Phase diagram of soybean phosphatidylcholine-diacylglycerol-water studied by x-ray diffraction and 31P- and pulsed field gradient 1H-NMR: evidence for reversed micelles in the cubic phase.

The phase equilibria of the system soybean phosphatidylcholine, diacylglycerol, and water has been determined using a combination of classical methods together with x-ray diffraction and NMR techniques. In particular, the extent of the phase regions of the lamellar, the reversed hexagonal, and the cubic phases have been determined. By pulsed field gradient 1H-NMR, the diffusion coefficients of all three components in a cubic phase composed of soybean phosphatidylcholine, diacylglycerol, and heavy water have been determined at 25 and 59 degrees C and also for the corresponding cubic phase composed of the chemically more well defined synthetic components 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dioleoylglycerol (DOG), and heavy water. The extension of the phase region of the cubic phase did not seem to change appreciably for the two ternary systems studied. The translational diffusion coefficient of DOPC in this cubic phase is more than an order of magnitude smaller (3 x 10(-13) m2 s-1, 59 degrees C) than the lateral diffusion coefficient of DOPC in an oriented lipid bilayer (5 x 10(-12) m2 s-1, 35 degrees C), whereas the diffusion coefficients of water and DOG were found to be about two orders of magnitude larger than DOPC at 59 degrees C. It is concluded that the cubic phase is built built up of closed reversed micelles in accordance with the suggestion from previous x-ray diffraction studies.     

A numerical model for studying the effect of plasma layer on the process of blood oxygenation in the pulmonary capillaries

A two layer model for the blood oxygenation in pulmonary capillaries is proposed. The model consists of a core of erythrocytes surrounded by a symmetrically placed plasma layer. The governing equations in the core describe the free molecular diffusion, convection, and facilitated diffusion due to the presence of haemoglobin. The corresponding equations in the plasma layer are based on the free molecular diffusion and the convective effect of the blood. According to the axial train model for the blood flow proposed by Whitmore (1967), the core will move with a uniform velocity whereas flow in the plasma layer will be fully developed. The resulting system of nonlinear partial differential equations is solved numerically. A fixed point iterative technique is used to deal with the nonlinearities. The distance traversed by the blood before getting fully oxygenated is computed. It is shown that the concentration of O2 increases continuously along the length of the capillary for a given ratio of core radius to capillary radius. It is found that the rate of oxygenation increases as the core to capillary ratio decreases. The equilibration length increases with a heterogeneous model in comparison to that in a homogeneous model. The effect of capillary diameters and core radii on the rate of oxygenation has also been examined.     

Pore network modelling of affinity chromatography: determination of the dynamic profiles of the pore diffusivity of beta-galactosidase and its effect on column performance as the loading of beta-galactosidase onto anti-beta-galactosidase varies with time.

A three-dimensional pore network model for diffusion in porous adsorbent particles was employed in a dynamic adsorption model that simulates the adsorption of a solute in porous particles packed in a chromatographic column. The solution of the combined model yielded the dynamic profiles of the pore diffusion coefficient of beta-galactosidase along the radius of porous adsorbent particles and along the length of the column as the loading of beta-galactosidase onto anti-beta-galactosidase immobilized on the surface of the pores of the particles occurred, and, the dynamic adsorptive capacity of the chromatographic column as a function of the design and operational parameters of the chromatographic system. It was found that for a given column length the dynamic profiles of the pore diffusion coefficient were influenced by (a) the superficial fluid velocity in the column, (b) the diameter of the adsorbent particles, and (c) the pore connectivity of the porous structure of the adsorbent particles. The effect of the magnitude of the pore connectivity on the dynamic profiles of the pore diffusion coefficient of beta-galactosidase increased as the diameter of the adsorbent particles and the superficial fluid velocity in the column increased. The dynamic adsorptive capacity of the column increased as (i) the particle diameter and the superficial fluid velocity in the column decreased, and (ii) the column length and the pore connectivity increased. In preparative affinity chromatography, it is desirable to obtain high throughputs within acceptable pressure gradients, and this may require the employment of larger diameter adsorbent particles. In such a case, longer column lengths satisfying acceptable pressure gradients with adsorbent particles having higher pore connectivity values could provide high dynamic adsorptive capacities. An alternative chromatographic system could be comprised of a long column packed with large particles which have fractal pores (fractal particles) that have high pore connectivities and which allow high intraparticle diffusional and convective flow mass transfer rates providing high throughputs and high dynamic adsorptive capacities. If large scale monoliths could be made to be reproducible and operationally stable, they could also offer an alternative mode of operation that could provide high throughputs and high dynamic adsorptive capacities.     

