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PubMedDate not supplied

The electron microscope band pattern of human fibrin: various stains, lateral order, and carbohydrate localization.

Human fibrin negatively contrasted with a variety of heavy metal compounds and examined by electron microscopy displays a distinctive, nonpolar band pattern with a repeat of 22.5 nm. These results together with a reversal of contrast observed in images of positively stained fibrin, indicate that the striations reflect the protein density along the fiber. All major features of the band pattern can be accounted for directly in terms of a model for the structure of fibrinogen. Optical and computed diffraction patterns of micrographs of fibrin show that most specimens are highly ordered along the fiber axis but have only diffuse equatorial reflections arising from the average spacing of the protofibrils, although occasional fibers have discrete reflections at about 19 nm. Finally, the resulting change in negative staining pattern upon binding of lectins to the carbohydrate moieties is distinctive and allows the carbohydrate-containing beta domain of the molecule to be localized.

Fibrin↗

PubMed2006

Oral bioavailability and intestinal secretion of amitriptyline: Role of P-glycoprotein?

The aim of the study was to evaluate the influence of quinidine, a P-glycoprotein inhibitor, on oral bioavailability and on intestinal secretion of amitriptyline, a tricyclic antidepressant. Amitriptyline was administrated intravenously (5 mg/kg) and orally (50 mg/kg) to rabbits, with and without quinidine. Jejunal segments of rats were mounted on diffusions chambers and the permeation of amitriptyline was measured across the tissue in luminal-serosal (LS) and serosal-luminal (SL) directions, with and without quinidine. Finally, an in situ recirculating intestinal perfusion model was performed in rabbits to study amitriptyline permeation in LS direction with and without quinidine. Absolute oral bioavailability (F) of amitriptyline was significantly increased more than three-fold in presence of quinidine (F = 0.6+/-0.4% versus 1.9+/-1.1%). The apparent permeability coefficients in SL direction were significantly higher than in LS direction (P(app (SL))=6.01+/-2.42 versus P(app (LS)) = 4.90+/-2.73 x 10(-4) cm min(-1)). In presence of quinidine, the intestinal absorption was increased (P(app (LS)) = 4.02+/-2.91 versus P(app (LS)) = 5.99+/-2.43 x 10(-4) cm min(-1)) and the intestinal secretion was decreased (P(app (SL)) = 4.58+/-0.54 versus P(app (LS)) = 3.63+/-1.46 x 10(-4) cm min(-1)) but not significantly. In conclusion, P-glycoprotein appears to be involved in oral amitriptyline absorption but other intestinal uptake and efflux transporters maybe implicated.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2006

Generating function methods in single-molecule spectroscopy.

Certain single-molecule measurements record a time series of individual physical events. Examples of such events include the emission of single photons or discrete fluctuations of molecular state (as in fluorescence blinking or spectral diffusion). The generating function formalism is a natural framework for studying these measurements both theoretically and numerically. Kinetic, stochastic, and quantum models for chromophore dynamics may all be extended to generating function calculations, enabling direct comparison to experiment with only slight extensions to familiar theoretical/computational tools.

Fluorescence↗

PubMed2005

Motion of single DNA molecules at a liquid-solid interface as revealed by variable-angle evanescent-field microscopy.

A variable-angle total-internal-reflection fluorescence microscope (VATIRFM) capable of providing a large range of incident angles was constructed for imaging single DNA molecule dynamics at a solid/liquid interface. An algorithm using a public-domain image-processing program, ImageJ, was developed for single-molecule counting. The experimental counts at various incident angles with different evanescent-field layer (EFL) thicknesses are affected by molecular diffusion. The dynamics of molecules near the surface and the observed counts in the VATIRFM are elucidated using a limited one-dimensional random-walk diffusion model. The simulation fits well with the experimental counting results. Further analysis using the simulation reveals the details of single-molecule motion. One implication is that the measured intensities cannot be used directly to determine the distances of molecules from the surface, though the majority of fluorescence does come from the EFL. Another implication is that rather than providing molecular concentrations within EFL the experimental counting results depict the distance-dependent dynamics of molecules near the surface. Thus, the VATIRFM could be a powerful technique to study the surface repulsion/attraction of molecules within a few hundred nanometers of the surface. Further studies show that molecules at low ionic strengths experience electrostatic repulsion at distances much further away from the surface than the calculated thickness of the electrical double layer.

