be 52.36 mg/g. Several types of synthetic zeolites such as zeolite X, zeolite Y, zeolite A, and sodalite were formed on surface of the modified slag through the modification process which might be enhanced the Cs adsorption capacity. Kinetic parameters were fitted by the pseudo-second order model. The adsorption isotherms data of modified slag were well-fitted to the Langmuir (R 2  = 0.989) and Freundlich isotherms (R 2  = 0.988). The thermodynamic studies indicated that the adsorption process by the modified slag was spontaneous and exothermic. In the competitive ions effect, the modified slag effectively captured the Cs ion in the presence of Na + and K + , especially at their lower concentrations. Moreover, the modified slag was reused for several cycles after the successful elution process with an appropriate eluting agent (0.5 M H 2 SO 4 ), without deterioration of its original performance. Therefore, the SSM modified slag could be effectively used as a low-cost potential adsorbent for high Cs adsorption from wastewater. Copyright © 2018 Elsevier Ltd. All rights reserved.

High removal performance of a magnetic FPA90-Cl anion resin for bromate and coexisting precursors: kinetics, thermodynamics, and equilibrium studies.

PubMed

Xu, Zhengming; Han, Dexia; Li, Yuan; Zhang, Pingling; You, Lijun; Zhao, Zhengang

2018-04-23

In this study, the FPA90-Cl resin was magnetized with supported Fe 3 O 4 particles using a chemical co-precipitation method and its removal performance of bromate and coexisting precursors was explored. The magnetized FPA90-Cl resin was structurally characterized by SEM, FT-IR, and XRD. The effects of the initial concentrations, temperature, and resin dosage on bromate and bromide ion removal in drinking water were investigated using batch experiments. The magnetized FPA90-Cl resin exhibited a high removal efficiency for bromate and bromide ions at three initial concentrations, and the residual bromate concentrations were under the maximum contaminant level (MCL) of 10 μg L -1 after 80 min. The adsorption data of bromate and bromide ion could be well described by a pseudo-first-order kinetic model (R 2  ˃ 0.98). The bromate removal alone was further studied by varying the initial solution pH, temperature, and competitive anions. The results showed that the magnetized FPA90-Cl resin could be used over a wide pH range (4.0-9.0). The maximum sorption capacity of the magnetized FPA90-Cl resin for bromate reached 132.83 mg g -1 at 298 K. The Freundlich and Redlich-Peterson isotherm models fit the bromate adsorption equilibrium better (R 2  ˃ 0.99) than the Langmuir isotherm model (R 2  ˃ 0.98). The thermodynamic analysis showed that the bromate adsorption process was endothermic. The negative ΔG and positive ΔS indicated that the process was spontaneous and that randomness increased after adsorption, respectively. The competition of coexisting anions with bromate was in the order of SO 4 2-  > CO 3 2-  > Cl -  > NO 3 -  > HCO 3 -  > PO 4 3- . Additionally, the magnetized FPA90-Cl resin could maintain a high bromate and bromide ion adsorption capacity after five cycles of regeneration by a 0.1 M NaCl solution. Graphical abstract ᅟ.

Oxidation of Methyl and Ethyl Nitrosamines by Cytochromes P450 2E1 and 2B1

PubMed Central

Chowdhury, Goutam; Calcutt, M. Wade; Nagy, Leslie D.; Guengerich, F. Peter

2012-01-01

Cytochrome P450 (P450) 2E1 is the major enzyme that oxidizes N-nitrosodimethylamine (N,N-dimethylnitrosamine, DMN), a carcinogen and also a representative of some nitrosamines formed endogenously. Oxidation of DMN by rat or human P450 2E1 to HCHO showed a high apparent intrinsic kinetic deuterium isotope effect (KIE), ≥ 8. The KIE was not attenuated in non-competitive intermolecular experiments with rat liver microsomes (DV 12.5, D(V/K) 10.9, nomenclature of Northrop, D.B. (1982) Methods Enzymol. 87, 607–625) but was with purified human P450 2E1 (DV 3.3, D(V/K) 3.7), indicating that C-H bond breaking is partially rate-limiting with human P450 2E1. With N-nitrosodiethylamine (N,N-diethylnitrosamine, DEN), the intrinsic KIE was slightly lower and was not expressed (e.g., D(V/K) 1.2) in non-competitive intermolecular experiments. The same general pattern of KIEs was also seen in the D(V/K) results with DMN and DEN for the minor products resulting from the denitrosation reactions (CH3NH2, CH3CH2NH2, and NO2−). Experiments with deuterated N-nitroso-N-methyl,N-ethylamine demonstrated that the lower KIEs associated for ethyl compared to methyl oxidation could be distinguished within a single molecule. P450 2E1 oxidized DMN and DEN to aldehydes and then to the carboxylic acids. No kinetic lags were observed in acid formation; pulse-chase experiments with carrier aldehydes showed only limited equilibration with P450 2E1-bound aldehydes, indicative of processive reactions, as reported for P450 2A6 (Chowdhury, G. et al. (2010) J. Biol. Chem. 285, 8031–8044). These same features (no lag phase for HCO2H formation, lack of equilibration in pulse-chase assays) were also seen with (rat) P450 2B1, which has lower catalytic efficiency for DMN oxidation and a larger active site. Thus, the processivity of dialkylnitrosamine oxidation appears to be shared by a number of P450s. PMID:23186213

5 CFR 6.3 - Method of filling excepted positions and status of incumbents.

Code of Federal Regulations, 2011 CFR

2011-01-01

... SERVICE RULES EXCEPTIONS FROM THE COMPETITIVE SERVICE (RULE VI) § 6.3 Method of filling excepted positions... persons without civil service eligibility or competitive status and such persons shall not acquire competitive status by reason of such appointment: Provided, That OPM, in its discretion, may by regulation...

5 CFR 6.3 - Method of filling excepted positions and status of incumbents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... SERVICE RULES EXCEPTIONS FROM THE COMPETITIVE SERVICE (RULE VI) § 6.3 Method of filling excepted positions... persons without civil service eligibility or competitive status and such persons shall not acquire competitive status by reason of such appointment: Provided, That OPM, in its discretion, may by regulation...

Metal–organic complexation in the marine environment

PubMed Central

Luther, George W; Rozan, Timothy F; Witter, Amy; Lewis, Brent

2001-01-01

We discuss the voltammetric methods that are used to assess metal–organic complexation in seawater. These consist of titration methods using anodic stripping voltammetry (ASV) and cathodic stripping voltammetry competitive ligand experiments (CSV-CLE). These approaches and a kinetic approach using CSV-CLE give similar information on the amount of excess ligand to metal in a sample and the conditional metal ligand stability constant for the excess ligand bound to the metal. CSV-CLE data using different ligands to measure Fe(III) organic complexes are similar. All these methods give conditional stability constants for which the side reaction coefficient for the metal can be corrected but not that for the ligand. Another approach, pseudovoltammetry, provides information on the actual metal–ligand complex(es) in a sample by doing ASV experiments where the deposition potential is varied more negatively in order to destroy the metal–ligand complex. This latter approach gives concentration information on each actual ligand bound to the metal as well as the thermodynamic stability constant of each complex in solution when compared to known metal–ligand complexes. In this case the side reaction coefficients for the metal and ligand are corrected. Thus, this method may not give identical information to the titration methods because the excess ligand in the sample may not be identical to some of the actual ligands binding the metal in the sample. PMID:16759421

Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics.

PubMed

Liu, Qingsong; Kirubakaran, Sivapriya; Hur, Wooyoung; Niepel, Mario; Westover, Kenneth; Thoreen, Carson C; Wang, Jinhua; Ni, Jing; Patricelli, Matthew P; Vogel, Kurt; Riddle, Steve; Waller, David L; Traynor, Ryan; Sanda, Takaomi; Zhao, Zheng; Kang, Seong A; Zhao, Jean; Look, A Thomas; Sorger, Peter K; Sabatini, David M; Gray, Nathanael S

2012-03-23

An intensive recent effort to develop ATP-competitive mTOR inhibitors has resulted in several potent and selective molecules such as Torin1, PP242, KU63794, and WYE354. These inhibitors are being widely used as pharmacological probes of mTOR-dependent biology. To determine the potency and specificity of these agents, we have undertaken a systematic kinome-wide effort to profile their selectivity and potency using chemical proteomics and assays for enzymatic activity, protein binding, and disruption of cellular signaling. Enzymatic and cellular assays revealed that all four compounds are potent inhibitors of mTORC1 and mTORC2, with Torin1 exhibiting ∼20-fold greater potency for inhibition of Thr-389 phosphorylation on S6 kinases (EC(50) = 2 nM) relative to other inhibitors. In vitro biochemical profiling at 10 μM revealed binding of PP242 to numerous kinases, although WYE354 and KU63794 bound only to p38 kinases and PI3K isoforms and Torin1 to ataxia telangiectasia mutated, ATM and Rad3-related protein, and DNA-PK. Analysis of these protein targets in cellular assays did not reveal any off-target activities for Torin1, WYE354, and KU63794 at concentrations below 1 μM but did show that PP242 efficiently inhibited the RET receptor (EC(50), 42 nM) and JAK1/2/3 kinases (EC(50), 780 nM). In addition, Torin1 displayed unusually slow kinetics for inhibition of the mTORC1/2 complex, a property likely to contribute to the pharmacology of this inhibitor. Our results demonstrated that, with the exception of PP242, available ATP-competitive compounds are highly selective mTOR inhibitors when applied to cells at concentrations below 1 μM and that the compounds may represent a starting point for medicinal chemistry efforts aimed at developing inhibitors of other PI3K kinase-related kinases.

Stochastic population dynamics in spatially extended predator-prey systems

NASA Astrophysics Data System (ADS)

Dobramysl, Ulrich; Mobilia, Mauro; Pleimling, Michel; Täuber, Uwe C.

2018-02-01

Spatially extended population dynamics models that incorporate demographic noise serve as case studies for the crucial role of fluctuations and correlations in biological systems. Numerical and analytic tools from non-equilibrium statistical physics capture the stochastic kinetics of these complex interacting many-particle systems beyond rate equation approximations. Including spatial structure and stochastic noise in models for predator-prey competition invalidates the neutral Lotka-Volterra population cycles. Stochastic models yield long-lived erratic oscillations stemming from a resonant amplification mechanism. Spatially extended predator-prey systems display noise-stabilized activity fronts that generate persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively via a Doi-Peliti field theory mapping of the master equation; related tools allow detailed characterization of extinction pathways. The critical steady-state and non-equilibrium relaxation dynamics at the predator extinction threshold are governed by the directed percolation universality class. Spatial predation rate variability results in more localized clusters, enhancing both competing species’ population densities. Affixing variable interaction rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of three-species competition with ‘rock-paper-scissors’ interactions metaphorically describe cyclic dominance. These models illustrate intimate connections between population dynamics and evolutionary game theory, underscore the role of fluctuations to drive populations toward extinction, and demonstrate how space can support species diversity. Two-dimensional cyclic three-species May-Leonard models are characterized by the emergence of spiraling patterns whose properties are elucidated by a mapping onto a complex Ginzburg-Landau equation. Multiple-species extensions to general ‘food networks’ can be classified on the mean-field level, providing both fundamental understanding of ensuing cooperativity and profound insight into the rich spatio-temporal features and coarsening kinetics in the corresponding spatially extended systems. Novel space-time patterns emerge as a result of the formation of competing alliances; e.g. coarsening domains that each incorporate rock-paper-scissors competition games.

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics

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

Masunov, Artëm E.; Wait, Elizabeth E.; Atlanov, Arseniy A.

In oxy-fuel combustion, the pure oxygen (O 2), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2O) are free from pollution by nitrogen oxides. Moreover, high pressures results in the near-liquid density of CO 2 at supercritical state (sCO 2). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. In order to assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of carbon dioxide melocule. All transitionmore » states, reactant and product complexes are reported for three reactions: H 2CO+HO 2→HCO+H 2O 2 (R1), 2HO 2→H 2O 2+O 2 (R2), and CO+OH→CO 2+H (R3). In the reaction R3, covalent binding of CO 2 to OH radical and then CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to bimolecular OH+CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol, and is expected to accelerate the reaction. This is the first report of autocatalytic effect in combustion. In case of hydroperoxyl self-reaction 2HO 2→H 2O 2+O 2 the intermediates, containing covalent bonds to CO 2 were found not to be competitive. However, the spectator CO 2 molecule is able to stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates was also discovered in H 2CO+HO 2→HCO+H 2O 2 reaction, but these specie lead to substantially higher activation barriers which makes them unlikely to play role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilized transition state and reduces reaction barrier. Lastly, these results indicate that CO 2 environment is likely to have catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2.« less

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics

DOE PAGES

Masunov, Artëm E.; Wait, Elizabeth E.; Atlanov, Arseniy A.; ...

2017-05-03

In oxy-fuel combustion, the pure oxygen (O 2), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2O) are free from pollution by nitrogen oxides. Moreover, high pressures results in the near-liquid density of CO 2 at supercritical state (sCO 2). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. In order to assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of carbon dioxide melocule. All transitionmore » states, reactant and product complexes are reported for three reactions: H 2CO+HO 2→HCO+H 2O 2 (R1), 2HO 2→H 2O 2+O 2 (R2), and CO+OH→CO 2+H (R3). In the reaction R3, covalent binding of CO 2 to OH radical and then CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to bimolecular OH+CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol, and is expected to accelerate the reaction. This is the first report of autocatalytic effect in combustion. In case of hydroperoxyl self-reaction 2HO 2→H 2O 2+O 2 the intermediates, containing covalent bonds to CO 2 were found not to be competitive. However, the spectator CO 2 molecule is able to stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates was also discovered in H 2CO+HO 2→HCO+H 2O 2 reaction, but these specie lead to substantially higher activation barriers which makes them unlikely to play role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilized transition state and reduces reaction barrier. Lastly, these results indicate that CO 2 environment is likely to have catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2.« less

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics.

PubMed

Masunov, Artëm E; Wait, Elizabeth E; Atlanov, Arseniy A; Vasu, Subith S

2017-05-18

In oxy-fuel combustion, the pure oxygen (O 2 ), diluted with CO 2 is used as oxidant instead air. Hence, the combustion products (CO 2 and H 2 O) are free from pollution by nitrogen oxides. Moreover, high pressures result in the near-liquid density of CO 2 at supercritical state (sCO 2 ). Unfortunately, the effects of sCO 2 on the combustion kinetics are far from being understood. To assist in this understanding, in this work we are using quantum chemistry methods. Here we investigate potential energy surfaces of important combustion reactions in the presence of the carbon dioxide molecule. All transition states and reactant and product complexes are reported for three reactions: H 2 CO + HO 2 → HCO + H 2 O 2 (R1), 2HO 2 → H 2 O 2 + O 2 (R2), and CO + OH → CO 2 + H (R3). In reaction R3, covalent binding of CO 2 to the OH radical and then the CO molecule opens a new pathway, including hydrogen transfer from oxygen to carbon atoms followed by CH bond dissociation. Compared to the bimolecular OH + CO mechanism, this pathway reduces the activation barrier by 5 kcal/mol and is expected to accelerate the reaction. In the case of hydroperoxyl self-reaction 2HO 2 → H 2 O 2 + O 2 the intermediates, containing covalent bonds to CO 2 are found not to be competitive. However, the spectator CO 2 molecule can stabilize the cyclic transition state and lower the barrier by 3 kcal/mol. Formation of covalent intermediates is also discovered in the H 2 CO + HO 2 → HCO + H 2 O 2 reaction, but these species lead to substantially higher activation barriers, which makes them unlikely to play a role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide also stabilizes the transition state and reduces the reaction barrier. These results indicate that the CO 2 environment is likely to have a catalytic effect on combustion reactions, which needs to be included in kinetic combustion mechanisms in supercritical CO 2 .

43 CFR 2710.0-6 - Policy.

Code of Federal Regulations, 2011 CFR

2011-10-01

... of public lands under this section shall be conducted under competitive bidding procedures... competitive bidding or without competitive bidding. In recognizing public policies, the Secretary shall give... considered in determining the method of sale. These factors include, but are not limited to: Competitive...

The use of dimethylsulfoxide as a solvent in enzyme inhibition studies: the case of aldose reductase.

PubMed

Misuri, Livia; Cappiello, Mario; Balestri, Francesco; Moschini, Roberta; Barracco, Vito; Mura, Umberto; Del-Corso, Antonella

2017-12-01

Aldose reductase (AR) is an enzyme devoted to cell detoxification and at the same time is strongly involved in the aetiology of secondary diabetic complications and the amplification of inflammatory phenomena. AR is subjected to intense inhibition studies and dimethyl sulfoxide (DMSO) is often present in the assay mixture to keep the inhibitors in solution. DMSO was revealed to act as a weak but well detectable AR differential inhibitor, acting as a competitive inhibitor of the L-idose reduction, as a mixed type of non-competitive inhibitor of HNE reduction and being inactive towards 3-glutathionyl-4-hydroxynonanal transformation. A kinetic model of DMSO action with respect to differently acting inhibitors was analysed. Three AR inhibitors, namely the flavonoids neohesperidin dihydrochalcone, rutin and phloretin, were used to evaluate the effects of DMSO on the inhibition studies on the reduction of L-idose and HNE.

Kinetic model of 1,3-specific triacylglycerols alcoholysis catalyzed by lipases.

PubMed

Pilarek, Maciej; Szewczyk, Krzysztof W

2007-01-20

A new model of enzymatic 1,3-specific alcoholysis of triacylglycerols has been developed. The irreversibility of the acyl bounds cleavage in glycerides, a reversible monoglycerides isomerization and an irreversible enzyme deactivation have been assumed. The Ping Pong Bi Bi mechanism with competitive inhibition by alcohol has been applied to describe rates of acyl bonds cleavage. The enzymatic propanolysis and iso-propanolysis of triacetin and tricaprylin catalyzed by immobilized lipase B from Candida antarctica (Novozym 435) have been investigated to verify the model. Good agreement between experimental data and calculations has been obtained. It was shown that the rate of tricaprylin alcoholysis is higher than the triacetin alcoholysis and that the rate of iso-propanolysis reactions are higher than propanolysis. The irreversible enzyme deactivation affects the conversion of glycerides whereas the competitive alcohol inhibition may be neglected. Empirical correlations of rates for monoglycerides isomerization and enzyme deactivation have been proposed.

Plant Photosynthesis-Irradiance Curve Responses to Pollution Show Non-Competitive Inhibited Michaelis Kinetics

PubMed Central

Lin, Maozi; Wang, Zhiwei; He, Lingchao; Xu, Kang; Cheng, Dongliang; Wang, Genxuan

2015-01-01

Photosynthesis-irradiance (PI) curves are extensively used in field and laboratory research to evaluate the photon-use efficiency of plants. However, most existing models for PI curves focus on the relationship between the photosynthetic rate (Pn) and photosynthetically active radiation (PAR), and do not take account of the influence of environmental factors on the curve. In the present study, we used a new non-competitive inhibited Michaelis-Menten model (NIMM) to predict the co-variation of Pn, PAR, and the relative pollution index (I). We then evaluated the model with published data and our own experimental data. The results indicate that the Pn of plants decreased with increasing I in the environment and, as predicted, were all fitted well by the NIMM model. Therefore, our model provides a robust basis to evaluate and understand the influence of environmental pollution on plant photosynthesis. PMID:26561863

α-Glucosidase inhibition by prenylated and lavandulyl compounds from Sophora flavescens roots and in silico analysis.

PubMed

Kim, Jang Hoon; Cho, Chong Woon; Kim, Hyo Young; Kim, Kyung Tae; Choi, Gug-Seoun; Kim, Hyeong-Hwang; Cho, In Sook; Kwon, Sun Jung; Choi, Seung-Kook; Yoon, Ju-Yeon; Yang, Seo Young; Kang, Jong Seong; Kim, Young Ho

2017-09-01

The enzyme α-glucosidase is a good drug target for the treatment of diabetes mellitus. Four minor flavonoids (1-4) from roots of Sophora flavescens showed the inhibitory activity, with IC 50 values ranging from 11.0±0.3 to 50.6±1.3μM, toward α-glucosidase. An enzyme kinetics analysis of them revealed that the compounds 1 and 4 were non-competitive, and compounds 2 and 3 were un-competitive inhibitors. For molecular docking, 3-dimensional structure of α-glucosidase was built by homology modeling. As the result, four compounds 1-4 were confirmed to interact into common binding site of α-glucosidase. In addition, all of the four prenylated and lavandulyl compounds (1-4) were abundant in an ethyl acetate fraction separated from a methanol extract, and the potential inhibitor (3) was extracted best using tetrahydrofuran. Copyright © 2017 Elsevier B.V. All rights reserved.

Towards Binding Mechanism of Cu2+ on Creatine Kinase from Pelodiscus sinensis: Molecular Dynamics Simulation Integrating Inhibition Kinetics Study.

PubMed

Cai, Yan; Lee, Jinhyuk; Wang, Wei; Park, Yong-Doo; Qian, Guo-Ying

2017-01-01

Cu2+ is well known to play important roles in living organisms having bifacial distinction: essential microelement that is necessary for a wide range of metabolic processes but hyper-accumulation of Cu2+ can be toxic. The physiological function of Cu2+ in ectothermic animals such as Pelodiscus sinensis (Chinese soft-shelled turtle) has not been elucidated. In this study, we elucidated effect of Cu2+ on the energy producing metabolic enzyme creatine kinase (CK), which might directly affect energy metabolism and homeostasis of P. sinensis. We first conducted molecular dynamics (MD) simulations between P-CK and Cu2+ and conducted the inactivation kinetics including spectrofluorimetry study. MD simulation showed that Cu2+ blocked the binding site of the ATP cofactor, indicating that Cu2+ could directly inactivate P-CK. We prepared the muscle type of CK (P-CK) and confirmed that Cu2+ conspicuously inactivated the activity of P-CK (IC50 = 24.3 μM) and exhibited non-competitive inhibition manner with creatine and ATP in a first-order kinetic process. This result was well matched to the MD simulation results that Cu2+-induced non-competitive inactivation of P-CK. The spectrofluorimetry study revealed that Cu2+ induced tertiary structure changes in PCK accompanying with the exposure of hydrophobic surfaces. Interestingly, the addition of osmolytes (glycine, proline, and liquaemin) effectively restored activity of the Cu2+-inactivated P-CK. Our study illustrates the Cu2+-mediated unfolding of P-CK with disruption of the enzymatic function and the protective restoration role of osmolytes on P-CK inactivation. This study provides information of interest on P-CK as a metabolic enzyme of ectothermic animal in response to Cu2+ binding. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Sphagnum Mosses - Masters of Efficient N-Uptake while Avoiding Intoxication

PubMed Central

Fritz, Christian; Lamers, Leon P. M.; Riaz, Muhammad; van den Berg, Leon J. L.; Elzenga, Theo J. T. M.

2014-01-01

Peat forming Sphagnum mosses are able to prevent the dominance of vascular plants under ombrotrophic conditions by efficiently scavenging atmospherically deposited nitrogen (N). N-uptake kinetics of these mosses are therefore expected to play a key role in differential N availability, plant competition, and carbon sequestration in Sphagnum peatlands. The interacting effects of rain N concentration and exposure time on moss N-uptake rates are, however, poorly understood. We investigated the effects of N-concentration (1, 5, 10, 50, 100, 500 µM), N-form (15N - ammonium or nitrate) and exposure time (0.5, 2, 72 h) on uptake kinetics for Sphagnum magellanicum from a pristine bog in Patagonia (Argentina) and from a Dutch bog exposed to decades of N-pollution. Uptake rates for ammonium were higher than for nitrate, and N-binding at adsorption sites was negligible. During the first 0.5 h, N-uptake followed saturation kinetics revealing a high affinity (Km 3.5–6.5 µM). Ammonium was taken up 8 times faster than nitrate, whereas over 72 hours this was only 2 times. Uptake rates decreased drastically with increasing exposure times, which implies that many short-term N-uptake experiments in literature may well have overestimated long-term uptake rates and ecosystem retention. Sphagnum from the polluted site (i.e. long-term N exposure) showed lower uptake rates than mosses from the pristine site, indicating an adaptive response. Sphagnum therefore appears to be highly efficient in using short N pulses (e.g. rainfall in pristine areas). This strategy has important ecological and evolutionary implications: at high N input rates, the risk of N-toxicity seems to be reduced by lower uptake rates of Sphagnum, at the expense of its long-term filter capacity and related competitive advantage over vascular plants. As shown by our conceptual model, interacting effects of N-deposition and climate change (changes in rainfall) will seriously alter the functioning of Sphagnum peatlands. PMID:24416125

Sphagnum mosses--masters of efficient N-uptake while avoiding intoxication.

