Folding, calcium binding, and structural characterization of a concatemer of the first and second ligand-binding modules of the low-density lipoprotein receptor

The ligand-binding domain of the low-density lipoprotein (LDL) receptor is comprised of seven tandemly repeated ligand-binding modules, each being approximately 40 amino acids long and containing six conserved cysteine residues. We have expressed and characterized a concatemer of the first two modules (LB1 and LB2) of the human LDL receptor. Oxidative folding of the recombinant concatemer (rLB(1-2)), in the presence of calcium ions, gave a single dominant isomer with six disulfide bonds. Peptic cleavage of the short Linker region that connects the last cysteine residue of LB1 and the first cysteine residue of LB2 yielded two discrete fragments, thus excluding the presence of intermodule disulfide bonds. The N-terminal module, LB1, reacted with a conformation-specific monoclonal antibody (IgG-C7) made to LB1 in the native LDL receptor. From this, we concluded that the first module was correctly folded, with the same set of disulfide bonds as LB1 of the LDL receptor. The disulfide bond connections of LB2 were identified from mass spectral analysis of fragments formed by digestion of the C-terminal peptic fragment with elastase. These data showed that the disulfide bonds of LB2 connected Cys(I) and Cys(III), Cys(II) and Cys(V), and Cys(IV) and Cys(VI). This pattern is identical to that found for recombinant LB1 and LB2. The concatemer has two high-affinity calcium-binding sites, one per module. An analysis of the secondary chemical shifts of C alpha protons shows that the conformations of LB1 and LB2 in the concatemer are very similar to those of the individual modules, with no evidence for strong interactions between the two modules.

Geochemical mass-balance and oxygen-isotope constrains on silcrete formation and its paleoclimatic implications in Southern Australia

Two geographically distinct silcrete associations are present in southern Australia, inland and eastern; these were sampled in central South Australia and central Victoria, respectively, At each site, both silicified and immediately adjacent unsilicified parent material were collected. Analytical data from these pairs were used to construct isocons, assuming Zr immobility, and to calculate the volume change and amount of silica introduced during silicification, These results, together with whole-rock oxygen isotope compositions, were used to determine the delta(18)O of th, introduced silica, The results show that the eastern silcretes in central Victoria are probably linked genetically to the associated basalts, weathering of which supplied the introduced silica, This conclusion is based on the close spatial connection between the two, as well as the substantial amount of introduced silica in the silcretes (greater than in the inland silcretes), resulting in volume increases in some eastern silcretes, Oxygen isotopic calculations for the silcretes indicate that the silica precipitated from groundwaters at temperatures slightly higher than present conditions. Silcrete formation apparently occurred during the Miocene and Pliocene (basalts in Victoria younger than Pliocene lack associated silcrete) and may reflect the much wetter climate in southeastern Australia at that time. The inland silcretes of central South Australia can be divided into pedogenic (the most common) and groundwater varieties. The pedogenic silcretes, which show typical soil features like columnar and nodular textures, contain moderate amounts of introduced silica that precipitated by evaporation from saline groundwaters, For the groundwater silcretes, which have massive textures and formed at or close to the water table, insufficient data are available to determine the mode of formation. The inland pedogenic silcretes have probably been farming from the Eocene-Miocene to the present, implying that conditions of seasonally high evaporation have occurred in central Australia during this time period. Thus silcrete formation depends on a complex interplay between climate and silica supply, and it is impossible to generalize that the presence of silcrete is indicative of a particular climate. Likewise, the elemental composition of silcretes, particularly Ti content, is not necessarily of climatic significance, Nevertheless, detailed geochemical and oxygen isotopic studies of a silcrete and its parent material can elucidate the mechanisms of silcrete formation, and if evaporation is indicated as a major factor in silcrete formation, then the climate at the time was likely to have been at least seasonally arid.

Reactivity of chars and carbons: New insights through molecular modeling

A new model proposed for the gasification of chars and carbons incorporates features of the turbostratic nanoscale structure that exists in such materials. The model also considers the effect of initial surface chemistry and different reactivities perpendicular to the edges and to the faces of the underlying crystallite planes comprising the turbostratic structure. It may be more realistic than earlier models based on pore or grain structure idealizations when the carbon contains large amounts of crystallite matter. Shrinkage of the carbon particles in the chemically controlled regime is also possible due to the random complete gasification of crystallitic planes. This mechanism can explain observations in the literature of particle size reduction. Based on the model predictions, both initial surface chemistry and the number of stacked planes in the crystallites strongly influence the reactivity and particle shrinkage. Its test results agree well with literature data on the air-oxidation of Spherocarb and show that it accurately predicts the variation of particle size with conversion. Model parameters are determined entirely from rate measurements.

