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At least 1,423 records · Page 79Linked to original sources
PubMed2001

Essential role of NHE3 in facilitating formate-dependent NaCl absorption in the proximal tubule.

The absorption of NaCl in the proximal tubule is markedly stimulated by formate. This stimulation of NaCl transport is consistent with a cell model involving Cl(-)-formate exchange in parallel with pH-coupled formate recycling due to nonionic diffusion of formic acid or H(+)-formate cotransport. The formate recycling process requires H(+) secretion. Although Na(+)-H(+) exchanger isoform NHE3 accounts for the largest component of H(+) secretion in the proximal tubule, 40-50% of the rates of HCO absorption or cellular H(+) extrusion persist in NHE3 null mice. The purpose of the present investigation is to use NHE3 null mice to directly test the role of apical membrane NHE3 in mediating NaCl absorption stimulated by formate. We demonstrate that formate stimulates NaCl absorption in the mouse proximal tubule microperfused in vivo, but the component of NaCl absorption stimulated by formate is absent in NHE3 null mice. In contrast, stimulation of NaCl absorption by oxalate is preserved in NHE3 null mice, indicating that oxalate-stimulated NaCl absorption is independent of Na(+)-H(+) exchange. The virtually complete dependence of formate-induced NaCl absorption on NHE3 activity raises the possibility that NHE3 and the formate transporters are functionally coupled in the brush border membrane.

Absorption↗
PubMed1985

Coupled reaction of immobilized aspartate aminotransferase and malate dehydrogenase. A plausible model for the cellular behaviour of these enzymes.

To study the effect of facilitated diffusion of the intermediate metabolite, oxaloacetate, on the coupled reaction of aspartate aminotransferase (L-aspartate: 2-oxoglutarate aminotransferase, EC 2.6.1.1) and malate dehydrogenase (L-malate:NAD+ oxidoreductase, EC 1.1.1.37), these enzymes were co-immobilized on the surface of a collagen film. The kinetic properties of the immobilized enzymes were compared with those observed with the enzymes in solution. Since the reactions correspond to the cytosolic enzymes, they have been studied in the direction aspartate aminotransferase toward malate dehydrogenase. Coupled enzymes in solution showed classical behaviour. A lag-time was observed before they reached a steady state and this lag-time was dependent on the kinetic properties of the second enzyme, malate dehydrogenase. The same lag-time was observed when malate dehydrogenase in solution was coupled with aspartate aminotransferase bound to the film. When aspartate aminotransferase in solution was coupled with malate dehydrogenase bound to the collagen film, a very long lag-time was observed. Theoretical considerations showed that in the latter case, the lag-time was dependent on the kinetic properties of the second enzyme and the transport coefficient of the intermediate substrate through the boundary layer near the surface of the film. Then both enzymes were co-immobilized on the collagen film. The coupled activity of aspartate aminotransferase and malate dehydrogenase was compared for films with an activity ratio of 5 and 0.8. In both cases, a highly efficient coupling was observed. In the former case, where malate dehydrogenase was rate-limiting, 81% of this limiting activity was observed. In the latter case, aspartate aminotransferase was rate-limiting and 82% of its rate was obtained for the final product formation. The linear increase of product formation with time corresponded fairly well to the theoretical equations developed in the paper. To interpret these rate equations, one should assume that the intermediate substrate oxaloacetate formed by aspartate aminotransferase was used by malate dehydrogenase in the diffusion layer near the film, before diffusing in the bulk solution.

Animals↗
PubMed2005

Solving the advection-diffusion equations in biological contexts using the cellular Potts model.