PubMed

Fritz, Christian; Lamers, Leon P M; Riaz, Muhammad; van den Berg, Leon J L; Elzenga, Theo J T M

2014-01-01

Peat forming Sphagnum mosses are able to prevent the dominance of vascular plants under ombrotrophic conditions by efficiently scavenging atmospherically deposited nitrogen (N). N-uptake kinetics of these mosses are therefore expected to play a key role in differential N availability, plant competition, and carbon sequestration in Sphagnum peatlands. The interacting effects of rain N concentration and exposure time on moss N-uptake rates are, however, poorly understood. We investigated the effects of N-concentration (1, 5, 10, 50, 100, 500 µM), N-form ((15)N-ammonium or nitrate) and exposure time (0.5, 2, 72 h) on uptake kinetics for Sphagnum magellanicum from a pristine bog in Patagonia (Argentina) and from a Dutch bog exposed to decades of N-pollution. Uptake rates for ammonium were higher than for nitrate, and N-binding at adsorption sites was negligible. During the first 0.5 h, N-uptake followed saturation kinetics revealing a high affinity (Km 3.5-6.5 µM). Ammonium was taken up 8 times faster than nitrate, whereas over 72 hours this was only 2 times. Uptake rates decreased drastically with increasing exposure times, which implies that many short-term N-uptake experiments in literature may well have overestimated long-term uptake rates and ecosystem retention. Sphagnum from the polluted site (i.e. long-term N exposure) showed lower uptake rates than mosses from the pristine site, indicating an adaptive response. Sphagnum therefore appears to be highly efficient in using short N pulses (e.g. rainfall in pristine areas). This strategy has important ecological and evolutionary implications: at high N input rates, the risk of N-toxicity seems to be reduced by lower uptake rates of Sphagnum, at the expense of its long-term filter capacity and related competitive advantage over vascular plants. As shown by our conceptual model, interacting effects of N-deposition and climate change (changes in rainfall) will seriously alter the functioning of Sphagnum peatlands.

Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation.

PubMed

Ushiki, Norisuke; Jinno, Masaru; Fujitani, Hirotsugu; Suenaga, Toshikazu; Terada, Akihiko; Tsuneda, Satoshi

2017-05-01

Nitrite oxidation is an aerobic process of the nitrogen cycle in natural ecosystems, and is performed by nitrite-oxidizing bacteria (NOB). Also, nitrite oxidation is a rate-limiting step of nitrogen removal in wastewater treatment plants (WWTPs). Although Nitrospira is known as dominant NOB in WWTPs, information on their physiological properties and kinetic parameters is limited. Here, we report the kinetic parameters and inhibition of nitrite oxidation by free ammonia in pure cultures of Nitrospira sp. strain ND1 and Nitrospira japonica strain NJ1, which were previously isolated from activated sludge in a WWTP. The maximum nitrite uptake rate ( [Formula: see text] ) and the half-saturation constant for nitrite uptake ( [Formula: see text] ) of strains ND1 and NJ1 were 45 ± 7 and 31 ± 5 (μmol NO 2 - /mg protein/h), and 6 ± 1 and 10 ± 2 (μM NO 2 - ), respectively. The [Formula: see text] and [Formula: see text] of two strains indicated that they adapt to low-nitrite-concentration environments like activated sludge. The half-saturation constants for oxygen uptake ( [Formula: see text] ) of the two strains were 4.0±2.5 and 2.6±1.1 (μM O 2 ), respectively. The [Formula: see text] values of the two strains were lower than those of other NOB, suggesting that Nitrospira in activated sludge could oxidize nitrite in the hypoxic environments often found in the interiors of biofilms and flocs. The inhibition thresholds of the two strains by free ammonia were 0.85 and 4.3 (mg-NH 3 l -1 ), respectively. Comparing the physiological properties of the two strains, we suggest that tolerance for free ammonia determines competition and partitioning into ecological niches among Nitrospira populations. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Replication of Simulated Prebiotic Amphiphilic Vesicles in a Finite Environment Exhibits Complex Behavior That Includes High Progeny Variability and Competition

PubMed Central

Armstrong, Don L.; Lancet, Doron

2018-01-01

Abstract We studied the simulated replication and growth of prebiotic vesicles composed of 140 phospholipids and cholesterol using our R-GARD (Real Graded Autocatalysis Replication Domain) formalism that utilizes currently extant lipids that have known rate constants of lipid-vesicle interactions from published experimental data. R-GARD normally modifies kinetic parameters of lipid-vesicle interactions based on vesicle composition and properties. Our original R-GARD model tracked the growth and division of one vesicle at a time in an environment with unlimited lipids at a constant concentration. We explore here a modified model where vesicles compete for a finite supply of lipids. We observed that vesicles exhibit complex behavior including initial fast unrestricted growth, followed by intervesicle competition for diminishing resources, then a second growth burst driven by better-adapted vesicles, and ending with a final steady state. Furthermore, in simulations without kinetic parameter modifications (“invariant kinetics”), the initial replication was an order of magnitude slower, and vesicles' composition variability at the final steady state was much lower. The complex kinetic behavior was not observed either in the previously published R-GARD simulations or in additional simulations presented here with only one lipid component. This demonstrates that both a finite environment (inducing selection) and multiple components (providing variation for selection to act upon) are crucial for portraying evolution-like behavior. Such properties can improve survival in a changing environment by increasing the ability of early protocellular entities to respond to rapid environmental fluctuations likely present during abiogenesis both on Earth and possibly on other planets. This in silico simulation predicts that a relatively simple in vitro chemical system containing only lipid molecules might exhibit properties that are relevant to prebiotic processes. Key Words: Phospholipid vesicles—Prebiotic compartments—Prebiotic vesicle competition—Prebiotic vesicle variability. Astrobiology 18, 419–430. PMID:29634319

7 CFR 1780.72 - Procurement methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 12 2012-01-01 2012-01-01 false Procurement methods. 1780.72 Section 1780.72..., Constructing and Inspections § 1780.72 Procurement methods. Procurement shall be made by one of the following methods: Small purchase procedures; competitive sealed bids (formal advertising); competitive negotiation...

7 CFR 1780.72 - Procurement methods.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 12 2013-01-01 2013-01-01 false Procurement methods. 1780.72 Section 1780.72..., Constructing and Inspections § 1780.72 Procurement methods. Procurement shall be made by one of the following methods: Small purchase procedures; competitive sealed bids (formal advertising); competitive negotiation...

7 CFR 1780.72 - Procurement methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 12 2014-01-01 2013-01-01 true Procurement methods. 1780.72 Section 1780.72..., Constructing and Inspections § 1780.72 Procurement methods. Procurement shall be made by one of the following methods: Small purchase procedures; competitive sealed bids (formal advertising); competitive negotiation...

7 CFR 1780.72 - Procurement methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Procurement methods. 1780.72 Section 1780.72..., Constructing and Inspections § 1780.72 Procurement methods. Procurement shall be made by one of the following methods: Small purchase procedures; competitive sealed bids (formal advertising); competitive negotiation...

7 CFR 1780.72 - Procurement methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 12 2011-01-01 2011-01-01 false Procurement methods. 1780.72 Section 1780.72..., Constructing and Inspections § 1780.72 Procurement methods. Procurement shall be made by one of the following methods: Small purchase procedures; competitive sealed bids (formal advertising); competitive negotiation...

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance.

PubMed

Kuzyakov, Yakov; Xu, Xingliang

2013-05-01

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 (15)N-labelling studies that investigated (15)N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on K(m) (Michaelis constant) and V(max) (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower K(m) values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (V(max)) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Spectral method for a kinetic swarming model

DOE PAGES

Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien

2015-04-28

Here we present the first numerical method for a kinetic description of the Vicsek swarming model. The kinetic model poses a unique challenge, as there is a distribution dependent collision invariant to satisfy when computing the interaction term. We use a spectral representation linked with a discrete constrained optimization to compute these interactions. To test the numerical scheme we investigate the kinetic model at different scales and compare the solution with the microscopic and macroscopic descriptions of the Vicsek model. Lastly, we observe that the kinetic model captures key features such as vortex formation and traveling waves.

Engineering of the function of diamond-like carbon binding peptides through structural design.

PubMed

Gabryelczyk, Bartosz; Szilvay, Géza R; Singh, Vivek K; Mikkilä, Joona; Kostiainen, Mauri A; Koskinen, Jari; Linder, Markus B

2015-02-09

The use of phage display to select material-specific peptides provides a general route towards modification and functionalization of surfaces and interfaces. However, a rational structural engineering of the peptides for optimal affinity is typically not feasible because of insufficient structure-function understanding. Here, we investigate the influence of multivalency of diamond-like carbon (DLC) binding peptides on binding characteristics. We show that facile linking of peptides together using different lengths of spacers and multivalency leads to a tuning of affinity and kinetics. Notably, increased length of spacers in divalent systems led to significantly increased affinities. Making multimers influenced also kinetic aspects of surface competition. Additionally, the multivalent peptides were applied as surface functionalization components for a colloidal form of DLC. The work suggests the use of a set of linking systems to screen parameters for functional optimization of selected material-specific peptides.

Kinetics of Social Contagion

NASA Astrophysics Data System (ADS)

Ruan, Zhongyuan; Iñiguez, Gerardo; Karsai, Márton; Kertész, János

2015-11-01

Diffusion of information, behavioral patterns or innovations follows diverse pathways depending on a number of conditions, including the structure of the underlying social network, the sensitivity to peer pressure and the influence of media. Here we study analytically and by simulations a general model that incorporates threshold mechanism capturing sensitivity to peer pressure, the effect of "immune" nodes who never adopt, and a perpetual flow of external information. While any constant, nonzero rate of dynamically introduced spontaneous adopters leads to global spreading, the kinetics by which the asymptotic state is approached shows rich behavior. In particular, we find that, as a function of the immune node density, there is a transition from fast to slow spreading governed by entirely different mechanisms. This transition happens below the percolation threshold of network fragmentation, and has its origin in the competition between cascading behavior induced by adopters and blocking due to immune nodes. This change is accompanied by a percolation transition of the induced clusters.

Multiphase OH oxidation kinetics of organic aerosol: The role of particle phase state and relative humidity

NASA Astrophysics Data System (ADS)

Slade, Jonathan H.; Knopf, Daniel A.

2014-07-01

Organic aerosol can exhibit different phase states in response to changes in relative humidity (RH), thereby influencing heterogeneous reaction rates with trace gas species. OH radical uptake by laboratory-generated levoglucosan and methyl-nitrocatechol particles, serving as surrogates for biomass burning aerosol, is determined as a function of RH. Increasing RH lowers the viscosity of amorphous levoglucosan aerosol particles enabling enhanced OH uptake. Conversely, OH uptake by methyl-nitrocatechol aerosol particles is suppressed at higher RH as a result of competitive coadsorption of H2O that occupies reactive sites. This is shown to have substantial impacts on organic aerosol lifetimes with respect to OH oxidation. The results emphasize the importance of organic aerosol phase state to accurately describe the multiphase chemical kinetics and thus chemical aging process in atmospheric models to better represent the evolution of organic aerosol and its role in air quality and climate.

Gallium(III)/4-(2-pyridylazo)resorcinol system in water and SDS solution: kinetics and thermodynamics.

PubMed

Biver, T; Boggioni, A; Secco, F; Venturini, M

2008-01-01

The equilibria and kinetics of the complex formation and dissociation reaction between gallium(III) and PAR [4-(2-pyridylazo)resorcinol] have been investigated in water and in the presence of SDS micelles. The reactive form of Ga(III) is GaOH2+ in both cases. The addition of SDS results in an increase of both the binding affinity and velocity, the maximum accelerating effect being observed just above the cmc value of SDS that, under the conditions of the experiments, is 5.6 x 10-3 M. At pH = 3.2, the maximum value of the equilibrium constant ratio Kapp(SDS)/Kapp(H2O) is 27.4, whereas that of the binding rate constants kf(SDS)/kf(H2O) is 16. The results are interpreted in terms of increased concentrations of the reactants on the micelle surface and on competition of PAR and SDS for GaOH2+.

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids.

PubMed

Nguyen, Hung D; Reddy, Vijay S; Brooks, Charles L

2007-02-01

Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly understood phenomenon of which elucidation may aid the exploration of beneficial applications of capsids in materials science and medicine. Using molecular dynamics simulations of coarse-grained models for capsid proteins, we show that the competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of elementary reactions in which free monomers are added to the growing oligomers on a downhill free-energy landscape. However, the insertion of the final subunits is the rate-limiting, energetically unfavorable step in viral capsid assembly. A phase diagram has been constructed to show the regions where capsids or nonidealized structures are stable at each concentration and temperature. We anticipate that our findings will provide guidance in identifying suitable conditions required for in vitro viral capsid assembly experiments.

Characterization of interactions between Nedd4 and beta and gammaENaC using surface plasmon resonance.

PubMed

Asher, C; Chigaev, A; Garty, H

2001-09-07

Cell surface expression of the epithelial Na(+) channel ENaC is regulated by the ubiquitin ligase Nedd4. Binding of the WW domains of Nedd4 to the PY region in the carboxy tails of beta and gammaENaC, results in channel ubiquitination and degradation. Kinetic analysis of these interactions has been done using surface plasmon resonance. Synthetic peptides corresponding to the PY regions of beta and gammaENaC were immobilized on a sensor chip and "real-time" kinetics of their binding to recombinant WW proteins was determined. Specificity of the interactions was established by competition experiment, as well as by monitoring effects of a point mutation known to impair Nedd4/ENaC binding. These data provides the first determination of association, dissociation and equilibrium constants for the interactions between WW2 and beta or gammaENaC. Copyright 2001 Academic Press.

3-Arylpropionylhydroxamic acid derivatives as Helicobacter pylori urease inhibitors: Synthesis, molecular docking and biological evaluation.

PubMed

Shi, Wei-Kang; Deng, Rui-Cheng; Wang, Peng-Fei; Yue, Qin-Qin; Liu, Qi; Ding, Kun-Ling; Yang, Mei-Hui; Zhang, Hong-Yu; Gong, Si-Hua; Deng, Min; Liu, Wen-Run; Feng, Qiu-Ju; Xiao, Zhu-Ping; Zhu, Hai-Liang

2016-10-01

Helicobacter pylori urease is involved in several physiologic responses such as stomach and duodenal ulcers, adenocarcinomas and stomach lymphomas. Thus, inhibition of urease is taken for a good chance to treat H. pylori-caused infections, we have therefore focused our efforts on seeking novel urease inhibitors. Here, a series of arylpropionylhydroxamic acids were synthesized and evaluated for urease inhibition. Out of these compounds, 3-(2-benzyloxy-5-chlorophenyl)-3-hydroxypropionylhydroxamic acid (d24) was the most active inhibitor with IC50 of 0.15±0.05μM, showing a mixed inhibition with both competitive and uncompetitive aspects. Non-linear fitting of kinetic data gives kinetics parameters of 0.13 and 0.12μg·mL(-1) for Ki and Ki', respectively. The plasma protein binding assays suggested that d24 exhibited moderate binding to human and rabbit plasma proteins. Copyright © 2016 Elsevier Ltd. All rights reserved.

In situ imaging of microstructure formation in electronic interconnections

PubMed Central

Salleh, M. A. A. Mohd; Gourlay, C. M.; Xian, J. W.; Belyakov, S. A.; Yasuda, H.; McDonald, S. D.; Nogita, K.

2017-01-01

The development of microstructure during melting, reactive wetting and solidification of solder pastes on Cu-plated printed circuit boards has been studied by synchrotron radiography. Using Sn-3.0Ag-0.5Cu/Cu and Sn-0.7Cu/Cu as examples, we show that the interfacial Cu6Sn5 layer is present within 0.05 s of wetting, and explore the kinetics of flux void formation at the interface between the liquid and the Cu6Sn5 layer. Quantification of the nucleation locations and anisotropic growth kinetics of primary Cu6Sn5 crystals reveals a competition between the nucleation of Cu6Sn5 in the liquid versus growth of Cu6Sn5 from the existing Cu6Sn5 layer. Direct imaging confirms that the β-Sn nucleates at/near the Cu6Sn5 layer in Sn-3.0Ag-0.5Cu/Cu joints. PMID:28079120

Thermodynamic properties of water in confined environments: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Gladovic, Martin; Bren, Urban; Urbic, Tomaž

2018-05-01

Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle distributions, hydrogen bond formation and thermodynamic quantities. Interestingly, temperature and space occupancy of matrix exhibit a similar effect on water properties following the competition between the kinetic and the potential energy of the system, whereby temperature increases the kinetic and matrix packing decreases the potential contribution. A novel thermodynamic decomposition approach was applied to gain insight into individual contributions of different types of inter-particle interactions. This decomposition proved to be useful and in good agreement with the total thermodynamic quantities especially at higher temperatures and matrix packings, where higher-order potential-energy mixing terms lose their importance.

Thymidine kinase 2 enzyme kinetics elucidate the mechanism of thymidine-induced mitochondrial DNA depletion.

PubMed

Sun, Ren; Wang, Liya

2014-10-07

Mitochondrial thymidine kinase 2 (TK2) is a nuclear gene-encoded protein, synthesized in the cytosol and subsequently translocated into the mitochondrial matrix, where it catalyzes the phosphorylation of thymidine (dT) and deoxycytidine (dC). The kinetics of dT phosphorylation exhibits negative cooperativity, but dC phosphorylation follows hyperbolic Michaelis-Menten kinetics. The two substrates compete with each other in that dT is a competitive inhibitor of dC phosphorylation, while dC acts as a noncompetitive inhibitor of dT phosphorylation. In addition, TK2 is feedback inhibited by dTTP and dCTP. TK2 also phosphorylates a number of pyrimidine nucleoside analogues used in antiviral and anticancer therapy and thus plays an important role in mitochondrial toxicities caused by nucleoside analogues. Deficiency in TK2 activity due to genetic alterations causes devastating mitochondrial diseases, which are characterized by mitochondrial DNA (mtDNA) depletion or multiple deletions in the affected tissues. Severe TK2 deficiency is associated with early-onset fatal mitochondrial DNA depletion syndrome, while less severe deficiencies result in late-onset phenotypes. In this review, studies of the enzyme kinetic behavior of TK2 enzyme variants are used to explain the mechanism of mtDNA depletion caused by TK2 mutations, thymidine overload due to thymidine phosphorylase deficiency, and mitochondrial toxicity caused by antiviral thymidine analogues.

Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine-deficient GAMT−/− mouse hearts

PubMed Central

Branovets, Jelena; Sepp, Mervi; Kotlyarova, Svetlana; Jepihhina, Natalja; Sokolova, Niina; Aksentijevic, Dunja; Lygate, Craig A.; Neubauer, Stefan; Birkedal, Rikke

2013-01-01

Disruption of the creatine kinase (CK) system in hearts of CK-deficient mice leads to changes in the ultrastructure and regulation of mitochondrial respiration. We expected to see similar changes in creatine-deficient mice, which lack the enzyme guanidinoacetate methyltransferase (GAMT) to produce creatine. The aim of this study was to characterize the changes in cardiomyocyte mitochondrial organization, regulation of respiration, and intracellular compartmentation associated with GAMT deficiency. Three-dimensional mitochondrial organization was assessed by confocal microscopy. On populations of permeabilized cardiomyocytes, we recorded ADP and ATP kinetics of respiration, competition between mitochondria and pyruvate kinase for ADP produced by ATPases, ADP kinetics of endogenous pyruvate kinase, and ATP kinetics of ATPases. These data were analyzed by mathematical models to estimate intracellular compartmentation. Quantitative analysis of morphological and kinetic data as well as derived model fits showed no difference between GAMT-deficient and wild-type mice. We conclude that inactivation of the CK system by GAMT deficiency does not alter mitochondrial organization and intracellular compartmentation in relaxed cardiomyocytes. Thus, our results suggest that the healthy heart is able to preserve cardiac function at a basal level in the absence of CK-facilitated energy transfer without compromising intracellular organization and the regulation of mitochondrial energy homeostasis. This raises questions on the importance of the CK system as a spatial energy buffer in unstressed cardiomyocytes. PMID:23792673

The electrooxidation mechanism of formic acid on platinum and on lead ad-atoms modified platinum studied with the kinetic isotope effect

NASA Astrophysics Data System (ADS)

Bełtowska-Brzezinska, M.; Łuczak, T.; Stelmach, J.; Holze, R.

2014-04-01

Kinetics and mechanism of formic acid (FA) oxidation on platinum and upd-lead ad-atoms modified platinum electrodes have been studied using unlabelled and deuterated compounds. Poisoning of the electrode surface by CO-like species was prevented by suppression of dissociative chemisorption of FA due to a fast competitive underpotential deposition of lead ad-atoms on the Pt surface from an acidic solution containing Pb2+ cations. Modification of the Pt electrode with upd lead induced a catalytic effect in the direct electrooxidation of physisorbed FA to CO2. With increasing degree of H/D substitution, the rate of this reaction decreased in the order: HCOOH > DCOOH ≥ HCOOD > DCOOD. HCOOH was oxidized 8.5-times faster on a Pt/Pb electrode than DCOOD. This primary kinetic isotope effect proves that the C-H- and O-H-bonds are simultaneously cleaved in the rate determining step. A secondary kinetic isotope effect was found in the dissociative chemisorption of FA in the hydrogen adsorption-desorption range on a bare Pt electrode after H/D exchange in the C-H bond, wherein the influence of deuterium substitution in the O-H group was negligibly small. Thus the C-H bond cleavage is accompanied by the C-OH and not the O-H bond split in the FA decomposition, producing CO-like species on the Pt surface sites.

A solvable model of Vlasov-kinetic plasma turbulence in Fourier-Hermite phase space

NASA Astrophysics Data System (ADS)

Adkins, T.; Schekochihin, A. A.

2018-02-01

A class of simple kinetic systems is considered, described by the one-dimensional Vlasov-Landau equation with Poisson or Boltzmann electrostatic response and an energy source. Assuming a stochastic electric field, a solvable model is constructed for the phase-space turbulence of the particle distribution. The model is a kinetic analogue of the Kraichnan-Batchelor model of chaotic advection. The solution of the model is found in Fourier-Hermite space and shows that the free-energy flux from low to high Hermite moments is suppressed, with phase mixing cancelled on average by anti-phase-mixing (stochastic plasma echo). This implies that Landau damping is an ineffective route to dissipation (i.e. to thermalisation of electric energy via velocity space). The full Fourier-Hermite spectrum is derived. Its asymptotics are -3/2$ at low wavenumbers and high Hermite moments ( ) and -1/2k-2$ at low Hermite moments and high wavenumbers ( ). These conclusions hold at wavenumbers below a certain cutoff (analogue of Kolmogorov scale), which increases with the amplitude of the stochastic electric field and scales as inverse square of the collision rate. The energy distribution and flows in phase space are a simple and, therefore, useful example of competition between phase mixing and nonlinear dynamics in kinetic turbulence, reminiscent of more realistic but more complicated multi-dimensional systems that have not so far been amenable to complete analytical solution.

Kinetic regulation of coated vesicle secretion

PubMed Central

Foret, Lionel; Sens, Pierre

2008-01-01

The secretion of vesicles for intracellular transport often relies on the aggregation of specialized membrane-bound proteins into a coat able to curve cell membranes. The nucleation and growth of a protein coat is a kinetic process that competes with the energy-consuming turnover of coat components between the membrane and the cytosol. We propose a generic kinetic description of coat assembly and the formation of coated vesicles and discuss its implication to the dynamics of COP vesicles that traffic within the Golgi and with the endoplasmic reticulum. We show that stationary coats of fixed area emerge from the competition between coat growth and the recycling of coat components, in a fashion resembling the treadmilling of cytoskeletal filaments. We further show that the turnover of coat components allows for a highly sensitive switching mechanism between a quiescent and a vesicle producing membrane, upon a slowing down of the exchange kinetics. We claim that the existence of this switching behavior, also triggered by factors, such as the presence of cargo and variation of the membrane mechanical tension, allows for efficient regulation of vesicle secretion. We propose a model, supported by different experimental observations, in which vesiculation of secretory membranes is impaired by the energy-consuming desorption of coat proteins, until the presence of cargo or other factors triggers a dynamical switch into a vesicle producing state. PMID:18824695

Tight coupling of Na+/K+-ATPase with glycolysis demonstrated in permeabilized rat cardiomyocytes.

PubMed

Sepp, Mervi; Sokolova, Niina; Jugai, Svetlana; Mandel, Merle; Peterson, Pearu; Vendelin, Marko

2014-01-01

The effective integrated organization of processes in cardiac cells is achieved, in part, by the functional compartmentation of energy transfer processes. Earlier, using permeabilized cardiomyocytes, we demonstrated the existence of tight coupling between some of cardiomyocyte ATPases and glycolysis in rat. In this work, we studied contribution of two membrane ATPases and whether they are coupled to glycolysis--sarcoplasmic reticulum Ca2+ ATPase (SERCA) and plasmalemma Na+/K+-ATPase (NKA). While SERCA activity was minor in this preparation in the absence of calcium, major role of NKA was revealed accounting to ∼30% of the total ATPase activity which demonstrates that permeabilized cell preparation can be used to study this pump. To elucidate the contribution of NKA in the pool of ATPases, a series of kinetic measurements was performed in cells where NKA had been inhibited by 2 mM ouabain. In these cells, we recorded: ADP- and ATP-kinetics of respiration, competition for ADP between mitochondria and pyruvate kinase (PK), ADP-kinetics of endogenous PK, and ATP-kinetics of total ATPases. The experimental data was analyzed using a series of mathematical models with varying compartmentation levels. The results show that NKA is tightly coupled to glycolysis with undetectable flux of ATP between mitochondria and NKA. Such tight coupling of NKA to PK is in line with its increased importance in the pathological states of the heart when the substrate preference shifts to glucose.

