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PubMed2003

On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation.

Analytical ultracentrifugation is one of the classical techniques for the study of protein interactions and protein self-association. Recent instrumental and computational developments have significantly enhanced this methodology. In this paper, new tools for the analysis of protein self-association by sedimentation velocity are developed, their statistical properties are examined, and considerations for optimal experimental design are discussed. A traditional strategy is the analysis of the isotherm of weight-average sedimentation coefficients s(w) as a function of protein concentration. From theoretical considerations, it is shown that integration of any differential sedimentation coefficient distribution c(s), ls-g(*)(s), or g(s(*)) can give a thermodynamically well-defined isotherm, as long as it provides a good model for the sedimentation profiles. To test this condition for the g(s(*)) distribution, a back-transform into the original data space is proposed. Deconvoluting diffusion in the sedimentation coefficient distribution c(s) can be advantageous to identify species that do not participate in the association. Because of the large number of scans that can be analyzed in the c(s) approach, its s(w) values are very precise and allow extension of the isotherm to very low concentrations. For all differential sedimentation coefficients, corrections are derived for the slowing of the sedimentation boundaries caused by radial dilution. As an alternative to the interpretation of the isotherm of the weight-average s value, direct global modeling of several sedimentation experiments with Lamm equation solutions was studied. For this purpose, a new software SEDPHAT is introduced, allowing the global analysis of several sedimentation velocity and equilibrium experiments. In this approach, information from the shape of the sedimentation profiles is exploited, which permits the identification of the association scheme and requires fewer experiments to precisely characterize the association. Further, under suitable conditions, fractions of incompetent material that are not part of the reversible equilibrium can be detected.

Algorithms↗
PubMed1993

Diffusion patterns on domains representing developing Xenopus retina.

The retinotectal map of mature Xenopus frogs has linear metrics. The regions of the Xenopus retina were modeled during embryonic and early larval development with a set of standard geometrical shapes. A disk was used to model the entire early retina, rings of various thickness were used to model the ciliary margin (the growth zone of the larval retina), and portions of a sphere were used to model the entire late embryonic and larval retina. Gradients produced by several reaction-diffusion pattern-generating configurations were considered: Gierer-Meinhardt and Kauffman-type activator-inhibitor systems; an ideal Turing-like two morphogen system; a point source with diffuse sinks; and variously placed point source-point sink combinations. A few special arrangements produced linear metrics: a point source-point sink system produced linear angular metrics on a thin ring; and ideal Turing system produced linear cartesian metrics on a thin ring; and carefully configured multiple sources and sinks produced linear metrics on a disk. These cases could lead to linear map metrics, but are biologically implausible. Thus linear map metrics are probably not a direct consequence of linear positional values, and more generally, most embryonic tissues probably use non-linear gradients of positional information. Formation of linear map metrics may be functionally important for Xenopus frogs, accounting in part for the evolutionary preservation of mechanisms for interactions among neighboring retinal fibers.

Animals↗
PubMed1995

Experimental allergic encephalomyelitis in non-human primates: diffusion imaging of acute and chronic brain lesions.

Diffusion imaging and T2-weighted magnetic resonance imaging were performed on 16 monkeys with experimental allergic encephalomyelitis (EAE), a model of the human demyelinating disease MS. The purpose of this study was to determine whether local changes in diffusion image intensity could be correlated with the formation of acute and chronic demyelinating lesions. Diffusion image analysis was restricted to the internal capsule of the brain because of its anatomic orientation of fiber pathways. Acute inflammatory EAE lesions were large and monophasic, as visualized by T2-weighted MRI, and were accompanied by a decrease in the diffusion MR image signal with the diffusion-sensitizing gradient in all three orthogonal directions (n = 27 brain regions, P < 0.005). Chronic demyelinating lesions were preceded by multiple inflammatory attacks, as visualized by MRI, and by a decrease in diffusion MR image signal with the diffusion-sensitizing gradient in the two orthogonal directions perpendicular to the fibers of the internal capsule (n = 18 brain regions, P < 0.005). However, for the chronic group, there was no significant change in the diffusion MR image signal with diffusion-sensitizing gradient parallel to the fibers of the internal capsule at the terminal scan, suggesting little change in the water diffusion within the nerve fibers. These results suggest that diffusion imaging holds promise for measuring subtle changes in water diffusion due to different types of brain damage.

Acute Disease↗
PubMed2001

Villous trophoblasts cultured on semi-permeable membranes form an effective barrier to the passage of high and low molecular weight particles.

