Determination of binding constants by affinity chromatography

This review summarizes developments in the use of affinity chromatography to characterize biospecific interactions in terms of reaction stoichiometry and equilibrium constant. In that regard, the biospecificity incorporated into the design of the experiment ensures applicability of the method regardless of the sizes of the reacting solutes. By the adoption of different experimental strategies (column chromatography, simple partition equilibrium, solid-phase immunoassay and biosensor technology protocols) quantitatiative affinity chromatography can be used to characterize interactions governed by an extremely broad range of binding affinities. In addition, the link between ligand-binding studies and quantitative affinity chromatography is illustrated by means of partition equilibrium studies of glycolytic enzyme interactions with muscle myofibrils. an exercise which emphasizes that the same theoretical expressions apply to naturally occurring examples of affinity chromatography in the cellular environment. (C) 2004 Elsevier B.V. All rights reserved.

Costs increase as ritualized fighting progresses within and between phases in the sierra dome spider, Neriene litigiosa

Magnitudes and patterns of energy expenditure in animal contests are seldom measured, but can be critical for predicting contest dynamics and understanding the evolution of ritualized fighting behaviour. In the sierra dome spider, males compete for sexual access to females and their webs. They show three distinct phases of fighting behaviour, escalating from ritualized noncontact display (phase 1) to cooperative wrestling (phase 2), and finally to unritualized, potentially fatal fighting (phase 3). Using CO2 respirometry, we estimated energetic costs of male-male combat in terms of mean and maximum metabolic rates and the rate of increase in energy expenditure. We also investigated the energetic consequences of age and body mass, and compared fighting metabolism to metabolism during courtship. All three phases involved mean energy expenditures well above resting metabolic rate (3.5 X, 7.4 X and 11.5 X). Both mean and maximum energy expenditure became substantially greater as fights escalated through successive phases. The rates of increase in energy use during phases 2 and 3 were much higher than in phase 1. In addition, age and body mass affected contest energetics. These results are consistent with a basic prediction of evolutionarily stable strategy contest models, that sequences of agonistic behaviours should be organized into phases of escalating energetic costs. Finally, higher energetic costs of escalated fighting compared to courtship provide a rationale for first-male sperm precedence in this spider species. (C) 2004 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Sorting nexin 5 is localized to a subdomain of the early endosomes and is recruited to the plasma imembrane following EGF stimulation

Sorting nexins are a large family of proteins that contain the phosphoinositide-binding Phox homology (PX) domain. A number of sorting nexins are known to bind to PtdIns(3)P, which mediates their localization to membranes of the endocytic pathway. We show here that sorting nexin 5 (SNX5) can be recruited to two distinct membrane compartments. In non-stimulated cells, the PX domain was independently targeted to endosomal structures and colocalized with full-length SNX5. The membrane binding of the PX domain was inhibited by the PI 3-kinase inhibitor, wortmannin. Although SNX5 colocalized with a fluid-phase marker and was found predominantly within a PtdIns(3)P-rich endosomal domain, very little colocalization was observed between SNX5 and the PtdIns(3)P-binding protein, EEA1. Using liposome-based binding assays, we have shown that the PX domain of SNX5 interacts not only with PtdIns(3)P but also with PtdIns(3,4)P-2. In response to EGF stimulation, either the SNX5-PX domain or full-length SNX5 was rapidly recruited to the plasma membrane. The localization of SNX1, which does not bind PtdIns(3,4)P-2, was unaffected by EGF signalling. Therefore, SNX5 is localized to a subdomain of the early endosome distinct from EEA1 and, following EGF stimulation and elevation of PtdIns(3,4)P-2, is also transiently recruited to the plasma membrane. These results indicate that SNX5 may have functions not only associated with endosomal sorting but also with the phosphoinositide-signalling pathway.

Morphological features of interfacial intermetallics and interfacial reaction rate in Al-11Si-2.5Cu-(0.15/0.60)Fe cast alloy/die steel couples

Soldering reactions are commonly observed during high pressure die casting of aluminium alloys, and involve the formation and growth of interfacial intermetallics between the die and the cast alloy. It is generally believed that close to 1% Fe is necessary in the aluminium alloy to reduce soldering. However, the role of iron in the interfacial reaction has not been studied in detail. In this investigation, reaction couples were formed between H13 tool steel substrates and an Al-11Si-2.5Cu melt containing either 0.15 or 0.60% Fe. Examination revealed distinctly different intermetallic layer morphology. The overall growth and chemistry of the reaction layer and the reaction rate measured by the consumption of the substrate were compared for the two alloy melts. It was demonstrated that a higher iron content reduces the rate of interfacial reaction, consistent with an observed thicker compact ( solid) intermetallic layer. Hence, the difference in reaction rate can be explained by a significant reduction in the diffusion flux due to a thicker compact layer. Finally, the mechanism of the growth of a thicker compact layer in the higher iron melt is proposed, based on the phase relations and diffusion both within and near the interfacial reaction zone. (C) 2004 Kluwer Academic Publishers.