Kinetics of nitrogenase of Klebsiella pneumoniae. Heterotropic interactions between magnesium-adenosine 5'-diphosphate and magnesium-adenosine 5'-triphosphate.

PubMed Central

Thorneley, R N; Cornish-Bowden, A

1977-01-01

The effects of MgADP and MgATP on the kinetics of a pre-steady-state electron-transfer reaction and on the steady-state kinetics of H2 evulution for nitrogenase proteins of K. pneumoniae were studied. MgADP was a competitive inhibitor of MgATP in the MgATP-induced electron transfer from the Fe-protein to the Mo-Fe-protein. A dissociation constant K'i = 20 micron was determined for MgADP. The release of MgADP or a coupled conformation change in the Fe-protein of K.pneumoniae occurred with a rate comparable with that of electron transfer, k approximately 2 X 10(2)S-1. Neither homotropic nor heterotropic interactions involving MgATP and MgADP were observed for this reaction. Steady-state kinetic data for H2 evolution exhibited heterotropic effects between MgADP and MgATP. The data have been fitted to symmetry and sequential-type models involving conformation changes in two identical subunits. The data suggest that the enzyme can bind up to molecules of either MgATP or MgADP, but is unable to bind both nucleotides simultaneously. The control of H2 evolution by the MgATP/MgADP ratio is not at the level of electron transfer between the Fe- and Mo-Fe-proteins. Images Fig. 2. PMID:336036

Effects of a Strength Training Session After an Exercise Inducing Muscle Damage on Recovery Kinetics.

PubMed

Abaïdia, Abd-Elbasset; Delecroix, Barthélémy; Leduc, Cédric; Lamblin, Julien; McCall, Alan; Baquet, Georges; Dupont, Grégory

2017-01-01

Abaïdia, A-E, Delecroix, B, Leduc, C, Lamblin, J, McCall, A, Baquet, G, and Dupont, G. Effects of a strength training session after an exercise inducing muscle damage on recovery kinetics. J Strength Cond Res 31(1): 115-125, 2017-The purpose of this study was to investigate the effects of an upper-limb strength training session the day after an exercise inducing muscle damage on recovery of performance. In a randomized crossover design, subjects performed the day after the exercise, on 2 separate occasions (passive vs. active recovery conditions) a single-leg exercise (dominant in one condition and nondominant in the other condition) consisting of 5 sets of 15 eccentric contractions of the knee flexors. Active recovery consisted of performing an upper-body strength training session the day after the exercise. Creatine kinase, hamstring strength, and muscle soreness were assessed immediately and 20, 24, and 48 hours after exercise-induced muscle damage. The upper-body strength session, after muscle-damaging exercise accelerated the recovery of slow concentric force (effect size = 0.65; 90% confidence interval = -0.06 to 1.32), but did not affect the recovery kinetics for the other outcomes. The addition of an upper-body strength training session the day after muscle-damaging activity does not negatively affect the recovery kinetics. Upper-body strength training may be programmed the day after a competition.

Methods for Kinetic and Thermodynamic Analysis of Aminoacyl-tRNA Synthetases

PubMed Central

Francklyn, Christopher S.; First, Eric A.; Perona, John J.; Hou, Ya-Ming

2008-01-01

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion. PMID:18241792

10 CFR 436.33 - Procedures and methods for contractor selection.

Code of Federal Regulations, 2010 CFR

2010-01-01

... for contractor selection. (a) Competitive selection. Competitive selections based on solicitation of... synopsizes the proposed contract action. (2) Each competitive solicitation— (i) Shall request technical and... from those within the competitive range. (b) Unsolicited proposals. Federal agencies may— (1) Consider...

The Functions and Methods of Mental Training on Competitive Sports

NASA Astrophysics Data System (ADS)

Xiong, Jianshe

Mental training is the major training method of the competitive sports and the main factor of athletes skill and tactics level.By combining the psychological factor with the current competitive sports characteristics, this paper presents the function of mental training forward athletes, and how to improve the comprehensive psychological quality by using mental training.

Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists

DOE PAGES

McCully, Alexandra L.; LaSarre, Breah; McKinlay, James B.; ...

2017-11-28

ABSTRACT Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer’s waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichiamore » coli and phototrophic Rhodopseudomonas palustris . In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris . In return, R. palustris cross-feeds E. coli ammonium (NH 4 + ), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH 4 + in each species. The model predicted that interpartner competition for NH 4 + could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH 4 + transporters in both NH 4 + competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH 4 + to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. IMPORTANCE Mutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical cycles. Cross-fed nutrients within these systems can be either waste products valued by only one partner or nutrients valued by both partners. Here, we explored how interpartner competition for a communally valuable cross-fed nutrient impacts mutualism dynamics. We discovered that mutualism stability necessitates that the recipient have a competitive advantage against the producer in obtaining the cross-fed nutrient, provided that the nutrient is generated intracellularly. We propose that the requirement for recipient-biased competition is a general rule for mutualistic coexistence based on the transfer of intracellularly generated, communally valuable resources.« less

Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists

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

McCully, Alexandra L.; LaSarre, Breah; McKinlay, James B.

ABSTRACT Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer’s waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichiamore » coli and phototrophic Rhodopseudomonas palustris . In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris . In return, R. palustris cross-feeds E. coli ammonium (NH 4 + ), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH 4 + in each species. The model predicted that interpartner competition for NH 4 + could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH 4 + transporters in both NH 4 + competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH 4 + to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. IMPORTANCE Mutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical cycles. Cross-fed nutrients within these systems can be either waste products valued by only one partner or nutrients valued by both partners. Here, we explored how interpartner competition for a communally valuable cross-fed nutrient impacts mutualism dynamics. We discovered that mutualism stability necessitates that the recipient have a competitive advantage against the producer in obtaining the cross-fed nutrient, provided that the nutrient is generated intracellularly. We propose that the requirement for recipient-biased competition is a general rule for mutualistic coexistence based on the transfer of intracellularly generated, communally valuable resources.« less

Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists.

PubMed

McCully, Alexandra L; LaSarre, Breah; McKinlay, James B

2017-11-28

Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer's waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris In return, R. palustris cross-feeds E. coli ammonium (NH 4 + ), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH 4 + in each species. The model predicted that interpartner competition for NH 4 + could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH 4 + transporters in both NH 4 + competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH 4 + to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. IMPORTANCE Mutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical cycles. Cross-fed nutrients within these systems can be either waste products valued by only one partner or nutrients valued by both partners. Here, we explored how interpartner competition for a communally valuable cross-fed nutrient impacts mutualism dynamics. We discovered that mutualism stability necessitates that the recipient have a competitive advantage against the producer in obtaining the cross-fed nutrient, provided that the nutrient is generated intracellularly. We propose that the requirement for recipient-biased competition is a general rule for mutualistic coexistence based on the transfer of intracellularly generated, communally valuable resources. Copyright © 2017 McCully et al.

Studies on collagen-tannic acid-collagenase ternary system: Inhibition of collagenase against collagenolytic degradation of extracellular matrix component of collagen.

PubMed

Krishnamoorthy, Ganesan; Sehgal, Praveen Kumar; Mandal, Asit Baran; Sadulla, Sayeed

2012-06-01

We report the detailed studies on the inhibitory effect of tannic acid (TA) on Clostridium histolyticum collagenase (ChC) activity against degradation of extracellular matrix component of collagen. The TA treated collagen exhibited 64% resistance against collagenolytic hydrolysis by ChC, whereas direct interaction of TA with ChC exhibited 99% inhibition against degradation of collagen and the inhibition was found to be concentration dependant. The kinetic inhibition of ChC has been deduced from the extent of hydrolysis of N-[3-(2-furyl) acryloyl]-Leu-Gly-Pro-Ala (FALGPA). This data provides a selective competitive mode of inhibition on ChC activity seems to be influenced strongly by the nature and structure of TA. TA showed inhibitor activity against the ChC by molecular docking method. This result demonstrated that TA containing digalloyl radical possess the ability to inhibit the ChC. The inhibition of ChC in gaining new insight into the mechanism of stabilization of collagen by TA is discussed.

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

Ye Jia; Lawrence Berkeley Laboratory, Berkeley, California 94720-8250; Li Youhong

Theoretical predictions indicate that ordered alloys can spontaneously develop a steady-state nanoscale microstructure when irradiated with energetic particles. This behavior derives from a dynamical competition between disordering in cascades and thermally activated reordering, which leads to self-organization of the chemical order parameter. We test this possibility by combining molecular dynamics (MD) and kinetic Monte Carlo (KMC) simulations. We first generate realistic distributions of disordered zones for Ni{sub 3}Al irradiated with 70 keV He and 1 MeV Kr ions using MD and then input this data into KMC to obtain predictions of steady state microstructures as a function of the irradiationmore » flux. Nanoscale patterning is observed for Kr ion irradiations but not for He ion irradiations. We illustrate, moreover, using image simulations of these KMC microstructures, that high-resolution transmission electron microscopy can be employed to identify nanoscale patterning. Finally, we indicate how this method could be used to synthesize functional thin films, with potential for magnetic applications.« less

Structure based discovery of clomifene as a potent inhibitor of cancer-associated mutant IDH1

PubMed Central

Luan, Shanshan; Li, Dan; Chen, Renqi; Zhang, Qian; Chen, Lixia; Huang, Jiangeng; Li, Hua

2017-01-01

Isocitrate dehydrogenase (IDH) plays an indispensable role in the tricarboxylic acid cycle, and IDH mutations are present in nearly 75% of glioma and 20% of acute myeloid leukemia. One IDH1R132H inhibitor (clomifene citrate) was found by virtual screening method, which can selectively suppress mutant enzyme activities in vitro and in vivo with a dose-dependent manner. The molecular docking indicated that clomifene occupied the allosteric site of the mutant IDH1. Enzymatic kinetics also demonstrated that clomifene inhibited mutant enzyme in a non-competitive manner. Moreover, knockdown of mutant IDH1 in HT1080 cells decreased the sensitivity to clomifene. In vivo studies indicated that clomifene significantly suppressed the tumor growth of HT1080-bearing CB-17/Icr-scid mice with oral administration of 100 mg/kg and 50 mg/kg per day. In short, our findings highlight clomifene may have clinical potential in tumor therapies as a safe and effective inhibitor of mutant IDH1. PMID:28498812

Characterization of Protein Tyrosine Phosphatase 1B Inhibition by Chlorogenic Acid and Cichoric Acid.

PubMed

Lipchock, James M; Hendrickson, Heidi P; Douglas, Bonnie B; Bird, Kelly E; Ginther, Patrick S; Rivalta, Ivan; Ten, Nicholas S; Batista, Victor S; Loria, J Patrick

2017-01-10

Protein tyrosine phosphatase 1B (PTP1B) is a known regulator of the insulin and leptin signaling pathways and is an active target for the design of inhibitors for the treatment of type II diabetes and obesity. Recently, cichoric acid (CHA) and chlorogenic acid (CGA) were predicted by docking methods to be allosteric inhibitors that bind distal to the active site. However, using a combination of steady-state inhibition kinetics, solution nuclear magnetic resonance experiments, and molecular dynamics simulations, we show that CHA is a competitive inhibitor that binds in the active site of PTP1B. CGA, while a noncompetitive inhibitor, binds in the second aryl phosphate binding site, rather than the predicted benzfuran binding pocket. The molecular dynamics simulations of the apo enzyme and cysteine-phosphoryl intermediate states with and without bound CGA suggest CGA binding inhibits PTP1B by altering hydrogen bonding patterns at the active site. This study provides a mechanistic understanding of the allosteric inhibition of PTP1B.

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Effects of adding LiBF4 on the glass-transition kinetics of 1,2-propanediol

NASA Astrophysics Data System (ADS)

Terashima, Yukio; Takeda, Kiyoshi

2017-11-01

By applying an isoconversional method to differential-scanning calorimetry (DSC) data, we have discovered that the addition of LiBF4 significantly affects the activation energy Eα of the glass transition of 1,2-propanediol. Depending upon its concentration, the dynamics of the glass transition are affected more by adding LiBF4 at an early stage of the glass-to-liquid transition rather than at later stages. As the mole fraction x of LiBF4 increases, the value of Eα initially increases, but it decreases dramatically during the glass transition. The abrupt decline in Eα suggests that the addition of LiBF4 breaks cooperative rearranging motions into smaller parts. The expansion of cooperativity, and its fragmentation with increasing temperature, can be explained in terms of competition between the hydrogen-bond networks of the alcohol solvent and the ionic interactions due to the added salt. The variability of Eα with temperature is found to correlate exponentially with the dynamic fragility.

Simulations of incompressible Navier Stokes equations on curved surfaces using discrete exterior calculus

NASA Astrophysics Data System (ADS)

Samtaney, Ravi; Mohamed, Mamdouh; Hirani, Anil

2015-11-01

We present examples of numerical solutions of incompressible flow on 2D curved domains. The Navier-Stokes equations are first rewritten using the exterior calculus notation, replacing vector calculus differential operators by the exterior derivative, Hodge star and wedge product operators. A conservative discretization of Navier-Stokes equations on simplicial meshes is developed based on discrete exterior calculus (DEC). The discretization is then carried out by substituting the corresponding discrete operators based on the DEC framework. By construction, the method is conservative in that both the discrete divergence and circulation are conserved up to machine precision. The relative error in kinetic energy for inviscid flow test cases converges in a second order fashion with both the mesh size and the time step. Numerical examples include Taylor vortices on a sphere, Stuart vortices on a sphere, and flow past a cylinder on domains with varying curvature. Supported by the KAUST Office of Competitive Research Funds under Award No. URF/1/1401-01.

Affinity of microbial transglutaminase to αs1-, β-, and acid casein under atmospheric and high pressure conditions.

PubMed

Menéndez, Orquídea; Schwarzenbolz, Uwe; Partschefeld, Claudia; Henle, Thomas

2009-05-27

Kinetics for the reaction of microbial transglutaminase (MTG) with individual caseins in a TRIS-acetate buffer at pH 6.0 was evaluated under atmospheric pressure (0.1 MPa) and high pressure (400 MPa) at 40 °C. The reaction was monitored under the following limitations: The kinetics from the initial velocities was obtained from nonprogressive enzymatic reactions assuming that the individual catalytic constants of reactive glutamine residues are represented by the reaction between MTG and casein monomers. Enzyme reaction kinetics carried out at 0.1 MPa at 40 °C showed Henri-Michaelis-Menten behavior with maximal velocities of 2.7 ± 0.02 × 10(-3), 0.8 ± 0.01 × 10(-3), and 1.3 ± 0.30 × 10(-3) mmol/L · min and K(m) values of 59 ± 2 × 10(-3), 64 ± 3 × 10(-3), and 50 ± 2 × 10(-3) mmol/L for β-, α(s1)-, and acid casein, respectively. Enzyme reaction kinetics of β-casein carried out at 400 MPa and 40 °C also showed a Henri-Michaelis-Menten behavior with a similar maximal velocity of 2.5 ± 0.33 × 10(-3) mmol/L · min, but, comparable to a competitive inhibition, the K(m) value increased to 144 ± 34 × 10(-3) mmol/L. The reaction of MTG with α(s1)-casein under high pressure did not fit in to Henri-Michaelis-Menten kinetics, indicating the complex influence of pressure on protein-enzyme interactions.

Determination of kinetic data for soot oxidation: Modeling of competition between oxygen diffusion and reaction during thermogravimetric analysis

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

Gilot, P.; Bonnefoy, F.; Marcuccilli, F.

1993-10-01

Kinetic data concerning carbon black oxidation in the temperature range between 600 and 900 C have been obtained using thermogravimetric analysis. Modeling of diffusion in a boundary layer above the pan and inside the porous medium coupled to oxygen reaction with carbon black is necessary to obtain kinetic constants as a function of temperature. These calculations require the knowledge of the oxidation rate at a given constant temperature as a function of the initial mass loading m[sub o]. This oxidation rate, expressed in milligrams of soot consumed per second and per milligram of initial soot loading, decreases when m[sub o]more » increases, in agreement with a reaction in an intermediary regime where the kinetics and the oxygen diffusion operate. The equivalent diffusivity of oxygen inside the porous medium is evaluated assuming two degrees of porosity: between soot aggregates and inside each aggregate. Below 700 C an activation energy of about 103 kJ/mol can be related to a combustion reaction probably kinetically controlled. Beyond 700 C the activation energy of about 20 kJ/ mol corresponds to a reaction essentially controlled by oxygen diffusion leading to a constant density oxidation with oxygen consumption at or near the particle surface. To validate these data, they are used in the modeling of a Diesel particulate trap regeneration. In this particular case, the oxidizing flux is forced across the carbon black deposit, oxygen diffusion being insignificant. A good agreement between experimental results and model predictions is obtained, proving the rate constants validity.« less

Synthetic spectral analysis of a kinetic model for slow-magnetosonic waves in solar corona

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

Ruan, Wenzhi; He, Jiansen; Tu, Chuanyi

We propose a kinetic model of slow-magnetosonic waves to explain various observational features associated with the propagating intensity disturbances (PIDs) occurring in the solar corona. The characteristics of slow mode waves, e.g, inphase oscillations of density, velocity, and thermal speed, are reproduced in this kinetic model. Moreover, the red-blue (R-B) asymmetry of the velocity distribution as self-consistently generated in the model is found to be contributed from the beam component, as a result of the competition between Landau resonance and Coulomb collisions. Furthermore, we synthesize the spectral lines and make the spectral analysis, based on the kinetic simulation data ofmore » the flux tube plasmas and the hypothesis of the surrounding background plasmas. It is found that the fluctuations of parameters of the synthetic spectral lines are basically consistent with the observations: (1) the line intensity, Doppler shift, and line width are fluctuating in phase; (2) the R-B asymmetry usually oscillate out of phase with the former three parameters; (3) the blueward asymmetry is more evident than the redward asymmetry in the R-B fluctuations. The oscillations of line parameters become weakened for the case with denser surrounding background plasmas. Similar to the observations, there is no doubled-frequency oscillation of the line width for the case with flux-tube plasmas flowing bulkly upward among the static background plasmas. Therefore, we suggest that the “wave + beam flow” kinetic model may be a viable interpretation for the PIDs observed in the solar corona.« less

Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA-Encoded Chemical Library.

PubMed

Cuozzo, John W; Centrella, Paolo A; Gikunju, Diana; Habeshian, Sevan; Hupp, Christopher D; Keefe, Anthony D; Sigel, Eric A; Soutter, Holly H; Thomson, Heather A; Zhang, Ying; Clark, Matthew A

2017-05-04

We have identified and characterized novel potent inhibitors of Bruton's tyrosine kinase (BTK) from a single DNA-encoded library of over 110 million compounds by using multiple parallel selection conditions, including variation in target concentration and addition of known binders to provide competition information. Distinct binding profiles were observed by comparing enrichments of library building block combinations under these conditions; one enriched only at high concentrations of BTK and was competitive with ATP, and another enriched at both high and low concentrations of BTK and was not competitive with ATP. A compound representing the latter profile showed low nanomolar potency in biochemical and cellular BTK assays. Results from kinetic mechanism of action studies were consistent with the selection profiles. Analysis of the co-crystal structure of the most potent compound demonstrated a novel binding mode that revealed a new pocket in BTK. Our results demonstrate that profile-based selection strategies using DNA-encoded libraries form the basis of a new methodology to rapidly identify small molecule inhibitors with novel binding modes to clinically relevant targets. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

National Clinical Skills Competition: an effective simulation-based method to improve undergraduate medical education in China.

PubMed

Jiang, Guanchao; Chen, Hong; Wang, Qiming; Chi, Baorong; He, Qingnan; Xiao, Haipeng; Zhou, Qinghuan; Liu, Jing; Wang, Shan

2016-01-01

Background The National Clinical Skills Competition has been held in China for 5 consecutive years since 2010 to promote undergraduate education reform and improve the teaching quality. The effects of the simulation-based competition will be analyzed in this study. Methods Participation in the competitions and the compilation of the questions used in the competition finals are summarized, and the influence and guidance quality are further analyzed. Through the nationwide distribution of questionnaires in medical colleges, the effects of the simulation-based competition on promoting undergraduate medical education reform were evaluated. Results The results show that approximately 450 students from more than 110 colleges (accounting for 81% of colleges providing undergraduate clinical medical education in China) participated in the competition each year. The knowledge, skills, and attitudes were comprehensively evaluated by simulation-based assessment. Eight hundred and eighty copies of the questionnaires were distributed to 110 participating medical schools in 2015. In total, 752 valid responses were received across 95 schools. The majority of the interviewees agreed or strongly agreed that competition promoted the adoption of advanced educational principles (76.8%), updated the curriculum model and instructional methods (79.8%), strengthened faculty development (84.0%), improved educational resources (82.1%), and benefited all students (53.4%). Conclusions The National Clinical Skills Competition is widely accepted in China. It has effectively promoted the reform and development of undergraduate medical education in China.

An ab initio/Rice-Ramsperger-Kassel-Marcus study of the hydrogen-abstraction reactions of methyl ethers, H(3)COCH(3-x)(CH(3))(x), x = 0-2, by OH; mechanism and kinetics.

PubMed

Zhou, Chong-Wen; Simmie, John M; Curran, Henry J

2010-07-14

A theoretical study of the mechanism and kinetics of the H-abstraction reaction from dimethyl (DME), ethylmethyl (EME) and iso-propylmethyl (IPME) ethers by the OH radical has been carried out using the high-level methods CCSD(T)/CBS, G3 and G3MP2BH&H. The computationally less-expensive methods of G3 and G3MP2BH&H yield results for DME within 0.2-0.6 and 0.7-0.9 kcal mol(-1), respectively, of the coupled cluster, CCSD(T), values extrapolated to the basis set limit. So the G3 and G3MP2BH&H methods can be confidently used for the reactions of the higher ethers. A distinction is made between the two different kinds of H-atoms, classified as in/out-of the symmetry plane, and it is found that abstraction from the out-of-plane H-atoms proceeds through a stepwise mechanism involving the formation of a reactant complex in the entrance channel and product complex in the exit channel. The in-plane H-atom abstractions take place through a more direct mechanism and are less competitive. Rate constants of the three reactions have been calculated in the temperature range of 500-3000 K using the Variflex code, based on the weak collision, master equation/microcanonical variational RRKM theory including tunneling corrections. The computed total rate constants (cm(3) mol(-1) s(-1)) have been fitted as follows: k(DME) = 2.74 xT(3.94) exp (1534.2/T), k(EME) = 20.93 xT(3.61) exp (2060.1/T) and k(IPME) = 0.55 xT(3.93) exp (2826.1/T). Expressions of the group rate constants for the three different carbon sites are also provided.

Extraction kinetic modelling of total polyphenols and total anthocyanins from saffron floral bio-residues: Comparison of extraction methods.

PubMed

Da Porto, Carla; Natolino, Andrea

2018-08-30

Analysis of the extraction kinetic modelling for natural compounds is essential for industrial application. The second order rate model was applied to estimate the extraction kinetics of conventional solid-liquid extraction (CSLE), ultrasound-assisted extraction (UAE) and microwave-assisted extraction (MAE) of total polyphenols (TPC) from saffron floral bio-residues at different solid-to-liquid ratios (R S/L )(1:10, 1:20, 1:30, 1:50 g ml -1 ), ethanol 59% as solvent and 66 °C temperature. The optimum solid-to-liquid ratios for TPC kinetics were 1:20 for CLSE, 1:30 for UAE and 1:50 for MAE. The kinetics of total anthocyanins (TA) and antioxidant activity (AA) were investigated for the optimum R S/L for each method. The results showed a good prediction of the model for extraction kinetics in all experiments (R 2  > 0.99; NRMS 0.65-3.35%). The kinetic parameters were calculated and discussed. UAE, compared with the other methods, had the greater efficiency for TPC, TA and AA. Copyright © 2018 Elsevier Ltd. All rights reserved.

Single and multi-component adsorption of psychiatric pharmaceuticals onto alternative and commercial carbons.

PubMed

Calisto, Vânia; Jaria, Guilaine; Silva, Carla Patrícia; Ferreira, Catarina I A; Otero, Marta; Esteves, Valdemar I

2017-05-01

This work describes the adsorptive removal of three widely consumed psychiatric pharmaceuticals (carbamazepine, paroxetine and oxazepam) from ultrapure water. Two different adsorbents were used: a commercial activated carbon and a non-activated waste-based carbon (PS800-150-HCl), produced by pyrolysis of primary paper mill sludge. These adsorbents were used in single, binary and ternary batch experiments in order to determine the adsorption kinetics and equilibrium isotherms of the considered pharmaceuticals. For the three drugs and both carbons, the equilibrium was quickly attained (with maximum equilibrium times of 15 and 120 min for the waste-based and the commercial carbons, respectively) even in binary and ternary systems. Single component equilibrium data were adequately described by the Langmuir model, with the commercial carbon registering higher maximum adsorption capacities (between 272 ± 10 and 493 ± 12 μmol g -1 ) than PS800-150-HCl (between 64 ± 2 and 74 ± 1 μmol g -1 ). Multi-component equilibrium data were also best fitted by the single component Langmuir isotherm, followed by the Langmuir competitive model. Overall, competitive effects did not largely affect the performance of both adsorbents. Binary and ternary systems maintained fast kinetics, the individual maximum adsorption capacities were not lower than half of the single component systems and both carbons presented improved total adsorption capacities for multi-component solutions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of herbicide resistance endowing Ile-1781-Leu and Asp-2078-Gly ACCase gene mutations on ACCase kinetics and growth traits in Lolium rigidum.

