Intra-crystalline protein diagenesis (IcPD) in Patella vulgata. Part II: Breakdown and temperature sensitivity

Artificial diagenesis of the intra-crystalline proteins isolated from Patella vulgata was induced by isothermal heating at 140 °C, 110 °C and 80 °C. Protein breakdown was quantified for multiple amino acids, measuring the extent of peptide bond hydrolysis, amino acid racemisation and decomposition. The patterns of diagenesis are complex; therefore the kinetic parameters of the main reactions were estimated by two different methods: 1) a well-established approach based on fitting mathematical expressions to the experimental data, e.g. first-order rate equations for hydrolysis and power-transformed first-order rate equations for racemisation; and 2) an alternative model-free approach, which was developed by estimating a “scaling” factor for the independent variable (time) which produces the best alignment of the experimental data. This method allows the calculation of the relative reaction rates for the different temperatures of isothermal heating. High-temperature data were compared with the extent of degradation detected in sub-fossil Patella specimens of known age, and we evaluated the ability of kinetic experiments to mimic diagenesis at burial temperature. The results highlighted a difference between patterns of degradation at low and high temperature and therefore we recommend caution for the extrapolation of protein breakdown rates to low burial temperatures for geochronological purposes when relying solely on kinetic data.

Size and molecular flexibility affect the binding of ellagitannins to bovine serum albumin

Binding to bovine serum albumin of monomeric (vescalagin and pedunculagin) and dimeric ellagitannins (roburin A, oenothein B, and gemin A) was investigated by isothermal titration calorimetry and fluorescence spectroscopy, which indicated two types of binding sites. Stronger and more specific sites exhibited affinity constants, K1, of 104–106 M–1 and stoichiometries, n1, of 2–13 and dominated at low tannin concentrations. Weaker and less-specific binding sites had K2 constants of 103–105 M–1 and stoichiometries, n2, of 16–30 and dominated at higher tannin concentrations. Binding to stronger sites appeared to be dependent on tannin flexibility and the presence of free galloyl groups. Positive entropies for all but gemin A indicated that hydrophobic interactions dominated during complexation. This was supported by an exponential relationship between the affinity, K1, and the modeled hydrophobic accessible surface area and by a linear relationship between K1 and the Stern–Volmer quenching constant, KSV.

Interactions between lipid-free apolipoprotein-AI and a lipopeptide incorporating the RGDS cell adhesion motif

The interaction of a designed bioactive lipopeptide C16-GGGRGDS, comprising a hexadecyl lipid chain attached to a functional heptapeptide, with the lipid-free apoliprotein, Apo-AI, is examined. This apolipoprotein is a major component of high density lipoprotein and it is involved in lipid metabolism and may serve as a biomarker for cardiovascular disease and Alzheimers’ disease. We find via isothermal titration calorimetry that binding between the lipopeptide and Apo-AI occurs up to a saturation condition, just above equimolar for a 10.7 μM concentration of Apo-AI. A similar value is obtained from circular dichroism spectroscopy, which probes the reduction in α-helical secondary structure of Apo-AI upon addition of C16-GGGRGDS. Electron microscopy images show a persistence of fibrillar structures due to self-assembly of C16-GGGRGDS in mixtures with Apo-AI above the saturation binding condition. A small fraction of spheroidal or possibly “nanodisc” structures was observed. Small-angle X-ray scattering (SAXS) data for Apo-AI can be fitted using a published crystal structure of the Apo-AI dimer. The SAXS data for the lipopeptide/ Apo-AI mixtures above the saturation binding conditions can be fitted to the contribution from fibrillar structures coexisting with flat discs corresponding to Apo-AI/lipopeptide aggregates.

Probing the mucoadhesive interactions between porcine gastric mucin and some water-soluble polymers

This study investigates the structural features of porcine gastric mucin (PGM) in aqueous dispersions and its interactions with water-soluble polymers (poly(acrylic acid) (PAA), poly(methacrylic acid) (PMAA), poly(ethylene oxide), and poly(ethylene glycol)) using isothermal titration calorimetry, turbidimetric titration, dynamic light scattering, and transmission electron microscopy. It is established that PAA (450 kDa) and PMAA (100 kDa) exhibit strong specific interactions with PGM causing further aggregation of its particles, while PAA (2 kDa), poly(ethylene oxide) (1 000 kDa), and poly(ethylene glycol) (10 kDa) do not show any detectable effects on mucin. Sonication of mucin dispersions prior to their mixing with PAA (450 kDa) and PMAA (100 kDa) leads to more pronounced intensity of interactions.