Effect of particle hydrophobicity on particle and water transport across a flotation froth

Froth recovery measurements have been conducted in both the presence (three-phase froth) and absence (two-phase froth) of particles of different contact angles in a specially modified laboratory flotation column. Increasing the particle hydrophobicity increased the flow rate of particles entering the froth, while the recovery of particles across the froth phase itself also increased for particle contact angles to 63 and at all vertical heights of the froth column. However, a further increase in the contact angle to 69 resulted in lower particle recovery across the froth phase. The reduced froth recovery for particles of 69 contact angle was linked to significant bubble coalescence within the froth phase. The reduced froth recovery occurred uniformly across the entire particle size range, and was, presumably, a result of particle detachment from coalescing bubbles. Water flow rates across the froth phase also varied with particle contact angle. The general trend was a decrease in the concentrate flow rate of water with increasing particle contact angle. An inverse relationship between water flow rate and bubble radius was also observed, possibly allowing prediction of water flow rate from bubble size measurements in the froth. Comparison of the froth structure, defined by bubble size, gas hold-up and bubble layer thickness, for two- and three-phase froths, at the same frother concentration, showed there was a relationship between water flow rate and froth structure. (c) 2005 Elsevier B.V. All rights reserved.

A reinvestigation of phase equilibria in the system Al2O3-SiO2-ZnO

The phase equilibria and liquidus temperatures in the binary SiO2-ZnO system and in the ternary Al2O3-SiO2-ZnO system at low Al2O3 concentrations have been experimentally determined using the equilibration and quenching technique followed by electron probe X-ray microanalysis. In the SiO2-ZnO system, two binary eutectics involving the congruently melting willemite (Zn2SiO4) were found at 1448 +/- 5 degrees C and 0.52 +/- 0.01 mole fraction ZnO and at 1502 +/- 5 degrees C and 0.71 +/- 0.01 mole fraction ZnO, respectively. The two ternary eutectics involving willemite previously reported in the Al2O3SiO2-ZnO system were found to be at 1315 +/- 5 degrees C and 1425 +/- 25 T, respectively. The compositions of the eutectics are 0.07, 0.52, and 0.41 and 0.05, 0.28, and 0.67 mole fraction Al2O3, SiO2, and ZnO, respectively. The results of the present investigation are significantly different from the results of previous studies.

Van der Waals-corrected density functional theory: benchmarking for hydrogen-nanotube and nanotube-nanotube interactions

Density functional theory (DFT) is a powerful approach to electronic structure calculations in extended systems, but suffers currently from inadequate incorporation of long-range dispersion, or Van der Waals (VdW) interactions. VdW-corrected DFT is tested for interactions involving molecular hydrogen, graphite, single-walled carbon nanotubes (SWCNTs), and SWCNT bundles. The energy correction, based on an empirical London dispersion term with a damping function at short range, allows a reasonable physisorption energy and equilibrium distance to be obtained for H-2 on a model graphite surface. The VdW-corrected DFT calculation for an (8, 8) nanotube bundle reproduces accurately the experimental lattice constant. For H-2 inside or outside an (8, 8) SWCNT, we find the binding energies are respectively higher and lower than that on a graphite surface, correctly predicting the well known curvature effect. We conclude that the VdW correction is a very effective method for implementing DFT calculations, allowing a reliable description of both short-range chemical bonding and long-range dispersive interactions. The method will find powerful applications in areas of SWCNT research where empirical potential functions either have not been developed, or do not capture the necessary range of both dispersion and bonding interactions.

Milk thistle and indinavir: a randomized controlled pharmacokinetics study and meta-analysis