PubMed

Vila-Aiub, Martin M; Yu, Qin; Han, Heping; Powles, Stephen B

2015-08-01

The rate of herbicide resistance evolution in plants depends on fitness traits endowed by alleles in both the presence and absence (resistance cost) of herbicide selection. The effect of two Lolium rigidum spontaneous homozygous target-site resistance-endowing mutations (Ile-1781-Leu, Asp-2078-Gly) on both ACCase activity and various plant growth traits have been investigated here. Relative growth rate (RGR) and components (net assimilation rate, leaf area ratio), resource allocation to different organs, and growth responses in competition with a wheat crop were assessed. Unlike plants carrying the Ile-1781-Leu resistance mutation, plants homozygous for the Asp-2078-Gly mutation exhibited a significantly lower RGR (30%), which translated into lower allocation of biomass to roots, shoots, and leaves, and poor responses to plant competition. Both the negligible and significant growth reductions associated, respectively, with the Ile-1781-Leu and Asp-2078-Gly resistance mutations correlated with their impact on ACCase activity. Whereas the Ile-1781-Leu mutation showed no pleiotropic effects on ACCase kinetics, the Asp-2078-Gly mutation led to a significant reduction in ACCase activity. The impaired growth traits are discussed in the context of resistance costs and the effects of each resistance allele on ACCase activity. Similar effects of these two particular ACCase mutations on the ACCase activity of Alopecurus myosuroides were also confirmed. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

The mechanistic basis for noncompetitive ibogaine inhibition of serotonin and dopamine transporters.

PubMed

Bulling, Simon; Schicker, Klaus; Zhang, Yuan-Wei; Steinkellner, Thomas; Stockner, Thomas; Gruber, Christian W; Boehm, Stefan; Freissmuth, Michael; Rudnick, Gary; Sitte, Harald H; Sandtner, Walter

2012-05-25

Ibogaine, a hallucinogenic alkaloid proposed as a treatment for opiate withdrawal, has been shown to inhibit serotonin transporter (SERT) noncompetitively, in contrast to all other known inhibitors, which are competitive with substrate. Ibogaine binding to SERT increases accessibility in the permeation pathway connecting the substrate-binding site with the cytoplasm. Because of the structural similarity between ibogaine and serotonin, it had been suggested that ibogaine binds to the substrate site of SERT. The results presented here show that ibogaine binds to a distinct site, accessible from the cell exterior, to inhibit both serotonin transport and serotonin-induced ionic currents. Ibogaine noncompetitively inhibited transport by both SERT and the homologous dopamine transporter (DAT). Ibogaine blocked substrate-induced currents also in DAT and increased accessibility of the DAT cytoplasmic permeation pathway. When present on the cell exterior, ibogaine inhibited SERT substrate-induced currents, but not when it was introduced into the cytoplasm through the patch electrode. Similar to noncompetitive transport inhibition, the current block was not reversed by increasing substrate concentration. The kinetics of inhibitor binding and dissociation, as determined by their effect on SERT currents, indicated that ibogaine does not inhibit by forming a long-lived complex with SERT, but rather binds directly to the transporter in an inward-open conformation. A kinetic model for transport describing the noncompetitive action of ibogaine and the competitive action of cocaine accounts well for the results of the present study.

The Mechanistic Basis for Noncompetitive Ibogaine Inhibition of Serotonin and Dopamine Transporters*

PubMed Central

Bulling, Simon; Schicker, Klaus; Zhang, Yuan-Wei; Steinkellner, Thomas; Stockner, Thomas; Gruber, Christian W.; Boehm, Stefan; Freissmuth, Michael; Rudnick, Gary; Sitte, Harald H.; Sandtner, Walter

2012-01-01

Ibogaine, a hallucinogenic alkaloid proposed as a treatment for opiate withdrawal, has been shown to inhibit serotonin transporter (SERT) noncompetitively, in contrast to all other known inhibitors, which are competitive with substrate. Ibogaine binding to SERT increases accessibility in the permeation pathway connecting the substrate-binding site with the cytoplasm. Because of the structural similarity between ibogaine and serotonin, it had been suggested that ibogaine binds to the substrate site of SERT. The results presented here show that ibogaine binds to a distinct site, accessible from the cell exterior, to inhibit both serotonin transport and serotonin-induced ionic currents. Ibogaine noncompetitively inhibited transport by both SERT and the homologous dopamine transporter (DAT). Ibogaine blocked substrate-induced currents also in DAT and increased accessibility of the DAT cytoplasmic permeation pathway. When present on the cell exterior, ibogaine inhibited SERT substrate-induced currents, but not when it was introduced into the cytoplasm through the patch electrode. Similar to noncompetitive transport inhibition, the current block was not reversed by increasing substrate concentration. The kinetics of inhibitor binding and dissociation, as determined by their effect on SERT currents, indicated that ibogaine does not inhibit by forming a long-lived complex with SERT, but rather binds directly to the transporter in an inward-open conformation. A kinetic model for transport describing the noncompetitive action of ibogaine and the competitive action of cocaine accounts well for the results of the present study. PMID:22451652

Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity

PubMed Central

Kasai, Yasuhiro; Shizuku, Hideki; Takagi, Yasuomi; Warashina, Masaki; Taira, Kazunari

2002-01-01

Exploitation of ribozymes in a practical setting requires high catalytic activity and strong specificity. The hammerhead ribozyme R32 has considerable potential in this regard since it has very high catalytic activity. In this study, we have examined how R32 recognizes and cleaves a specific substrate, focusing on the mechanism behind the specificity. Comparing rates of cleavage of a substrate in a mixture that included the correct substrate and various substrates with point mutations, we found that R32 cleaved the correct substrate specifically and at a high rate. To clarify the source of this strong specificity, we quantified the weak interactions between R32 and various truncated substrates, using truncated substrates as competitive inhibitors since they were not readily cleaved during kinetic measurements of cleavage of the correct substrate, S11. We found that the strong specificity of the cleavage reaction was due to a closed form of R32 with a hairpin structure. The self-complementary structure within R32 enabled the ribozyme to discriminate between the correct substrate and a mismatched substrate. Since this hairpin motif did not increase the Km (it did not inhibit the binding interaction) or decrease the kcat (it did not decrease the cleavage rate), this kind of hairpin structure might be useful for the design of new ribozymes with strong specificity and high activity. PMID:12034825

Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA

PubMed Central

Mekler, Vladimir; Minakhin, Leonid; Semenova, Ekaterina; Kuznedelov, Konstantin; Severinov, Konstantin

2016-01-01

CRISPR-Cas9 is widely applied for genome engineering in various organisms. The assembly of single guide RNA (sgRNA) with the Cas9 protein may limit the Cas9/sgRNA effector complex function. We developed a FRET-based assay for detection of CRISPR–Cas9 complex binding to its targets and used this assay to investigate the kinetics of Cas9 assembly with a set of structurally distinct sgRNAs. We find that Cas9 and isolated sgRNAs form the effector complex efficiently and rapidly. Yet, the assembly process is sensitive to the presence of moderate concentrations of non-specific RNA competitors, which considerably delay the Cas9/sgRNA complex formation, while not significantly affecting already formed complexes. This observation suggests that the rate of sgRNA loading into Cas9 in cells can be determined by competition between sgRNA and intracellular RNA molecules for the binding to Cas9. Non-specific RNAs exerted particularly large inhibitory effects on formation of Cas9 complexes with sgRNAs bearing shortened 3′-terminal segments. This result implies that the 3′-terminal segment confers sgRNA the ability to withstand competition from non-specific RNA and at least in part may explain the fact that use of sgRNAs truncated for the 3′-terminal stem loops leads to reduced activity during genomic editing. PMID:26945042

The kinetics of the arginine deiminase pathway in the meat starter culture Lactobacillus sakei CTC 494 are pH-dependent.

PubMed

Rimaux, T; Vrancken, G; Pothakos, V; Maes, D; De Vuyst, L; Leroy, F

2011-05-01

Lactobacillus sakei is frequently present as the dominant lactic acid bacterium in spontaneously fermented meat products, demonstrating its competitiveness in and adaptation to the meat environment. Since meat is generally low in carbohydrate content, the ability to utilize other energy sources to generate ATP, such as arginine via the arginine deiminase (ADI) pathway, represents a competitive benefit. In this study, the kinetics of growth and arginine conversion capabilities of Lb. sakei CTC 494 were analyzed, and a model was set up to describe the influence of pH on growth and arginine conversion. A series of in vitro batch fermentations using reconstituted MRS medium at different constant pH values (pH 4.50-pH 7.75) was performed. Arginine conversion through the ADI pathway, which was activated from the stationary growth phase on, resulted in the production of both citrulline and ornithine for all pH conditions tested. However, the pattern and the ratio of the end-products of the ADI pathway were influenced by pH. For certain pH values (between pH 5.0 and 6.5), a further conversion of citrulline into ornithine was found when all arginine was depleted. Characterization of responses of the ADI pathway in Lb. sakei CTC 494 to environmental conditions will allow a better understanding and control of this important starter culture in meat fermentations. Copyright © 2010 Elsevier Ltd. All rights reserved.

Binding of Cimetidine to Balb/C Mouse Liver Catalase; Kinetics and Conformational Studies.

PubMed

Jahangirvand, Mahboubeh; Minai-Tehrani, Dariush; Yazdi, Fatemeh; Minai-Tehrani, Arash; Razmi, Nematollah

2016-01-01

Catalase is responsible for converting hydrogen peroxide (H2O2) into water and oxygen in cells. This enzyme has high affinity for hydrogen peroxide and can protect the cells from oxidative stress damage. Catalase is a tetramer protein and each monomer contains a heme group. Cimetidine is a histamine H2 receptor blocker which inhibits acid release from stomach and is used for gasterointestinal diseases. In this research, effect of cimetidine on the activity of liver catalase was studied and the kinetic parameters of this enzyme and its conformational changes were investigated. Cell free extract of mouse liver was used for the catalase assay. The activity of the catalase was detected in the absence and presence of cimetidine by monitoring hydrogen peroxide reduction absorbance at 240 nm. The purified enzyme was used for conformational studies by Fluorescence spectrophotometry. The data showed that cimetidine could inhibit the enzyme in a non-competitive manner. Ki and IC50 values of the drug were determined to be about 0.75 and 0.85 uM, respectively. The Arrhenius plot showed that activation energy was 6.68 and 4.77 kJ/mol in the presence and absence of the drug, respectively. Fluorescence spectrophotometry revealed that the binding of cimetidine to the purified enzyme induced hyperchromicity and red shift which determined the conformational change on the enzyme. Cimetidine could non-competitively inhibit the liver catalase with high affinity. Binding of cimetidine to the enzyme induced conformational alteration in the enzyme.

PTP1B inhibitors from Selaginella tamariscina (Beauv.) Spring and their kinetic properties and molecular docking simulation.

PubMed

Le, Duc Dat; Nguyen, Duc Hung; Zhao, Bing Tian; Seong, Su Hui; Choi, Jae Sue; Kim, Seok Kyu; Kim, Jeong Ah; Min, Byung Sun; Woo, Mi Hee

2017-06-01

Diabetes is one of the most popular worldwide diseases, regulated by the defects in insulin secretion, insulin action, or both. The overexpression of protein tyrosine phosphatase 1B (PTP1B) was found to down-regulate the insulin-receptor activation. PTP1B has been known as a strategy for the treatment of diabetes via the regulation of insulin signal transduction pathway. Herein, we investigated the PTP1B inhibitors isolated from natural sources. The chemical investigation of Selaginella tamariscina (Beauv.) Spring revealed seven unsaturated alkynyl phenols 1-7, four new selaginellins T-W 1-4 together with three known compounds 5-7 isolated from the aerial parts. The structures of the isolates were determined by spectroscopic techniques (1D/2D-NMR, MS, and CD). The inhibitory effects of these isolates on the PTP1B enzyme activity were investigated. Among them, compounds 2-7 significantly exhibited the inhibitory effects with the IC 50 values ranging from 4.8 to 15.9μM. Compound 1 moderately displayed the inhibitory activity with an IC 50 of 57.9μM. Furthermore, active compounds were discovered from their kinetic and molecular docking analysis. The results revealed that compounds 2 and 4-7 were mixed-competitive inhibitors, whereas compound 3 was a non-competitive inhibitor. This data confirm that these compounds exhibited potential inhibitory effect on the PTP1B enzyme activity. Copyright © 2017 Elsevier Inc. All rights reserved.

In Vitro Evaluation of Fluorescence Glucose Biosensor Response

PubMed Central

Aloraefy, Mamdouh; Pfefer, T. Joshua; Ramella-Roman, Jessica C.; Sapsford, Kim E.

2014-01-01

Rapid, accurate, and minimally-invasive glucose biosensors based on Förster Resonance Energy Transfer (FRET) for glucose measurement have the potential to enhance diabetes control. However, a standard set of in vitro approaches for evaluating optical glucose biosensor response under controlled conditions would facilitate technological innovation and clinical translation. Towards this end, we have identified key characteristics and response test methods, fabricated FRET-based glucose biosensors, and characterized biosensor performance using these test methods. The biosensors were based on competitive binding between dextran and glucose to concanavalin A and incorporated long-wavelength fluorescence dye pairs. Testing characteristics included spectral response, linearity, sensitivity, limit of detection, kinetic response, reversibility, stability, precision, and accuracy. The biosensor demonstrated a fluorescence change of 45% in the presence of 400 mg/dL glucose, a mean absolute relative difference of less than 11%, a limit of detection of 25 mg/dL, a response time of 15 min, and a decay in fluorescence intensity of 72% over 30 days. The battery of tests presented here for objective, quantitative in vitro evaluation of FRET glucose biosensors performance have the potential to form the basis of future consensus standards. By implementing these test methods for a long-visible-wavelength biosensor, we were able to demonstrate strengths and weaknesses with a new level of thoroughness and rigor. PMID:25006996

In vitro evaluation of fluorescence glucose biosensor response.

PubMed

Aloraefy, Mamdouh; Pfefer, T Joshua; Ramella-Roman, Jessica C; Sapsford, Kim E

2014-07-08

Rapid, accurate, and minimally-invasive glucose biosensors based on Förster Resonance Energy Transfer (FRET) for glucose measurement have the potential to enhance diabetes control. However, a standard set of in vitro approaches for evaluating optical glucose biosensor response under controlled conditions would facilitate technological innovation and clinical translation. Towards this end, we have identified key characteristics and response test methods, fabricated FRET-based glucose biosensors, and characterized biosensor performance using these test methods. The biosensors were based on competitive binding between dextran and glucose to concanavalin A and incorporated long-wavelength fluorescence dye pairs. Testing characteristics included spectral response, linearity, sensitivity, limit of detection, kinetic response, reversibility, stability, precision, and accuracy. The biosensor demonstrated a fluorescence change of 45% in the presence of 400 mg/dL glucose, a mean absolute relative difference of less than 11%, a limit of detection of 25 mg/dL, a response time of 15 min, and a decay in fluorescence intensity of 72% over 30 days. The battery of tests presented here for objective, quantitative in vitro evaluation of FRET glucose biosensors performance have the potential to form the basis of future consensus standards. By implementing these test methods for a long-visible-wavelength biosensor, we were able to demonstrate strengths and weaknesses with a new level of thoroughness and rigor.

Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

PubMed

Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

2016-10-01

Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Fundamental electrode kinetics

NASA Technical Reports Server (NTRS)

Elder, J. P.

1968-01-01

Report presents the fundamentals of electrode kinetics and the methods used in evaluating the characteristic parameters of rapid-charge transfer processes at electrode-electrolyte interfaces. The concept of electrode kinetics is outlined, followed by the principles underlying the experimental techniques for the investigation of electrode kinetics.

Level set method for image segmentation based on moment competition

NASA Astrophysics Data System (ADS)

Min, Hai; Wang, Xiao-Feng; Huang, De-Shuang; Jin, Jing; Wang, Hong-Zhi; Li, Hai

2015-05-01

We propose a level set method for image segmentation which introduces the moment competition and weakly supervised information into the energy functional construction. Different from the region-based level set methods which use force competition, the moment competition is adopted to drive the contour evolution. Here, a so-called three-point labeling scheme is proposed to manually label three independent points (weakly supervised information) on the image. Then the intensity differences between the three points and the unlabeled pixels are used to construct the force arms for each image pixel. The corresponding force is generated from the global statistical information of a region-based method and weighted by the force arm. As a result, the moment can be constructed and incorporated into the energy functional to drive the evolving contour to approach the object boundary. In our method, the force arm can take full advantage of the three-point labeling scheme to constrain the moment competition. Additionally, the global statistical information and weakly supervised information are successfully integrated, which makes the proposed method more robust than traditional methods for initial contour placement and parameter setting. Experimental results with performance analysis also show the superiority of the proposed method on segmenting different types of complicated images, such as noisy images, three-phase images, images with intensity inhomogeneity, and texture images.

Skating mechanics of change-of-direction manoeuvres in ice hockey players.

PubMed

Fortier, Antoine; Turcotte, René A; Pearsall, David J

2014-11-01

Ice hockey requires rapid transitions between skating trajectories to effectively navigate about the ice surface. Player performance relates in large part to effective change-of-direction manoeuvres, but little is known about how those skills are performed mechanically and the effect of equipment design on them. The purpose of this study was to observe the kinetics involved in those manoeuvres as well as to compare whether kinetic differences may result between two skate models of varying ankle mobility. Eight subjects with competitive ice hockey playing experience performed rapid lateral (90°) left and right change-of-direction manoeuvres. Kinetic data were collected using force strain gauge transducers on the blade holders of the skates. Significantly greater forces were applied by the outside skate (50-70% body weight, %BW) in comparison to the inside skate (12-24%BW, p < 0.05). Skate model and turn direction had no main effect, though significant mixed interactions between leg side (inside/outside) with skate model or turn direction (p < 0.05) were observed, with a trend for left-turn dominance. This study demonstrates the asymmetric dynamic behaviour inherent in skating change-of-direction tasks.

Thermodynamic and kinetic analysis of the reaction between biological catecholamines and chlorinated methylperoxy radicals

NASA Astrophysics Data System (ADS)

Dimić, Dušan S.; Milenković, Dejan A.; Marković, Jasmina M. Dimitrić; Marković, Zoran S.

2018-05-01

The antiradical potency of catecholamines (dopamine, epinephrine, norepinephrine, L-DOPA), metabolites of dopamine (homovanillic acid, 3-methoxytyramine and 3,4-dihydroxyphenylacetic acid) and catechol towards substituted methylperoxy radicals is investigated. The thermodynamic parameters, together with the kinetic approach, are used to determine the most probable mechanism of action. The natural bond orbital and quantum theory of atoms in molecules are utilised to explain the highest reactivity of trichloromethylperoxy radical. The preferred mechanism is dependent both on the thermodynamic and kinetic parameters . The number of chlorine atoms on radical, the presence of intra-molecular hydrogen bond and number of hydroxy groups attached to the aromatic ring significantly influence the mechanism. The results suggest that sequential proton loss electron transfer (SPLET) is the most probable for reaction with methylperoxy and hydrogen atom transfer (HAT) for reaction with trichloromethylperoxy radicals, with a gradual transition between SPLET and HAT for other two radicals. Due to the significant deprotonation of molecules containing the carboxyl group, the respective anions are also investigated. The HAT and SPLET mechanisms are highly competitive in reaction with MP radical, while the dominant mechanism towards chlorinated radicals is HAT. The reactions in methanol and benzene are also discussed.

New application of superconductors: High sensitivity cryogenic light detectors

NASA Astrophysics Data System (ADS)

Cardani, L.; Bellini, F.; Casali, N.; Castellano, M. G.; Colantoni, I.; Coppolecchia, A.; Cosmelli, C.; Cruciani, A.; D'Addabbo, A.; Di Domizio, S.; Martinez, M.; Tomei, C.; Vignati, M.

2017-02-01

In this paper we describe the current status of the CALDER project, which is developing ultra-sensitive light detectors based on superconductors for cryogenic applications. When we apply an AC current to a superconductor, the Cooper pairs oscillate and acquire kinetic inductance, that can be measured by inserting the superconductor in a LC circuit with high merit factor. Interactions in the superconductor can break the Cooper pairs, causing sizable variations in the kinetic inductance and, thus, in the response of the LC circuit. The continuous monitoring of the amplitude and frequency modulation allows to reconstruct the incident energy with excellent sensitivity. This concept is at the basis of Kinetic Inductance Detectors (KIDs) that are characterized by natural aptitude to multiplexed read-out (several sensors can be tuned to different resonant frequencies and coupled to the same line), resolution of few eV, stable behavior over a wide temperature range, and ease in fabrication. We present the results obtained by the CALDER collaboration with 2×2 cm2 substrates sampled by 1 or 4 Aluminum KIDs. We show that the performances of the first prototypes are already competitive with those of other commonly used light detectors, and we discuss the strategies for a further improvement.

Complete kinetic mechanism for recycling of the bacterial ribosome

PubMed Central

Borg, Anneli; Pavlov, Michael

2016-01-01

How EF-G and RRF act together to split a post-termination ribosomal complex into its subunits has remained obscure. Here, using stopped-flow experiments with Rayleigh light scattering detection and quench-flow experiments with radio-detection of GTP hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. Ribosome splitting requires that EF-G binds to an already RRF-containing ribosome. EF-G binding to RRF-free ribosomes induces futile rounds of GTP hydrolysis and inhibits ribosome splitting, implying that while RRF is purely an activator of recycling, EF-G acts as both activator and competitive inhibitor of RRF in recycling of the post-termination ribosome. The ribosome splitting rate and the number of GTPs consumed per splitting event depend strongly on the free concentrations of EF-G and RRF. The maximal recycling rate, here estimated as 25 sec−1, is approached at very high concentrations of EF-G and RRF with RRF in high excess over EF-G. The present in vitro results, suggesting an in vivo ribosome recycling rate of ∼5 sec−1, are discussed in the perspective of rapidly growing bacterial cells. PMID:26527791

Bubble contraction in free-boundary Hele-Shaw flow with surface tension and kinetic undercooling regularisation

NASA Astrophysics Data System (ADS)

Dallaston, Michael; McCue, Scott

2012-11-01

When an inviscid bubble expands into a viscous fluid in a Hele-Shaw cell, the bubble boundary is unstable, in general forming long fingers (the Saffman-Taylor instability). In order to make the problem well-posed, a regularising boundary effect must be included. The most widely studied of these are surface tension, which penalises high curvatures, and kinetic undercooling, which penalises high velocities. Both these effects act as a stabilising influence on the free boundary. Less attention has been paid to the case of contracting bubbles, which shrink to a single point (or points) in finite time. In this case, the two effects are in competition, as surface tension stabilises the boundary, while kinetic undercooling destabilises it. This leads to bifurcation behaviour in the asymptotic (near-extinction) shape of the bubble as the relative strengths of the two effects are varied. In particular, there is a critical range of parameter values for which both circular and slit-type bubbles are stable, with a third (unstable) oval-type shape also present. We discuss some numerical and analytic techniques for solving the full free boundary problem and for exploring this interesting extinction behaviour.

Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

PubMed

Pereira, Félix Monteiro; Oliveira, Samuel Conceição

2016-11-01

In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.; Beddard, Godfrey S.; Paci, Emanuele; Glowacki, David R.

2012-10-01

Molecular dynamics (MD) methods are increasingly widespread, but simulation of rare events in complex molecular systems remains a challenge. We recently introduced the boxed molecular dynamics (BXD) method, which accelerates rare events, and simultaneously provides both kinetic and thermodynamic information. We illustrate how the BXD method may be used to obtain high-resolution kinetic data from explicit MD simulations, spanning picoseconds to microseconds. The method is applied to investigate the loop formation dynamics and kinetics of cyclisation for a range of polypeptides, and recovers a power law dependence of the instantaneous rate coefficient over six orders of magnitude in time, in good agreement with experimental observations. Analysis of our BXD results shows that this power law behaviour arises when there is a broad and nearly uniform spectrum of reaction rate coefficients. For the systems investigated in this work, where the free energy surfaces have relatively small barriers, the kinetics is very sensitive to the initial conditions: strongly non-equilibrium conditions give rise to power law kinetics, while equilibrium initial conditions result in a rate coefficient with only a weak dependence on time. These results suggest that BXD may offer us a powerful and general algorithm for describing kinetics and thermodynamics in chemical and biochemical systems.

In-Space Propulsion, Logistics Reduction, and Evaluation of Steam Reformer Kinetics: Problems and Prospects

NASA Technical Reports Server (NTRS)

Jaworske, D. A.; Palaszewski, B. A.; Kulis, M. J.; Gokoglu, S. A.

