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PubMed2007

A PGSE diffusion and electrophoretic NMR study of Cs+ and Na+ dynamics in aqueous crown ether systems.

Multinuclear pulsed gradient spin-echo (PGSE) NMR diffusion and linewidth measurements were used to probe binding and transport in aqueous Na+-15-crown-5, Na+-18-crown-6, Cs+-15-crown-5 and Cs+-18-crown-6 systems. Since direct PGSE observation of many alkali cations is precluded by either low inherent sensitivity or rapid relaxation (or both), the feasibility of proton-detected electrophoretic NMR (ENMR) measurements to complement PGSE data was investigated. ENMR measurements were performed on aqueous Cs+-, Li+-, Na+-, K+-, and Rb+- 18-crown-6 systems. The data analysis is based on a two-site binding model and its corresponding association constants. Cs+ was found to bind considerably more tightly to 18-crown-6 (K=8 M-1) than to 15-crown-5 (K approximately 2 M-1), whereas Na+ had almost equal affinity (K approximately 4.5 M-1) for 15-crown-5 and 18-crown-6. The difficulties encountered in analysing the NMR parameters, methodological limitations and the implied need for more complicated binding models are discussed.

Cesium↗
PubMed1999

Non-linear model of cancer growth and metastasis: a limiting nutrient as a major determinant of tumor shape and diffusion.

A new approach for modelling the spatio-temporal evolution of tumors is presented. To test its validity, a very basic model is considered, which, in spite of its simplicity, is capable of generating a multiplicity of morphologies and growth and migration rates. From an in-vivo scenario of basic life processes, cancer cell proliferation is described as a competition for basic nutrients. The chosen mathematical treatment and simulation techniques permit a direct implementation of the local nonlinear couplings existing between the various cell populations and the free and bound nutrient concentration. A discussion of the results and proposed improvements and applications of the model is also presented.

Cell Division↗
PubMed2004

Experimental and theoretical investigation of directional permeability of human vertebral cancellous bone for cement infiltration.

The use of acrylic polymers in infiltrating the porous bone structure is an emerging procedure for the augmentation of osteoporotic vertebrae. Although this procedure is employed frequently, it is performed based on empirical knowledge, and therefore, does not take into consideration the porosity-dependent permeability of human vertebral cancellous bone. The purpose of this study was to: (a). experimentally and theoretically investigate interdependence of the vertebral cancellous bone permeability and porosity, and (b). examine if the bone permeability of spinal cancellous bone can be predicted using bone mineral density measurements. If these relations can be established, they can be useful in optimizing the injection conditions for predicable cement infiltration. To determine the porosity-dependent and directional permeability, 34 bone cores-20 samples in the superior-inferior (SI) direction and 14 in the anterior-posterior (AP) direction-were cut from 20 lumbar vertebrae and infiltrated with silicone oil with a viscosity matching that of PMMA. The permeability of the cores was determined based on Darcy's law. The mean permeability of SI and AP cores was 4.45+/-1.72 x 10(-8) and 3.44+/-1.26 x 10(-8)m(2), respectively. An interesting finding of this study was that the permeability of the AP cores was approximately 78% of that of SI cores, though the porosity of the SI and AP cores taken from the same vertebra was approximately equal. In addition, we provided a theoretical model for the porosity-dependent permeability that accurately described non-linear dependency of the bone permeability and porosity in both directions. Although the relation of the bone permeability and porosity was established, bone mineral density was a weak predictor of the bone permeability. The experimental and theoretical results of this study can be used to understand polymer flow in cement infiltration procedures.

Adsorption↗
PubMed1983

Rotational diffusion of Escherichia coli RNA polymerase free and bound to deoxyribonucleic acid in nonspecific complexes.