Objectives: To determine whether ingestion of milk thistle affects the pharmacokinetics of indinavir. Methods: We conducted a three-period, randomized controlled trial with 16 healthy participants. We randomized participants to milk thistle or control. All participants received initial dosing of indinavir, and baseline indinavir levels were obtained (AUC(0-8)) (phase I). The active group were then given 450 mg milk-thistle extract capsules to be taken t.i.d. from day 2 to day 30. The control group received no plant extract. On day 29 and day 30, indinavir dosing and sampling was repeated in both groups as before (phase II). After a wash-out period of 7 days, indinavir dosing and sampling were repeated as before (phase III). Results: All participants completed the trial, but two were excluded from analysis due to protocol violation. There were no significant between-group differences. Active group mean AUC(0-8) indinavir decreased by 4.4% (90% CI, -27.5% to -26%, P=0.78) from phase I to phase II in the active group, and by 17.3% (90% CI, -37.3% to +9%, P=0.25) in phase III. Control group mean AUC(0-8) decreased by 21.5% (90% CI, -43% to +8%, P=0.2) from phase I to phase II and by 38.5% (90% CI, -55.3% to -15.3%, P=0.01) of baseline at phase III. To place our findings in context, milk thistle-oindinavir trials were identified through systematic searches of the literature. A meta-analysis of three milk thistle-indinavir trials revealed a non-significant pooled mean difference of 1% in AUC(0-8) (95% CI, -53% to 55%, P=0.97). Conclusions: Indinavir levels were not reduced significantly in the presence of milk thistle.

Evaluation of 1-site and 5-site models of methane on its adsorption on graphite and in graphitic slit pores

In this paper, we evaluate the performance of the 1- and 5-site models of methane on the description of adsorption on graphite surfaces and in graphitic slit pores. These models have been known to perform well in the description of the fluid-phase behavior and vapor-liquid equilibria. Their performance in adsorption is evaluated in this work for nonporous graphitized thermal carbon black, and simulation results are compared with the experimental data of Avgul and Kiselev (Chemistry and Physics of Carbon; Dekker: New York, 1970; Vol. 6, p 1). On this nonporous surface, it is found that these models perform as well on isotherms at various temperatures as they do on the experimental isosteric heat for adsorption on a graphite surface. They are then tested for their performance in predicting the adsorption isotherms in graphitic slit pores, in which we would like to explore the effect of confinement on the molecule packing. Pore widths of 10 and 20 angstrom are chosen in this investigation, and we also study the effects of temperature by choosing 90.7, 113, and 273 K. The first two are for subcritical conditions, with 90.7 K being the triple point of methane and 113 K being its boiling point. The last temperature is chosen to represent the supercritical condition so that we can investigate the performance of these models at extremely high pressures. We have found that for the case of slit pores investigated in this paper, although the two models yield comparable pore densities (provided the accessible pore width is used in the calculation of pore density), the number of particles predicted by the I-site model is always greater than that predicted by the 5-site model, regardless of whether temperature is subcritical or supercritical. This is due to the packing effect in the confined space such that a methane molecule modeled as a spherical particle in the I-site model would pack better than the fused five-sphere model in the case of the 5-site model. Because the 5-site model better describes the liquid- and solid-phase behavior, we would argue that the packing density in small pores is better described with a more detailed 5-site model, and care should be exercised when using the 1-site model to study adsorption in small pores.

Permeability of subcritical hydrocarbons in activated carbon

A new diffusion and flow model is presented to describe the behavior of hydrocarbon vapors in activated carbon. The micro/mesopore size distribution (PSD) is obtained according to Do's method which consists of two sequential processes of pore layering and pore filling. This model uses the micro/meso PSD obtained from each adsorbate equilibrium isotherm, which reflects the dynamics behavior of adsorbing molecules through the solid. The initial rise in total permeability is mainly attributed to adsorbed-phase diffusion (that is, surface diffusion), whereas the decrease over reduced pressure of about 0.9 is attributed to the reduction of pore space available for gas phase diffusion and flow. A functional form of surface diffusivity is proposed and validated with experimental data. This model predicts well the permeability of condensable hydrocarbon vapors in activated carbon. (C) 2005 American Institute of Chemical Engineers.

Adsorption in slit pores and pore-size distribution: A molecular layer structure theory

A new approach is developed to analyze the thermodynamic properties of a sub-critical fluid adsorbed in a slit pore of activated carbon. The approach is based on a representation that an adsorbed fluid forms an ordered structure close to a smoothed solid surface. This ordered structure is modelled as a collection of parallel molecular layers. Such a structure allows us to express the Helmholtz free energy of a molecular layer as the sum of the intrinsic Helmholtz free energy specific to that layer and the potential energy of interaction of that layer with all other layers and the solid surface. The intrinsic Helmholtz free energy of a molecular layer is a function (at given temperature) of its two-dimensional density and it can be readily obtained from bulk-phase properties, while the interlayer potential energy interaction is determined by using the 10-4 Lennard-Jones potential. The positions of all layers close to the graphite surface or in a slit pore are considered to correspond to the minimum of the potential energy of the system. This model has led to accurate predictions of nitrogen and argon adsorption on carbon black at their normal boiling points. In the case of adsorption in slit pores, local isotherms are determined from the minimization of the grand potential. The model provides a reasonable description of the 0-1 monolayer transition, phase transition and packing effect. The adsorption of nitrogen at 77.35 K and argon at 87.29 K on activated carbons is analyzed to illustrate the potential of this theory, and the derived pore-size distribution is compared favourably with that obtained by the Density Functional Theory (DFT). The model is less time-consuming than methods such as the DFT and Monte-Carlo simulation, and most importantly it can be readily extended to the adsorption of mixtures and capillary condensation phenomena.