The first structurally characterized discrete dinuclear mu-cyano hexacyanoferrate complex

Mixed valence complexes containing ferro- and ferricyanide have been known for almost 300 years, but no dinuclear, non-polymeric examples of these complexes have been structurally characterized. Here we report the first such example, comprising ferrocyanide coordinated to a pentaaminecobalt(III) complex. This Fe-II-Co-III complex may be reversibly oxidized to the Fe-III-Co-III analogue.

Modeling the optical constants of GaP, InP, and InAs

An extension of the Adachi model with the adjustable broadening function, instead of the Lorentzian one, is employed to model the optical constants of GaP, InP, and InAs. Adjustable broadening is modeled by replacing the damping constant with the frequency-dependent expression. The improved flexibility of the model enables achieving an excellent agreement with the experimental data. The relative rms errors obtained for the refractive index equal 1.2% for GaP, 1.0% for InP, and 1.6% for InAs. (C) 1999 American Institute of Physics. [S0021-8979(99)05807-7].

Modeling the fluid-flow-induced stress and collapse in a dendritic network

An analytical approach to the stress development in the coherent dendritic network during solidification is proposed. Under the assumption that stresses are developed in the network as a result of the friction resisting shrinkage-induced interdendritic fluid flow, the model predicts the stresses in the solid. The calculations reflect the expected effects of postponed dendrite coherency, slower solidification conditions, and variations of eutectic volume fraction and shrinkage. Comparing the calculated stresses to the measured shear strength of equiaxed mushy zones shows that it is possible for the stresses to exceed the strength, thereby resulting in reorientation or collapse of the dendritic network.

Growth and lactic acid production in batch culture of Lactobacillus rhamnosus in a defined medium

To facilitate metabolic analysis, batch fermentations of Lactobacillus rhamnosus were carried out in a new defined medium. Biomass at 10.5 g/l and lactic acid at 67 g/l with a Y-P/S of 0.84 were achieved. The maximum specific growth rate and the average productivity were 0.49/h and 2.48 g/l.h, respectively. These are comparable to those of this organism and related organisms in complex media. Preliminary amino acid studies were also conducted, highlighting the importance of serine, asparagine, glutamine and cysteine. Kinetic analysis revealed that lactic acid production was predominantly growth-associated with growth associated and non-growth associated lactic acid constants of 0.389 mol/g-cell and 0.0025 mol/g-cell.h, respectively. Finally a kinetic model has been included to describe the fermentation of L. rhamnosus.

Modeling the optical constants of AlxGa1-xAs alloys

The extension of Adachi's model with a Gaussian-like broadening function, in place of Lorentzian, is used to model the optical dielectric function of the alloy AlxGa1-xAs. Gaussian-like broadening is accomplished by replacing the damping constant in the Lorentzian line shape with a frequency dependent expression. In this way, the comparative simplicity of the analytic formulas of the model is preserved, while the accuracy becomes comparable to that of more intricate models, and/or models with significantly more parameters. The employed model accurately describes the optical dielectric function in the spectral range from 1.5 to 6.0 eV within the entire alloy composition range. The relative rms error obtained for the refractive index is below 2.2% for all compositions. (C) 1999 American Institute of Physics. [S0021-8979(99)00512-5].

A numerical study of pore-fluid, thermal and mass flow iu fluid-saturated porous rock basins

We present a numerical methodology for the study of convective pore-fluid, thermal and mass flow in fluid-saturated porous rock basins. lit particular, we investigate the occurrence and distribution pattern of temperature gradient driven convective pore-fluid flow and hydrocarbon transport in the Australian North West Shelf basin. The related numerical results have demonstrated that: (1) The finite element method combined with the progressive asymptotic approach procedure is a useful tool for dealing with temperature gradient driven pore-fluid flow and mass transport in fluid-saturated hydrothermal basins; (2) Convective pore-fluid flow generally becomes focused in more permeable layers, especially when the layers are thick enough to accommodate the appropriate convective cells; (3) Large dislocation of strata has a significant influence off the distribution patterns of convective pore;fluid flow, thermal flow and hydrocarbon transport in the North West Shelf basin; (4) As a direct consequence of the formation of convective pore-fluid cells, the hydrocarbon concentration is highly localized in the range bounded by two major faults in the basin.

Finite element modelling of reactive mass transport problems in fluid-saturated porous media

We use the finite element method to solve reactive mass transport problems in fluid-saturated porous media. In particular, we discuss the mathematical expression of the chemical reaction terms involved in the mass transport equations for an isothermal, non-equilibrium chemical reaction. It has turned out that the Arrhenius law in chemistry is a good mathematical expression for such non-equilibrium chemical reactions especially from the computational point of view. Using the finite element method and the Arrhenius law, we investigate the distributions of PH (i.e. the concentration of H+) and the relevant reactive species in a groundwater system. Although the main focus of this study is on the contaminant transport problems in groundwater systems, the related numerical techniques and principles are equally applicable to the orebody formation problems in the geosciences. Copyright (C) 1999 John Wiley & Sons, Ltd.