We have studied the rotational diffusion of Escherichia coli RNA polymerase free in solution and bound nonspecifically to DNA fragments. The rotational motion was measured by the decay in anisotropy of the triplet-triplet absorption by using as probes either the liganded enzyme inhibitor Rose Bengal or eosin 5'-isothiocyanate conjugated to the protein. The time resolution extended from 10 ns to 1 ms. Free RNA polymerase (holoenzyme) at high salt concentration (1 M NaCl) is monomeric and diffuses at 5 degrees C with a rotational correlation time of 0.66 microseconds, corresponding to an equivalent hydrodynamic sphere with a radius of 7.4 nm. These values and the known molecular weight are most compatible with a nonspherical shape, e.g., an oblate ellipsoid with an axial ratio of about 3. In 0.1 M NaCl, the holoenzyme is dimeric and has a rotational correlation time of 2 microseconds. The decay of anisotropy is at least biexponential upon binding RNA polymerase to calf thymus DNA or to poly[d(A-T)]. The fast component with half of the amplitude has decay kinetics comparable to those seen with the free monomeric enzyme. The slow component has a rotational correlation time of about 14 microseconds and is independent of DNA chain length in the range greater than 180 base pairs. Both rotational correlation times decrease with temperature, and the relative amplitudes change such that the faster component dominates at higher temperature. The rotational relaxation of the enzyme-DNA complexes is discussed in terms of alternative models involving rigid rod-sphere diffusion, conformational changes in the enzyme and/or DNA, sliding motions of the protein along the DNA, and torsional-bending motions of DNA envisioned as a deformable rod.

Circular Dichroism↗
PubMed2003

Facilitated transport of sodium or potassium chloride across vesicle membranes using a ditopic salt-binding macrobicycle.

A synthetic receptor, with an ability to bind sodium or potassium chloride as a contact ion-pair, is shown to effectively transport either salt across vesicle membranes. Significant transport is observed even when the transporter: phospholipid ratio is as low as 1:2500. Chloride efflux from unilamellar vesicles is monitored using a chloride selective electrode. Mechanistic studies indicate that the facilitated efflux is due to the uncomplexed transporter diffusing into the vesicle and the transporter-salt complex diffusing out. Vesicle influx experiments are also reported, where the facilitated influx of chloride and sodium ions into vesicles is observed directly by 35Cl and 23Na NMR, respectively.

Biological Transport↗
PubMed1999

[Attempts at innovations in the practice of teaching and practicing psychiatric nursing].

In the context of recent changes that are taking place in the field of mental health care in Brazil, the University has the responsibility to redimensioning human resources qualification of mental health workers. At the Mental Health Care and Educational Program of the University of São Paulo and São Paulo Health Office (São Paulo/Brazil), an experience still in course, the nursing students attending to psychiatric nurse training evaluated that theoretical-practical education dealing with health care issue in the field of Psychosocial Rehabilitation purpose, at the same time that directly interferes in the qualification of practices, simultaneously develops the students attitudes and knowledge that qualify them to perform coherent practices in accordance with rehabilitation models of care.

Attitude of Health Personnel↗
PubMed2003

Role of charges on cytochrome f from the cyanobacterium Phormidium laminosum in its interaction with plastocyanin.

The role of charge on the surface of cytochrome f from the cyanobacterium Phormidium laminosum in the reaction with plastocyanin was investigated in vitro using site-directed mutagenesis. Charge was neutralized at five acidic residues individually and introduced at a residue close to the interface between the two proteins. The effects on the kinetics of the reaction were measured using stopped-flow spectrophotometry, and the midpoint potentials of the mutant proteins were determined. The dependence of the bimolecular rate constant of reaction, k(2), on ionic strength was determined for the reactions of the cytochrome f mutants with wild-type and mutant forms of plastocyanin. Double mutant cycle analysis was carried out to probe for the presence of specific electrostatic interactions. The effects of mutations on Cyt f were smaller than those seen previously for mutants of plastocyanin [Schlarb-Ridley, B. G. et al. (2002) Biochemistry 41, 3279-3285]. One specific short-range interaction between charged residues of wild-type plastocyanin (Arg93) and wild-type cytochrome f (Asp63) was identified. The kinetic evidence from this study and that of Schlarb-Ridley et al., 2002, appears to conflict with the NMR structure of the P. laminosum complex, which suggests the absence of electrostatic interactions in the final complex [Crowley, P. et al. (2001) J. Am. Chem. Soc. 123, 10444-10453]. The most likely explanation of the apparent paradox is that the overall rate is diffusion controlled and that electrostatics specifically influence the encounter complex and not the reaction complex.

Amino Acid Substitution↗
PubMed2006

Analysis of lung parenchyma as a parametric porous medium.