DNA↗

PubMed2005

Steady-state analysis of polymer adsorption at and transport across an interface between two polymer phases.

We consider a mutually incompatible polymer mixture composed of two major components AN and BN and a third minority component C(N). The interactions, parameterized by short-range Flory-Huggins interaction parameters, are chosen such that C wets the A/B interface completely at three-phase coexistence. At sub-saturated conditions the adsorption of C remains necessarily microscopic. We study such a system in a stationary off-equilibrium state: due to imposed chemical potential gradients, polymer AN diffuses from the A-rich bulk phase through the interface to the A-poor bulk phase. Polymer BN travels in the opposite direction. Symmetric conditions are selected for which the polymer CN that accumulates at the A/B-interface has no net flux in the stationary state. This system is described by the Mean Field Stationary Diffusion (MFSD) model, an approach that solves the Scheutjens Fleer self-consistent-field (SF-SCF) equations with the boundary condition that the chemical potentials in the two bulk phases are different (but constant) so that a stationary state can be described. When the chemical potentials in the two bulk phases are the same, MFSD reduces to the equilibrium SF-SCF results. From the MFSD method we obtain the stationary volume fraction profiles and segmental fluxes. By forcing the system further from three-phase coexistence, i.e. by imposing larger concentration gradients, the adsorption of C goes unexpectedly from a thin adsorption layer to a thick adsorption film. The susceptibility partial differential J(A)/partial differential Delta(phi)A of the flux of A (equal to minus the flux of B) with respect to the imposed concentration gradient changes abruptly at the transition in adsorption behaviour. Interestingly, upon variation of the concentration gradients, the fluxes of A and B are enhanced by the accumulation of C at the interface. This means that the adsorbed C-film does not behave as an inert barrier.

Journal Article↗

PubMed2004

Curvature induced periodic attractor on growth interface.

We experimentally address the long-time dynamics of an artificially curved growth interface in directional solidification. Repetitive cell nucleations are found to appear in a disordered way but to eventually organize themselves coherently, at long times. This behavior is recovered by simulation of a nonlinear advection-diffusion model for the phase dynamics. The existence of a periodic attractor is shown by deriving a Liapunov functional for the cellular pattern organization on time ranges that include the singular events of cell nucleation.

Journal Article↗

PubMed2004

Drift of rigidly rotating spirals under periodic and noisy illuminations.

Under the weak deformation approximation, the motion of rigidly rotating spirals induced by periodic and noisy illuminations are investigated analytically. We derive an approximate but explicit formula of the spiral drift velocity directly from the original reaction-diffusion equation. With this formula we are able to explain the main features in the periodic and noisy illuminations induced spiral drift problems. Numerical computations of the Oregonator model are carried out as well, and they agree with the main qualitative conclusions of our analytical results.

Journal Article↗

PubMed1999

Polyglutamine pathogenesis.