The cellular Potts model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or matrix (ECM). Standard diffusion solvers applied to the cellular potts model use finite difference methods on the underlying CPM lattice. However, these methods produce a diffusing field tied to the underlying lattice, which is inaccurate in many biological situations in which cell or ECM movement causes advection rapid compared to diffusion. Finite difference schemes suffer numerical instabilities solving the resulting advection-diffusion equations. To circumvent these problems we simulate advection diffusion within the framework of the CPM using off-lattice finite-difference methods. We define a set of generalized fluid particles which detach advection and diffusion from the lattice. Diffusion occurs between neighboring fluid particles by local averaging rules which approximate the Laplacian. Directed spin flips in the CPM handle the advective movement of the fluid particles. A constraint on relative velocities in the fluid explicitly accounts for fluid viscosity. We use the CPM to solve various diffusion examples including multiple instantaneous sources, continuous sources, moving sources, and different boundary geometries and conditions to validate our approximation against analytical and established numerical solutions. We also verify the CPM results for Poiseuille flow and Taylor-Aris dispersion.

Algorithms↗
PubMed2002

Modeling the gel electrophoresis of short duplex DNA by Brownian dynamics: cubic gel lattice with direct interaction.

The technique of Brownian dynamics is used to model the electrophoretic mobility of spherical and rod-like particles in a three-dimensional cubic gel lattice. In addition to excluded volume interactions between the migrating particle and the gel, direct interactions are also included. The methodology is first applied to spherical particles in the absence of direct interactions and the resulting mobilities are shown to agree with independent studies. The methodology is then applied to rod-like models of short duplex DNA fragments 10-50 base pairs in length. In the absence of direct interactions between gel and DNA, calculated mobilities show a much weaker dependence on gel concentration than observed in experiments of DNA in Tris-acetate buffer and polyacrylamide gels. When an attractive interaction between gel and DNA of approximately -0.3 k(B)T per base pair at contact is included, good agreement between calculated and experimental mobilities is achieved.

DNA↗
PubMed1968

Permeability of lipid bilayer membranes to organic solutes.

A sensitive fluorescence technique was used to measure transport of organic solutes through lipid bilayer membranes and to relate permeability to the functional groups of the solute, lipid composition of the membrane, and pH of the medium. Indole derivatives having ethanol, acetate, or ethylamine in the 3-position, representing neutral, acidic, and basic solutes, respectively, were the primary models. The results show: (a) Neutral solute permeability is not greatly affected by changes in lipid composition but presence or absence of cholesterol in the membranes could greatly alter permeability of the dissociable substrates. (b) Indole acetate permeability was reduced by introduction of phosphatidylserine into membranes to produce a net negative charge on the membranes. (c) Permeability response of dissociable solutes to variation in pH was in the direction predicted but not always of the magnitude expected from changes in the calculated concentrations of the undissociated solute in the bulk aqueous phase. Concentration gradients of amines across the membranes caused substantial diffusion potentials, suggesting that some transport of the cationic form of the amine may occur. It is suggested that factors such as interfacial charge and hydration structure, interfacial polar forces, and lipid organization and viscosity, in addition to the expected solubility-diffusion relations, may influence solute flux.

Acetates↗
PubMed2001

New insights into the mechanism of protein-protein association.

Association of a protein complex follows a two-step mechanism, with the first step being the formation of an encounter complex that evolves into the final complex. Here, we analyze recent experimental data of the association of TEM1-beta-lactamase with BLIP using theoretical calculations and simulation. We show that the calculated Debye-Hückel energy of interaction for a pair of proteins during association resembles an energy funnel, with the final complex at the minima. All attraction is lost at inter-protein distances of 20 A, or rotation angles of >60 degrees from the orientation of the final complex. For faster-associating protein complexes, the energy funnel deepens and its volume increases. Mutations with the largest impact on association (hotspots for association) have the largest effect on the size and depth of the energy funnel. Analyzing existing evidence, we suggest that the transition state along the association pathway is the formation of the final complex from the encounter complex. Consequently, pairs of proteins forming an encounter complex will tend to dissociate more readily than to evolve into the final complex. Increasing directional diffusion by increasing favorable electrostatic attraction results in a faster forming and slower dissociating encounter complex. The possible applicability of electrostatic calculations for protein-protein docking is discussed.