The dynamic behavior of the lung in health and disease depends on its viscoelastic properties. To better understand these properties, several mathematical models have been utilized by many investigators. In the present work, we present a new approach that characterizes the dynamics of gas flow into a viscoelastic porous medium that models the lung structure. This problem is considered in terms of the lung input impedance on a macro level and parenchymal tissue impedance on the level of an alveolar wall. We start from a basic theoretical analysis in which macroscopic tissue deformations are represented in accordance with the linearized Navier-Stokes equations. This approach has strong theoretical underpinnings in other situations but has not been applied to analyze the impedance of the inflated lung. Our analysis provides a theoretical basis for analyzing the interaction between flow into the lungs as a biophysical diffusion process and parenchymal viscoelasticity described phenomenologically, within the frameworks of standard viscoelasticity and structural damping. This lung impedance incorporates parameters of porosity, permeability, and viscoelasticity on micro and macro levels of parenchymal tissue. The analysis shows the theoretical basis of the transformation from the impedance of alveolar walls or isolated tissue strips to that of the intact parenchyma. We also show how the loading impedance at the lung boundary may have a significant impact on the dynamic behavior of whole lung viscoelasticity. Our analysis may be useful in directing specific tests of different models and for analyzing experimental measurements of viscoelastic parameters of lung material under normal and pathological conditions.

Animals↗
PubMed2004

Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations.

Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that the electrophoretic mobility increases with increasing RNA length, consistent with experiment. Diffusion coefficients of RNA, corrected for finite-size effects and solvent viscosity, agree well with those estimated from experiments and hydrodynamic calculations. The diffusion coefficients and electrophoretic mobilities satisfy a Nernst-Einstein relation in which the effective charge of RNA is reduced by the charge of transiently bound counterions. Fluctuations in the counterion atmosphere are shown to enhance the diffusive spread of RNA molecules drifting along the direction of the external electric field. As a consequence, apparent diffusion coefficients measured by capillary zone electrophoresis can be significantly larger than the actual values at certain experimental conditions.

Computer Simulation↗
PubMed2006

Flying high: a theoretical analysis of the factors limiting exercise performance in birds at altitude.

The ability of some bird species to fly at extreme altitude has fascinated comparative respiratory physiologists for decades, yet there is still no consensus about what adaptations enable high altitude flight. Using a theoretical model of O(2) transport, we performed a sensitivity analysis of the factors that might limit exercise performance in birds. We found that the influence of individual physiological traits on oxygen consumption (Vo2) during exercise differed between sea level, moderate altitude, and extreme altitude. At extreme altitude, haemoglobin (Hb) O(2) affinity, total ventilation, and tissue diffusion capacity for O(2) (D(To2)) had the greatest influences on Vo2; increasing these variables should therefore have the greatest adaptive benefit for high altitude flight. There was a beneficial interaction between D(To2) and the P(50) of Hb, such that increasing D(To2) had a greater influence on Vo2 when P(50) was low. Increases in the temperature effect on P(50) could also be beneficial for high flying birds, provided that cold inspired air at extreme altitude causes a substantial difference in temperature between blood in the lungs and in the tissues. Changes in lung diffusion capacity for O(2), cardiac output, blood Hb concentration, the Bohr coefficient, or the Hill coefficient likely have less adaptive significance at high altitude. Our sensitivity analysis provides theoretical suggestions of the adaptations most likely to promote high altitude flight in birds and provides direction for future in vivo studies.

Adaptation, Physiological↗
PubMed2001

Autonomous multispecies reaction-diffusion systems with more-than-two-site interactions.

Autonomous multispecies systems with more-than-two-neighbor interactions are studied. Conditions necessary and sufficient for the closedness of the evolution equations of the n-point functions are obtained. The average numbers of the particles at each site for one species and three-site interactions, and its generalization to the more-than-three-site interactions, are explicitly obtained. Generalizations of the Glauber model in different directions, using generalized rates, generalized numbers of states at each site, and generalized numbers of interacting sites, are also investigated.

Journal Article↗
PubMed1999

A comparative study of acquisition schemes for diffusion tensor imaging using MRI.

This study has investigated the effects of the selection of the diffusion-weighted (DW) gradient directions on the precision of a diffusion tensor imaging (DTI) experiment. The theoretical analysis provided a quantitative framework in which the noise performance of DTI schemes could be assessed objectively and for the development of novel DTI schemes, which employ multiple DW gradient directions. This generic framework was first applied to the examination of two commonly used DTI schemes, which employed 6 DW gradient directions and hitherto were used indiscriminately under the sole condition of noncollinearity. It was then used to design and assess a novel 12-DW-gradient-direction DTI protocol, which employed the same total number of DW acquisitions as the two conventional schemes (12). This theoretical investigation was then corroborated using rigorous simulation and DTI experiments on both an isotropic phantom and a healthy human brain. Both the theoretical and the experimental analysis demonstrated that the two conventional schemes showed a significantly different noise performance and that use of the new multiple-DW-gradient-direction scheme clearly improved the precision of the DTI measurements.

