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At least 217 records · Page 12Linked to original sources
PubMed2001

Thermal stability and DPPC/Ca2+ interactions of pulmonary surfactant SP-A from bulk-phase and monolayer IR spectroscopy.

Surfactant protein A (SP-A), the most abundant pulmonary surfactant protein, is implicated in multiple biological functions including surfactant homeostasis, biophysical activity, and host defense. SP-A forms ternary complexes with lipids and Ca2+ which are important for protein function. The current study uses infrared (IR) transmission spectroscopy to investigate the bulk-phase interaction between SP-A, 1,2-dipalmitoylphosphatidylcholine (DPPC), and Ca2+ ions along with IR reflection-absorption spectroscopy (IRRAS) to examine protein secondary structure and lipid orientational order in monolayer films in situ at the air/water interface. The amide I contour of SP-A reveals two features at 1653 and 1636 cm(-1) arising from the collagen-like domain and a broad feature at 1645 cm(-1) suggested to arise from the carbohydrate recognition domain (CRD). SP-A secondary structure is unchanged in lipid monolayers. Thermal denaturation of SP-A in the presence of either DPPC or Ca2+ ion reveals a sequence of events involving the initial melting of the collagen-like region, followed by formation of intermolecular extended forms. Interestingly, these spectral changes were inhibited in the ternary system, showing that the combined presence of both DPPC and Ca2+ confers a remarkable thermal stability upon SP-A. The ternary interaction was revealed by the enhanced intensity of the asymmetric carboxylate stretching vibration. The IRRAS measurements indicated that incorporation of SP-A into preformed DPPC monolayers at a surface pressure of 10 mN/m induced a decrease in the average acyl chain tilt angle from 35 degrees to 28 degrees. In contrast, little change in chain tilt was observed at surface pressures of 25 or 40 mN/m. These results are consistent with and extend the fluorescence microscopy studies of Keough and co-workers [Ruano, M. L. F., et al. (1998) Biophys. J. 74, 1101-1109] in which SP-A was suggested to accumulate at the liquid-expanded/liquid-condensed boundary. Overall these experiments reveal the remarkable stability of SP-A in diverse, biologically relevant environments.

Androstanes↗
PubMed1994

Seeing morphemes: loss of visibility during the retinal stabilization of compound and pseudocompound words.

When stabilized, a retinal image fades from vision. Earlier studies suggested that knowledge constrains the loss of vision, as disappearing images fragment into familiar subpatterns. Effects of image stabilization on word perception were used in the current study to examine effects of morphemic knowledge on stimulus fragmentations. Bimorphemic compound words (in which beginning and ending trigrams formed morphemic subword units) and monomorphemic pseudo-compound words (with a similar trigram structure) were stabilized. Stimulus fragmentations generally resulted in the visibility of lexically nondistinct strings of letters. However, internal morpheme boundaries also affected the loss of vision when compound words were stabilized. Two follow-up experiments indicated that morpheme-related loss of vision was neither the result of differential forgetting rates nor of guessing bias.

Fixation, Ocular↗
PubMed1988

Oxygen ordering and twinning in YBa2Cu3O7-x.

Direct structure images of the YBa2Cu3O7-x high Tc superconducting ceramic (also called the 1-2-3 compound) at 1.7 A resolution have been obtained for the [100] and [001] orientations. It was found that for the purposes of studying oxygen ordering in this compound it is better to use lattice images of lower resolution. The oxygen ordering was studied via the measurement of the bending of (100) and (110) lattice planes on crossing the (110) twin boundaries in crystals oriented in the [001] zone. Significant variations were found in the b/a ratios, owning to a variation in oxygen ordering, between different crystal grains, and between different regions in the same grain. For the three different 1-2-3 samples studied, the average b/a ratio was 1.016, the same value as was found in neutron diffraction studies. The twin boundaries in the orthorhombic 1-2-3 phase are sharp and planar. It seems likely that the transformation from the high-temperature tetragonal phase to the lower-temperature orthorhombic phase is martensitic in nature. A new phase has been discovered on some of the twin boundaries. The new phase can be indexed as tetragonal with a = 7.5 +/- 0.2 A, and c = 6.8 +/- 0.2 A. It is possible that the new phase is stabilized by the stress which occurs at the twin boundaries.

Barium↗
PubMed1999

Probing the stability of S-layer-supported planar lipid membranes.