Bacterial Proteins↗
PubMed1996

Agonist-releasable intracellular calcium stores and the phenomenon of store-dependent calcium entry. A novel hypothesis based on calcium stores in organelles of the endo- and exocytotic apparatus.

Store-dependent calcium entry represents a little characterized calcium permeation pathway that is present in a variety of cell types. It is activated in an unknown way by depletion of intracellular calcium stores, for example in the course of phospholipase C stimulation. Current hypotheses propose that depleted calcium stores signal their filling state to this permeation pathway either by direct, protein-mediated interaction or by release of a small, diffusible messenger. The further characterization of store-dependent calcium entry will benefit from progress in the identification of the intracellular calcium storing compartments. Recent findings reviewed here suggest that these compartments include parts of the organelle system that is involved in endo- and exocytosis. This commentary describes a novel model of store-dependent calcium entry based on calcium stores belonging to the endo- and exocytotic organelle system. Such calcium stores could establish a tubule-like connection with the extracellular space, in analogy to the cellular compartments that contain the insulin-sensitive glucose transporter or the gastric proton pump. This connection will provide a pathway for store-dependent calcium entry. Under store depletion, extracellular calcium will permeate through the tubule-like connection into the store lumen and from there into the cytosol. The consequences of this model for the development of drugs modulating store-dependent calcium entry are discussed.

Animals↗
PubMed1987

Theory and delivery of health programming in the community: the Pawtucket Heart Health Program.

The Pawtucket Heart Health Program is one of the community studies examining whether population-based efforts to lower cardiovascular risk factors will reduce cardiovascular morbidity and mortality. The Pawtucket Heart Health Program intervention is based on a blend of social learning theory, community organization models, community psychology tenets, and diffusion research. This model allows for multifaceted programs that target individuals, groups, organizations, and the entire community to alter their cardiovascular risk through managing blood pressure, lowering blood cholesterol, quitting smoking, increasing fitness, and maintaining desirable weight levels. A dominant feature of the intervention is the emphasis that it places on volunteers for program delivery. The role of volunteers in providing direct services to help citizens lower their blood pressure and lose weight is highlighted to demonstrate the feasibility and effectiveness of these services. In addition, church-based programming which utilizes volunteers to manage and direct programs is also presented as an example of community-based health promotion efforts that promote collective efficacy.

Adolescent↗
PubMed2005

Comparison of outdoor activity size distributions of 220Rn and 222Rn progeny.

Inhalation of 222Rn and 220Rn progeny from the domestic environment contributes the greatest fraction of the natural radiation exposure to the public. Dosimetric models are most often used in the assessment of human lung doses due to inhaled radioactivity because of the difficulty in making direct measurements. These models require information about the parameters of activity size distributions of thoron and radon progeny. The present study presents measured data on the attached and unattached activity size distributions of thoron and radon progeny in outdoor air in El-Minia, Egypt. The attached fraction was collected using a low-pressure Berner cascade impactor technique. A screen diffusion battery was used for collecting the unattached fraction. Most of the attached activities for 222Rn and 220Rn progeny were associated with aerosol particles of the accumulation mode. The activity size distribution of thoron progeny was found to be shifted to slightly smaller particle size compared to radon progeny.

Journal Article↗
PubMed2006

Simple expressions for diffusion coefficient determination of adsorption within spherical and cylindrical absorbents using direct simulation method.

Various analytical expressions for solute adsorption kinetics within porous absorbents of defined geometry (planar sheet, cylinder, and sphere) are available in the literature. However, these expressions are limited for practical numerical evaluation because they are based on infinite series. An investigation of these expressions has been carried out and then accurate but simple expressions derived that enable rapid determination of effective diffusion coefficients for adsorption within geometrically categorical absorbents. These involve directly fitting calculated kinetic adsorption curves to experimental ones. A simple one point method is also proposed to estimate the effective diffusion coefficient for an adsorption process within these simple geometrical absorbents as an initial value for a best fit.

Absorption↗
PubMed2004

Mapping backbone dynamics in solution with site-directed spin labeling: GCN4-58 bZip free and bound to DNA.