An effective in vitro model of the placental villous syncytium cultured on semi-permeable substrata is essential for studies of infectious pathogen transmission from mother to fetus. Current models using amniotic membranes or thinner artificial membranes show significant leakage, suggesting disruption of tight junctions or the presence of gaps between syncytial units. Such disruption and discontinuity of trophoblast cultures are probably the result of high stromal cell contamination, poor viability and lack of proliferation in culture. We have successfully cultured confluent layers of tight-junctioned syncytium on semi-permeable insert membranes using highly viable purified cytotrophoblasts and an alternating multiple seeding and differentiation technique. Using criteria including transepithelial diffusion of high and low molecular weight substances, electrical resistance and directional secretion of the matrix metalloproteinase, MMP-9, we demonstrate that these cultures form effective and functional physical barriers that can be maintained for up to 1 month.

Adult↗
PubMed2004

Crystal and molecular structure of methyl 4-O-methyl-beta-D-ribo-hex-3-ulopyranoside.

Methyl 4-O-methyl-beta-D-ribo-hex-3-ulopyranoside (2), a model compound for partially oxidized anhydroglucose units in cellulose, was crystallized from CHCl(3)/n-hexane by vapor diffusion to give colorless plates. Crystal structure determination revealed the monoclinic space group P2(1) with Z = 2C(8)H(14)O(6) and unit cell parameters of a = 8.404(2), b = 4.5716(10), c = 13.916(3)A, and beta = 107.467(4) degrees. The structure was solved by direct methods and refined to R = 0.0476 for 1655 reflections and 135 parameters. The hexulopyranoside occurs in a distorted chair conformation. Both hydroxyls are involved in hydrogen bonding and form zigzag bond chains along the b-axis. One of the two hydrogen bonds is bifurcated. The solid-state (13)C NMR spectrum of exhibits eight carbon resonances, with well-separated signals for the two methoxyls (1-OMe: 55.72 ppm, 4-OMe: 61.25 ppm) and a keto resonance with relatively large downfield shift (206.90 ppm). Differences in the C-4 and the methoxyls' chemical shifts in the solid and liquid states were found.

Carbohydrate Conformation↗
PubMed2005

Investigating the light absorption in a single pass through the photoreceptor layer by means of the lipofuscin fluorescence.

Reflection densitometry has been widely used to measure the density difference of the bleachable cone photopigments in human eyes. Most such measurements make a series of assumptions concerning the amount of scattered light to derive an estimate of the true cone photopigment density from the density difference measurements. The current study made three types of measurements of the light returning from the eye before and after bleaching: the amount of light returning in the "directed" reflection, which is a double-pass estimate of the cone photopigment density; the amount of light in undirected or diffuse reflection; and the amount of fluorescence from lipofuscin in the RPE, which provides a single-pass measurement of optical density difference. For a 1 deg foveally fixated field, the density difference estimates for the three measurements were 0.68, 0.21, and 0.22 respectively. The lipofuscin fluorescence was found to be unguided. The background density difference was non-negligible and very close to the single pass estimate from fluorescence. These measurements each involve potentially different pathways of light through the retina, and therefore place different constraints on models of these pathways. A simple model comparing the directional and the fluorescence optical densities produced retinal coverage estimates around 70-75%. Estimates of the shape factor of the single pass optical Stiles-Crawford effect were evaluated from the dark-adapted and bleached fluorescence measurements. The values were closer to those obtained from psychophysical methods than to the double pass optical Stiles-Crawford shape factors obtained directly from retinal reflectometry.

Adult↗
PubMed2001

Pore-to-pore hopping model for the interpretation of the pulsed gradient spin echo attenuation of water diffusion in cell suspension systems.

A simplified pore-to-pore hopping model for the two-phase diffusion problem is developed for the analysis of the pulsed gradient spin echo (PGSE) attenuation of water diffusion in the condensed cell suspension systems. In this model, the two phases inside and outside the cells are treated as two different kinds of pores, and the spin-bearing molecules perform hopping diffusion between them. The size and the orientations of those two respective pores are considered, and then the diffraction pattern of the PGSE attenuation may be well simulated. Nevertheless, the intensity of the characteristic peak decreases with increasing membrane permeability, from which the exchange time may be estimated. We then analyze the experimental 1H PGSE results of the erythrocytes suspension system. The water-residence lifetime in the erythrocyte is obtained to be 10 ms, which is the same as that estimated from the two-region approximation. Furthermore, the PGSE attenuation curve of addition of p-Chloromercuribenzenesulfonate (p-CMBS) is also discussed. It predicts that the alignment of erythrocytes will become normal to the magnetic field direction after the addition of p-CMBS, and inspection using a light microscope confirms that result.