2015-01-01

Human space missions generate waste materials. A 70-kg crewmember creates a waste stream of 1 kg per day, and a four-person crew on a deep space habitat for a 400+ day mission would create over 1600 kg of waste. Converted into methane, the carbon could be used as a fuel for propulsion or power. The NASA Advanced Exploration Systems (AES) Logistics Reduction and Repurposing (LRR) project is investing in space resource utilization with an emphasis on repurposing logistics materials for useful purposes and has selected steam reforming among many different competitive processes as the preferred method for repurposing organic waste into methane. Already demonstrated at the relevant processing rate of 5.4 kg of waste per day, high temperature oxygenated steam consumes waste and produces carbon dioxide, carbon monoxide, and hydrogen which can then be converted into methane catalytically. However, the steam reforming process has not been studied in microgravity. Data are critically needed to understand the mechanisms that allow use of steam reforming in a reduced gravity environment. This paper reviews the relevant literature, identifies gravity-dependent mechanisms within the steam gasification process, and describes an innovative experiment to acquire the crucial kinetic information in a small-scale reactor specifically designed to operate within the requirements of a reduced gravity aircraft flight. The experiment will determine if the steam reformer process is mass-transport limited, and if so, what level of forced convection will be needed to obtain performance comparable to that in 1-g.

Modeling the Kinetics of Contaminants Oxidation and the Generation of Manganese(III) in the Permanganate/Bisulfite Process.

PubMed

Sun, Bo; Dong, Hongyu; He, Di; Rao, Dandan; Guan, Xiaohong

2016-02-02

Permanganate can be activated by bisulfite to generate soluble Mn(III) (noncomplexed with ligands other than H2O and OH(-)) which oxidizes organic contaminants at extraordinarily high rates. However, the generation of Mn(III) in the permanganate/bisulfite (PM/BS) process and the reactivity of Mn(III) toward emerging contaminants have never been quantified. In this work, Mn(III) generated in the PM/BS process was shown to absorb at 230-290 nm for the first time and disproportionated more easily at higher pH, and thus, the utilization rate of Mn(III) for decomposing organic contaminant was low under alkaline conditions. A Mn(III) generation and utilization model was developed to get the second-order reaction rate parameters of benzene oxidation by soluble Mn(III), and then, benzene was chosen as the reference probe to build a competition kinetics method, which was employed to obtain the second-order rate constants of organic contaminants oxidation by soluble Mn(III). The results revealed that the second-order rate constants of aniline and bisphenol A oxidation by soluble Mn(III) were in the range of 10(5)-10(6) M(-1) s(-1). With the presence of soluble Mn(III) at micromolar concentration, contaminants could be oxidized with the observed rates several orders of magnitude higher than those by common oxidation processes, implying the great potential application of the PM/BS process in water and wastewater treatment.

Differential Proteomic Analysis of Lactic Acid Bacteria-Escherichia coli O157:H7 Interaction and Its Contribution to Bioprotection Strategies in Meat.

PubMed

Orihuel, Alejandra; Terán, Lucrecia; Renaut, Jenny; Vignolo, Graciela M; De Almeida, André M; Saavedra, María L; Fadda, Silvina

2018-01-01

Human infection by Enterohemorrhagic Escherichia (E.) coli (EHEC) occurs through the ingestion of contaminated foods such as milk, vegetable products, water-based drinks, and particularly minced meats. Indeed EHEC is a pathogen that threatens public health and meat industry. The potential of different Lactic Acid Bacteria (LAB) strains to control EHEC in a meat-based medium was evaluated by using a simple and rapid method and by analyzing the growth kinetics of co-cultures (LAB-EHEC) in a meat-based medium. The activity of LAB toward EHEC in co-cultures showed variable inhibitory effect. Although, LAB were able to control EHEC, neither the produced acid nor bacteriocins were responsible of the inhibition. The bacteriocinogenic Enteroccus (Ent.) mundtii CRL35 presented one of the highest inhibition activities. A proteomic approach was used to evaluate bacterial interaction and antagonistic mechanisms between Ent. mundtii and EHEC. Physiological observations, such as growth kinetics, acidification ability and EHEC inhibitory potential were supported by the proteomic results, demonstrating significant differences in protein expression in LAB: (i) due to the presence of the pathogen and (ii) according to the growth phase analyzed. Most of the identified proteins belonged to carbohydrate/amino acid metabolism, energy production, transcription/translation, and cell division. These results contribute to the knowledge of competition strategies used by Ent. mundtii during its co-culture with EHEC setting new perspectives for the use of LAB to control this pathogen in meat.

A BAYESIAN METHOD OF ESTIMATING KINETIC PARAMETERS FOR THE INACTIVATION OF CRYPTOSPORIDIUM PARVUM OOCYSTS WITH CHLORINE DIOXIDE AND OZONE

EPA Science Inventory

The main objective of this paper is to use Bayesian methods to estimate the kinetic parameters for the inactivation kinetics of Cryptosporidium parvum oocysts with chlorine dioxide or ozone which are characterized by the delayed Chick-Watson model, i.e., a lag phase or shoulder f...

Measurement of Enzyme Kinetics by Use of a Blood Glucometer: Hydrolysis of Sucrose and Lactose

ERIC Educational Resources Information Center

Heinzerling, Peter; Schrader, Frank; Schanze, Sascha

2012-01-01

An alternative analytical method for measuring the kinetic parameters of the enzymes invertase and lactase is described. Invertase hydrolyzes sucrose to glucose and fructose and lactase hydrolyzes lactose to glucose and galactose. In most enzyme kinetics studies, photometric methods or test strips are used to quantify the derivates of the…

An in vivo, label-free quick assay for xylose transport in Escherichia coli.

PubMed

Chen, Tingjian; Zhang, Jingqing; Liang, Ling; Yang, Rong; Lin, Zhanglin

2009-07-01

Efficient use of xylose is necessary for economic production of biochemicals and biofuels from lignocellulosic materials. Current studies on xylose uptake for various microorganisms have been hampered by the lack of a facile assay for xylose transport. In this work, a rapid in vivo, label-free method for measuring xylose transport in Escherichia coli was developed by taking advantage of the Bacillus pumilus xylosidase (XynB), which cleaved a commercially available xylose analog, p-nitrophenyl-beta-d-xylopyranoside (pNPX), to release a chromogenic group, p-nitrophenol (pNP). XynB was expressed alone or in conjunction with a Zymomonas mobilis glucose facilitator protein (Glf) capable of transporting xylose. This XynB-mediated transport assay was demonstrated in test tubes and 96-well plates with submicromolar concentrations of pNPX. Kinetic inhibition experiments validated that pNPX and xylose were competitive substrates for the transport process, and the addition of glucose (20 g/L) in the culture medium clearly diminished the transmembrane transport of pNPX and, thus, mimicked its inhibitory action on xylose uptake. This method should be useful for engineering of the xylose transport process in E. coli, and similar assay schemes can be extended to other microorganisms.

Disentangling niche competition from grazing mortality in phytoplankton dilution experiments

PubMed Central

Weitz, Joshua S.

2017-01-01

The dilution method is the principal tool used to infer in situ microzooplankton grazing rates. However, grazing is the only mortality process considered in the theoretical model underlying the interpretation of dilution method experiments. Here we evaluate the robustness of mortality estimates inferred from dilution experiments when there is concurrent niche competition amongst phytoplankton. Using a combination of mathematical analysis and numerical simulations, we find that grazing rates may be overestimated—the degree of overestimation is related to the importance of niche competition relative to microzooplankton grazing. In response, we propose a conceptual method to disentangle the effects of niche competition and grazing by diluting out microzooplankton, but not phytoplankton. Our theoretical results suggest this revised “Z-dilution” method can robustly infer grazing mortality, regardless of the dominant phytoplankton mortality driver in our system. Further, we show it is possible to independently estimate both grazing mortality and niche competition if the classical and Z-dilution methods can be used in tandem. We discuss the significance of these results for quantifying phytoplankton mortality rates; and the feasibility of implementing the Z-dilution method in practice, whether in model systems or in complex communities with overlap in the size distributions of phytoplankton and microzooplankton. PMID:28505212

36 CFR 223.88 - Bidding methods.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Bidding methods. 223.88... methods. (a) Competitive sales of National Forest timber shall be offered through either sealed or oral auction bidding. The method chosen for each sale will: (1) Insure open and fair competition, (2) Insure...

A study of the kinetics of isothermal nicotine desorption from silicon dioxide

NASA Astrophysics Data System (ADS)

Adnadjevic, Borivoj; Lazarevic, Natasa; Jovanovic, Jelena

2010-12-01

The isothermal kinetics of nicotine desorption from silicon dioxide (SiO 2) was investigated. The isothermal thermogravimetric curves of nicotine at temperatures of 115 °C, 130 °C and 152 °C were recorded. The kinetic parameters ( Ea, ln A) of desorption of nicotine were calculated using various methods (stationary point, model constants and differential isoconversion method). By applying the "model-fitting" method, it was found that the kinetic model of nicotine desorption from silicon dioxide was a phase boundary controlled reaction (contracting volume). The values of the kinetic parameters, Ea,α and ln Aα, complexly change with changing degree of desorption and a compensation effect exists. A new mechanism of activation for the desorption of the absorbed molecules of nicotine was suggested in agreement with model of selective energy transfer.

Kinetic Description of the Impedance Probe

NASA Astrophysics Data System (ADS)

Oberrath, Jens; Lapke, Martin; Mussenbrock, Thomas; Brinkmann, Ralf

2011-10-01

Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. The authors acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG) via the Ruhr University Research School and the Federal Ministry of Education and Research in frame of the PluTO project.

Optimization of a direct spectrophotometric method to investigate the kinetics and inhibition of sialidases

PubMed Central

2012-01-01

Backgrounds Streptococcus pneumoniae expresses three distinct sialidases, NanA, NanB, and NanC, that are believed to be key virulence factors and thus, potential important drug targets. We previously reported that the three enzymes release different products from sialosides, but could share a common catalytic mechanism before the final step of product formation. However, the kinetic investigations of the three sialidases have not been systematically done thus far, due to the lack of an easy and steady measurement of sialidase reaction rate. Results In this work, we present further kinetic characterization of pneumococcal sialidases by using a direct spectrophotometric method with the chromogenic substrate p-nitrophenyl-N-acetylneuraminic acid (p-NP-Neu5Ac). Using our assay, the measured kinetic parameters of the three purified pneumococcal sialidase, NanA, NanB and NanC, were obtained and were in perfect agreement with the previously published data. The major advantage of this alternative method resides in the direct measurement of the released product, allowing to readily determine of initial reaction rates and record complete hydrolysis time courses. Conclusion We developed an accurate, fast and sensitive spectrophotometric method to investigate the kinetics of sialidase-catalyzed reactions. This fast, sensitive, inexpensive and accurate method could benefit the study of the kinetics and inhibition of sialidases in general. PMID:23031230

Pseudo-second order models for the adsorption of safranin onto activated carbon: comparison of linear and non-linear regression methods.

PubMed

Kumar, K Vasanth

2007-04-02

Kinetic experiments were carried out for the sorption of safranin onto activated carbon particles. The kinetic data were fitted to pseudo-second order model of Ho, Sobkowsk and Czerwinski, Blanchard et al. and Ritchie by linear and non-linear regression methods. Non-linear method was found to be a better way of obtaining the parameters involved in the second order rate kinetic expressions. Both linear and non-linear regression showed that the Sobkowsk and Czerwinski and Ritchie's pseudo-second order models were the same. Non-linear regression analysis showed that both Blanchard et al. and Ho have similar ideas on the pseudo-second order model but with different assumptions. The best fit of experimental data in Ho's pseudo-second order expression by linear and non-linear regression method showed that Ho pseudo-second order model was a better kinetic expression when compared to other pseudo-second order kinetic expressions.

National Clinical Skills Competition: an effective simulation-based method to improve undergraduate medical education in China

PubMed Central

Jiang, Guanchao; Chen, Hong; Wang, Qiming; Chi, Baorong; He, Qingnan; Xiao, Haipeng; Zhou, Qinghuan; Liu, Jing; Wang, Shan

2016-01-01

Background The National Clinical Skills Competition has been held in China for 5 consecutive years since 2010 to promote undergraduate education reform and improve the teaching quality. The effects of the simulation-based competition will be analyzed in this study. Methods Participation in the competitions and the compilation of the questions used in the competition finals are summarized, and the influence and guidance quality are further analyzed. Through the nationwide distribution of questionnaires in medical colleges, the effects of the simulation-based competition on promoting undergraduate medical education reform were evaluated. Results The results show that approximately 450 students from more than 110 colleges (accounting for 81% of colleges providing undergraduate clinical medical education in China) participated in the competition each year. The knowledge, skills, and attitudes were comprehensively evaluated by simulation-based assessment. Eight hundred and eighty copies of the questionnaires were distributed to 110 participating medical schools in 2015. In total, 752 valid responses were received across 95 schools. The majority of the interviewees agreed or strongly agreed that competition promoted the adoption of advanced educational principles (76.8%), updated the curriculum model and instructional methods (79.8%), strengthened faculty development (84.0%), improved educational resources (82.1%), and benefited all students (53.4%). Conclusions The National Clinical Skills Competition is widely accepted in China. It has effectively promoted the reform and development of undergraduate medical education in China. PMID:26894586

The progamic phase of an early-divergent angiosperm, Annona cherimola (Annonaceae)

PubMed Central

Lora, J.; Hormaza, J. I.; Herrero, M.

2010-01-01

Background and Aims Recent studies of reproductive biology in ancient angiosperm lineages are beginning to shed light on the early evolution of flowering plants, but comparative studies are restricted by fragmented and meagre species representation in these angiosperm clades. In the present study, the progamic phase, from pollination to fertilization, is characterized in Annona cherimola, which is a member of the Annonaceae, the largest extant family among early-divergent angiosperms. Beside interest due to its phylogenetic position, this species is also an ancient crop with a clear niche for expansion in subtropical climates. Methods The kinetics of the reproductive process was established following controlled pollinations and sequential fixation. Gynoecium anatomy, pollen tube pathway, embryo sac and early post-fertilization events were characterized histochemically. Key Results A plesiomorphic gynoecium with a semi-open carpel shows a continuous secretory papillar surface along the carpel margins, which run from the stigma down to the obturator in the ovary. The pollen grains germinate in the stigma and compete in the stigma-style interface to reach the narrow secretory area that lines the margins of the semi-open stylar canal and is able to host just one to three pollen tubes. The embryo sac has eight nuclei and is well provisioned with large starch grains that are used during early cellular endosperm development. Conclusions A plesiomorphic simple gynoecium hosts a simple pollen–pistil interaction, based on a support–control system of pollen tube growth. Support is provided through basipetal secretory activity in the cells that line the pollen tube pathway. Spatial constraints, favouring pollen tube competition, are mediated by a dramatic reduction in the secretory surface available for pollen tube growth at the stigma–style interface. This extramural pollen tube competition contrasts with the intrastylar competition predominant in more recently derived lineages of angiosperms. PMID:19939980

Binary Colloidal Alloy Test-5: Compete

NASA Technical Reports Server (NTRS)

Frisken, Barbara J.; Bailey, Arthur E.; Weitz, David A.

2008-01-01

The Binary Colloidal Alloy Test - 5: Compete (BCAT-5-Compete) investigation will photograph andomized colloidal samples onboard the International Space Station (ISS) to determine their resulting structure over time. The use of EarthKAM software and hardware will allow the scientists to capture the kinetics (evolution) of their samples, as well as the final equilibrium state of each sample. BCAT-5-Compete will utilize samples 6 - 8 in the BCAT-5 hardware to study the competition between phase separation and crystallization, which is important in the manufacture of plastics and other materials.

Tyrosinase inhibitor activity of coumarin-resveratrol hybrids.

PubMed

Fais, Antonella; Corda, Marcella; Era, Benedetta; Fadda, M Benedetta; Matos, Maria Joao; Quezada, Elias; Santana, Lourdes; Picciau, Carmen; Podda, Gianni; Delogu, Giovanna

2009-07-13

In the present work we report on the contribution of the coumarin moiety to tyrosinase inhibition. Coumarin-resveratrol hybrids 1-8 have been resynthesized to investigate the structure-activity relationships and the IC(50) values of these compounds were measured. The results showed that these compounds exhibited tyrosinase inhibitory activity. Compound 3-(3',4',5'-trihydroxyphenyl)-6,8-dihydroxycoumarin (8)is the most potentcompound (0.27 mM), more so than umbelliferone (0.42 mM), used as reference compound. The kinetic studies revealed that compound 8 caused non-competitive tyrosinase inhibition.

F-12509A, a new sphingosine kinase inhibitor, produced by a discomycete.

PubMed

Kono, K; Tanaka, M; Ogita, T; Hosoya, T; Kohama, T

2000-05-01

In the course of our screening for inhibitors of sphingosine kinase, we found an active compound from a culture broth of a discomycete, Trichopezizella barbata SANK 25395. The structure of the compound, named F-12509A, was elucidated by a combination of spectroscopic analyses, to be a new sesquiterpene quinone consisting of a drimane moiety and a dihydroxybenzoquinone. Enzyme kinetic analyses showed that F-12509A inhibits sphingosine kinase activity in a competitive manner with respect to sphingosine, with a Ki value of 18 microM.

Calculation of kinetic rate constants from thermodynamic data

NASA Technical Reports Server (NTRS)

Marek, C. John

1995-01-01

A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

High-order continuum kinetic method for modeling plasma dynamics in phase space

DOE PAGES

Vogman, G. V.; Colella, P.; Shumlak, U.

2014-12-15

Continuum methods offer a high-fidelity means of simulating plasma kinetics. While computationally intensive, these methods are advantageous because they can be cast in conservation-law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Advances in continuum method capabilities for modeling kinetic phenomena in plasmas require the development of validation tools in higher dimensional phase space and an ability to handle non-cartesian geometries. To that end, a new benchmark for validating Vlasov-Poisson simulations in 3D (x,v x,v y) is presented. The benchmark is based on the Dory-Guest-Harris instability and is successfully used to validate a continuummore » finite volume algorithm. To address challenges associated with non-cartesian geometries, unique features of cylindrical phase space coordinates are described. Preliminary results of continuum kinetic simulations in 4D (r,z,v r,v z) phase space are presented.« less

Critical Evaluation of Kinetic Method Measurements: Possible Origins of Nonlinear Effects

NASA Astrophysics Data System (ADS)

Bourgoin-Voillard, Sandrine; Afonso, Carlos; Lesage, Denis; Zins, Emilie-Laure; Tabet, Jean-Claude; Armentrout, P. B.

2013-03-01

The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities ( ΔH° acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.

Simulating Chemical Kinetics Without Differential Equations: A Quantitative Theory Based on Chemical Pathways.

PubMed

Bai, Shirong; Skodje, Rex T

2017-08-17

A new approach is presented for simulating the time-evolution of chemically reactive systems. This method provides an alternative to conventional modeling of mass-action kinetics that involves solving differential equations for the species concentrations. The method presented here avoids the need to solve the rate equations by switching to a representation based on chemical pathways. In the Sum Over Histories Representation (or SOHR) method, any time-dependent kinetic observable, such as concentration, is written as a linear combination of probabilities for chemical pathways leading to a desired outcome. In this work, an iterative method is introduced that allows the time-dependent pathway probabilities to be generated from a knowledge of the elementary rate coefficients, thus avoiding the pitfalls involved in solving the differential equations of kinetics. The method is successfully applied to the model Lotka-Volterra system and to a realistic H 2 combustion model.

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

PubMed

Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

2013-03-07

Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

Thermo-kinetic instabilities in model reactors. Examples in experimental tests

NASA Astrophysics Data System (ADS)

Lavadera, Marco Lubrano; Sorrentino, Giancarlo; Sabia, Pino; de Joannon, Mara; Cavaliere, Antonio; Ragucci, Raffaele

2017-11-01

The use of advanced combustion technologies (such as MILD, LTC, etc.) is among the most promising methods to reduce emission of pollutants. For such technologies, working temperatures are enough low to boost the formation of several classes of pollutants, such as NOx and soot. To access this temperature range, a significant dilution as well as preheating of reactants is required. Such conditions are usually achieved by a strong recirculation of exhaust gases that simultaneously dilute and pre-heat the fresh reactants. These peculiar operative conditions also imply strong fuel flexibility, thus allowing the use of low calorific value (LCV) energy carriers with high efficiency. However, the intersection of low combustion temperatures and highly diluted mixtures with intense pre-heating alters the evolution of the combustion process with respect to traditional flames, leading to features such as the susceptibility to oscillations, which are undesirable during combustion. Therefore, an effective use of advanced combustion technologies requires a thorough analysis of the combustion kinetic characteristics in order to identify optimal operating conditions and control strategies with high efficiency and low pollutant emissions. The present work experimentally and numerically characterized the ignition and oxidation processes of methane and propane, highly diluted in nitrogen, at atmospheric pressure, in a Plug Flow Reactor and a Perfectly Stirred Reactor under a wide range of operating conditions involving temperatures, mixture compositions and dilution levels. The attention was focused particularly on the chemistry of oscillatory phenomena and multistage ignitions. The global behavior of these systems can be qualitatively and partially quantitatively modeled using the detailed kinetic models available in the literature. Results suggested that, for diluted conditions and lower adiabatic flame temperatures, the competition among several pathways, i.e. intermediate- and high-temperature branching, branching and recombination channels, oxidation and recombination/pyrolysis pathways, is enhanced, thus permitting the onset of phenomena that are generally hidden during conventional combustion processes.

An Inner-Sphere Mechanism for Molecular Oxygen Reduction Catalyzed by Copper Amine Oxidases

PubMed Central

Mukherjee, Arnab; Smirnov, Valeriy V.; Lanci, Michael P.; Brown, Doreen E.; Shepard, Eric M.; Dooley, David M.; Roth, Justine P.

2008-01-01

Copper and topaquinone (TPQ) containing amine oxidases utilize O2 for the metabolism of biogenic amines while concomitantly generating H2O2 for use by the cell. The mechanism of O2 reduction has been the subject of long-standing debate due to the obscuring influence of a proton-coupled electron transfer between the tyrosine-derived TPQ and copper, a rapidly established equilibrium precluding assignment of the enzyme in its reactive form. Here we show that substrate-reduced pea seedling amine oxidase (PSAO) exists predominantly in the CuI, TPQ semiquinone state. A new mechanistic proposal for O2 reduction is advanced on the basis of thermodynamic considerations together with kinetic studies (at varying pH, temperature and viscosity), the identification of steady-state intermediates and the analysis of competitive oxygen kinetic isotope effects: 18O KIEs, [kcat/KM(16,16O2)]/[kcat/KM(16,18O2)]. The 18O KIE = 1.0136 ± 0.0013 at pH 7.2 is independent of temperature from 5 to 47°C and insignificantly changed to 1.0122 ± 0.0020 upon raising the pH to 9, thus indicating the absence of kinetic complexity. Using density functional methods, the effect is found to be precisely in the range expected for reversible O2 binding to CuI to afford a superoxide, [CuII(η1-O2)−I]+, intermediate. Electron transfer from the TPQ semiquinone follows in the first irreversible step to form a peroxide, CuII(η1-O2)−II, intermediate driving the reduction of O2. The similar 18O KIEs reported for copper amine oxidases from other sources raise the possibility that all enzymes react by related inner-sphere mechanisms although additional experiments are needed to test this proposal. PMID:18582059

Experimental and Modeling Investigation of the Low-Temperature Oxidation of Dimethyl Ether.

PubMed

Rodriguez, Anne; Frottier, Ophélie; Herbinet, Olivier; Fournet, René; Bounaceur, Roda; Fittschen, Christa; Battin-Leclerc, Frédérique

2015-07-16

The oxidation of dimethyl ether (DME) was studied using a jet-stirred reactor over a wide range of conditions: temperatures from 500 to 1100 K; equivalence ratios of 0.25, 1, and 2; residence time of 2 s; pressure of 106.7 kPa (close to the atmospheric pressure); and an inlet fuel mole fraction of 0.02 (with high dilution in helium). Reaction products were quantified using two analysis methods: gas chromatography and continuous wave cavity ring-down spectroscopy (cw-CRDS). cw-CRDS enabled the quantification of formaldehyde, which is one of the major products from DME oxidation, as well as that of hydrogen peroxide, which is an important branching agent in low-temperature oxidation chemistry. Experimental data were compared with data computed using models from the literature with important deviations being observed for the reactivity at low-temperature. A new detailed kinetic model for the oxidation of DME was developed in this study. Kinetic parameters used in this model were taken from literature or calculated in the present work using quantum calculations. This new model enables a better prediction of the reactivity in the low-temperature region. Under the present JSR conditions, error bars on predictions were given. Simulations were also successfully compared with experimental flow reactor, jet-stirred reactor, shock tube, rapid compression machine, and flame data from literature. The kinetic analysis of the model enabled the highlighting of some specificities of the oxidation chemistry of DME: (1) the early reactivity which is observed at very low-temperature (e.g., compared to propane) is explained by the absence of inhibiting reaction of the radical directly obtained from the fuel (by H atom abstraction) with oxygen yielding an olefin + HO2·; (2) the low-temperature reactivity is driven by the relative importance of the second addition to O2 (promoting the reactivity through branching chain) and the competitive decomposition reactions with an inhibiting effect.

Competition, Education and Assessment: Connecting History with Recent Scholarship

ERIC Educational Resources Information Center

Nelson, Robert; Dawson, Phillip

2017-01-01

In this article, we investigate competition in education, asking if it is good or bad, and especially if it is old and necessary or new and questionable. Using philological methods, we trace the history of competition and relate it to contemporary educational ideas. In history and modern pedagogical research, competition has a "dark…

The utility of salivary testosterone and cortisol concentration measures for assessing the stress responses of junior athletes during a sporting competition.