In site-directed spin labeling, a nitroxide-containing side chain is introduced at selected sites in a protein. The EPR spectrum of the labeled protein encodes information about the motion of the nitroxide on the nanosecond time scale, which has contributions from the rotary diffusion of the protein, from internal motions in the side chain, and from backbone fluctuations. In the simplest model for the motion of noninteracting (surface) side chains, the contribution from the internal motion is sequence independent, as is that from protein rotary diffusion. Hence, differences in backbone motions should be revealed by comparing the sequence-dependent motions of nitroxides at structurally homologous sites. To examine this model, nitroxide side chains were introduced, one at a time, along the GCN4-58 bZip sequence, for which NMR (15)N relaxation experiments have identified a striking gradient of backbone mobility along the DNA-binding region [Bracken et al. (1999) J. Mol. Biol. 285, 2133]. Spectral simulation techniques and a simple line width measure were used to extract dynamical parameters from the EPR spectra, and the results reveal a mobility gradient similar to that observed in NMR relaxation, indicating that side chain motions mirror backbone motions. In addition, the sequence-dependent side chain dynamics were analyzed in the DNA/protein complex, which has not been previously investigated by NMR relaxation methods. As anticipated, the backbone motions are damped in the DNA-bound state, although a gradient of motion persists with residues at the DNA-binding site being the most highly ordered, similar to those of helices on globular proteins.

DNA↗
PubMed2004

Mechanism of the transition between lamellar and gyroid phases formed by a diblock copolymer in aqueous solution.

The mechanism of the transition from a lamellar phase to a gyroid phase in an aqueous solution of a diblock copolymer has been studied by time-resolved synchrotron small-angle X-ray scattering. The transition occurs via a metastable perforated lamellar structure. The perforations initially have liquidlike ordering before developing hexagonal packing. The transient phase of irregularly perforated layers is revealed by the development of diffuse scattering peaks, just below the Bragg peaks of the lamellar structure. The diffuse scattering is modeled by Monte Carlo simulations of perforated layers. Following the formation of perforations, Bragg peaks characteristic of a hexagonal structure signal an ordering into a hexagonal lattice (with the concomitant loss of diffuse scattering). Computer simulations based on a dynamic density functional model reproduce these features. The hexagonal perforated lamellar phase is rapidly replaced by the gyroid phase. The domain spacing of the gyroid phase is larger than that of the perforated lamellar structure. The perforated lamellar and gyroid phases coexist for a defined period. The reverse transition from gyroid to lamellae occurs directly, with no transient or metastable intermediates.

Computer Simulation↗
PubMed1988

Dialysate volume measurements required for determining peritoneal solute transport.

Solute transport parameters for the peritoneal membrane have been previously determined using dialysate volumes measured by the indicator dilution method. Recent work has shown that the indicator dilution volume (IDV) exceeds true dialysate volume (TV) because the indicator or index solute is lost from the peritoneal cavity. A peritoneal transport model that includes significant solute loss from the peritoneal cavity is here described. Theory suggests that simultaneous measurements of both IDV and TV are required to calculate solute transport parameters for the peritoneal membrane when solutes are lost from the peritoneal cavity. The magnitude of systematic errors incurred by the use of either IDV or TV alone was determined in the calculated diffusive permeability-area product (PA) for creatinine during a two hour exchange in a rabbit model of peritoneal dialysis. IDV was measured using dextran (2 X 10(6) daltons) and TV by the dilution of multiple injections of Evans blue-albumin complex. Best estimates of PA using either or both volume measurements were determined in the blood to dialysate direction with isotonic (N = 9) and hypertonic (N = 7) solutions and in the dialysate to blood direction with isotonic (N = 4) and hypotonic (N = 4) solutions. Systematic errors in PA using either IDV alone or TV alone were small with either isotonic or hypertonic solutions but were increased with hypotonic solutions. Moreover, systematic errors were larger when using TV alone thaN IDV alone. When solute transport parameters for the peritoneal membrane are approximately determined employing only a single volume measurement, the use of IDV leads to less systematic error than TV.