A modelling approach to estimate the effect of exotic pollinators on exotic weed population dynamics: bumblebees and broom in Australia

The role of mutualisms in contributing to species invasions is rarely considered, inhibiting effective risk analysis and management options. Potential ecological consequences of invasion of non-native pollinators include increased pollination and seed set of invasive plants, with subsequent impacts on population growth rates and rates of spread. We outline a quantitative approach for evaluating the impact of a proposed introduction of an invasive pollinator on existing weed population dynamics and demonstrate the use of this approach on a relatively data-rich case study: the impacts on Cytisus scoparius (Scotch broom) from proposed introduction of Bombus terrestris. Three models have been used to assess population growth (matrix model), spread speed (integrodifference equation), and equilibrium occupancy (lattice model) for C. scoparius. We use available demographic data for an Australian population to parameterize two of these models. Increased seed set due to more efficient pollination resulted in a higher population growth rate in the density-independent matrix model, whereas simulations of enhanced pollination scenarios had a negligible effect on equilibrium weed occupancy in the lattice model. This is attributed to strong microsite limitation of recruitment in invasive C. scoparius populations observed in Australia and incorporated in the lattice model. A lack of information regarding secondary ant dispersal of C. scoparius prevents us from parameterizing the integrodifference equation model for Australia, but studies of invasive populations in California suggest that spread speed will also increase with higher seed set. For microsite-limited C. scoparius populations, increased seed set has minimal effects on equilibrium site occupancy. However, for density-independent rapidly invading populations, increased seed set is likely to lead to higher growth rates and spread speeds. The impacts of introduced pollinators on native flora and fauna and the potential for promoting range expansion in pollinator-limited 'sleeper weeds' also remain substantial risks.

A bang-bang PLL employing dynamic gain control for low jitter and fast lock times

Bang-bang phase detector based PLLs are simple to design, suffer no systematic phase error, and can run at the highest speed a process can make a working flip-flop. For these reasons designers are employing them in the design of very high speed Clock Data Recovery (CDR) architectures. The major drawback of this class of PLL is the inherent jitter due to quantized phase and frequency corrections. Reducing loop gain can proportionally improve jitter performance, but also reduces locking time and pull-in range. This paper presents a novel PLL design that dynamically scales its gain in order to achieve fast lock times while improving fitter performance in lock. Under certain circumstances the design also demonstrates improved capture range. This paper also analyses the behaviour of a bang-bang type PLL when far from lock, and demonstrates that the pull-in range is proportional to the square root of the PLL loop gain.