Modeling the optical properties of AlSb, GaSb, and InSb

Optical constants of AlSb, GaSb, and InSb are modeled in the 1-6 eV spectral range. We employ an extension of Adachi's model of the optical constants of semiconductors. The model takes into account transitions at E-0, E-0 + Delta(0), E-1, and E-1 + Delta(1) critical points, as well as higher-lying transitions which are modeled with three damped harmonic oscillators. We do not consider indirect transitions contribution, since it represents a second-order perturbation and its strength should be low. Also, we do not take into account excitonic effects at E-1, E-1 + Delta(1) critical points, since we model the room temperature data. In spite of fewer contributions to the dielectric function compared to previous calculations involving Adachi's model, our calculations show significantly improved agreement with the experimental data. This is due to the two main distinguishing features of calculations presented here: use of adjustable line broadening instead of the conventional Lorentzian one, and employment of a global optimization routine for model parameter determination.

Changes in quantum efficiency of Photosystem II of symbiotic dinoflagellates of corals after heat stress, and of bleached corals sampled after the 1998 Great Barrier Reef mass bleaching event Ross J. Jones , Selina Ward, Affendi Yang Amri and Ove Hoegh-Guldberg

Pulse-amplitude-modulation chlorophyll fluorometry was used to examine changes in dark-adapted F-v/F-m of endosymbiotic dinoflagellate microalgae within the tissues of the temperate coral Plesiastrea versipora exposed to elevated seawater temperature. The F-v/F-m was markedly reduced following exposure of corals to 28 degrees C for 48 h. When corals were returned to ambient (24 degrees C) conditions, F-v/F-m increased in an initial rapid and then secondary slower phase. Tissue discolouration (coral bleaching), caused by a significant decrease in the density of algae, was observed during the first 2-3 days of the recovery period. After 14 days, F-v/F-m was still significantly lower than in control corals. The recovery of F-v/F-m is discussed in terms of repair processes within the symbiotic algae, division of healthy algae and also the selective removal of photo-damaged dinoflagellates. Under field conditions, bleached corals sampled at Heron Island Reef during a bleaching event had significantly lower F-v/F-m than non-bleached colonies; four months after the bleaching event, there were no differences in F-v/F-m or algal density in corals marked as having bleached or having shown no signs of colour loss. The results of this laboratory and field study are consistent with the hypothesis that an impairment of photosynthesis occurs during heat-stress, and is the underlying cause of coral bleaching.

Modeling of hepatic elimination and organ distribution kinetics with the extended convection-dispersion model

The conventional convection-dispersion (also called axial dispersion) model is widely used to interrelate hepatic availability (F) and clearance (Cl) with the morphology and physiology of the liver and to predict effects such as changes in liver blood flow on F and Cl. An extended form of the convection-dispersion model has been developed to adequately describe the outflow concentration-time profiles for vascular markers at both short and long times after bolus injections into perfused livers. The model, based on flux concentration and a convolution of catheters and large vessels, assumes that solute elimination in hepatocytes follows either fast distribution into or radial diffusion in hepatocytes. The model includes a secondary vascular compartment, postulated to be interconnecting sinusoids. Analysis of the mean hepatic transit time (MTT) and normalized variance (CV2) of solutes with extraction showed that the discrepancy between the predictions of MTT and CV2 for the extended and conventional models are essentially identical irrespective of the magnitude of rate constants representing permeability, volume, and clearance parameters, providing that there is significant hepatic extraction. In conclusion, the application of a newly developed extended convection-dispersion model has shown that the unweighted conventional convection-dispersion model can be used to describe the disposition of extracted solutes and, in particular, to estimate hepatic availability and clearance in booth experimental and clinical situations.

Strain-dependent fluid flow defined through rock mass classification schemes

Strain-dependent hydraulic conductivities are uniquely defined by an environmental factor, representing applied normal and shear strains, combined with intrinsic material parameters representing mass and component deformation moduli, initial conductivities, and mass structure. The components representing mass moduli and structure are defined in terms of RQD (rock quality designation) and RMR (rock mass rating) to represent the response of a whole spectrum of rock masses, varying from highly fractured (crushed) rock to intact rock. These two empirical parameters determine the hydraulic response of a fractured medium to the induced-deformations The constitutive relations are verified against available published data and applied to study one-dimensional, strain-dependent fluid flow. Analytical results indicate that both normal and shear strains exert a significant influence on the processes of fluid flow and that the magnitude of this influence is regulated by the values of RQD and RMR.