Animals↗
PubMed2000

Kramers problem for a polymer in a double well

We consider a long chain molecule, initially confined to the metastable side of a biased double well potential. It can escape from this side to the other by the motion of its N segments across the barrier. We assume that the length of the molecule is much larger than the width w of the barrier. The width w is taken to be sufficiently large that a continuum description is applicable to even the portion over the barrier. We use the Rouse model and analyze the mechanism of crossing the barrier. There can be two dominant mechanisms: end crossing and hairpin crossing. We find the free energy of activation for the hairpin crossing to be two times that for end crossing. The pre-exponential factor for hairpin crossing is proportional to N, while it is independent of N for end crossing. In both cases, the activation energy has a square root dependence on the temperature T, leading to a non-Arrhenius form for the rate. We also show that there is a special time dependent solution of the model, which corresponds to a kink in the chain, confined to the region of the barrier. The movement of the polymer from one side to the other is equivalent to the motion of the kink on the chain in the reverse direction. If there is no free energy difference between the two sides of the barrier, then the kink moves by diffusion and the time of crossing t(cross) approximately N(2)/T(3/2). If there is a free energy difference, then the kink moves with a nonzero velocity from the lower free energy side to the other, leading to t(cross) approximately N/sqrt[T]. We also discuss the applicability of the mechanism to the recent experiments of Kasianowicz [Proc. Natl. Acad. Sci. USA 93, 13 770 (1996)], where DNA molecules were driven through a nanopore by the application of an electric field. The prediction that t(cross) approximately N is in agreement with these experiments. Our results are in agreement with the recent experimental observations of Han, Turner, and Craighead [Phys. Rev. Lett. 83, 1688 (1999)]. We also consider the translocation of hydrophilic polypeptides across hydrophobic pores, a process that is quite common in biological systems. Biological systems accomplish this by having a hydrophobic signal sequence at the end that goes in first. We find that for such a molecule, the transition state resembles a hook, and this is in agreement with presently accepted view in cell biology.

Journal Article↗
PubMed2005

Monte Carlo charged-particle tracking and energy deposition on a Lagrangian mesh.

A Monte Carlo algorithm for alpha particle tracking and energy deposition on a cylindrical computational mesh in a Lagrangian hydrodynamics code used for inertial confinement fusion (ICF) simulations is presented. The straight line approximation is used to follow propagation of "Monte Carlo particles" which represent collections of alpha particles generated from thermonuclear deuterium-tritium (DT) reactions. Energy deposition in the plasma is modeled by the continuous slowing down approximation. The scheme addresses various aspects arising in the coupling of Monte Carlo tracking with Lagrangian hydrodynamics; such as non-orthogonal severely distorted mesh cells, particle relocation on the moving mesh and particle relocation after rezoning. A comparison with the flux-limited multi-group diffusion transport method is presented for a polar direct drive target design for the National Ignition Facility. Simulations show the Monte Carlo transport method predicts about earlier ignition than predicted by the diffusion method, and generates higher hot spot temperature. Nearly linear speed-up is achieved for multi-processor parallel simulations.

Journal Article↗
PubMed1998

Factor Xa generation at the surface of cultured rat vascular smooth muscle cells in an in vitro flow system.

The purpose of the present investigation was to explore the effects of well-defined flow conditions on the activity of tissue factor (TF) expressed on the surface of cultured rat vascular smooth muscle cells. Cells were cultured to confluence on Permanox brand slides and stimulated to express TF by a 90 min incubation with fresh growth medium containing 10 percent calf serum. The stimulated cells were then placed in a parallel plate flow chamber and perfused with Hank's Balanced Salt Solution containing factor VIIa, factor X (FX), and calcium. The chamber effluent was collected and assayed for factor Xa (FXa) and the steady-state flux of FXa was calculated. The flux values were 68.73, 94.81, 139.75, 138.19, 316.82, and 592.92 fmole/min/cm2 at wall shear rates of 10, 20, 40, 80, 320, and 1280 s-1, respectively. The FXa flux depended on the wall shear rate to a greater degree than predicted by classical mass transport theory. The flux at each shear rate was three to five times less than that calculated according to the Leveque solution. These features of the experimental data imply nonclassical behavior, which may partially result from a direct effect of flow on the cell layer.