PubMed

Crewther, Blair T; Obmiński, Zbigniew; Orysiak, Joanna; Al-Dujaili, Emad A S

2018-01-01

This study examined the utility of salivary testosterone (T) and cortisol (C) concentration measures for assessing the acute stress responses of junior athletes during a sporting competition. Paired capillary blood and saliva samples were taken from 71 junior athletes (45 males, 26 females) before and after a simulated Olympic weightlifting competition. The concentration measures of salivary T and C were referenced against blood total T (TT) and C (TC) concentrations. All hormones were tested by immunoassay. The competition promoted an increase in the blood TT concentrations of the male (10.1%±18.7%) and female (12.9%±19.9%) athletes (P<.05), with TC also rising in females (37.5%±69%) and tending to increase in males (23.2%±56.1%). No significant changes in salivary T or C were identified. Locally-weighted regression revealed that salivary T was strongly related to blood TT in males (r 2 =.84), but not females (r 2 =-.15), whereas salivary C was moderately related to blood TC in both sexes (r 2 =.43, r 2 =.48), respectively. A short, high-intensity competition promoted a predictable stress-induced rise in blood TT and TC concentrations. We observed no hormonal stress responses in saliva under the current format, which could be explained by individual variability and blood-saliva differences in hormone kinetics. Still, the salivary T and C measures did show a moderate to strong ability to track individual blood TT (males only) and TC (both sexes) concentrations in a young athletic cohort across a broad physiological range. Recommendations for researchers and practitioners are presented. © 2017 Wiley Periodicals, Inc.

Global stability and pattern formation in a nonlocal diffusive Lotka-Volterra competition model

NASA Astrophysics Data System (ADS)

Ni, Wenjie; Shi, Junping; Wang, Mingxin

2018-06-01

A diffusive Lotka-Volterra competition model with nonlocal intraspecific and interspecific competition between species is formulated and analyzed. The nonlocal competition strength is assumed to be determined by a diffusion kernel function to model the movement pattern of the biological species. It is shown that when there is no nonlocal intraspecific competition, the dynamics properties of nonlocal diffusive competition problem are similar to those of classical diffusive Lotka-Volterra competition model regardless of the strength of nonlocal interspecific competition. Global stability of nonnegative constant equilibria are proved using Lyapunov or upper-lower solution methods. On the other hand, strong nonlocal intraspecific competition increases the system spatiotemporal dynamic complexity. For the weak competition case, the nonlocal diffusive competition model may possess nonconstant positive equilibria for some suitably large nonlocal intraspecific competition coefficients.

Different competitive capacities of Stat4- and Stat6-deficient CD4+ T cells during lymphophenia-driven proliferation.

PubMed

Sanchez-Guajardo, Vanesa; Borghans, José A M; Marquez, Maria-Elena; Garcia, Sylvie; Freitas, Antonio A

2005-02-01

The outcome of an immune response relies on the competitive capacities acquired through differentiation of CD4(+) T cells into Th1 or Th2 effector cells. Because Stat4 and Stat6 proteins are implicated in the Th1 vs Th2 generation and maintenance, respectively, we compare in this study the kinetics of Stat4(-/-) and Stat6(-/-) CD4(+) T cells during competitive bone marrow reconstitution and lymphopenia-driven proliferation. After bone marrow transplantation, both populations reconstitute the peripheral T cell pools equally well. After transfer into lymphopenic hosts, wild-type and Stat6(-/-) CD4(+) T cells show a proliferation advantage, which is early associated with the expression of an active phospho-Stat4 and the down-regulation of Stat6. Despite these differences, Stat4- and Stat6-deficient T cells reach similar steady state numbers. However, when both Stat4(-/-) and Stat6(-/-) CD4(+) T cells are coinjected into the same hosts, the Stat6(-/-) cells become dominant and out-compete Stat4(-/-) cells. These findings suggest that cell activation, through the Stat4 pathway and the down-regulation of Stat6, confers to pro-Th1 T cells a slight proliferation advantage that in a competitive situation has major late repercussions, because it modifies the final homeostatic equilibrium of the populations and favors the establishment of Th1 CD4(+) T cell dominance.

Oncogenic Nras has bimodal effects on stem cells that sustainably increase competitiveness.

PubMed

Li, Qing; Bohin, Natacha; Wen, Tiffany; Ng, Victor; Magee, Jeffrey; Chen, Shann-Ching; Shannon, Kevin; Morrison, Sean J

2013-12-05

'Pre-leukaemic' mutations are thought to promote clonal expansion of haematopoietic stem cells (HSCs) by increasing self-renewal and competitiveness; however, mutations that increase HSC proliferation tend to reduce competitiveness and self-renewal potential, raising the question of how a mutant HSC can sustainably outcompete wild-type HSCs. Activating mutations in NRAS are prevalent in human myeloproliferative neoplasms and leukaemia. Here we show that a single allele of oncogenic Nras(G12D) increases HSC proliferation but also increases reconstituting and self-renewal potential upon serial transplantation in irradiated mice, all prior to leukaemia initiation. Nras(G12D) also confers long-term self-renewal potential to multipotent progenitors. To explore the mechanism by which Nras(G12D) promotes HSC proliferation and self-renewal, we assessed cell-cycle kinetics using H2B-GFP label retention and 5-bromodeoxyuridine (BrdU) incorporation. Nras(G12D) had a bimodal effect on HSCs, increasing the frequency with which some HSCs divide and reducing the frequency with which others divide. This mirrored bimodal effects on reconstituting potential, as rarely dividing Nras(G12D) HSCs outcompeted wild-type HSCs, whereas frequently dividing Nras(G12D) HSCs did not. Nras(G12D) caused these effects by promoting STAT5 signalling, inducing different transcriptional responses in different subsets of HSCs. One signal can therefore increase HSC proliferation, competitiveness and self-renewal through bimodal effects on HSC gene expression, cycling and reconstituting potential.

A second-order accurate kinetic-theory-based method for inviscid compressible flows

NASA Technical Reports Server (NTRS)

Deshpande, Suresh M.

1986-01-01

An upwind method for the numerical solution of the Euler equations is presented. This method, called the kinetic numerical method (KNM), is based on the fact that the Euler equations are moments of the Boltzmann equation of the kinetic theory of gases when the distribution function is Maxwellian. The KNM consists of two phases, the convection phase and the collision phase. The method is unconditionally stable and explicit. It is highly vectorizable and can be easily made total variation diminishing for the distribution function by a suitable choice of the interpolation strategy. The method is applied to a one-dimensional shock-propagation problem and to a two-dimensional shock-reflection problem.

Differential equation methods for simulation of GFP kinetics in non-steady state experiments.

PubMed

Phair, Robert D

2018-03-15

Genetically encoded fluorescent proteins, combined with fluorescence microscopy, are widely used in cell biology to collect kinetic data on intracellular trafficking. Methods for extraction of quantitative information from these data are based on the mathematics of diffusion and tracer kinetics. Current methods, although useful and powerful, depend on the assumption that the cellular system being studied is in a steady state, that is, the assumption that all the molecular concentrations and fluxes are constant for the duration of the experiment. Here, we derive new tracer kinetic analytical methods for non-steady state biological systems by constructing mechanistic nonlinear differential equation models of the underlying cell biological processes and linking them to a separate set of differential equations governing the kinetics of the fluorescent tracer. Linking the two sets of equations is based on a new application of the fundamental tracer principle of indistinguishability and, unlike current methods, supports correct dependence of tracer kinetics on cellular dynamics. This approach thus provides a general mathematical framework for applications of GFP fluorescence microscopy (including photobleaching [FRAP, FLIP] and photoactivation to frequently encountered experimental protocols involving physiological or pharmacological perturbations (e.g., growth factors, neurotransmitters, acute knockouts, inhibitors, hormones, cytokines, and metabolites) that initiate mechanistically informative intracellular transients. When a new steady state is achieved, these methods automatically reduce to classical steady state tracer kinetic analysis. © 2018 Phair. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Merit Evaluation Of Competitors In Debate And Recitation Competitions By Fuzzy Approach

NASA Astrophysics Data System (ADS)

Mukherjee, Supratim; Bhattacharyya, Rupak; Chatterjee, Amitava; Kar, Samarjit

2010-10-01

Co-curricular activities have a great importance in students' life, especially to grow their personality and communication skills. In different process of evaluating competitors in such competitions, generally crisp techniques are used. In this paper, we introduce a new fuzzy set theory based method of evaluation of competitors in co-curricular activities like debate and recitation competitions. The proposed method is illustrated by two examples.

Non-animal approaches for toxicokinetics in risk evaluations of food chemicals.

PubMed

Punt, Ans; Peijnenburg, Ad A C M; Hoogenboom, Ron L A P; Bouwmeester, Hans

2017-01-01

The objective of the present work was to review the availability and predictive value of non-animal toxicokinetic approaches and to evaluate their current use in European risk evaluations of food contaminants, additives and food contact materials, as well as pesticides and medicines. Results revealed little use of quantitative animal or human kinetic data in risk evaluations of food chemicals, compared with pesticides and medicines. Risk evaluations of medicines provided sufficient in vivo kinetic data from different species to evaluate the predictive value of animal kinetic data for humans. These data showed a relatively poor correlation between the in vivo bioavailability in rats and dogs versus that in humans. In contrast, in vitro (human) kinetic data have been demonstrated to provide adequate predictions of the fate of compounds in humans, using appropriate in vitro-in vivo scalers and by integration of in vitro kinetic data with in silico kinetic modelling. Even though in vitro kinetic data were found to be occasionally included within risk evaluations of food chemicals, particularly results from Caco-2 absorption experiments and in vitro data on gut-microbial conversions, only minor use of in vitro methods for metabolism and quantitative in vitro-in vivo extrapolation methods was identified. Yet, such quantitative predictions are essential in the development of alternatives to animal testing as well as to increase human relevance of toxicological risk evaluations. Future research should aim at further improving and validating quantitative alternative methods for kinetics, thereby increasing regulatory acceptance of non-animal kinetic data.

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

NASA Astrophysics Data System (ADS)

Chowdhury, Debashish

2013-08-01

A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors “transduce” input energy into mechanical work. All the nano-motors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multi-module motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular nano-motors, we consider the porters, sliders and rowers, pistons and hooks, exporters, importers, packers and movers as well as those that also synthesize, manipulate and degrade “macromolecules of life”. We review mostly the quantitative models for the kinetics of these motors. We also describe several of those motor-driven intracellular stochastic processes for which quantitative models are yet to be developed. In part I, we discuss mainly the methodology and the generic models of various important classes of molecular motors. In part II, we review many specific examples emphasizing the unity of the basic mechanisms as well as diversity of operations arising from the differences in their detailed structure and kinetics. Multi-disciplinary research is presented here from the perspective of physicists.

Oxidation process of MoO xC y to MoO 3: kinetics and mechanism

NASA Astrophysics Data System (ADS)

Aleman-Vázquez, L. O.; Torres-García, E.; Rodríguez-Gattorno, G.; Ocotlán-Flores, J.; Camacho-López, M. A.; Cano, J. L.

2004-10-01

A non-isothermal kinetic study of the oxidation of "carbon-modified MoO3" in the temperature range of 150-550°C by simultaneous TGA-DTA was investigated. During the oxidation process, two thermal events were detected, which are associated with the oxidation of carbon in MoOxCy and MoO2 to MoO3. The model-free and model-fitting kinetic approaches have been applied to TGA experimental data. The solid state-kinetics of the oxidation of MoOxCy to MoO3 is governed by F1 (unimolecular decay), which suggests that the reaction is of the first order with respect to oxygen concentration. The constant (Ea)α value (about 115±5 kJ/mol) for this first stage can be related to the nature of the reaction site in the MoO3 matrix. This indicates that oxidation occurs in well-defined lattice position sites (energetically equivalent). On the other hand, for the second stage of oxidation, MoO2 to MoO3, the isoconversional analysis shows a complex (Ea)α dependence on (α) and reveals a typical behavior for competitive reaction. A D2 (two-dimensional diffusion) mechanism with a variable activation energy value in the range 110-200 kJ/mol was obtained. This can be interpreted as an inter-layer oxygen diffusion in the solid bulk, which does not exclude other simultaneous mechanism reactions.

KINETIC EVOLUTION OF CORONAL HOLE PROTONS BY IMBALANCED ION-CYCLOTRON WAVES: IMPLICATIONS FOR MEASUREMENTS BY SOLAR PROBE PLUS

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

Isenberg, Philip A.; Vasquez, Bernard J.

We extend the kinetic guiding-center model of collisionless coronal hole protons presented in Isenberg and Vasquez to consider driving by imbalanced spectra of obliquely propagating ion-cyclotron waves. These waves are assumed to be a small by-product of the imbalanced turbulent cascade to high perpendicular wavenumber, and their total intensity is taken to be 1% of the total fluctuation energy. We also extend the kinetic solutions for the proton distribution function in the resulting fast solar wind to heliocentric distances of 20 solar radii, which will be attainable by the Solar Probe Plus spacecraft. We consider three ratios of outward-propagating tomore » inward-propagating resonant intensities: 1, 4, and 9. The self-consistent bulk flow speed reaches fast solar wind values in all cases, and these speeds are basically independent of the intensity ratio. The steady-state proton distribution is highly organized into nested constant-density shells by the resonant wave-particle interaction. The radial evolution of this kinetic distribution as the coronal hole plasma flows outward is understood as a competition between the inward- and outward-directed large-scale forces, causing an effective circulation of particles through the (v{sub ∥}, v{sub ⊥}) phase space and a characteristic asymmetric shape to the distribution. These asymmetries are substantial and persist to the outer limit of the model computation, where they should be observable by the Solar Probe Plus instruments.« less

Compositional redistribution in alloy films under high-voltage electron microscope irradiation

NASA Astrophysics Data System (ADS)

Lam, Nghi Q.; Leaf, O. K.; Minkoff, M.

1983-10-01

The problem of nonequilibrium segregation in alloy films under high-voltage electron microscope (HVEM) irradiation at elevated temperatures is re-examined in the present work, taking into account the damage-rate gradients caused by radial variation in the electron flux. Axial and radial compositional redistributions in model solid solutions, representative of concentrated Ni-Cu, Ni-Al and Ni-Si alloys, were calculated as a function of time, temperature, and film thickness, using a kinetic theory of segregation in binary alloys. The numerical results were achieved by means of a new software package (DISPL2) for solving convection-diffusion-kinetics problems with general orthogonal geometries. It was found that HVEM irradiation-induced segregation in thin films consists of two stages. Initially, due to the proximity of the film surfaces as sinks for point defects, the usual axial segregation (to surfaces) occurs at relatively short irradiation times, and rapidly attains quasi-steady state. Then, radial segregation becomes more and more competitive, gradually affecting the kinetics of axial segregation. At a given temperature, the buildup time to steady state is much longer in the present situation than in the simple case of one-dimensional segregation with uniform defect production. Changes in the alloy composition occur in a much larger zone than the irradiated volume. As a result, the average alloy composition within the irradiated region can differ greatly from that of the unirradiated alloy. The present calculations may be useful in the interpretation of the kinetics of certain HVEM irradiation-induced processes in alloys.

A second dihydroorotate dehydrogenase (Type A) of the human pathogen Enterococcus faecalis: expression, purification, and steady-state kinetic mechanism.

PubMed

Marcinkeviciene, J; Jiang, W; Locke, G; Kopcho, L M; Rogers, M J; Copeland, R A

2000-05-01

We report the identification, expression, and characterization of a second Dihydroorotate dehydrogenase (DHODase A) from the human pathogen Enterococcus faecalis. The enzyme consists of a polypeptide chain of 322 amino acids that shares 68% identity with the cognate type A enzyme from the bacterium Lactococcus lactis. E. faecalis DHODase A catalyzed the oxidation of l-dihydroorotate while reducing a number of substrates, including fumarate, coenzyme Q(0), and menadione. The steady-state kinetic mechanism has been determined with menadione as an oxidizing substrate at pH 7.5. Initial velocity and product inhibition data suggest that the enzyme follows a two-site nonclassical ping-pong kinetic mechanism. The absorbance of the active site FMN cofactor is quenched in a concentration-dependent manner by titration with orotate and barbituric acid, two competitive inhibitors with respect to dihydroorotate. In contrast, titration of the enzyme with menadione had no effect on FMN absorbance, consistent with nonoverlapping binding sites for dihyroorotate and menadione, as suggested from the kinetic mechanism. The reductive half-reaction has been shown to be only partially rate limiting, and an attempt to evaluate the slow step in the overall reaction has been made by simulating orotate production under steady-state conditions. Our data indicate that the oxidative half-reaction is a rate-limiting segment, while orotate, most likely, retains significant affinity for the reduced enzyme, as suggested by the product inhibition pattern. Copyright 2000 Academic Press.

Pseudo second order kinetics and pseudo isotherms for malachite green onto activated carbon: comparison of linear and non-linear regression methods.

PubMed

Kumar, K Vasanth; Sivanesan, S

2006-08-25

Pseudo second order kinetic expressions of Ho, Sobkowsk and Czerwinski, Blanachard et al. and Ritchie were fitted to the experimental kinetic data of malachite green onto activated carbon by non-linear and linear method. Non-linear method was found to be a better way of obtaining the parameters involved in the second order rate kinetic expressions. Both linear and non-linear regression showed that the Sobkowsk and Czerwinski and Ritchie's pseudo second order model were the same. Non-linear regression analysis showed that both Blanachard et al. and Ho have similar ideas on the pseudo second order model but with different assumptions. The best fit of experimental data in Ho's pseudo second order expression by linear and non-linear regression method showed that Ho pseudo second order model was a better kinetic expression when compared to other pseudo second order kinetic expressions. The amount of dye adsorbed at equilibrium, q(e), was predicted from Ho pseudo second order expression and were fitted to the Langmuir, Freundlich and Redlich Peterson expressions by both linear and non-linear method to obtain the pseudo isotherms. The best fitting pseudo isotherm was found to be the Langmuir and Redlich Peterson isotherm. Redlich Peterson is a special case of Langmuir when the constant g equals unity.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data.

PubMed

Kotasidis, F A; Mehranian, A; Zaidi, H

2016-05-07

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

NASA Astrophysics Data System (ADS)

Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

2016-05-01

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Effects of climate on competitive dynamics in mixed conifer forests of the Sierra Nevada

Treesearch

Christal Johnson; Sophan Chhin; Jianwei Zhang

2017-01-01

Trees in more competitive environments appear to respond to climate differently than trees in less competitive environments. In turn, climate patterns may affect inter- or intra-specific competition, favoring certain individuals over others. Using dendrochronological methods, we sampled cores from dominant pine trees and their nearby competitors in 40 stands in the...

Electronic Commerce and Competitive Procurement

DTIC Science & Technology

1991-06-01

electronic commerce techniques ( electronic Jata interchange (EDI). electronic mail ( E -mail), electronic bulletin boards and facsimile] to competitive ...The ability to conduct discussions and negotiations with offerors electronically by E -mail supports the competitive proposal solicitation method...software vendors understand the dimensions of the DoD electronic commerce market , they may through competitive forces provide EDI capability. If their

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method.

PubMed

Polidori, David; Rowley, Clarence

2014-07-22

The indocyanine green dilution method is one of the methods available to estimate plasma volume, although some researchers have questioned the accuracy of this method. We developed a new, physiologically based mathematical model of indocyanine green kinetics that more accurately represents indocyanine green kinetics during the first few minutes postinjection than what is assumed when using the traditional mono-exponential back-extrapolation method. The mathematical model is used to develop an optimal back-extrapolation method for estimating plasma volume based on simulated indocyanine green kinetics obtained from the physiological model. Results from a clinical study using the indocyanine green dilution method in 36 subjects with type 2 diabetes indicate that the estimated plasma volumes are considerably lower when using the traditional back-extrapolation method than when using the proposed back-extrapolation method (mean (standard deviation) plasma volume = 26.8 (5.4) mL/kg for the traditional method vs 35.1 (7.0) mL/kg for the proposed method). The results obtained using the proposed method are more consistent with previously reported plasma volume values. Based on the more physiological representation of indocyanine green kinetics and greater consistency with previously reported plasma volume values, the new back-extrapolation method is proposed for use when estimating plasma volume using the indocyanine green dilution method.

Impacts of regulated competition on pricing in Chinese pharmaceutical market under urban employee basic medical insurance.

PubMed

Zhao, Mingyue; Wu, Jing

2017-06-01

Examine the effects of regulated competition on the drug pricing in China. Based on product-level data, a regression method was employed for pricing by using data from Tianjin Urban Employee Basic Medical Insurance (UEBMI) database. The market competition measures distinguished generic competition within the same molecule from therapeutic competition within the same therapeutic class. The increases in pricing are inversely related to the number of generic competitions. The generic sub-group results vary from the originator sub-group. For the generics, generic competition has a significantly reduced effect on the price; however, only therapeutic competition has a significantly reduced effect on the originator price. Regulated competition has a positive role in shaping the pharmaceutical market. Furthermore, regulated competition affects the price differently for the sub-groups. The promotion of competition between generic and originator in order to reap full competition benefit and reduce frictions among policies are necessary.

Nucleation-controlled microstructures and anomalous eutectic formation in undercooled Co-Sn and Ni-Si eutectic melts

NASA Astrophysics Data System (ADS)

Li, Mingjun; Kuribayashi, Kazuhiko

2003-12-01

Co-20.5 at. pct Sn and Ni-21.4 at. pct Si eutectic alloys have been levitated and undercooled in an electromagnetic levitator (EML) and then solidified spontaneously at different undercoolings. The original surface and cross-sectional morphologies of these solidified samples consist of separate eutectic colonies regardless of melt undercooling, indicating that microstructures in the free solidification of the eutectic systems are nucleation controlled. Regular lamellae always grow from the periphery of an independent anomalous eutectic grain in each eutectic colony. This typical morphology shows that the basic unit should be a single eutectic colony, when discussing the solidification behavior. Special emphasis is focused on the anomalous eutectic formation after a significant difference in linear kinetic coefficients is recognized for terminal eutectic phases, in particular when a eutectic reaction contains a nonfaceted disordered solid solution and a faceted ordered intermetallic compound as the terminal eutectic phases. It is this remarkable difference in the linear kinetic coefficients that leads to a pronounced difference in kinetic undercoolings. The sluggish kinetics in the interface atomic attachment of the intermetallic compound originates the occurrence of the decoupled growth of two eutectic phases. Hence, the current eutectic models are modified to incorporate kinetic undercooling, in order to account for the competitive growth behavior of eutectic phases in a single eutectic colony. The critical condition for generating the decoupled growth of eutectic phases is proposed. Further analysis reveals that a dimensionless critical undercooling may be appropriate to show the tendency for the anomalous eutectic-forming ability when considering the difference in linear kinetic coefficients of terminal eutectic phases. This qualitative criterion, albeit crude with several approximations and assumptions, can elucidate most of the published experimental results with the correct order of magnitude. Solidification modes in some eutectic alloys are predicted on the basis of the present criterion. Future work that may result in some probable errors is briefly directed to improve the model.

Comment on: "Split kinetic energy method for quantum systems with competing potentials", Ann. Phys. 327 (2012) 2061

NASA Astrophysics Data System (ADS)

Fernández, Francisco M.

2018-06-01

We show that the kinetic-energy partition method (KEP) is a particular example of the well known Rayleigh-Ritz variational method. We discuss some of the KEP results and compare them with those coming from other approaches.

New strategy to identify radicals in a time evolving EPR data set by multivariate curve resolution-alternating least squares.

PubMed

Fadel, Maya Abou; de Juan, Anna; Vezin, Hervé; Duponchel, Ludovic

2016-12-01

Electron paramagnetic resonance (EPR) spectroscopy is a powerful technique that is able to characterize radicals formed in kinetic reactions. However, spectral characterization of individual chemical species is often limited or even unmanageable due to the severe kinetic and spectral overlap among species in kinetic processes. Therefore, we applied, for the first time, multivariate curve resolution-alternating least squares (MCR-ALS) method to EPR time evolving data sets to model and characterize the different constituents in a kinetic reaction. Here we demonstrate the advantage of multivariate analysis in the investigation of radicals formed along the kinetic process of hydroxycoumarin in alkaline medium. Multiset analysis of several EPR-monitored kinetic experiments performed in different conditions revealed the individual paramagnetic centres as well as their kinetic profiles. The results obtained by MCR-ALS method demonstrate its prominent potential in analysis of EPR time evolved spectra. Copyright © 2016 Elsevier B.V. All rights reserved.

Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

PubMed

Varga, Matthew J; Schwartz, Steven D

2016-04-12

In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.

Inclusive Competitive Game Play Through Balanced Sensory Feedback.

PubMed

Westin, Thomas; Söderström, David; Karlsson, Olov; Peiris, Ranil

2017-01-01

While game accessibility has improved significantly the last few years, there are still barriers for equal participation and multiplayer issues have been less researched. Game balance is here about making the game fair in a player versus player competitive game. One difficult design task is to balance the game to be fair regardless of visual or hearing capabilities, with clearly different requirements. This paper explores a tentative design method for enabling inclusive competitive game-play without individual adaptations of game rules that could spoil the game. The method involved applying a unified design method to design an unbalanced game, then modifying visual feedback as a hypothetical balanced design, and testing the game with totally 52 people with and without visual or hearing disabilities in three workshops. Game balance was evaluated based on score differences and less structured qualitative data, and a redesign of the game was made. Conclusions are a tentative method for balancing a multiplayer, competitive game without changing game rules and how the method can be applied.