An increasing number of neurodegenerative disorders have been found to be caused by expanding CAG triplet repeats that code for polyglutamine. Huntington's disease (HD) is the most common of these disorders and dentatorubral-pallidoluysian atrophy (DRPLA) is very similar to HD, but is caused by mutation in a different gene, making them good models to study. In this review, we will concentrate on the roles of protein aggregation, nuclear localization and proteolytic processing in disease pathogenesis. In cell model studies of HD, we have found that truncated N-terminal portions of huntingtin (the HD gene product) with expanded repeats form more aggregates than longer or full length huntingtin polypeptides. These shorter fragments are also more prone to aggregate in the nucleus and cause more cell toxicity. Further experiments with huntingtin constructs harbouring exogenous nuclear import and nuclear export signals have implicated the nucleus in direct cell toxicity. We have made mouse models of HD and DRPLA using an N-terminal truncation of huntingtin (N171) and full-length atrophin-1 (the DRPLA gene product), respectively. In both models, diffuse neuronal nuclear staining and nuclear inclusion bodies are observed in animals expressing the expanded glutamine repeat protein, further implicating the nucleus as a primary site of neuronal dysfunction. Neuritic pathology is also observed in the HD mice. In the DRPLA mouse model, we have found that truncated fragments of atrophin-1 containing the glutamine repeat accumulate in the nucleus, suggesting that proteolysis may be critical for disease progression. Taken together, these data lead towards a model whereby proteolytic processing, nuclear localization and protein aggregation all contribute to pathogenesis.

Animals↗

PubMed1999

Triangular anisotropies in driven diffusive systems: reconciliation of up and down.

Deterministic coarse-grained descriptions of driven diffusive systems (DDS) have been hampered by apparent inconsistencies with the kinetic Ising models of DDS. In the evolution towards the driven steady-state, "triangular" anisotropies in the two systems point in opposite directions with respect to the drive field. We show that this is nonuniversal behavior in the sense that the triangular anisotropy "flips" with local modifications of the Ising interactions. The sign and magnitude of the triangular anisotropy also vary with temperature. We have also flipped the anisotropy of coarse-grained models, though not yet at the latest stages of evolution. Our results illustrate the comparison of deterministic coarse-grained and stochastic Ising DDS studies to identify universal phenomena in driven systems. Coarse-grained systems are particularly attractive in terms of analysis and computational efficiency.

Journal Article↗

PubMed2003

Self-consistent theory of collective Brownian dynamics: theory versus simulation.

A recently developed theory of collective diffusion in colloidal suspensions is tested regarding the quantitative accuracy of its description of the dynamics of monodisperse model colloidal systems without hydrodynamic interactions. The idea is to exhibit the isolated effects of the direct interactions, which constitute the main microscopic relaxation mechanism, in the absence of other effects, such as hydrodynamic interactions. Here we compare the numerical solution of the fully self-consistent theory with the results of Brownian dynamics simulation of the van Hove function G(r,t) and/or the intermediate scattering function F(k,t) of four simple model systems. Two of them are representative of short-ranged soft-core repulsive interactions [(sigma/r)(mu), with mu>>1], in two and in three dimensions. The other two involve long-ranged repulsive forces in two (dipolar, r(-3) potential) and in three (screened Coulomb, or repulsive Yukawa interactions) dimensions. We find that the theory, without any sort of adjustable parameters or rescaling prescriptions, provides an excellent approximate description of the collective dynamics of these model systems, particularly in the short- and intermediate-time regimes. We also compare our results with those of the single exponential approximation and with the competing mode-mode coupling theory.

Journal Article↗

PubMed2006

Salt stress upregulates periplasmic arabinogalactan proteins: using salt stress to analyse AGP function.

Arabinogalactan proteins (AGPs) are implicated in cell expansion by unknown mechanisms, thus AGP content and cell-expansion rate might be correlated. We used Yariv reagent to quantify release rates and distribution of AGP at the cell surface of tobacco BY-2 cells: plasma membrane (M); soluble periplasmic AGPs released by cell rupture (S); cell wall (W); and growth medium (Gsink). In contrast to earlier reports, we observed massive upregulation of AGPs in salt-stressed cells, and hence the absence of a simple, direct cause-and-effect relationship between growth rate and AGP release. There was a more subtle connection. A dynamic flux model, M-->S-->W-->Gsink, indicated that turnover was nondegradative, with little free diffusion of AGPs trapped in the pectic matrix of nonadapted cells where transmural migration of high molecular-weight AGPs occurred mainly by plug flow (apposition and extrusion). In contrast, however, an up to sixfold increased AGP release rate in the slower-growing salt-adapted cells indicated a greatly increased rate of AGP diffusion through a much more highly porous pectic network. We hypothesize that classical AGPs act as pectin plasticizers. This explains how beta-D-glycosyl Yariv reagents might inhibit expansion growth by crosslinking monomeric AGPs, and thus mimic an AGP loss-of-function mutation.