Vibrational dynamics and structure of natural feldspars

The present study gives a contribution to the knowledge on the Na-feldspar and plagioclases, extending the database of the Raman spectra of plagioclases with different chemical compositions and structural orders. This information may be used for the future planetary explorations by “rovers”, for the investigation of ceramics nanocrystal materials and for the mineralogical phase identification in sediments. Na-feldspar and plagioclase solid solution have been investigated by Raman spectroscopy in order to determine the relationships between the vibrational changes and the plagioclase crystal chemistry and structure. We focused on the Raman micro-spectroscopy technique, being a non-destructive method, suited for contactless analysis with high spatial resolution. Chemical and structural analyses have been performed on natural samples to test the usefulness of Raman spectroscopy as a tool in the study of the pressure-induced structural deformations, the disordering processes due to change in the Al-Si distribution in the tetrahedral sites and, finally, in the determination of the anorthitic content (Anx) in plagioclase minerals. All the predicted 39 Ag Raman active modes have been identified and assigned to specific patterns of atomic vibrational motion. A detailed comparison between experimental and computed Raman spectra has been performed and previous assignments have been revised, solving some discrepancies reported in recent literature. The ab initio calculation at the hybrid HF/DFT level with the WC1LYP Hamiltonian has proven to give excellent agreement between calculated and experimentally measured Raman wavenumbers and intensities in triclinic minerals. A short digression on the 36 infrared active modes of Na-feldspar has been done too. The identification of all 39 computed Raman modes in the experimentally measured spectra of the fully ordered Na-feldspar, known as low albite, along with the detailed description of each vibrational mode, has been essential to extend the comparative analysis to the high pressure and high temperature structural forms of albite, which reflect the physical–chemical conditions of the hosting rocks. The understanding of feldspar structure response to pressure and temperature is crucial in order to constrain crustal behaviour. The compressional behaviour of the Na-feldspar has been investigated for the first time by Raman spectroscopy. The absence of phase transitions and the occurrence of two secondary compression mechanisms acting at different pressures have been confirmed. Moreover, Raman data suggest that the internal structural changes are confined to a small pressure interval, localized around 6 GPa, not spread out from 4 to 8 GPa as suggested by previous X-rays studies on elasticity. The dominant compression mechanisms act via tetrahedral tilting, while the T-O bond lengths remain nearly constant at moderate compressional regimes. At the spectroscopic level, this leads to the strong pressure dependencies of T-O-T bending modes, as found for the four modes at 478, 508, 578 and 815 cm-1. The Al-Si distribution in the tetrahedral sites affects also the Raman spectrum of Na-feldspar. In particular, peak broadening is more sensitive than peak position to changes in the degree of order. Raman spectroscopy is found to be a good probe for local ordering, in particular being sensitive to the first annealing steps, when the macroscopic order parameter is still high. Even though Raman data are scattered and there are outliers in the estimated values of the degree of order, the average peak linewidths of the Na-feldspar characteristic doublet band, labelled here as υa and υb, as a function of the order parameter Qod show interesting trends: both peak linewidths linearly increase until saturation. From Qod values lower than 0.6, peak broadening is no more affected by the Al-Si distribution. Moreover, the disordering process is found to be heterogeneous. SC-XRD and Raman data have suggested an inter-crystalline inhomogeneity of the samples, i.e., the presence of regions with different defect density on the micrometric scale. Finally, the influence of Ca-Na substitution in the plagioclase Raman spectra has been investigated. Raman spectra have been collected on a series of well characterized natural, low structural plagioclases. The variations of the Raman modes as a function of the chemical composition and the structural order have been determined. The number of the observed Raman bands at each composition gives information about the unit-cell symmetry: moving away from the C1 structures, the number of the Raman bands enhances, as the number of formula units in the unit cell increases. The modification from an “albite-like” Raman spectrum to a more “anorthite-like” spectrum occurs from sample An78 onwards, which coincides with the appearance of c reflections in the diffraction patterns of the samples. The evolution of the Raman bands υa and υb displays two changes in slope at ~An45 and ~An75: the first one occurs between e2 and e1 plagioclases, the latter separates e1 and I1 plagioclases with only b reflections in their diffraction patterns from I1 and P1 samples having b and c reflections too. The first variation represents exactly the e2→e1 phase transitions, whereas the second one corresponds in good approximation to the C1→I1 transition, which has been determined at ~An70 by previous works. The I1→P1 phase transition in the anorthite-rich side of the solid solution is not highlighted in the collected Raman spectra. Variations in peak broadening provide insights into the behaviour of the order parameter on a local scale, suggesting an increase in the structural disorder within the solid solution, as the structures have to incorporate more Al atoms to balance the change from monovalent to divalent cations. All the information acquired on these natural plagioclases has been used to produce a protocol able to give a preliminary estimation of the chemical composition of an unknown plagioclase from its Raman spectrum. Two calibration curves, one for albite-rich plagioclases and the other one for the anorthite-rich plagioclases, have been proposed by relating the peak linewidth of the most intense Raman band υa and the An content. It has been pointed out that the dependence of the composition from the linewidth can be obtained only for low structural plagioclases with a degree of order not far away from the references. The proposed tool has been tested on three mineralogical samples, two of meteoric origin and one of volcanic origin. Chemical compositions by Raman spectroscopy compare well, within an error of about 10%, with those obtained by elemental techniques. Further analyses on plagioclases with unknown composition will be necessary to validate the suggested method and introduce it as routine tool for the determination of the chemical composition from Raman data in planetary missions.

Threshold-induced phase transitions in perceptrons

Error rates of a Boolean perceptron with threshold and either spherical or Ising constraint on the weight vector are calculated for storing patterns from biased input and output distributions derived within a one-step replica symmetry breaking (RSB) treatment. For unbiased output distribution and non-zero stability of the patterns, we find a critical load, α p, above which two solutions to the saddlepoint equations appear; one with higher free energy and zero threshold and a dominant solution with non-zero threshold. We examine this second-order phase transition and the dependence of α p on the required pattern stability, κ, for both one-step RSB and replica symmetry (RS) in the spherical case and for one-step RSB in the Ising case.