Clarifications regarding the use of model-fitting methods of kinetic analysis for determining the activation energy from a single non-isothermal curve.

PubMed

Sánchez-Jiménez, Pedro E; Pérez-Maqueda, Luis A; Perejón, Antonio; Criado, José M

2013-02-05

This paper provides some clarifications regarding the use of model-fitting methods of kinetic analysis for estimating the activation energy of a process, in response to some results recently published in Chemistry Central journal. The model fitting methods of Arrhenius and Savata are used to determine the activation energy of a single simulated curve. It is shown that most kinetic models correctly fit the data, each providing a different value for the activation energy. Therefore it is not really possible to determine the correct activation energy from a single non-isothermal curve. On the other hand, when a set of curves are recorded under different heating schedules are used, the correct kinetic parameters can be clearly discerned. Here, it is shown that the activation energy and the kinetic model cannot be unambiguously determined from a single experimental curve recorded under non isothermal conditions. Thus, the use of a set of curves recorded under different heating schedules is mandatory if model-fitting methods are employed.

Wheelchair pushrim kinetics measurement: A method to cancel inaccuracies due to pushrim weight and wheel camber.

PubMed

Chénier, Félix; Aissaoui, Rachid; Gauthier, Cindy; Gagnon, Dany H

2017-02-01

The commercially available SmartWheel TM is largely used in research and increasingly used in clinical practice to measure the forces and moments applied on the wheelchair pushrims by the user. However, in some situations (i.e. cambered wheels or increased pushrim weight), the recorded kinetics may include dynamic offsets that affect the accuracy of the measurements. In this work, an automatic method to identify and cancel these offsets is proposed and tested. First, the method was tested on an experimental bench with different cambers and pushrim weights. Then, the method was generalized to wheelchair propulsion. Nine experienced wheelchair users propelled their own wheelchairs instrumented with two SmartWheels with anti-slip pushrim covers. The dynamic offsets were correctly identified using the propulsion acquisition, without needing a separate baseline acquisition. A kinetic analysis was performed with and without dynamic offset cancellation using the proposed method. The most altered kinetic variables during propulsion were the vertical and total forces, with errors of up to 9N (p<0.001, large effect size of 5). This method is simple to implement, fully automatic and requires no further acquisitions. Therefore, we advise to use it systematically to enhance the accuracy of existing and future kinetic measurements. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Iterative Addition of Kinetic Effects to Cold Plasma RF Wave Solvers

NASA Astrophysics Data System (ADS)

Green, David; Berry, Lee; RF-SciDAC Collaboration

2017-10-01

The hot nature of fusion plasmas requires a wave vector dependent conductivity tensor for accurate calculation of wave heating and current drive. Traditional methods for calculating the linear, kinetic full-wave plasma response rely on a spectral method such that the wave vector dependent conductivity fits naturally within the numerical method. These methods have seen much success for application to the well-confined core plasma of tokamaks. However, quantitative prediction of high power RF antenna designs for fusion applications has meant a requirement of resolving the geometric details of the antenna and other plasma facing surfaces for which the Fourier spectral method is ill-suited. An approach to enabling the addition of kinetic effects to the more versatile finite-difference and finite-element cold-plasma full-wave solvers was presented by where an operator-split iterative method was outlined. Here we expand on this approach, examine convergence and present a simplified kinetic current estimator for rapidly updating the right-hand side of the wave equation with kinetic corrections. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Simulated maximum likelihood method for estimating kinetic rates in gene expression.

PubMed

Tian, Tianhai; Xu, Songlin; Gao, Junbin; Burrage, Kevin

2007-01-01

Kinetic rate in gene expression is a key measurement of the stability of gene products and gives important information for the reconstruction of genetic regulatory networks. Recent developments in experimental technologies have made it possible to measure the numbers of transcripts and protein molecules in single cells. Although estimation methods based on deterministic models have been proposed aimed at evaluating kinetic rates from experimental observations, these methods cannot tackle noise in gene expression that may arise from discrete processes of gene expression, small numbers of mRNA transcript, fluctuations in the activity of transcriptional factors and variability in the experimental environment. In this paper, we develop effective methods for estimating kinetic rates in genetic regulatory networks. The simulated maximum likelihood method is used to evaluate parameters in stochastic models described by either stochastic differential equations or discrete biochemical reactions. Different types of non-parametric density functions are used to measure the transitional probability of experimental observations. For stochastic models described by biochemical reactions, we propose to use the simulated frequency distribution to evaluate the transitional density based on the discrete nature of stochastic simulations. The genetic optimization algorithm is used as an efficient tool to search for optimal reaction rates. Numerical results indicate that the proposed methods can give robust estimations of kinetic rates with good accuracy.

Improving University Ranking to Achieve University Competitiveness by Management Information System

NASA Astrophysics Data System (ADS)

Dachyar, M.; Dewi, F.

2015-05-01

One way to increase university competitiveness is through information system management. A literature review was done to find information system factors that affect university performance in Quacquarelli Symonds (QS) University Ranking: Asia evaluation. Information system factors were then eliminated using Delphi method through consensus of 7 experts. Result from Delphi method was used as measured variables in PLS-SEM. Estimation with PLS-SEM method through 72 respondents shows that the latent variable academic reputation and citation per paper have significant correlation to university competitiveness. In University of Indonesia (UI) the priority to increase university competitiveness as follow: (i) network building in international conference, (ii) availability of research data to public, (iii) international conference information, (iv) information on achievements and accreditations of each major, (v) ease of employment for alumni.

Kinetics of caesium and potassium absorption by roots of three grass pastures and competitive effects of potassium on caesium uptake in Cynodon sp.

NASA Astrophysics Data System (ADS)

Ayub, J. Juri; Valverde, L. Rubio; Garcia-Sanchez, M. J.; Fernandez, J. A.; Velasco, R. H.

2008-08-01

Caesium uptake by plant roots has been normally associated with the uptake of potassium as the potassium transport systems present in plants have also the capacity to transport caesium. Three grass species (Eragrostis curvula, Cynodon sp and Distichlis spicata) growing in seminatural grassland of central Argentina were selected to study their capability to incorporate Cs+ (and K+) using electrophysiological techniques. Although the 137Cs soil inventory ranged between 328-730 Bq m-2 in this region, no 137Cs activity was detected in these plants. However, all the species, submitted previously to K+ starvation, showed the uptake of both Cs+ and K+ when micromolar concentrations of these cations were present in the medium. The uptake showed saturation kinetics for both cations that could be fitted to the Michelis-Menten model. KM values were smaller for K+ than for Cs+, indicating a higher affinity for the first cation. The presence of increasing K+ concentrations in the assay medium inhibited Cs+ uptake in Cynodon sp., as expected if both cations are transported by the same transport systems. This effect is due to the competition of both ions for the union sites of the high affinity potassium transporters. In field situation, where soil concentration of Cs+ is smaller than K+ concentration, is then expectable that caesium activity in plants is not detectable. Nevertheless, the studied plants would have the capacity to incorporate caesium if its availability in soil solution increases. In addition, studies of Cs/K interaction can help us to understand the variability in transfer factors.

Fatty acid transport protein-2 inhibitor Grassofermata/CB5 protects cells against lipid accumulation and toxicity

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

Saini, Nipun; Black, Paul N.; Montefusco, David

The inhibition of the fatty acid uptake into non-adipose tissues provides an attractive target for prevention of lipotoxicity leading to obesity-associated non-alcoholic fatty liver disease and type 2 diabetes. Fatty acid transport proteins (FATPs) are bifunctional proteins involved in the uptake and activation of fatty acids by esterification with coenzyme A. Here we characterize Grassofermata/CB5, previously identified as a fatty acid uptake inhibitor directed against HsFATP2. The compound was effective in inhibiting the uptake of fatty acids in the low micro-molar range (IC{sub 50} 8–11 μM) and prevented palmitate-mediated lipid accumulation and cell death in cell lines that are models formore » intestines, liver, muscle and pancreas. In adipocytes, uptake inhibition was less effective (IC{sub 50} 58 μM). Inhibition was specific for long chain fatty acids and was ineffective toward medium chain fatty acids, which are transported by diffusion. Kinetic analysis of Grassofermata-dependent FA transport inhibition verified a non-competitive mechanism. By comparison with Grassofermata, several atypical antipsychotic drugs previously implicated as inhibitors of FA uptake were ineffectual. In mice Grassofermata decreased absorption of {sup 13}C-oleate demonstrating its potential as a therapeutic agent. - Highlights: • Grassofermata is a small compound inhibitor of FATP2. • Uptake inhibition is specific for long chain fatty acids. • Uptake kinetics shows low specificity for adipocytes compared to other cell types. • Inhibition is by a non-competitive mechanism. • Atypical antipsychotics do not inhibit FA uptake by comparison with Grassofermata.« less

Removal of binary dyes mixtures with opposite and similar charges by adsorption, coagulation/flocculation and catalytic oxidation in the presence of CeO2/H2O2 Fenton-like system.

PubMed

Issa Hamoud, Houeida; Finqueneisel, Gisèle; Azambre, Bruno

2017-06-15

In this study, the removal of binary mixtures of dyes with similar (Orange II/Acid Green 25) or opposite charges (Orange II/Malachite Green) was investigated either by simple adsorption on ceria or by the heterogeneous Fenton reaction in presence of H 2 O 2 . First, the CeO 2 nanocatalyst with high specific surface area (269 m 2 /g) and small crystal size (5 nm) was characterized using XRD, Raman spectroscopy and N 2 physisorption at 77 K. The adsorption of single dyes was studied either from thermodynamic and kinetic viewpoints. It is shown that the adsorption of dyes on ceria surface is highly pH-dependent and followed a pseudo-second order kinetic model. Adsorption isotherms fit well the Langmuir model with a complete monolayer coverage and higher affinity towards Orange II at pH 3, compared to other dyes. For the (Orange II/Acid Green 25) mixture, both the amounts of dyes adsorbed on ceria surface and discoloration rates measured from Fenton experiments were decreased by comparison with single dyes. This is due to the adsorption competition existing onto the same surface Ce x+ sites and the reaction competition with hydroxyl radicals, respectively. The behavior of the (Orange II/Malachite Green) mixture is markedly different. Dyes with opposite charges undergo paired adsorption on ceria as well as homogeneous and heterogeneous coagulation/flocculation processes, but can also be removed by heterogeneous Fenton process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Competitive adsorption of textile dyes using peat: adsorption equilibrium and kinetic studies in monosolute and bisolute systems.

PubMed

Sepulveda, L; Troncoso, F; Contreras, E; Palma, C

2008-09-01

The purpose of this study is to investigate the adsorption by peat of four reactive textile dyes with the following commercial names: Yellow CIBA WR 200% (Y), Dark Blue CIBA WR (DB), Navy CIBA WB (N), and Red CIBA WB 150% (R), used in a cotton-polyester fabric finishing plant. The decolorization levels obtained varied between 5% and 30%, and the most significant variables were pH and ionic strength. Equilibrium studies were carried out at pH 2.8 and temperature of 25 degrees C. Maximum adsorption capacities were between 15 and 20 mg g(-1). Experimental data were fitted to the models of Langmuir. The equilibrium studies for bisolute systems were DB-R and Y-N mixtures. The Langmuir extended model indicated that there is competition for adsorption sites and without interaction between dyes. The results of the kinetic adsorption studies on monosolute and bisolute systems were fitted to the film-pore diffusion, variable diffusivity and quasi-stationary models. They showed that the diffusivity coefficients obtained varied between 2.0 x 10(-8) and 8.5 x 10(-8) cm2s(-1) when the variable diffusivity mass transfer model (VDM) was used and effective diffusion coefficient was fitted between 3.3 x 10(-7) and 56.0 x 10(-7) cm2s(-1) for the film-pore diffusion model (FPDM). The root of average of squares relative error obtained varied between 0.8% and 47.0% for the VDM and FPDM models, respectively.

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

Monochloramine disinfection kinetics of Nitrosomonas europaea by propidium monoazide quantitative PCR and Live/Dead BacLight Methods

EPA Science Inventory

Monochloramine disinfection kinetics were determined for the pure culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture independent methods: (1) LIVE/DEAD® BacLight™ (LD) and (2) propidium monoazide quantitative PCR (PMA-qPCR). Both methods were f...

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.

PubMed

Khan, Nymul; Maezato, Yukari; McClure, Ryan S; Brislawn, Colin J; Mobberley, Jennifer M; Isern, Nancy; Chrisler, William B; Markillie, Lye Meng; Barney, Brett M; Song, Hyun-Seob; Nelson, William C; Bernstein, Hans C

2018-01-10

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized - and confirmed - that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

A General Strategy for Nanohybrids Synthesis via Coupled Competitive Reactions Controlled in a Hybrid Process

PubMed Central

Wang, Rongming; Yang, Wantai; Song, Yuanjun; Shen, Xiaomiao; Wang, Junmei; Zhong, Xiaodi; Li, Shuai; Song, Yujun

2015-01-01

A new methodology based on core alloying and shell gradient-doping are developed for the synthesis of nanohybrids, realized by coupled competitive reactions, or sequenced reducing-nucleation and co-precipitation reaction of mixed metal salts in a microfluidic and batch-cooling process. The latent time of nucleation and the growth of nanohybrids can be well controlled due to the formation of controllable intermediates in the coupled competitive reactions. Thus, spatiotemporal-resolved synthesis can be realized by the hybrid process, which enables us to investigate nanohybrid formation at each stage through their solution color changes and TEM images. By adjusting the bi-channel solvents and kinetic parameters of each stage, the primary components of alloyed cores and the second components of transition metal doping ZnO or Al2O3 as surface coatings can be successively formed. The core alloying and shell gradient-doping strategy can efficiently eliminate the crystal lattice mismatch in different components. Consequently, varieties of gradient core-shell nanohybrids can be synthesized using CoM, FeM, AuM, AgM (M = Zn or Al) alloys as cores and transition metal gradient-doping ZnO or Al2O3 as shells, endowing these nanohybrids with unique magnetic and optical properties (e.g., high temperature ferromagnetic property and enhanced blue emission). PMID:25818342

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

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

Khan, Nymul; Maezato, Yukari; McClure, Ryan S.

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesizedmore » – and confirmed – that co-cultivation under glucose as the sole carbon source would result in a competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.« less

Modeling the competition between antenna size mutant and wild type microalgae in outdoor mass culture.

PubMed

de Mooij, Tim; Schediwy, Kira; Wijffels, René H; Janssen, Marcel

2016-12-20

Under high light conditions, microalgae are oversaturated with light which significantly reduces the light use efficiency. Microalgae with a reduced pigment content, antenna size mutants, have been proposed as a potential solution to increase the light use efficiency. The goal of this study was to investigate the competition between antenna size mutants and wild type microalgae in mass cultures. Using a kinetic model and literature-derived experimental data from wild type Chlorella sorokiniana, the productivity and competition of wild type cells and antenna size mutants were simulated. Cultivation was simulated in an outdoor microalgal raceway pond production system which was assumed to be limited by light only. Light conditions were based on a Mediterranean location (Tunisia) and a more temperate location (the Netherlands). Several wild type contamination levels were simulated in each mutant culture separately to predict the effect on the productivity over the cultivation time of a hypothetical summer season of 100days. The simulations demonstrate a good potential of antenna size reduction to increase the biomass productivity of microalgal cultures. However, it was also found that after a contamination with wild type cells the mutant cultures will be rapidly overgrown resulting in productivity loss. Copyright © 2016 Elsevier B.V. All rights reserved.

In vivo competitive studies between normal and common gamma chain-defective bone marrow cells: implications for gene therapy.

PubMed

Otsu, M; Sugamura, K; Candotti, F

2000-09-20

Corrective gene transfer into hematopoietic stem cells (HSCs) is being investigated as therapy for X-linked severe combined immunodeficiency (XSCID) and it is hoped that selective advantage of gene-corrected HSCs will help in achieving full immune reconstitution after treatment. Lines of evidence from the results of allogeneic bone marrow transplantation in patients with XSCID support this hypothesis that, however, has not been rigorously tested in an experimental system. We studied the competition kinetics between normal and XSCID bone marrow (BM) cells using a murine bone marrow transplantation (BMT) model. For easy chimerism determination, we used genetic marking with retrovirus-mediated expression of the enhanced green fluorescent protein (EGFP). We found that XSCID BM cells were able to compete with normal BM cells for engraftment of myeloid lineages in a dose-dependent manner, whereas we observed selective repopulation of T, B, and NK cells deriving from normal BM cells. This was true despite the evidence of competitive engraftment of XSCID lineage marker-negative/c-Kit-positive (Lin-/c-Kit+) cells in the bone marrow of treated animals. From these results we extrapolate that genetic correction of XSCID HSCs will result in selective advantage of gene-corrected lymphoid lineages with consequent restoration of lymphocyte populations and high probability of clinical benefit.

Simulation of Nuclear Reactor Kinetics by the Monte Carlo Method

NASA Astrophysics Data System (ADS)

Gomin, E. A.; Davidenko, V. D.; Zinchenko, A. S.; Kharchenko, I. K.

2017-12-01

The KIR computer code intended for calculations of nuclear reactor kinetics using the Monte Carlo method is described. The algorithm implemented in the code is described in detail. Some results of test calculations are given.

The Impact of Nursing Students' Chemistry Learning Performance Assessment in Taiwan: Competitive versus Non-Competitive Student Team Achievement Division Approaches

ERIC Educational Resources Information Center

Wang, Kai-Ping

2012-01-01

Purpose: The purpose of this study was to determine the effectiveness of competitive Student Team Achievement Division (STAD), non-competitive STAD, and traditional learning on chemistry learning and learning perceptions. Sample, design and methods: By adopting the STAD approach, this study examined 144 nursing students at a five-year junior…

Sorption of norfloxacin, sulfamerazine and oxytetracycline by KOH-modified biochar under single and ternary systems.

PubMed

Luo, Jiwei; Li, Xue; Ge, Chengjun; Müller, Karin; Yu, Huamei; Huang, Peng; Li, Jiatong; Tsang, Daniel C W; Bolan, Nanthi S; Rinklebe, Jörg; Wang, Hailong

2018-05-08

Pollution of water by single antibiotics has been investigated in depth. However, in reality, a wide range of different contaminants is often mixed in the aquatic environment (contaminant cocktail). Here, single and competitive sorption dynamics of ionizable norfloxacin (NOR), sulfamerazine (SMR) and oxytetracycline (OTC) by both pristine and modified biochars were investigated. Sorption kinetics of the three antibiotics was faster in ternary-solute than single-solute system. Sorption efficiency was enhanced in the competitive system for NOR by the pristine biochar, and for OTC by both the pristine biochar and the modified biochar, while SMR sorption by the pristine biochar and the KOH-modified biochar was inhibited. Sorption was governed by electrostatic interactions, π-π EDA and H-bonds for antibiotics sorption by biochar. SMR and OTC sorption by biochar was influenced by cation bridging and surface complexation, respectively. This research finding will guide the development of treatment procedures for water polluted by multiple antibiotics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro

PubMed Central

Yacoby, Iftach; Pochekailov, Sergii; Toporik, Hila; Ghirardi, Maria L.; King, Paul W.; Zhang, Shuguang

2011-01-01

Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evidence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for competition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADP+-oxidoreductase (FNR), and NADP+. Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen production and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport. PMID:21606330

Identification of tyrosinase specific inhibitors from Xanthium strumarium fruit extract using ultrafiltration-high performance liquid chromatography.

PubMed

Wang, Zhiqiang; Hwang, Seung Hwan; Huang, Bo; Lim, Soon Sung

2015-10-01

In this study, a strategy based on ultrafiltration-high performance liquid chromatography coupled with diode array detection (UF-HPLC-DAD) was proposed for screening tyrosinase specific inhibitors in Xanthii fructus. The false negatives were distinguished by optimizing the UF-HPLC-DAD parameters to reduce the background noise; the false positives were distinguished by introducing a blocked tyrosinase in the control group for comparison. To obtain the best blocker, the competitive experiments were performed using various known ligands. Using this strategy, three competitive inhibitors (protocatechuic acid; 3,5-di-O-caffeoylquinic acid; and 1,5-di-O-caffeoylquinic acid) and one mixed-type inhibitor (chlorogenic acid) were identified. These results were verified using tyrosinase inhibition assay, kinetic analysis, and structural simulation of the complex. Our experimental results suggest that the proposed strategy could be useful for high-throughput identification of tyrosinase specific inhibitors in natural products. Copyright © 2015 Elsevier B.V. All rights reserved.

Energetics and dynamics through time-resolved measurements in mass spectrometry

NASA Astrophysics Data System (ADS)

Lifshitz, Chava

Results of recent work on time-resolved photoionization and electron ionization mass spectrometry carried out in Jerusalem are reviewed. Time-resolved photoionization mass spectrometry in the vacuum ultraviolet is applied to polycyclic aromatic hydrocarbons, for example naphthalene, pyrene and fluoranthene as well as to some bromo derivatives (bromonaphthalene and bromoanthracene). Time-resolved photoionization efficiency curves are modelled by Rice-Ramsperger-Kassel-Marcus QET rate-energy k ( E ) dependences of the unimolecular dissociative processes and by the rate process infrared radiative relaxation k . Experimental results are augmented by time-resolved photorad dissociation data for the same species, whenever available. Kinetic shifts, conventional and intrinsic (due to competition between dissociative and radiative decay), are evaluated. Activation parameters (activation energies and entropies) are deduced. Thermochemical information is obtained including bond energies and ionic heats of formation. Fullerenes, notably C , are studied by time-resolved electron ionization and a large intrinsic shift, due to competition with black-bodylike radiative decay in the visible is discussed.

Inhibition studies of soybean (Glycine max) urease with heavy metals, sodium salts of mineral acids, boric acid, and boronic acids.

PubMed

Kumar, Sandeep; Kayastha, Arvind M

2010-10-01

Various inhibitors were tested for their inhibitory effects on soybean urease. The K(i) values for boric acid, 4-bromophenylboronic acid, butylboronic acid, and phenylboronic acid were 0.20 +/- 0.05 mM, 0.22 +/- 0.04 mM, 1.50 +/- 0.10 mM, and 2.00 +/- 0.11 mM, respectively. The inhibition was competitive type with boric acid and boronic acids. Heavy metal ions including Ag(+), Hg(2+), and Cu(2+) showed strong inhibition on soybean urease, with the silver ion being a potent inhibitor (IC(50) = 2.3 x 10(-8) mM). Time-dependent inhibition studies exhibited biphasic kinetics with all heavy metal ions. Furthermore, inhibition studies with sodium salts of mineral acids (NaF, NaCl, NaNO(3), and Na(2)SO(4)) showed that only F(-) inhibited soybean urease significantly (IC(50) = 2.9 mM). Competitive type of inhibition was observed for this anion with a K(i) value of 1.30 mM.

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

Rao, Linfeng

A literature survey has been conducted to collect information on the International R&D activities in the extraction of uranium from seawater for the period from the 1960s till the year of 2010. The reported activities, on both the laboratory scale bench experiments and the large scale marine experiments, were summarized by country/region in this report. Among all countries where such activities have been reported, Japan has carried out the most advanced large scale marine experiments with the amidoxime-based system, and achieved the collection efficiency (1.5 g-U/kg-adsorbent for 30 days soaking in the ocean) that could justify the development of industrialmore » scale marine systems to produce uranium from seawater at the price competitive with those from conventional uranium resources. R&D opportunities are discussed for improving the system performance (selectivity for uranium, loading capacity, chemical stability and mechanical durability in the sorption-elution cycle, and sorption kinetics) and making the collection of uranium from seawater more economically competitive.« less

Catalytic and immunochemical properties of arylsulphatase A from urine, modified by potassium ferrate.

PubMed

Laidler, P M; Steczko, J

1986-01-01

Arylsulphatase A (EC 3.1.6.1.) from urine was inactivated with potassium ferrate, a strong oxidizing agent. The inhibition could be prevented by competitive inhibitors, tetraborate and orthophosphate. Tetraborate which was shown to be a powerful competitive inhibitor (determined Ki = 4 X 10(-5) M) gave more efficient protection. The partially inactivated enzyme exhibited a Km value similar to that of the unmodified arylsulphatase A, and its Vmax decreased in proportion to the loss of enzymatic activity. The partially modified enzyme did not lose its ability to catalyse hydrolysis of p-nitrocatechol sulphate according to the "anomalous kinetics" exhibited towards this substrate and characteristic for arylsulphatase A. The immunochemical properties of arylsulphatase A either fully or partially inactivated were similar to those of the native enzyme. The results allow to conclude that ferrate reacts with arylsulphatase A in its active site. Thus ferrate seems to be a very sensitive probe for amino acid residues essential for catalytic activity of arylsulphatase A.

Kinetic Studies with Ion Selective Electrodes: Determination of Creatinine in Urine with a Picrate Ion Selective Electrode: A Laboratory Experiment.