Enzymatically-triggered, isothermally responsive polymers: re-programming poly(oligoethylene glycols) to respond to phosphatase

Polymers which can respond to externally applied stimuli have found much application in the biomedical field due to their (reversible) coil–globule transitions. Polymers displaying a lower critical solution temperature are the most commonly used, but for blood-borne (i.e., soluble) biomedical applications the application of heat is not always possible, nor practical. Here we report the design and synthesis of poly(oligoethylene glycol methacrylate)-based polymers whose cloud points are easily varied by alkaline phosphatase-mediated dephosphorylation. By fine-tuning the density of phosphate groups on the backbone, it was possible to induce an isothermal transition: A change in solubility triggered by removal of a small number of phosphate esters from the side chains activating the LCST-type response. As there was no temperature change involved, this serves as a model of a cell-instructed polymer response. Finally, it was found that both polymers were non cytotoxic against MCF-7 cells (at 1 mg·mL–1), which confirms promise for biomedical applications.

Astringency reduction in red wine by whey proteins

Whey is a by-product of cheese manufacturing and therefore investigating new applications of whey proteins will contribute towards the valorisation of whey and hence waste reduction. This study shows for the first time a detailed comparison of the effectiveness of gelatin and β-lactoglobulin (β-LG) as fining agents. Gelatin was more reactive than whey proteins to tannic acid as shown by both the astringency method (with ovalbumin as a precipitant) and the tannins determination method (with methylcellulose as a precipitant). The two proteins showed similar selectivity for polyphenols but β-LG did not remove as much catechin. The fining agent was removed completely or to a trace level after centrifugation followed by filtration which minimises its potential allergenicity. In addition, improved understanding of protein–tannin interactions was obtained by fluorescence, size measurement and isothermal titration calorimetry (ITC). Overall this study demonstrates that whey proteins have the potential of reducing astringency in red wine and can find a place in enology.

A new topology of ACBP from Moniliophthora perniciosa

Acyl-CoA binding protein (ACBP) is a housekeeping protein and is an essential protein in human cell lines and in Trypanosoma brucei. The ACBP of Moniliophthora perniciosa is composed of 104 amino acids and is possibly a non-classic isoform exclusively from Basidiomycetes. The M. perniciosa acbp gene was cloned, and the protein was expressed and purified. Acyl-CoA ester binding was analyzed by isoelectric focusing, native gel electrophoresis and isothermal titration calorimetry. Our results suggest an increasing affinity of ACBP for longer acyl-CoA esters, such as myristoyl-CoA to arachidoyl-CoA, and best fit modeling indicates two binding sites. ACBP undergoes a shift from a monomeric to a dimeric state, as shown by dynamic light scattering, fluorescence anisotropy and native gel electrophoresis in the absence and presence of the ligand. The protein`s structure was determined at 1.6 angstrom resolution and revealed a new topology for ACBP, containing five a-helices instead of four. alpha-helices 1, 2, 3 and 4 adopted a bundled arrangement that is unique from the previously determined four-helix folds of ACBP, while alpha-helices 1, 2, 4 and 5 formed a classical four-helix bundle. A MES molecule was found in the CoA binding site, suggesting that the CoA site could be a target for small compound screening. (C) 2009 Elsevier B.V. All rights reserved.

Non-LTE Monte Carlo radiative transfer. II. Nonisothermal solutions for viscous Keplerian disks

We discuss the basic hydrodynamics that determines the density structure of the disks around hot stars. Observational evidence supports the idea that these disks are Keplerian (rotationally supported) gaseous disks. A popular scenario in the literature, which naturally leads to the formation of Keplerian disks, is the viscous decretion model. According to this scenario, the disks are hydrostatically supported in the vertical direction, while the radial structure is governed by the viscous transport. This suggests that the temperature is one primary factor that governs the disk density structure. In a previous study we demonstrated, using three-dimensional non-LTE Monte Carlo simulations, that viscous Keplerian disks can be highly nonisothermal. In this paper we build on our previous work and solve the full problem of the steady state nonisothermal viscous diffusion and vertical hydrostatic equilibrium. We find that the self-consistent solution departs significantly from the analytic isothermal density, with potentially large effects on the emergent spectrum. This implies that nonisothermal disk models must be used for a detailed modeling of Be star disks.