4-Chloromercuribenzenesulfonate↗
PubMed2003

Freezing transition and correlated motion in a quasi-two-dimensional colloid suspension.

Recent experiments have demonstrated that the deviation of the single-particle displacement distribution from Gaussian form in a dense quasi-two-dimensional colloid suspension is a result of heterogenous dynamics that involves cooperative motions of neighboring colloid particles [J. Chem. Phys. 47, 9142 (2001)]. In this paper, we report the results of molecular dynamics (MD) simulations of a quasi-two-dimensional assembly of nearly hard-sphere colloid particles. The colloid-colloid interaction we use is short ranged and everywhere repulsive; it is related to the Marcus-Rice (MR) and modified MR interactions used in a previous study [Phys. Rev. E 58, 7529 (1998)]. As is the case for those systems, the one we study supports liquid, hexatic, and solid phases. Our calculations show that the deviation of the single-particle displacement distribution from Gaussian form is present in the liquid phase, and that a sharp increase in its magnitude occurs at the liquidus density and extends into the crystalline phase. For densities greater than the liquidus density we find three dynamical relaxation processes that include, at intermediate times, a slowing down in the rate of growth of the diffusive displacement of a particle due to the cage effect. As the density increases toward the solidus density, the dependence of the mean squared displacement on time, at intermediate times, changes from sublinear to zero. The onset of the long-time relaxation mode corresponds to the time at which the deviation of the particle displacement distribution from Gaussian form is a maximum. At this time, which increases exponentially with the density, the self-part of the van Hove function exhibits multiple maxima with respect to r while the distinct part of the van Hove function is a maximum at the origin, thereby signaling jump dynamics. At long times the particle mean square displacement has diffusive character at all densities including solid phase densities. A remarkable feature of our findings is the continuity of character of the particle displacement from the liquid phase through the hexatic phase and into the solid phase. Cooperative jumps that lead to diffusive process in crystals can be explained by a mechanism that involves many such correlated hops in random locations and random directions (but along the crystallographic axes) thereby generating effective random walk behavior. We argue that the collective motion we have found is generated by superpositions of instantaneous normal mode vibrations along diffusive paths. The diffusive paths are along the directions with strong bond orientation correlation, and start to grow in amplitude rapidly on entry into the hexatic phase.

Biophysical Phenomena↗
PubMed2002

Parallel flow measurements in microstructures by use of a multifocal 4 x 1 diffractive optical fan-out element.

We have developed a multifocal optical fluorescence correlation spectroscopy system for parallel flow analyses. Multifocal excitation was made possible through a 4 x 1 diffractive optical fan-out element, which produces uniform intensity in all four foci. Autocorrelation flow analyses inside a 20 microm x 20 microm square microchannel, with the 4 x 1 fan-out foci perpendicular to the flow direction, made it possible to monitor different flows in all four foci simultaneously. We were able to perform cross-correlation flow analyses by turning the microstructure, thereby having all four foci parallel to the direction of flow. Transport effects of the diffusion as a function of flow and distance could then also be studied.

Fluorescent Dyes↗
PubMed1994

Introducing new technology: confusion or order?

A model is explained for assessing the components and potential relationships which should be considered before introduction of a new or updated piece of equipment, improved supplies or a new process in nursing care. Some principles are offered to direct the weighting of various factors involved in selecting and implementing the introduction of new technology. Use of such a model can reduce staff frustration and improve quality of patient care.

Diffusion of Innovation↗
PubMed2001

Polymer additive migration to foods--a direct comparison of experimental data and values calculated from migration models for polypropylene.