Selection of nest sites by a hole-nesting duck, the Goldeneye Bucephala clangula

Nest site preferences were examined for a population of Goldeneye Ducks breeding in nest boxes in Värmland, central Sweden. Some nest boxes were occupied more often than others even if females returning to the same nest box were excluded from the analysis. Nest boxes located higher up trees were occupied more often than those close to the ground and some spatial 'cluster groups' of boxes were occupied more often than others. Otherwise nest site prefernces were not related to any measured physical attributes of the boxes. Prefernces for nest boxes seemed to be based mainly on a tendency for females to select those that had been occupied by other females in the preceding year, especially if they had bred successfully. As a result of this, the occupancy of nest boxes was not random over years but rather progressed in a series of runs; a period of consecutive years in which a box was occupied was followed by a period of years in which it was empty.
There were reproductive consequences for these prefernces in that females occupying preferred boxes were less likely to lose their clutch to a predator. These females also bred earlier in the year and produced larger clutches and broods than females breeding in other boxes.     

The influence of the simulation box geometry in solid-state molecular simulations: phase behaviour of lithium iodide in a dynamic Monte Carlo simulation

In thermodynamic computer simulations, it is common to use cubic simulation boxes, which are then regarded as unit cells of an infinitely large cubic lattice. While this approach is adequate for gases and liquids at low densities, for dense liquids and solid cuboid boxes forming an orthorhombic lattice or parallelepiped boxes forming a triclinic lattice are shown to be advantageous, because they do not predetermine the structure of the simulated system. In this work, an extension of the Ewald summation formalism towards a parallelepiped lattice symmetry is given. Monte Carlo simulations of lithium iodide with cubic, cuboid and parallelepiped box geometries are reported; the latter is found to offer little improvement over the cuboid geometry. The existence of two hexagonal solid phases is discussed.     

Lipid and water diffusion in bicontinuous cubic phases measured by NMR.

Lipid and water diffusion coefficients in bicontinuous cubic liquid crystalline phases have been determined with the NMR pulsed magnetic field gradient technique. In the monoolein-water system, a discontinuity in the variation of the water diffusion coefficient with water content is observed, which coincides with the two-phase region between the two cubic phases in this system. The degree of water association to the lipid has been determined, considering the obstruction factor for diffusion in the cubic phases. The lipid diffusion coefficient increases with increased unsaturation of the lipid, and decreases when larger amphiphile molecules like cholesterol, gramicidin-A, and lyso-oleoyl-phosphatidylcholine are solubilized in the cubic phase. In a cubic liquid crystal of monoolein (MO), dioleoylphosphatidylcholine (DOPC), and water, the individual lipid diffusion coefficients have been determined simultaneously in the same sample. The diffusion coefficients of MO and DOPC differ by a factor of two, and both decrease with increasing DOPC content. The results are discussed in relation to probe techniques for measurements of lipid diffusion.     

Microscopic diffusion and hydrodynamic interactions of hemoglobin in red blood cells

The cytoplasm of red blood cells is congested with the oxygen storage protein hemoglobin occupying a quarter of the cell volume. The high protein concentration leads to a reduced mobility; the self-diffusion coefficient of hemoglobin in blood cells is six times lower than in dilute solution. This effect is generally assigned to excluded volume effects in crowded media. However, the collective or gradient diffusion coefficient of hemoglobin is only weakly dependent on concentration, suggesting the compensation of osmotic and friction forces. This would exclude hydrodynamic interactions, which are of dynamic origin and do not contribute to the osmotic pressure. Hydrodynamic coupling between protein molecules is dominant at short time- and length scales before direct interactions are fully established. Employing neutron spin-echo-spectroscopy, we study hemoglobin diffusion on a nanosecond timescale and protein displacements on the scale of a few nanometers. A time- and wave-vector dependent diffusion coefficient is found, suggesting the crossover of self- and collective diffusion. Moreover, a wave-vector dependent friction function is derived, which is a characteristic feature of hydrodynamic interactions. The wave-vector and concentration dependence of the long-time self-diffusion coefficient of hemoglobin agree qualitatively with theoretical results on hydrodynamics in hard spheres suspensions. Quantitative agreement requires us to adjust the volume fraction by including part of the hydration shell: Proteins exhibit a larger surface/volume ratio compared to standard colloids of much larger size. It is concluded that hydrodynamic and not direct interactions dominate long-range molecular transport at high concentration.     