Isolated protein subunits of the crystalline bacterial cell surface layer (S-layer) of Bacillus coagulans E38-66 have been recrystallized on one side of planar black lipid membranes (BLMs) and their influence on the electrical properties, rupture kinetics and mechanical stability of the BLM was investigated. The effect on the boundary potential, the capacitance or the conductance of the membrane was negligible whereas the mechanical properties were considerably changed. The mechanical stability was characterized by applying voltage pulses or ramps to induce irreversible rupture. The amplitude of the voltage pulse leading to rupture allows conclusions on the ability of membranes to resist external forces. Surprisingly, these amplitudes were significantly lower for composite S-layer/lipid membranes compared to undecorated BLMs. In contrast, the delay time between the voltage pulse and the appearance of the initial defect was found to be drastically longer for the S-layer-supported lipid bilayer. Furthermore, the kinetics of the rupture process was recorded. Undecorated membranes show a fast linear increase of the pore conductance in time, indicating an inertia-limited defect growth. The attachment of an S-layer causes a slow exponential increase in the conductance during rupture, indicating a viscosity-determined widening of the pore. In addition, the mechanical properties on a longer time scale were investigated by applying a hydrostatic pressure across the BLMs. This causes the BLM to bulge, as monitored by an increase in capacitance. Compared to undecorated BLMs, a significantly higher pressure gradient has to be applied on the S-layer face of the composite BLMs to observe any change in capacitance.

Bacillus↗
PubMedDate not supplied

Gelatine-alginate complex gel: a new acoustically tissue-equivalent material.

Methods are described for the preparation of gelatine-alginate complex gels and measurements are reported of certain of their acoustic and physical properties relevant to their use as tissue-equivalent phantoms in medical ultrasonics applications. Speed of sound at 20 degrees C is 1520 ms-1 with a coefficient of +2.6 ms-1/degrees C. Attenuation coefficient in unloaded gel is 0.12 dB cm-1 MHz-1 (varying approximately linearly with frequency) but can readily be increased to at least 0.5 dB cm-1 MHz-1 by loading the gel with polyethylene or lipid microspheres. Volume stability under conditions of water immersion without an impermeable boundary layer is within about +/- 2% over a 300 day period, an improvement by a factor of at least 25 on both simple and cross-linked gelatine gels, and stability against chemical or bacterial degradation can also readily be maintained.

Alginates↗
PubMed2000

Stabilization of RNA tertiary structure by monovalent cations.

The effects of monovalent cations (Li(+), Na(+), K(+), Rb(+), Cs(+), and NH4(+)) on the thermal stability of RNA tertiary structure were investigated by UV melting. We show that with the RNA used here (nucleotides 1051-1108 of Escherichia coli 23 S rRNA with four base substitutions), monovalent cations and Mg(2+) compete in stabilizing the RNA tertiary structure, and that the competition takes place between two boundaries: one where Mg(2+) concentration is zero and the other where it is maximally stabilizing ("saturating"). The pattern of competition is the same for all monovalent cations and depends on the cation's ability to displace Mg(2+) from the RNA, its ability to stabilize tertiary structure in the absence of Mg(2+), and its ability to stabilize tertiary structure at saturating Mg(2+) concentrations. The stabilizing ability of a monovalent cation depends on its unhydrated ionic radius, and at a low monovalent cation concentration and saturating Mg(2+), there is a (calculated) net release of a single monovalent cation/RNA molecule when tertiary structure is denatured. The implications are that under these conditions there is at least one binding site for monovalent cations on the RNA, the site is specifically associated with formation of stable tertiary structure, K(+) is the most effective of the tested cations, and Mg(2+) appears ineffective at this site. At high ionic strength, and in the absence of Mg(2+), stabilization of tertiary structure is still monovalent-cation specific and ionic-radius dependent, but a larger number of cations ( approximately eight) are released upon RNA tertiary structure denaturation, and NH(4)(+) appears to be the most effective cation in stabilizing tertiary structure under these conditions. In the majority of the experiments, methanol was added as a cosolvent to the buffer. Its use allowed the examination of the behavior of monovalent ions under conditions where their effects would otherwise have been too weak to be observed. Methanol stabilizes tertiary but not secondary structure of the RNA. There was no evidence that it either causes qualitative changes in cation-binding properties of the RNA or a change in the pattern of monovalent cation/Mg(2+) competition.

Base Sequence↗
PubMed2005

Vaccination against multiple HPV types.

Vaccines against the most common human papillomavirus (HPV) types are currently under development. Epidemiologic data suggest that the transmission dynamics of different HPV types are not independent. Some studies indicate that interactions among HPV types are synergistic, where infection with one type facilitates concurrent or subsequent infection with another HPV type. Other studies point to antagonistic interference among HPV types. Here we develop a mathematical model to explore how these interactions may either enhance or diminish the effectiveness of vaccination programs designed to reduce the prevalence of the HPV types associated with cervical cancer. We analyze the local stability of the infection-free and boundary equilibria and characterize the conditions leading to a coexistence equilibrium. We also illustrate the results with numerical simulations using realistic model parameters. We show that if interactions among HPV types are synergistic, mass vaccination may reduce the prevalence of types that are not even included in the vaccine.