Animals↗
PubMed1982

[Thermal effects of Nd:YAG and Co2 lasers on biological tissues].

The surgical use of CO2 c.w. laser as a knife and of Nd:YAG laser as photocoagulator is generally explained in terms of the different absorption coefficients of the water contained in high amount in the living tissues at the operating wavelengths of the two sources (alphaCO2 congruent to 10(2) cm(-1), alpha Nd congruent to 1cm(-1)). This approach can be shown to be incorrect once spectrophotometric measurements carried out on a mucous membrane and blood give the values gammaCO2 = 200 cm(-1) and gamma Nd = 10 cm(-1) for the effective absorption coefficient (the effective coefficient is gamma = alpha + beta where beta is the internal light scattering coefficient). It is worth noting that gammaCO2 congruent to alpha CO2 but gammaNd congruent to 10alphaNd. Then we have calculated the temperature distribution on tissues irradiated either by Co2 or by Nd laser. In the Co2 irradiation two energy transfer mechanisms are present: the surface optical absorption and the thermal diffusion in the bulk of the tissue. Under Nd irradiation the optical absorption of internally scattered radiation must also be taken into account. The calculation model is based on the classical heat equation, but assuming a "source" given by the expression S (r,z; t) = alpha [IB (r,z; t)+IS (r,z;t)], where IB and IS are respectively the direct and scattered components of a beam propagating along a z direction perpendicular to the tissue surface. The general expression of the temperature increases deltaT (r,z;t) have been obtained for both laser sources. The calculation show that even a few watts CO2 laser can induce a surface temperature rise of about 60 degrees C with negligible bulk effects, depending only on the thermal conductivity and on the irradiation time (knife effect). On the contrary a 40 w Nd:YAG laser induces a 50 degrees C temperature rise in the whole thickness of the tissue becoming in this way unable to "cut" even though it coagulates a region much larger than the beam dimensions.

Carbon Dioxide↗
PubMed1999

Ultrastructural model for size selectivity in glomerular filtration.

A theoretical model was developed to relate the size selectivity of the glomerular barrier to the structural characteristics of the individual layers of the capillary wall. Thicknesses and other linear dimensions were evaluated, where possible, from previous electron microscopic studies. The glomerular basement membrane (GBM) was represented as a homogeneous material characterized by a Darcy permeability and by size-dependent hindrance coefficients for diffusion and convection, respectively; those coefficients were estimated from recent data obtained with isolated rat GBM. The filtration slit diaphragm was modeled as a single row of cylindrical fibers of equal radius but nonuniform spacing. The resistances of the remainder of the slit channel, and of the endothelial fenestrae, to macromolecule movement were calculated to be negligible. The slit diaphragm was found to be the most restrictive part of the barrier. Because of that, macromolecule concentrations in the GBM increased, rather than decreased, in the direction of flow. Thus the overall sieving coefficient (ratio of Bowman's space concentration to that in plasma) was predicted to be larger for the intact capillary wall than for a hypothetical structure with no GBM. In other words, because the slit diaphragm and GBM do not act independently, the overall sieving coefficient is not simply the product of those for GBM alone and the slit diaphragm alone. Whereas the calculated sieving coefficients were sensitive to the structural features of the slit diaphragm and to the GBM hindrance coefficients, variations in GBM thickness or filtration slit frequency were predicted to have little effect. The ability of the ultrastructural model to represent fractional clearance data in vivo was at least equal to that of conventional pore models with the same number of adjustable parameters. The main strength of the present approach, however, is that it provides a framework for relating structural findings to the size selectivity of the glomerular barrier.

Animals↗