Signals for TBP/TATA box recognition

The TATA box-binding protein (TBP) recognizes its target sites (TATA boxes) by indirectly reading the DNA sequence through its conformation effects (indirect readout). Here, we explore the molecular mechanisms underlying indirect readout of TATA boxes by TBP by studying the binding of TBP to adenovirus major late promoter (AdMLP) sequence variants, including alterations inside as well as in the sequences flanking the TATA box. We measure here the dissociation kinetics of complexes of TBP with AdMLP targets and, by phase-sensitive assay, the intrinsic bending in the TATA box sequences as well as the bending of the same sequence induced by TBP binding. In these experiments we observe a correlation of the kinetic stability to sequence changes within the TATA recognition elements. Comparison of the kinetic data with structural properties of TATA boxes in known crystalline TBP/TATA box complexes reveals several "signals" for TATA box recognition, which are both on the single base-pair level, as well as larger DNA tracts within the TATA recognition element. The DNA bending induced by TBP on its binding sites is not correlated to the stability of TBP/TATA box complexes. Moreover, we observe a significant influence on the kinetic stability of alteration in the region flanking the TATA box. This effect is limited however to target sites with alternating TA sequences, whereas the AdMLP target, containing an A tract, is not influenced by these changes.     

Interactions of molecular probes with living cells and tissues. Part 1. Some general mechanistic proposals, making use of a simplistic Chinese box model

A simple and generalised model-termed the simplistic Chinese box [SCB] model-for the interaction of molecular probes with living systems is described. The SCB model includes the following assumptions. That living systems may be considered as built from biologically defined boxes, e.g. whole cell, nucleus, nucleoli. That movement of molecular probes into and through these boxes is strongly influenced by box wall permeability, which in turn is largely dependent on the simple physicochemical properties of probe and wall. That retention of probes in boxes is influenced by permeability of the walls and by trapping of probes by boxes and walls, the latter effect also being strongly dependent on simple physicochemical properties. That important physicochemical properties include electric charge, hydrophilicity/lipophilicity, non-specific protein binding, and molecular size. That, since all these factors can be expressed or modelled numerically, SAR methodology is an appropriate technique for analysing molecular probe investigations.     

Improved staining boxes for fast, uniform staining of ultrathin sections on grids.

A standard LKB (LKB-Produkter Ab. S-161, 25 Brommma 1, Sweden) grid storage box is converted into several grid staining boxes by sawing the body of the box into segments along rows of its grid storage cavities. The staining boxes can be cut out to any required size or shape. The polymethyacrylate storage box cover is discarded. Covers for the staining boxes are cut from thin sheet vinyl, which is more chemically resistant than polymethyacrylate. Corresponding 2 mm diameter holes are drilled through the vinyl covers and the bottoms of the grid storage cavities of the staining boxes to convert the storage cavities into staining chambers. For staining, the covers are tied to the boxes with sewing thread and the assembled units are put into vials. The separate staining chambers prevent intermingling of and mechanical damage to grids during the staining procedure. Ultrathin sections are more cleanly and uniformly stained in bulk by the use of these staining boxes than they are when stained individually by a standard method.     