To reduce the amount of compliance testing for food contact polymers the use of migration modelling is under discussion and being evaluated by an EU Commission funded project (Evaluation of Migration Models No. SMT4-CT98-7513). The work reported in this paper was exclusively funded by industry to provide data for the independent evaluation of a diffusion based model using eight different samples of polypropylene (PP) covering the range of polymers specification and five commonly used plastics additives. One hundred and fifty experimental migration data have been obtained in triplicate and used to evaluate a Fickian-based migration model in the prediction of specific migration of five additives into olive oil. All tests were conducted using olive oil, representing the most severe case for fatty foods, with test conditions of 2h at 121 degrees C, 2h at 70 degrees C and 10 days at 40 degrees C, representing short term exposures at high temperatures and room temperature storage. Predicted migration values were calculated using the Piringer 'Migratest Lite' model by entering the measured initial concentration of additive in the polymers(Cp.0) in to the equations together with known variables such as additive molecular weight, temperature and exposure time. Where necessary the data generated in this study have been used to update the model. The results indicate the Piringer migration model, using the 'exact' calculations of the Migratest Lite program, predicted migration values into olive oil close to, or in excess of, the experimental results for > 97% of the migration values generated in this study. For all measurements, the predicted migration from the Migratest Lite program was greater than 70% of the observed value. This study has identified the possibility, that random co-polymers of propylene and ethylene give higher migration than other grades of polypropylenes and could be treated as a separate case. However, further work on more samples of random co-polymers is required to confirm this finding.

Chromatography, High Pressure Liquid↗
PubMed2005

Phosphorus-discharge hysteresis during storm events along a river catchment: the River Swale, UK.

Variations in the concentration of determinands in rivers during storms often result in a hysteresis effect with different concentration during the rising and falling limb of the hydrograph. This is investigated here by measuring total phosphorus, particulate phosphorus and soluble reactive phosphorus at 3-h intervals at three points along the River Swale. Phosphorus concentration-discharge hysteresis from 10 storm events were quantified using an empirical model. The size and direction of the hysteresis loops were described by a response factor, and the slope of the loop quantified by a gradient constant. The modelled loops produced acceptable agreement with the field measurements. Hysteresis patterns for all phosphorus fractions changed markedly downstream, with predominantly anticlockwise trajectories in the upland moors (indicating a slow diffuse phosphorus delivery to the river) and clockwise in the intensively farmed lowland (indicating mobilisation of within-channel and riverbank phosphorus, and rapid inputs from field drains). The size of the hysteresis loops increased downstream, indicating an increased capacity for phosphorus storage and mobilisation within the lower catchment. During a succession of storms, lowland hysteresis loops decreased in magnitude, tending towards anticlockwise behaviour, indicating a depletion of mobile phosphorus from the river channel and margins. The modelling of hysteresis trajectories offers a convenient method of determining the relative contributions of diffuse and within-channel phosphorus sources.

Agriculture↗
PubMed1993

Single ion channel models incorporating aggregation and time interval omission.

We present a general theoretical framework, incorporating both aggregation of states into classes and time interval omission, for stochastic modeling of the dynamic aspects of single channel behavior. Our semi-Markov models subsume the standard continuous-time Markov models, diffusion models and fractal models. In particular our models allow for quite general distributions of state sojourn times and arbitrary correlations between successive sojourn times. Another key feature is the invariance of our framework with respect to time interval omission: that is, properties of the aggregated process incorporating time interval omission can be derived directly from corresponding properties of the process without it. Even in the special case when the underlying process is Markov, this leads to considerable clarification of the effects of time interval omission. Among the properties considered are equilibrium behavior, sojourn time distributions and their moments, and auto-correlation and cross-correlation functions. The theory is motivated by ion channel mechanisms drawn from the literature, and illustrated by numerical examples based on these.

Biophysical Phenomena↗
PubMed2003

Some properties of two-dimensional stochastic regimes of double-diffusive convection in plane layer.

The existence of a two-dimensional attracting manifold is established for trajectories emanating from the vicinity of static solution. The structure of this manifold is studied with the help of succession map of points in intersection of trajectories with some coordinate plane. The structure of the attracting manifold varies depending on Rayleigh numbers of heat and salinity. With growth of Rayleigh numbers of heat and salinity the structure of one-dimensional curve becomes more irregular and sophisticated. The convergence of Bubnov-Galerkin approximation with a large number of basic functions was demonstrated in norms of kinetic energy, dissipation function, and directly by norm evaluation of the residual (noncompensated terms in substitution of Bubnov-Galerkin approximation to the initial double-diffusive convection system).

Computer Simulation↗
PubMed2006

Organization pattern of nacre in Pteriidae (Bivalvia: Mollusca) explained by crystal competition.