Anisotropy↗
PubMed1976

Reversible particle movements associated with unstacking and restacking of chloroplast membranes in vitro.

Freeze-fracture and freeze-etch techniques have been employed to study the supramolecular structure of isolated spinach chloroplast membranes and to monitor structural changes associated with in vitro unstacking and restacking of these membranes. High-resolution particle size histograms prepared from the four fracture faces of normal chloroplast membranes reveal the presence of four distinct categories of intramembranous particles that are nonrandomly distributed between grana and stroma membranes. The large surface particles show a one to one relationship with the EF-face particles. Since the distribution of these particles between grana and stroma membranes coincides with the distribution of photosystem II (PS II) activity, it is argued that they could be structural equivalents of PS II complexes. An interpretative model depicting the structural relationship between all categories of particles is presented. Experimental unstacking of chloroplast membranes in low-salt medium for at least 45 min leads to a reorganization of the lamellae and to a concomitant intermixing of the different categories of membrane particles by means of translational movements in the plane of the membrane. In vitro restacking of such experimentally unstacked chloroplast membranes can be achieved by adding 2-20 mM MgCl2 or 100-200 mM NaCl to the membrane suspension. Membranes allowed to restack for at least 1 h at room temperature demonstrate a resegregation of the EF-face particles into the newly formed stacked membrane regions to yield a pattern and a size distribution nearly indistinguishable from the normally stacked controls. Restacking occurs in two steps: a rapid adhesion of adjoining stromal membrane surfaces with little particle movement, and a slower diffusion of additional large intramembranous particles into the stacked regions where they become trapped. Chlorophyll a:chlorophyll b ratios of membrane fraction obtained from normal, unstacked, and restacked membranes show that the particle movements are paralleled by movements of pigment molecules. The directed and reversible movements of membrane particles in isolated chloroplasts are compared with those reported for particles of plasma membranes.

Chloroplasts↗
PubMed1998

Mass spectrometric mapping of ion channel proteins (porins) and identification of their supramolecular membrane assembly.

Mass spectrometric peptide mapping, particularly by matrix-assisted laser desorption-ionization (MALDI-MS), has recently been shown to be an efficient tool for the primary structure characterization of proteins. In combination with in situ proteolytic digestion of proteins separated by one- and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), mass spectrometric peptide mapping permits identification of proteins from complex mixtures such as cell lysates. In this study we have investigated several ion channel membrane proteins (porins) and their supramolecular assembly in mitochondrial membranes by peptide mapping in solution and upon digestion in the gel matrix. Porins are integral membrane proteins serving as nonspecific diffusion pores or as specific systems for the transport of substrates through bacterial and mitochondrial membranes. The well-characterized porin from Rhodobacter capsulatus (R.c.-porin) has been found to be a native trimeric complex by the crystal structure and was used as a model system in this study. R.c.-porin was characterized by MALDI-MS peptide mapping in solution, and by direct in situ-gel digestion of the trimer. Furthermore, in this study we demonstrate the direct identification of the noncovalent complex between a mitochondrial porin and the adenine nucleotide translocator from rat liver, by MALDI-MS determination of the specific peptides due to both protein sequences in the SDS-PAGE gel band. The combination of native gel electrophoresis and mass spectrometric peptide mapping of the specific gel bands should be developed as a powerful tool for the molecular identification of protein interactions.

Electrophoresis, Polyacrylamide Gel↗
PubMed1995

Investigation of the delamination of polymer films from galvanized steel with the Scanning Kelvinprobe.

The applicability of a new experimental technique - the Scanning Kelvinprobe - for the analysis of the delamination of polymer films from galvanized steel is discussed. Defect ions having direct access to the zinc/ polymer interface will diffuse along this interface, a process, which can be monitored by the Kelvinprobe in a very early state with a high local resolution. After incorporation of ions a galvanic element is formed, the local cathode being at the delamination front, where oxygen is reduced, and the local anode at the zinc coated defect. For the model polymer under investigation the interaction between the film and the substrate is weak and the rate determining step for the delamination is the diffusion of cations from the local anode to the local cathode. An exposure to a highly CO(2)-containing atmosphere before the delamination prolongs the incubation time of delamination. If there is no zinc layer at the defect, an anodic delamination mechanism occurs. Zinc is dissolved under the polymer film, while the steel surface is cathodically protected.