Detection and characterization of actin monomers, oligomers, and filaments in solution by measurement of fluorescence photobleaching recovery

Fluorescence photobleaching recovery (FPR) was measured to determine the diffusion coefficient of fluorescein-labeled G-actin in low-salt buffer. The result obtained, 7.15 +/- 0.35 X 10(-7) cm2/s, is in good agreement with that computed from the molecular weight, partial specific volume, and sedimentation coefficient, but is higher than previously obtained values. It is demonstrated from theory that at low ionic strength, the electrostatic contribution to the intrinsic viscosity leads to an overestimate of the hydrodynamic eccentricity of G-actin. Data from FPR, sedimentation, and fluorescence polarization experiments all indicate that the true low-salt form of the actin monomer has an axial ratio less than or equal to 3.0. The G-F transformation of actin was also observed by measurement of FPR during the assembly phase, in the steady state, and in the presence of ligands such as cytochalasin and aldolase. Each FPR record in general yields three data: relative proportion of rapidly and slowly diffusing actin, diffusion coefficient for the high-mobility fraction, and a mean diffusion coefficient for the low-mobility fraction. A relation between the mean low-mobility diffusion coefficient and the number-average filament length is derived and applied to the analysis of FPR data. Under typical conditions, the average filament length was much greater than 10 micron in the steady state. Cytochalasin D was found to decrease filament length and total amount of filament proportionally; total filament number was not greatly affected. In all polymerizations of G-actin, the high-mobility material observed in situ was found to be essentially monomeric actin. Relatively stable oligomers of actin were separated by fractionating G-AF-actin by gel filtration in 50 microM MgCl2 at 4 degrees C. On the basis of the diffusion coefficient, we conclude that monomer and dimer constitute the major particle types present under these conditions. Sedimentation of labeled actin polymerized in 1.0 mM MgCl2 yielded a graded supernatant that contained actin oligomers significantly larger than the monomer.     

Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics

Five long-timescale (10 ns) explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide dimer are performed using the GROMOS 45A4 force field and the simple-point-charge water model, in order to investigate the effect of the treatment of long-range electrostatic interactions as well as of the box shape and size on the structure and dynamics of the molecule (starting from an idealised B-DNA conformation). Long-range electrostatic interactions are handled using either a lattice-sum (LS) method (particle–particle–particle–mesh; one simulation performed within a cubic box) or a cutoff-based reaction-field (RF) method (four simulations, with long-range cutoff distances of 1.4 or 2.0 nm and performed within cubic or truncated octahedral periodic boxes). The overall double-helical structure, including Watson–Crick (WC) base-pairing, is well conserved in the simulation employing the LS scheme. In contrast, the WC base-pairing is nearly completely disrupted in the four simulations employing the RF scheme. These four simulations result in highly distorted compact (cutoff distance of 1.4 nm) or extended (cutoff distance of 2 nm) structures, irrespective of the shape and size of the computational box. These differences observed between the two schemes seem correlated with large differences in the radial distribution function between charged entities (backbone phosphate groups and sodium counterions) within the system.     

Interactions of molecular probes with living cells and tissues. Part 1. Some general mechanistic proposals,making use of a simplistic Chinese box model

Summary A simple and generalised model — termed the simplistic Chinese box [SCB] model — for the interaction of molecular probes with living systems is described. The SCB model includes the following assumptions. That living systems may be considered as built from biologically defined boxes, e.g. whole cell nucleus nucleoli. That movement of molecular probes into and through these boxes is strongly infuenced by box wall permeability, which in turn is largely dependent on the simple physicochemical properties of probe and wall. That retention of probes in boxes is influenced by permeability of the walls and by trapping of probes by boxes and walls, the latter effect also being strongly dependent on simple physicochemical, properties. That important physicochemical properties include electric charge, hydrophilicity/lipophilicity, non-specific protein binding, and molecular size. That, since all these factors can be expressed or modelled numerically, SAR methodology is an appropriate technique for analysing molecular probe investigations. This paper is dedicated to the memory of Prof. A.W. Rogers     

Dispersion of protein solutions in short, open capillary tubes as a method for rapid molecular weight determination

A method has been developed by which the molecular weight of proteins and other freely diffusing species can be estimated on the basis of chromatographic peak shapes developed by injection of a sample into an open capillary tube in a liquid chromatography system. In chromatographic peaks obtained from such a system, there are contributions from both convection and diffusion. Thus, peak shape is dependent upon the diffusion coefficient of the molecular species, the flow rate, and the length of the capillary tube. In the work reported here it has been found that for samples of different proteins ranging from 2000 to 14,000 molecular weight, each injected at the same mobile phase flow rate, the ratio (R) of h1, the height of the peak primarily due to convection, to h2, the height of the "makeup" peak, primarily due to diffusion from the capillary wall, is a direct measure of protein molecular weight. Linear plots of R vs molecular weight are obtained under certain conditions.     