DENSITY PROFILE, VELOCITY ANISOTROPY, AND LINE-OF-SIGHT EXTERNAL CONVERGENCE OF SLACS GRAVITATIONAL LENSES

Data from 58 strong-lensing events surveyed by the Sloan Lens ACS Survey are used to estimate the projected galaxy mass inside their Einstein radii by two independent methods: stellar dynamics and strong gravitational lensing. We perform a joint analysis of these two estimates inside models with up to three degrees of freedom with respect to the lens density profile, stellar velocity anisotropy, and line-of-sight (LOS) external convergence, which incorporates the effect of the large-scale structure on strong lensing. A Bayesian analysis is employed to estimate the model parameters, evaluate their significance, and compare models. We find that the data favor Jaffe`s light profile over Hernquist`s, but that any particular choice between these two does not change the qualitative conclusions with respect to the features of the system that we investigate. The density profile is compatible with an isothermal, being sightly steeper and having an uncertainty in the logarithmic slope of the order of 5% in models that take into account a prior ignorance on anisotropy and external convergence. We identify a considerable degeneracy between the density profile slope and the anisotropy parameter, which largely increases the uncertainties in the estimates of these parameters, but we encounter no evidence in favor of an anisotropic velocity distribution on average for the whole sample. An LOS external convergence following a prior probability distribution given by cosmology has a small effect on the estimation of the lens density profile, but can increase the dispersion of its value by nearly 40%.

Palaeomagnetism, rock magnetism and AMS of the Cabo Magmatic Province, NE Brazil, and the opening of South Atlantic

P>Reconstruction of the South Atlantic opening has long been a matter of debate and several models have been proposed. One problem in tracing properly the Atlantic history arises from the existence of a long interval without geomagnetic reversals, the Cretaceous Normal Superchron, for which ages are difficult to assign. Palaeomagnetism may help in addressing this issue if high-quality palaeomagnetic poles are available for the two drifting continental blocks, and if precise absolute ages are available. In this work we have investigated the Cabo Magmatic Province, northeastern Brazil, recently dated at 102 +/- 1 Ma (zircon fission tracks, Ar39/Ar40). All volcanic and plutonic rocks showed stable thermal and AF demagnetization patterns, and exhibit primary magnetic signatures. AMS data also support a primary origin for the magnetic fabric and is interpreted to be contemporaneous of the rock formation. The obtained pole is located at 335.9 degrees E/87.9 degrees S (N = 24; A(95) = 2.5; K = 138) and satisfies modern quality criteria, resulting in a reference pole for South America at similar to 100 Ma. This new pole also gives an insight to test and discuss the kinematic models currently proposed for the South Atlantic opening during mid-Cretaceous.

VELOCITY FIELD OF COMPRESSIBLE MAGNETOHYDRODYNAMIC TURBULENCE: WAVELET DECOMPOSITION AND MODE SCALINGS

We study compressible magnetohydrodynamic turbulence, which holds the key to many astrophysical processes, including star formation and cosmic-ray propagation. To account for the variations of the magnetic field in the strongly turbulent fluid, we use wavelet decomposition of the turbulent velocity field into Alfven, slow, and fast modes, which presents an extension of the Cho & Lazarian decomposition approach based on Fourier transforms. The wavelets allow us to follow the variations of the local direction of the magnetic field and therefore improve the quality of the decomposition compared to the Fourier transforms, which are done in the mean field reference frame. For each resulting component, we calculate the spectra and two-point statistics such as longitudinal and transverse structure functions as well as higher order intermittency statistics. In addition, we perform a Helmholtz-Hodge decomposition of the velocity field into incompressible and compressible parts and analyze these components. We find that the turbulence intermittency is different for different components, and we show that the intermittency statistics depend on whether the phenomenon was studied in the global reference frame related to the mean magnetic field or in the frame defined by the local magnetic field. The dependencies of the measures we obtained are different for different components of the velocity; for instance, we show that while the Alfven mode intermittency changes marginally with the Mach number, the intermittency of the fast mode is substantially affected by the change.

Synthesis of biodegradable polyhydroxyalcanoate copolymer from a renewable source by alternate feeding

Polyhydroxyalcanoates copolymers with 3-hydroxybutirate (3HB) and 3-hydroxyvalerate (3HV) co-monomers, P3(HB-co-x%HV), were produced in fed-batch culture by Ralstonia eutropha DSM428 using fructose as a single carbon source in the first step and adding propionic acid in the second step by alternating feeding. Polymer yield was 0.18 g/L with a content of 24 mol% of the 3HV fraction determined by H-1 NMR. NMR measurements indicated that the polymer obtained is isotactic. The copolymer attained 35% of crystallinity according to X-ray diffraction measurements, and two (020) planes were observed. Thermal behavior presented melting temperature at 154 degrees C and the crystallization temperature was 65 degrees C. A glass transition temperature was observed at -10 degrees C. Average molecular weight measured by GPC was 4.9 x 10(5) Dalton. Isothermal radial growth rates of spherulites of P3(HB-co-24%HV) were studied. All experimental facts and the analysis of the sequence distribution of diads and triads of 3HB and 3HV units led to the conclusion that it is not a completely statistical random copolymer once it contains different types of segments. POLYM.