Journal Article↗
PubMed1999

Nuclear magnetic resonance imaging measurements of water diffusion in the perfused hippocampal slice during N-methyl-D-aspartate-induced excitotoxicity.

Significant changes in the apparent diffusion coefficient of water are observed in nuclear magnetic resonance images of patients with acute ischemic stroke. However, the underlying mechanisms of these apparent diffusion coefficient changes are still unresolved. To analyse possible mechanisms, this study applies nuclear magnetic resonance imaging on a 14.1 Tesla narrow-bore magnet to quantitatively study water diffusion in individually perfused brain slices following exposure to N-methyl-D-aspartate excitotoxicity. The results indicate that brain slices have at least two distinct diffusing water compartments with apparent diffusion coefficients of 0.96+/-0.10x10(-3) mm2/s and 0.06+/-0.01x10(-3) mm2/s. When excitotoxicity was induced with N-methyl-D-aspartate, there was a significant decrease in the fraction of the fast diffusing water component in the slices (P<0.001). However, neither apparent diffusion coefficient changed significantly. Prior treatment with dizocilpine maleate (MK-801) depressed the effects of N-methyl-D-aspartate (P<0.01, ANOVA). The results demonstrate brain slice compartmental changes resulting from direct receptor stimulation and provide evidence for tissue water redistribution as an important mechanism for changes in apparent diffusion coefficient seen in clinical magnetic resonance imaging. The brain slice preparation affords a well-controlled method to study the mechanisms of tissue nuclear magnetic resonance contrast, bridging the gap between basic nuclear magnetic resonance studies and clinical magnetic resonance imaging. The brain slice model also offers a new way to test the utility of potential anti-stroke drugs using high field nuclear magnetic resonance imaging.

Algorithms↗
PubMed2004

On the adsorption kinetics of surface-chemically pure n-dodecanoic acid at the air/water interface.

The dynamic surface tension data for n-dodecanoic acid in 0.005 M hydrochloric acid, for as-received as well as for surface-chemically pure solutions, show the presence of a prolonged induction period, clearly indicating that the adsorption of this nonionic surfactant is not simply diffusion-controlled. A kinetic model for the reversible formation of monolayer islands, long known in the field of electrochemistry, is shown to also apply to the adsorption of n-dodecanoic acid at the air/water interface. The rate constant increases linearly with increasing bulk concentration, while the induction time decreases exponentially. The phenomenon of nucleation at the air/water interface is consistent with the direct experimental observation of the formation of solid-like patches as the interfacial region is drastically compressed.

Adsorption↗
PubMed1998

Regulation of extrinsic pathway factor Xa formation by tissue factor pathway inhibitor.

Tissue factor (TF) pathway inhibitor (TFPI) regulates factor X activation through the sequential inhibition of factor Xa and the VIIa.TF complex. Factor Xa formation was studied in a purified, reconstituted system, at plasma concentrations of factor X and TFPI, saturating concentrations of factor VIIa, and increasing concentrations of TF reconstituted into phosphatidylcholine:phosphatidylserine membranes (TF/PCPS) or PC membranes (TF/PC). The initial rate of factor Xa formation was equivalent in the presence or absence of 2.4 nM TFPI. However, reaction extent was small (<20%) relative to that observed in the absence of TFPI, implying the rapid inhibition of VIIa.TF during factor X activation. Initiation of factor Xa formation using increasing concentrations of TF/PCPS or TF/PC in the presence of TFPI yielded families of progress curves where both initial rate and reaction extent were linearly proportional to the concentration of VIIa.TF. These observations were consistent with a kinetic model in which the rate-limiting step represents the initial inhibition of newly formed factor Xa. Numerical analyses of progress curves yielded a rate constant for inhibition of VIIa.TF by Xa.TFPI (>10(8) M-1.s-1) that was substantially greater than the value (7.34 +/- 0.8 x 10(6) M-1.s-1) directly measured. Thus, VIIa.TF is inhibited at near diffusion-limited rates by Xa.TFPI formed during catalysis which cannot be explained by studies of the isolated reaction. We propose that the predominant inhibitory pathway during factor X activation may involve the initial inhibition of factor Xa either bound to or in the near vicinity of VIIa.TF on the membrane surface. As a result, VIIa.TF inhibition is unexpectedly rapid, and the concentration of active factor Xa that escapes regulation is linearly dependent on the availability of TF.

Animals↗