Female↗
PubMed1998

Hydration of the dienic lipid dioctadecadienoylphosphatidylcholine in the lamellar phase--an infrared linear dichroism and x-ray study on headgroup orientation, water ordering, and bilayer dimensions.

In the phospholipid 1,2-bis(2,4-octadecadienoyl)-sn-glycero-3-phosphorylcholine (DODPC) in each of the fatty acid chains, a rigid diene group is inserted in a position near the polar/apolar boundary that is exceptionally sensitive for membrane stability. DODPC transforms upon gradual dehydration from the liquid-crystalline to a metastable gel state, which rearranges into two subgel phases at low and intermediate degrees of hydration. The molecular dimensions of the respective bilayers were determined by means of x-ray diffraction. Infrared linear dichroism of selected vibrations of the phosphate and trimethylammonium groups and of the nu13(OH) band of water adsorbed onto the lipid was used to study the molecular order in the polar part of the bilayers in macroscopically oriented samples. The dense packing of the tilted acyl chains in the subgel causes the in-plane orientation of the phosphatidylcholine headgroups with direct interactions between the phosphate and trimethylammonium groups, and a strong orientation of adsorbed water molecules. In the more disordered gel, the thickness of the polar part of the bilayer increases and the lateral interactions between the lipid headgroups weaken. The higher order in the headgroup region of the subgels correlates with shorter decay lengths of the repulsive forces acting between opposite membrane surfaces. This result can be understood if the work to dehydrate the lipid is determined to a certain degree by the work to break up the lipid-water interactions without compensation by adequate lipid-lipid contacts. Almost similar area compressibility moduli are found in the liquid-crystalline and solid phases. Obviously, the lipid avoids lateral stress by the structural rearrangement.

Biophysical Phenomena↗
PubMed2005

Reversible flocculation of silica across the phase boundary of poly(vinyl caprolactam) in aqueous solution.

The colloid stability of silica dispersions in water in the presence of poly(vinyl caprolactam) (PVCAP) has been studied below and above the lower consolute temperature (LCT) of its solutions. The dispersion sediments slowly without PVCAP in the temperature range studied (26-40 degrees C) or with PVCAP below the LCT ( approximately 30 degrees C). In contrast, with PVCAP above the LCT, rapid flocculation occurs at acid pH, with re-dispersal on cooling. Reversible flocculation is also obtained above the LCT by cycling the pH from alkaline to acid and back. The flocculation observed above the LCT may also be regarded as heterocoagulation between the silica particles and the aggregates of the polymer.

Journal Article↗
PubMed1983

Escherichia coli single-strand binding protein stabilizes specific denatured sites in superhelical DNA.

Escherichia coli single-strand binding protein relaxes supercoiled DNA molecules containing the Drosophila melanogaster histone gene repeat unit, by stabilizing denaturation bubbles that map near the boundaries of the genes, at sites that in native chromatin have been shown to be hypersensitive to nucleases. A similar process may contribute to the propagation of such hypersensitive sites after their induction on the activation of gene expression.

Bacterial Proteins↗
PubMed2002

Exact discrete breather compactons in nonlinear Klein-Gordon lattices.

We demonstrate the existence of exact discrete compact breather solutions in nonlinear Klein-Gordon systems, and complete the work of Tchofo Dinda and Remoissenet [Phys. Rev. E 60, 6218 (1999)], by showing that the breathers stability is related principally to the lattice boundary conditions, the coupling term, and the harmonicity parameter.

Journal Article↗
PubMed2005

Least-squares finite-element scheme for the lattice Boltzmann method on an unstructured mesh.

A numerical model of the lattice Boltzmann method (LBM) utilizing least-squares finite-element method in space and the Crank-Nicolson method in time is developed. This method is able to solve fluid flow in domains that contain complex or irregular geometric boundaries by using the flexibility and numerical stability of a finite-element method, while employing accurate least-squares optimization. Fourth-order accuracy in space and second-order accuracy in time are derived for a pure advection equation on a uniform mesh; while high stability is implied from a von Neumann linearized stability analysis. Implemented on unstructured mesh through an innovative element-by-element approach, the proposed method requires fewer grid points and less memory compared to traditional LBM. Accurate numerical results are presented through two-dimensional incompressible Poiseuille flow, Couette flow, and flow past a circular cylinder. Finally, the proposed method is applied to estimate the permeability of a randomly generated porous media, which further demonstrates its inherent geometric flexibility.

Journal Article↗
PubMed2006

Shear-induced crystallization of a dense rapid granular flow: hydrodynamics beyond the melting point.