ERIC Educational Resources Information Center

Diamandis, E. P.; And Others

1983-01-01

The kinetic of the Jaffe reaction with picrate ion selective electrode (ISE) and a kinetic method for determining creatinine in urine is presented. The experiment could be used to familarize students with the application of ISE in kinetic studies and chemical analysis. (Author/JN)

Layer-selective synthesis of bilayer graphene via chemical vapor deposition

NASA Astrophysics Data System (ADS)

Yang, Ning; Choi, Kyoungjun; Robertson, John; Park, Hyung Gyu

2017-09-01

A controlled synthesis of high-quality AB-stacked bilayer graphene by chemical vapor deposition demands a detailed understanding of the mechanism and kinetics. By decoupling the growth of the two layers via a growth-and-regrowth scheme, we report the kinetics and termination mechanisms of the bilayer graphene growth on copper. We observe, for the first time, that the secondary layer growth follows Gompertzian kinetics. Our observations affirm the postulate of a time-variant transition from a mass-transport-limited to a reaction-limited regimes and identify the mechanistic disparity between the monolayer growth and the secondary-layer expansion underneath the monolayer cover. It is the continuous carbon supply that drives the expansion of the graphene secondary layer, rather than the initially captured carbon amount, suggesting an essential role of the surface diffusion of reactant adsorbates in the interspace between the top graphene layer and the underneath copper surface. We anticipate that the layer selectivity of the growth relies on the entrance energetics of the adsorbed reactants to the graphene-copper interspace across the primary-layer edge, which could be engineered by tailoring the edge termination state. The temperature-reliant saturation area of the secondary-layer expansion is understood as a result of competitive attachment of carbon and hydrogen adatoms to the secondary-layer graphene edge.

Selective and slow-binding inhibition of shikonin derivatives isolated from Lithospermum erythrorhizon on glycosyl hydrolase 33 and 34 sialidases.

PubMed

Kim, Ji Young; Jeong, Hyung Jae; Park, Ji-Young; Kim, Young Min; Park, Su-Jin; Cho, Jung Keun; Park, Ki Hun; Ryu, Young Bae; Lee, Woo Song

2012-03-01

Sialidases are enzymes that catalyze the hydrolysis of sialic acid residues from various glycoconjugates, which are widely found in a number of viral and microbial pathogens. In this study, we investigated the biological evaluation of isolated six shikonins (1-6) and three shikonofurans (7-9) from Lithospermum erythrorhizon. The nine isolated compounds 1-9 showed strong and selective inhibition of glycosyl hydrolase (GH) 33 and -34 sialidases activities. In GH33 bacterial-sialidase inhibition assay, the inhibitory activities against GH33 siadliase of all shikonofuran derivatives (7-9) were greater than shikonin derivatives (1-6). Shikonofuran E (8) exhibited the most potent inhibitory activity toward GH33 sialidases (IC(50)=0.24μM). Moreover, our detailed kinetic analysis of these species unveiled that they are all competitive and simple reversible slow-binding inhibitors. Otherwise, they showed different inhibitory capacities and kinetic modes to GH34 viral-sialidase activity. All the naphthoquinone derivatives (1-6) were of almost equal efficiency with IC(50) value of 40μM and shikonofurans (7-9) did not show the significant inhibitory effect to GH34 sialidase. Kinetic analyses indicated that naphthoquinones acted via a noncompetitive mechanism. Copyright © 2012 Elsevier Ltd. All rights reserved.

Gradual Ordering in Red Abalone Nacre

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

Gilbert, P. U. P. A.; Metzler, Rebecca A.; Zhou, Dong

2008-09-03

Red abalone (Haliotis rufescens) nacre is a layered composite biomineral that contains crystalline aragonite tablets confined by organic layers. Nacre is intensely studied because its biologically controlled microarchitecture gives rise to remarkable strength and toughness, but the mechanisms leading to its formation are not well understood. Here we present synchrotron spectromicroscopy experiments revealing that stacks of aragonite tablet crystals in nacre are misoriented with respect to each other. Quantitative measurements of crystal orientation, tablet size, and tablet stacking direction show that orientational ordering occurs not abruptly but gradually over a distance of 50 {micro}m. Several lines of evidence indicate thatmore » different crystal orientations imply different tablet growth rates during nacre formation. A theoretical model based on kinetic and gradual selection of the fastest growth rates produces results in qualitative and quantitative agreement with the experimental data and therefore demonstrates that ordering in nacre is a result of crystal growth kinetics and competition either in addition or to the exclusion of templation by acidic proteins as previously assumed. As in other natural evolving kinetic systems, selection of the fastest-growing stacks of tablets occurs gradually in space and time. These results suggest that the self-ordering of the mineral phase, which may occur completely independently of biological or organic-molecule control, is fundamental in nacre formation.« less

Kinetics and equilibrium modelling of lead uptake by algae Gelidium and algal waste from agar extraction industry.

PubMed

Vilar, Vítor J P; Botelho, Cidália M S; Boaventura, Rui A R

2007-05-08

Pb(II) biosorption onto algae Gelidium, algal waste from agar extraction industry and a composite material was studied. Discrete and continuous site distribution models were used to describe the biosorption equilibrium at different pH (5.3, 4 and 3), considering competition among Pb(II) ions and protons. The affinity distribution function of Pb(II) on the active sites was calculated by the Sips distribution. The Langmuir equilibrium constant was compared with the apparent affinity calculated by the discrete model, showing higher affinity for lead ions at higher pH values. Kinetic experiments were conducted at initial Pb(II) concentrations of 29-104 mgl(-1) and data fitted to pseudo-first Lagergren and second-order models. The adsorptive behaviour of biosorbent particles was modelled using a batch mass transfer kinetic model, which successfully predicts Pb(II) concentration profiles at different initial lead concentration and pH, and provides significant insights on the biosorbents performance. Average values of homogeneous diffusivity, D(h), are 3.6 x 10(-8); 6.1 x 10(-8) and 2.4 x 10(-8)cm(2)s(-1), respectively, for Gelidium, algal waste and composite material. The concentration of lead inside biosorbent particles follows a parabolic profile that becomes linear near equilibrium.

An operando FTIR spectroscopic and kinetic study of carbon monoxide pressure influence on rhodium-catalyzed olefin hydroformylation.

PubMed

Kubis, Christoph; Sawall, Mathias; Block, Axel; Neymeyr, Klaus; Ludwig, Ralf; Börner, Armin; Selent, Detlef

2014-09-08

The influence of carbon monoxide concentration on the kinetics of the hydroformylation of 3,3-dimethyl-1-butene with a phosphite-modified rhodium catalyst has been studied for the pressure range p(CO)=0.20-3.83 MPa. Highly resolved time-dependent concentration profiles of the organometallic intermediates were derived from IR spectroscopic data collected in situ for the entire olefin-conversion range. The dynamics of the catalyst and organic components are described by enzyme-type kinetics with competitive and uncompetitive inhibition reactions involving carbon monoxide taken into account. Saturation of the alkyl-rhodium intermediates with carbon monoxide as a cosubstrate occurs between 1.5 and 2 MPa of carbon monoxide pressure, which brings about a convergence of aldehyde regioselectivity. Hydrogenolysis of the acyl intermediate is fast at 30 °C and low pressure of p(CO)=0.2 MPa, but is of minus first order with respect to the solution concentration of carbon monoxide. Resting 18-electron hydrido and acyl complexes that correspond to early and late rate-determining states, respectively, coexist as long as the conversion of the substrate is not complete. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fluorescence stopped-flow study of the interaction of tubulin with the antimitotic drug MDL 27048.

PubMed

Silence, K; D'Hoore, A; Engelborghs, Y; Peyrot, V; Briand, C

1992-11-17

The kinetics of the binding of MDL 27048 to tubulin have been studied by fluorescence stopped flow. The binding is accompanied by a fluorescence increase. The time course can be described by a sum of two exponentials, assumed to be due to the presence of two major tubulin isoforms. The observed rate constants depend in a nonlinear way on the concentration of MDL in pseudo-first-order conditions. This concentration dependence can be described by the presence of a fast equilibrium of low affinity, followed by an isomerization of the initial complex. The dissociation kinetics have been studied by displacement experiments, in which MTC was used as a competitive ligand. The reaction enthalpy change for the first binding equilibrium and the activation energies for the forward and reverse steps of the isomerization were determined from the temperature dependence. This was possible for the two tubulin isotype populations. The kinetics of the binding of MDL to tubulin are slowed down in the presence of 3',4',5'-trimethoxyacetophenone, a fast binding analog of the colchicine A-ring, but are not influenced by the binding of tropolone methyl ether, indicating that the binding site of MDL has the A-subsite in common with colchicine, but not the C-subsite.

Detailed Modelling of Kinetic Biodegradation Processes in a Laboratory Mmicrocosm

NASA Astrophysics Data System (ADS)

Watson, I.; Oswald, S.; Banwart, S.; Mayer, U.

2003-04-01

Biodegradation of organic contaminants in soil and groundwater usually takes places via different redox processes happening sequentially as well as simultaneously. We used numerical modelling of a long-term lab microcosm experiment to simulate the dynamic behaviour of fermentation and respiration in the aqueous phase in contact with the sandstone material, and to develop a conceptual model describing these processes. Aqueous speciation, surface complexation, mineral dissolution and precipitation were taken into account also. Fermentation can be the first step of the degradation process producing intermediate species, which are subsequently consumed by TEAPs. Microbial growth and substrate utilisation kinetics are coupled via a formulation that also includes aqueous speciation and other geochemical reactions including surface complexation, mineral dissolution and precipitation. Competitive exclusion between TEAPs is integral to the conceptual model of the simulation, and the results indicate that exclusion is not complete, but some overlap is found between TEAPs. The model was used to test approaches like the partial equilibrium approach that currently make use of hydrogen levels to diagnose prevalent TEAPs in groundwater. The observed pattern of hydrogen and acetate concentrations were reproduced well by the simulations, and the results show the relevance of kinetics, lag times and inhibition, and especially that intermediate products play a key role.

Effect of soil parameters on the kinetics of the displacement of Fe from FeEDDHA chelates by Cu.

PubMed

Schenkeveld, Walter D C; Reichwein, Arjen M; Temminghoff, Erwin J M; van Riemsdijk, Willem H

2012-06-28

In soil application, o,o-FeEDDHA (iron (3+) ethylene diamine-N,N'-bis(2-hydroxy phenyl acetic acid) complex) is the active ingredient of FeEDDHA chelate-based Fe fertilizers. The effectiveness of o,o-FeEDDHA is potentially compromised by the displacement of Fe from FeEDDHA by Cu. The actual impact of Cu competition is codetermined by the kinetics of the displacement reaction. In this study, the influence of soil parameters on the displacement kinetics has been examined in goethite suspensions. The displacement reaction predominantly takes place on the reactive surface rather than in solution. The rate at which the o,o-FeEDDHA concentration declined depended on the available reactive surface area, the Cu loading, and the FeEDDHA loading. Soil factors reducing FeEDDHA adsorption (high ionic strength, humic acid adsorption onto the goethite surface, and monovalent instead of divalent cations in the electrolyte) decreased the displacement rate. For meso o,o-FeEDDHA, the displacement rate equation was derived, which is first order in FeEDDHA loading and half order in Cu loading. For soil conditions, the equation can be simplified to an exponential decay function in meso o,o-FeEDDHA solution concentration.

A point mutation of valine-311 to methionine in Bacillus subtilis protoporphyrinogen oxidase does not greatly increase resistance to the diphenyl ether herbicide oxyfluorfen.

PubMed

Jeong, Eunjoo; Houn, Thavrak; Kuk, Yongin; Kim, Eun-Seon; Chandru, Hema Kumar; Baik, Myunggi; Back, Kyoungwhan; Guh, Ja-Ock; Han, Oksoo

2003-10-01

In an effort to asses the effect of Val311Met point mutation of Bacillus subtilis protoporphyrinogen oxidase on the resistance to diphenyl ether herbicides, a Val311Met point mutant of B. subtilis protoporphyrinogen oxidase was prepared, heterologously expressed in Escherichia coli, and the purified recombinant Val311Met mutant protoporphyrinogen oxidase was kinetically characterized. The mutant protoporphyrinogen oxidase showed very similar kinetic patterns to wild type protoporphyrinogen oxidase, with slightly decreased activity dependent on pH and the concentrations of NaCl, Tween 20, and imidazole. When oxyfluorfen was used as a competitive inhibitor, the Val311Met mutant protoporphyrinogen oxidase showed an increased inhibition constant about 1.5 times that of wild type protoporphyrinogen oxidase. The marginal increase of the inhibition constant indicates that the Val311Met point mutation in B. subtilis protoporphyrinogen oxidase may not be an important determinant in the mechanism that protects protoporphyrinogen oxidase against diphenyl ether herbicides.

Dynamic Covalent Synthesis of Aryleneethynylene Cages through Alkyne Metathesis: Dimer, Tetramer, or Interlocked Complex?

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

Wang, Qi; Yu, Chao; Zhang, Chenxi

A dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) was explored. Our study on the relationship of the COP structures and the geometry of their building blocks reveals that the topology of aryleneethynylene COPs strongly depends on the size of the building blocks. A tetramer (D2h symmetric), dimer, or interlocked complex can be formed from monomers with the same face-to-edge angle but in different sizes. As alkyne metathesis is a self-exchange reaction and non-directional, the cyclooligomerization of multi-alkyne monomers involves both intramolecular cyclization and intermolecular metathesis reaction, resulting in complicated thermodynamic process disturbed by kinetic competition. Although amore » tetrahedron-shaped tetramer (Td symmetric) has comparable thermodynamic stability to a D2h symmetric tetramer, its formation is kinetically disfavored and was not observed experimentally. Aryleneethynylene COPs consist of purely unsaturated carbon backbones and exhibit large internal cavities, which would have interesting applications in host-guest chemistry and development of porous materials.« less

Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

PubMed

Chakraborty, Debayan; Wales, David J

2018-01-04

The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.

[Influence of CNTs on Photodegradation of Salbutamol in Water Environment].

PubMed

Wang, Qi; Han, Jia-rui; Wei, Bo-fan; Zhou, Lei; Zhang, Ya; Yang, Xi

2015-08-01

The influence of CNTs on the photolysis of organic pollutant was investigated by studying the photodegradation kinetics of SAL under 1000 W Xenon lamp, in the presence of three kinds of CNTs (SCNT, MWNT-COOH, MWNT-OH). In addition, the interaction between CNTs and Fe3" was also investigated. The results showed that the photodegradation of salbutamol followed pseudo-first-order kinetics, which could be inhibited by all three kinds of CNTs through light screening effect. Formation of singlet oxygen was detected during the photolysis, using the molecular probe furfuryl alcohol. All three kinds of CNTs could absorb electrons through competition, i.e., inhibit SAL photodegradation by light screening effect; meanwhile, the CNTs could generate singlet oxygen through photoexcitation to promote the photodegradation reaction. Both mechanisms coexisted, and in most cases, the inhibition effect was dominant. In addition, CNTs could inactivate the photoactive substance Fe3 in the water body by electrostatic adsorption, and affect the photochemical behavior of organic pollutants in natural water body.

Sensing multiple ligands with single receptor

NASA Astrophysics Data System (ADS)

Singh, Vijay; Nemenman, Ilya

2015-03-01

Cells use surface receptors to measure concentrations of external ligand molecules. Limits on the accuracy of such sensing are well-known for the scenario where concentration of one molecular species is being determined by one receptor [Endres]. However, in more realistic scenarios, a cognate (high-affinity) ligand competes with many non-cognate (low-affinity) ligands for binding to the receptor. We analyze effects of this competition on the accuracy of sensing. We show that maximum-likelihood statistical inference allows determination of concentrations of multiple ligands, cognate and non-cognate, by the same receptor concurrently. While it is unclear if traditional biochemical circuitry downstream of the receptor can implement such inference exactly, we show that an approximate inference can be performed by coupling the receptor to a kinetic proofreading cascade. We characterize the accuracy of such kinetic proofreading sensing in comparison to the exact maximum-likelihood approach. We acknowledge the support from the James S. McDonnell Foundation and the Human Frontier Science Program.

Batch kinetics of Pseudomonas sp. growth on benzene. Modeling of product and substrate inhibitions.

PubMed

Monero, Alessandra; Lanza, Luca; Zilli, Mario; Sene, Luciane; Converti, Attilio

2003-01-01

Batch tests of benzene degradation were performed in liquid phase at 30 degrees C, pH 6.8 +/- 0.2, and 200 rpm in two 3-L stirred tank bioreactors, using the benzene-degrading bacterium Pseudomonas sp. NCIMB 9688. A relatively high starting biomass level (220-270 mg(X)/L) and starting benzene concentration ranging from 20 to 200 mg(S)/L were selected as conditions to investigate possible inhibition phenomena. Volumetric as well as specific rates of biomass formation and substrate consumption were calculated from experimental data of both growth and benzene degradation and used to propose and check a new overall kinetic model for cell growth simultaneously accounting for both product and substrate inhibitions. The results of the present study evidenced the occurrence of a competitive-type product inhibition due to 2-hydroxymuconic semialdehyde (K(iP)' = 0.902 mg(S)/L), which was stronger than the uncompetitive-type inhibition exerted by substrate (K(iS) = 7.69 mg(S)/L).

Polysaccharide chemistry regulates kinetics of calcite nucleation through competition of interfacial energies.

PubMed

Giuffre, Anthony J; Hamm, Laura M; Han, Nizhou; De Yoreo, James J; Dove, Patricia M

2013-06-04

Calcified skeletons are produced within complex assemblages of proteins and polysaccharides whose roles in mineralization are not well understood. Here we quantify the kinetics of calcite nucleation onto a suite of high-purity polysaccharide (PS) substrates under controlled conditions. The energy barriers to nucleation are PS-specific by a systematic relationship to PS charge density and substrate structure that is rooted in minimization of the competing substrate-crystal and substrate-liquid interfacial energies. Chitosan presents a low-energy barrier to nucleation because its near-neutral charge favors formation of a substrate-crystal interface, thus reducing substrate interactions with water. Progressively higher barriers are measured for negatively charged alginates and heparin that favor contact with the solution over the formation of new substrate-crystal interfaces. The findings support a directing role for PS in biomineral formation and demonstrate that substrate-crystal interactions are one end-member in a larger continuum of competing forces that regulate heterogeneous crystal nucleation.

Polysaccharide chemistry regulates kinetics of calcite nucleation through competition of interfacial energies

PubMed Central

Hamm, Laura M.; Han, Nizhou; De Yoreo, James J.; Dove, Patricia M.

2013-01-01

Calcified skeletons are produced within complex assemblages of proteins and polysaccharides whose roles in mineralization are not well understood. Here we quantify the kinetics of calcite nucleation onto a suite of high-purity polysaccharide (PS) substrates under controlled conditions. The energy barriers to nucleation are PS-specific by a systematic relationship to PS charge density and substrate structure that is rooted in minimization of the competing substrate–crystal and substrate–liquid interfacial energies. Chitosan presents a low-energy barrier to nucleation because its near-neutral charge favors formation of a substrate–crystal interface, thus reducing substrate interactions with water. Progressively higher barriers are measured for negatively charged alginates and heparin that favor contact with the solution over the formation of new substrate–crystal interfaces. The findings support a directing role for PS in biomineral formation and demonstrate that substrate–crystal interactions are one end-member in a larger continuum of competing forces that regulate heterogeneous crystal nucleation. PMID:23690577

Kinetic model for dependence of thin film stress on growth rate, temperature, and microstructure

NASA Astrophysics Data System (ADS)

Chason, E.; Shin, J. W.; Hearne, S. J.; Freund, L. B.

2012-04-01

During deposition, many thin films go through a range of stress states, changing from compressive to tensile and back again. In addition, the stress depends strongly on the processing and material parameters. We have developed a simple analytical model to describe the stress evolution in terms of a kinetic competition between different mechanisms of stress generation and relaxation at the triple junction where the surface and grain boundary intersect. The model describes how the steady state stress scales with the dimensionless parameter D/LR where D is the diffusivity, R is the growth rate, and L is the grain size. It also explains the transition from tensile to compressive stress as the microstructure evolves from isolated islands to a continuous film. We compare calculations from the model with measurements of the stress dependence on grain size and growth rate in the steady state regime and of the evolution of stress with thickness for different temperatures.

Discovery of potent α-glucosidase inhibitor flavonols: Insights into mechanism of action through inhibition kinetics and docking simulations.

PubMed

Şöhretoğlu, Didem; Sari, Suat; Barut, Burak; Özel, Arzu

2018-05-17

Beside other pharmaceutical benefits, flavonoids are known for their potent α-glucosidase inhibition. In the present study, we investigated α-glucosidase inhibitory effects of structurally related 11 flavonols, among which quercetin-3-O-(3″-O-galloyl)-β-galactopyranoside (8) and quercetin 3-O-(6″-O-galloyl)-β-glucopyranoside (9) showed significant inhibition compared to the positive control, acarbose, with IC 50 values of 0.97 ± 0.02 and 1.35 ± 0.06 µM, respectively. It was found that while sugar substitution to C3-OH of C ring reduced the α-glucosidase inhibitory effect, galloyl substitution to these sugar units increased it. An enzyme kinetics analysis revealed that 7 was competitive, whereas 1, 2, 8, and 9 were uncompetitive inhibitors. In the light of these findings, we performed molecular docking studies to predict their inhibition mechanisms at atomic level. Copyright © 2018 Elsevier Inc. All rights reserved.

Bio-reduction of N-nitrosodimethylamine (NDMA) using a hydrogen-based membrane biofilm reactor.

PubMed

Chung, Jinwook; Ahn, Chang-Hoon; Chen, Zhuo; Rittmann, Bruce E

2008-01-01

N-Nitrosodimethylamine (NDMA) is a disinfection by-product shown to be carcinogenic, mutagenic, and teratogenic. A feasible detoxification pathway for NDMA is a three-step bio-reduction that leads to ammonia and dimethylamine. This study examines the bio-reduction of NDMA in a H2-based membrane biofilm reactor (MBfR) that also is active in nitrate and sulfate reductions. In particular, the study investigates the effects of H2 availability and the relative loadings of NDMA, nitrate, and sulfate, which potentially are competing electron acceptors. The results demonstrate that NDMA was bio-reduced to a major extent (i.e., at least 96%) in a H2-based MBfR in which the electron-equivalent fluxes from H2 oxidation were dominated by nitrate and sulfate reductions. NDMA reduction kinetics responded to NDMA concentration, H2 pressure, and the presence of competing acceptors. The most important factor controlling NDMA-reduction kinetics was the H2 availability, controlled primarily by the H2 pressure, and secondarily by competition from nitrate reduction.

Sperm motility in fish: technical applications and perspectives through CASA-Mot systems.

PubMed

Gallego, V; Asturiano, J F

2018-03-09

Although a relatively high number of sperm quality biomarkers have been reported over the years in several fish species, sperm motility is nowadays considered the best biomarker for fish spermatozoa. The first scientific reports focusing on fish sperm motility date from a century ago, but the objective assessment allowed by computer-aided sperm analysis (CASA-Mot) systems was not applied to fish species until the mid-1980s. Since then, a high number of sperm kinetic parameters from more than 170 fish species have been reported in more than 700 scientific articles, covering a wide range of topics, such as sperm physiology, sperm storage, broodstock management, the phenomenon of sperm competition, ecotoxicology and understanding the life cycle of the species. The sperm kinetic parameters provided by CASA-Mot systems can serve as powerful and useful tools for aquaculture and ecological purposes, and this review provides an overview of the major research areas in which fish sperm motility assessment by a CASA-Mot system has been used successfully.

Decomposition mechanisms and kinetics of novel energetic molecules BNFF-1 and ANFF-1: quantum-chemical modeling.

PubMed

Tsyshevsky, Roman V; Kuklja, Maija M

2013-07-18

Decomposition mechanisms, activation barriers, Arrhenius parameters, and reaction kinetics of the novel explosive compounds, 3,4-bis(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (BNFF-1), and 3-(4-amino-1,2,5-oxadiazol-3-yl)-4-(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (ANFF-1) were explored by means of density functional theory with a range of functionals combined with variational transition state theory. BNFF-1 and ANFF-1 were recently suggested to be good candidates for insensitive high energy density materials. Our modeling reveals that the decomposition initiation in both BNFF-1 and ANFF-1 molecules is triggered by ring cleavage reactions while the further process is defined by a competition between two major pathways, the fast C-NO₂ homolysis and slow nitro-nitrite isomerization releasing NO. We discuss insights on design of new energetic materials with targeted properties gained from our modeling.

Fatty Acids Change the Conformation of Uncoupling Protein 1 (UCP1)*

PubMed Central

Divakaruni, Ajit S.; Humphrey, Dickon M.; Brand, Martin D.

2012-01-01

UCP1 catalyzes proton leak across the mitochondrial inner membrane to disengage substrate oxidation from ATP production. It is well established that UCP1 is activated by fatty acids and inhibited by purine nucleotides, but precisely how this regulation occurs remains unsettled. Although fatty acids can competitively overcome nucleotide inhibition in functional assays, fatty acids have little effect on purine nucleotide binding. Here, we present the first demonstration that fatty acids induce a conformational change in UCP1. Palmitate dramatically changed the binding kinetics of 2′/3′-O-(N-methylanthraniloyl)-GDP, a fluorescently labeled nucleotide analog, for UCP1. Furthermore, palmitate accelerated the rate of enzymatic proteolysis of UCP1. The altered kinetics of both processes indicate that fatty acids change the conformation of UCP1, reconciling the apparent discrepancy between existing functional and ligand binding data. Our results provide a framework for how fatty acids and nucleotides compete to regulate the activity of UCP1. PMID:22952235