Bivalve nacre is a brick-wall-patterned biocomposite of aragonite platelets surrounded by organic matter. SEM-electron back scatter diffraction analysis of nacre of the bivalve family Pteriidae reveals that early aragonite crystals grow with their c-axes oriented perpendicular to the growth surface but have their a- and b-axes disoriented. With the accumulation of successive lamellae, crystals progressively orient themselves with their b-axes mutually parallel and towards the growth direction. We propose that progressive orientation is a result of competition between nacre crystals at the growth front of lamellae, which favours selection of crystals whose fastest growth axis (b-axis) is oriented parallel to the direction of propagation of the lamella. A theoretical model has been developed, which simulates competition of rhombic plates at the lamellar growth front as well as epitaxial growth of crystals onto those of the preceding lamella. The model predicts that disordered nacre progressively produces bivalve-like oriented nacre. As growth fronts become diffuse (as is the common case in bivalves) it takes longer for nacre to become organized. Formation of microdomains of nacre platelets with different orientations is also reproduced. In conclusion, not only the organic matrix component, but also the mineral phase plays an active role in organizing the final microstructure.

Animals↗
PubMed2000

The relation of communication to risk judgment and preventive behavior related to lead in tap water.

More and more communities are becoming concerned about health risks posed by lead and other health hazards in their drinking water. Our study, applying the model of innovation diffusion to the adoption of preventive health behaviors, found that reliance on health professionals for information about lead in tap water was associated with residents perceiving risk from this hazard, their sense of efficacy in dealing with it, and their adoption of preventive behaviors. Mass media and pamphlets mailed directly to residents were relatively ineffective. Results suggest that interpersonal channels may be the best way to reach individuals who live in areas of highest risk from tap water lead.

Communication↗
PubMed2005

Quantification of contaminant sorption-desorption time scales from batch experiments.

The ability to predict rates of contaminant sorption and desorption in the environment is essential in order to determine contaminant bioavailability, predict contaminant fate and transport, and assess risk. In this paper, we present a new method to determine sorption-desorption time scales from the temporal moments of batch experimental data. Here, the term time scale has a precise meaning: Time scales are defined in terms of the parameters of kinetic sorption models. The method can be implemented with either a diffusion-based model (t(diff) = a2/15D) or a linear-driving-force model (t(LDF) = I/k) for sorption kinetics and can be implemented with either a discrete or a continuous distribution of rate parameters. Three advantages to the new method are that the time scales t(diff) or t(LDF) can be calculated directly without best-fitting the experimental data, the calculated sorption-desorption time scales are not dependent on an arbitrarily chosen distribution (e.g., the commonly used gamma or lognormal distributions), and the time scales implied by the analysis are consistent with the time scale of the actual experiment. We apply the method to previously reported experiments of 1,2-dichlorobenzene (DCB) sorption onto four natural sorbents. Comparing the newly calculated sorption-desorption time scales to those reported previously indicates a different order for the four sorbents with regard to DCB sorption rate. Further applications and limitations of the method are discussed.

Adsorption↗
PubMed2003

Structural and rheological characterization of Scleroglucan/borax hydrogel for drug delivery.

The polysaccharide Scleroglucan, one of the most rigid polymers found in nature, can form a chemical/physical gel, in the presence of borax. The obtained hydrogel was loaded with three different model molecules (Theophylline, Vitamin B12 and Myoglobin) and then, after freeze-drying, was used as a matrix for tablets. The release profiles of the substances from the dosage forms were evaluated; the matrix appeared capable to modulate the diffusion of the chosen molecules, and different diffusion rates were observed, according to the different radii of the tested molecules. Interestingly, in the dissolution medium the matrix undergoes an anisotropic swelling taking place only in the axial direction, while a negligible radial variation occurs. The water uptake of the matrix occurs according to a Fickian process. Samples at two different polymer concentrations (0.7 and 2.3%, w/v) were characterized in terms of rheological and mechanical parameters and the properties were interpreted in terms of the molecular structure obtained by conformational analysis. The flow curves acquired in the viscoelasticity interval, show the effect of the borate ion in improving the resistance of the gel in comparison to the polymer alone. The evaluation of the moduli indicates that the system is viscoelastic, with an appreciable liquid component that increases as the polymer concentration decreases. Also the cohesion of the gel is higher in comparison to the Scleroglucan and is strongly dependent on temperature. The combination of experimental and theoretical conformational analysis approaches, allowed us to propose a model for the structure of the macromolecular network and to give an explanation to the anomalous swelling that was observed. It came out that the polymer can built up a channel structure, mediated via borax ion interaction, that can accommodate guest molecules of different size.

Borates↗