We investigate shear-induced crystallization in a very dense flow of monodisperse inelastic hard spheres. We consider a steady plane Couette flow under constant pressure and neglect gravity. We assume that the granular density is greater than the melting point of the equilibrium phase diagram of elastic hard spheres. We employ a Navier-Stokes hydrodynamics with constitutive relations all of which (except the shear viscosity) diverge at the crystal-packing density, while the shear viscosity diverges at a smaller density. The phase diagram of the steady flow is described by three parameters: an effective Mach number, a scaled energy loss parameter, and an integer number m: the number of half-oscillations in a mechanical analogy that appears in this problem. In a steady shear flow the viscous heating is balanced by energy dissipation via inelastic collisions. This balance can have different forms, producing either a uniform shear flow or a variety of more complicated, nonlinear density, velocity, and temperature profiles. In particular, the model predicts a variety of multilayer two-phase steady shear flows with sharp interphase boundaries. Such a flow may include a few zero-shear (solidlike) layers, each of which moving as a whole, separated by fluidlike regions. As we are dealing with a hard sphere model, the granulate is fluidized within the "solid" layers: the granular temperature is nonzero there, and there is energy flow through the boundaries of the solid layers. A linear stability analysis of the uniform steady shear flow is performed, and a plausible bifurcation diagram of the system, for a fixed m, is suggested. The problem of selection of m remains open.

Journal Article↗
PubMed2006

Vortex formation by active agents as a model for Daphnia swarming.

We propose a self-propelled particle model for the swarming of Daphnia that takes into account mutual repulsion and attraction to a center. Surprisingly, a vortex is formed only for an intermediate strength of propulsion. The phase diagram and the transitions between states with and without a vortex are analyzed, and the nature of the phase boundaries is discussed based on a linear stability analysis of the motion of individual swimmers. This allows us to identify various key parameters determining the characteristic features of the collective motion.

Animals↗
PubMed2004

Atomistic and lattice model of a grain boundary defaceting phase transition.

Recent calculations have shown that grain boundary (GB) stress is too small to stabilize finite GB facets, suggesting that the existing theory of GB defaceting phase transitions is incomplete. We perform molecular dynamics calculations, which show a reversible phase transition at approximately 400 K with a concerted shuffle of two atoms at the facet junction as the elementary excitation. Based on this excitation we formulate an appropriate lattice model, perform Monte Carlo simulations, and establish an analytical relationship between the elementary excitation energy and the transition temperature.

Journal Article↗
PubMed1985

Effects of detergents and phospholipids on the pyridine nucleotide-independent aldehyde dehydrogenase from membranes of Acetobacter rancens.

The pyridine nucleotide-independent aldehyde dehydrogenase solubilized and purified from membranes of Acetobacter rancens CCM 1774 requires the presence of detergents for activity. While several detergents could stimulate the enzyme activity the stability of the enzyme-detergent complexes was rather low. Phospholipid substitution experiments revealed the reversibility of the loss of activity caused by phospholipid removal. Enzyme-phospholipid complexes generated from a complex phospholipid fraction exhibited an increased stability. The predominant effect of phosphatidylglycerol on both enzyme activity and stability is discussed in terms of essential boundary layer phospholipids.

Acetobacter↗
PubMed2005

Tilt grain boundary instabilities in three-dimensional lamellar patterns.

We identify a finite wave-number instability of a 90 degrees tilt grain boundary in three-dimensional lamellar phases which is absent in two-dimensional configurations. Both a stability analysis of the slowly varying amplitude or envelope equation for the boundary, and a direct numerical solution of an order parameter model equation are presented. The instability mode involves two-dimensional perturbations of the planar base boundary, and is suppressed for purely one-dimensional perturbations. We find that both the most unstable wave numbers and their growth rate increase with epsilon , the dimensionless distance away from threshold of the lamellar phase.

Journal Article↗
PubMed2002

Symmetry-breaking instability in a prototypical driven granular gas.

Symmetry-breaking instability of a laterally uniform granular cluster (strip state) in a prototypical driven granular gas is investigated. The system consists of smooth hard disks in a two-dimensional box, colliding inelastically with each other and driven, at zero gravity, by a "thermal" wall. The limit of nearly elastic particle collisions is considered, and granular hydrodynamics with the Jenkins-Richman constitutive relations is employed. The hydrodynamic problem is completely described by two scaled parameters and the aspect ratio of the box. Marginal stability analysis predicts a spontaneous symmetry-breaking instability of the strip state, similar to that predicted recently for a different set of constitutive relations. If the system is big enough, the marginal stability curve becomes independent of the details of the boundary condition at the driving wall. In this regime, the density perturbation is exponentially localized at the elastic wall opposite the thermal wall. The short- and long-wavelength asymptotics of the marginal stability curves are obtained analytically in the dilute limit. The physics of the symmetry-breaking instability is discussed.

Journal Article↗