Binding of the TorR regulator to cis-acting direct repeats activates tor operon expression

The expression of the Escherichia coli torCAD operon, which encodes the anaerobically expressed trimethylamine N-oxide (TMAO) reductase respiratory system, requires the presence of TMAO in the medium. The response regulator, TorR, has recently been identified as the regulatory protein that controls the expression of the torCAD operon in response to TMAO. The torC regulatory region contains four direct repeats of a decameric consensus motif designated the tor boxes. Alteration by base substitutions of any of the four tor boxes in a plasmid containing a torC'-lacZ fusion dramatically reduces TorR-dependent torC expression. In addition, deletion of the distal tor box (box1) abolishes torC induction whereas the presence of a DNA fragment starting three bases upstream from box1 suffices for normal torC expression. Footprinting and gel-retardation experiments unambiguously demonstrated that TorR binds to the torC regulatory region. Three distinct regions are protected by TorR binding. One of approximately 24 nucleotides covers the first two tor boxes (box1 and box2); the second is located upstream from the −35 promoter sequence and includes the third tor box (box3); the last is found downstream from the −35 sequence and corresponds to the fourth tor box (box4). Binding to the upstream tor boxes (box1 and box2) appears to be stronger than binding to the downstream tor boxes (box3 and box4) since only the upstream region is protected at the lower concentration of TorR used in the footprinting experiments.
We propose a model in which multiple binding sites (i.e. the tor boxes) contribute to the formation of a nucleoprotein complex, but only one particular proximal site positions TorR properly so that it interacts with RNA polymerase.     

Improved Staining Boxes for Fast, Uniform Staining of Ultrathin Sections on Grids

A standard LKB (LKB-Produkter Ab. S161, 45 Bromma 1, Sweden) grid storage box is converted into several grid staining boxes by sawing the body of the box into segments along rows of its grid storage cavities. the staining boxes can be cut out to any required size or shape. the polymethacrylate storage box cover is discarded. Covers for the staining boxes are cut from thin sheet vinyl, which is more chemically resistant thin polymethacrylate. Corresponding 2 mm diameter holes are drilled through the vinyl covers and the bottoms of the grid storage cavities of the staining boxes to convert the storage cavities into staining chambers. for staining, the covers are tied to the boxes with sewing thread and the assembled units are put into vials. the separate staining chambers prevent intermingling of and mechanical damage to grids during the staining procedure. Ultrathin sections are more cleanly and uniformly stained in bulk by the use of these staining boxes than they are when stained individually by a standard method.     

Egg box conformation of oligogalacturonides: the time-dependent stabilization of the elicitor-active conformation increases its biological activity

Circular dichroism spectrometry was used on oligogalacturonides (OGAs) and showed the existence of a calcium/sodium-induced conformational state that is intermediate between single-isolated chains and calcium-associated multimer chains. This conformation is interpreted as being egg box dimers. Using the 2F4 monoclonal antibody that specifically binds such an egg box dimer conformation of pectin, the stability of OGA dimers was investigated over a period of 24 hours. The extent to which egg box dimers were recognized by the antibody was dependent on the temperature and duration of preincubation of the OGA. This suggests a "maturation" process of the egg-box structure that consists in a progressive increase in the length of the junction sequences between two chains that slide along each other in order to form a maximum number of calcium bridges and dimer ends. The maturation of egg boxes induced both a significant increase in their binding to wall-associated kinase 1 (WAK1) and an increased extracellular alkalinization when applied to Arabidopsis thaliana cell suspensions. The chemical modification of the reducing end of the OGAs largely diminished their elicitating activity but did not hinder either dimerization or binding of these end-reduced egg boxes to WAK1. We conclude that there are at least two different perception systems for egg box dimers. One binds egg box junctions and the other binds egg box ends. The relevance of these results is discussed in terms of pectic signal perception and plant-pathogen interaction.