An unstructured CVFEM and moving interface algorithm for non-Newtonian Hele-Shaw flows in injection molding

Purpose - The purpose of this paper is to develop a novel unstructured simulation approach for injection molding processes described by the Hele-Shaw model. Design/methodology/approach - The scheme involves dual dynamic meshes with active and inactive cells determined from an initial background pointset. The quasi-static pressure solution in each timestep for this evolving unstructured mesh system is approximated using a control volume finite element method formulation coupled to a corresponding modified volume of fluid method. The flow is considered to be isothermal and non-Newtonian. Findings - Supporting numerical tests and performance studies for polystyrene described by Carreau, Cross, Ellis and Power-law fluid models are conducted. Results for the present method are shown to be comparable to those from other methods for both Newtonian fluid and polystyrene fluid injected in different mold geometries. Research limitations/implications - With respect to the methodology, the background pointset infers a mesh that is dynamically reconstructed here, and there are a number of efficiency issues and improvements that would be relevant to industrial applications. For instance, one can use the pointset to construct special bases and invoke a so-called ""meshless"" scheme using the basis. This would require some interesting strategies to deal with the dynamic point enrichment of the moving front that could benefit from the present front treatment strategy. There are also issues related to mass conservation and fill-time errors that might be addressed by introducing suitable projections. The general question of ""rate of convergence"" of these schemes requires analysis. Numerical results here suggest first-order accuracy and are consistent with the approximations made, but theoretical results are not available yet for these methods. Originality/value - This novel unstructured simulation approach involves dual meshes with active and inactive cells determined from an initial background pointset: local active dual patches are constructed ""on-the-fly"" for each ""active point"" to form a dynamic virtual mesh of active elements that evolves with the moving interface.

Structural characterization of supported nanocrystalline ZnO thin films prepared by dip-coating

Nanocrystalline ZnO thin films prepared by the sol-gel dip-coating technique were characterized by grazing incidence X-ray diffraction (GIXD), atomic force microscopy (AFM), X-ray reflectivity (XR) and grazing incidence small-angle X-ray scattering (GISAXS). The structures of several thin films subjected to (i) isochronous annealing at 350, 450 and 550 degrees C, and (ii) isothermal annealing at 450 degrees C during different time periods, were characterized. The studied thin films are composed of ZnO nanocrystals as revealed by analysing several GIXD patterns, from which their average sizes were determined. Thin film thickness and roughness were determined from quantitative analyses of AFM images and XR patterns. The analysis of XR patterns also yielded the average density of the studied films. Our GISAXS study indicates that the studied ZnO thin films contain nanopores with an ellipsoidal shape, and flattened along the direction normal to the substrate surface. The thin film annealed at the highest temperature, T = 550 degrees C, exhibits higher density and lower thickness and nanoporosity volume fraction, than those annealed at 350 and 450 degrees C. These results indicate that thermal annealing at the highest temperature (550 degrees C) induces a noticeable compaction effect on the structure of the studied thin films. (C) 2011 Elsevier B.V. All rights reserved.

Growth and Melting of Metallic Nanoclusters in Glass: A Review of Recent Investigations

The mechanisms of nucleation and growth and the solid-to-liquid transition of metallic nanoclusters embedded in sodium borate glass were recently studied in situ via small-angle X-ray scattering (SAXS) and wide-an-le X-ray scattering (WAXS). SAXS results indicate that, under isothermal annealing conditions, the formation and growth of Bi or Ag nanoclusters embedded in sodium borate glass occurs through two successive stages after a short incubation period. The first stage is characterized by the nucleation and growth of spherical metal clusters promoted by the diffusion of Bi or Ag atoms through the initially supersaturated glass phase. The second stage is named the coarsening stage and occurs when the (Bi- or Ag-) doping level of the vitreous matrix is close to the equilibrium value. The experimental results demonstrated that, at advanced stages of the growth process, the time dependence of the average radius and density number of the clusters is in agreement with the classical Lifshitz-Slyozov-Waoner (LSW) theory. However, the radius distribution function is better described by a lognormal function than by the function derived from the theoretical LSW model. From the results of SAXS measurements at different temperatures, the activation energies for the diffusion of Ag and Bi through sodium borate glass were determined. In addition, via combination of the results of simultaneous WAXS and SAXS measurements at different temperatures, the crystallographic structure and the dependence of melting temperature T(m) on crystal radius R of Bi nanocrystals were established. The experimental results indicate that T(m) is a linear and decreasing function of nanocrystal reciprocal radius 1/R, in agreement with the Couchman and Jesser theoretical model. Finally, a weak contraction in the lattice parameters of Bi nanocrystals with respect to bulk crystals was established.