Acclimatization↗

PubMed2000

Contributions of the extracellular and cytoplasmic domains of platelet-endothelial cell adhesion molecule-1 (PECAM-1/CD31) in regulating cell-cell localization.

PECAM-1/CD31, a vascular cell adhesion/signaling molecule that has been implicated in a number of vascular functions (including angiogenesis and the transmigration of leukocytes through endothelium) is highly enriched at the cell-cell borders of adjacent endothelial cells. To identify the mechanisms responsible for this localization, a series of PECAM-1 mutants and chimeric PECAM-1 molecules were transfected into non-PECAM-expressing cells and the ability of the constructs to move to cell-cell borders of adjacent cells was determined using immunohistochemistry and confocal microscopy. Although neither the extracellular domain, by itself, nor the cytoplasmic domain, by itself, was sufficient to direct cell-cell localization, the combination of the extracellular and transmembrane domains with a small group of highly charged amino acids in a membrane proximal region of the cytoplasmic domain was sufficient to direct efficient localization of the molecule to cell-cell borders. Importantly, only constructs that supported PECAM-1 mediated adhesion localized to cell-cell borders. Our data are consistent with a 'diffusion trapping' model in which movement of PECAM-1 in the cell membrane occurs relatively freely until the 'stablized' extracellular domain of the molecule encounters its ligand on an adjacent cell. When this occurs, the complex is 'captured' at the cell-cell interface leading to localization at cell-cell borders.

Cell Membrane↗

PubMed2006

Analytic algorithms for determining radiative transfer optical properties of ocean waters.

A synthetic model for the scattering phase function is used to develop simple algebraic equations, valid for any water type, for evaluating the ratio of the backscattering to absorption coefficients of spatially uniform, very deep waters with data from upward and downward planar irradiances and the remotely sensed reflectance. The phase function is a variable combination of a forward-directed Dirac delta function plus isotropic scattering, which is an elementary model for strongly forward scattering such as that encountered in oceanic optics applications. The incident illumination at the surface is taken to be diffuse plus a collimated beam. The algorithms are compared with other analytic correlations that were previously derived from extensive numerical simulations, and they are also numerically tested with forward problem results computed with a modified FN method.

Journal Article↗

PubMed1999

Parabolic quantitative structure-activity relationships and photodynamic therapy: application of a three-compartment model with clearance to the in vivo quantitative structure-activity relationships of a congeneric series of pyropheophorbide derivatives used as photosensitizers for photodynamic therapy.

An open three-compartment pharmacokinetic model was applied to the in vivo quantitative structure-activity relationship (QSAR) data of a homologous series of pyropheophorbide photosensitizers for photodynamic therapy (PDT). The physical model was a lipid compartment sandwiched between two identical aqueous compartments. The first compartment was assumed to clear irreversibly at a rate K0. The measured octanol-water partition coefficients, P(i) (where i is the number of carbons in the alkyl chain) and the clearance rate K0 determined the clearance kinetics of the drugs. Solving the coupled differential equations of the three-compartment model produced clearance kinetics for each of the sensitizers in each of the compartments. The third compartment was found to contain the target of PDT. This series of compounds is quite lipophilic. Therefore these drugs are found mainly in the second compartment. The drug level in the third compartment represents a small fraction of the tissue level and is thus not accessible to direct measurement by extraction. The second compartment of the model accurately predicted the clearance from the serum of mice of the hexyl ether of pyropheophorbide a, one member of this series of compounds. The diffusion and clearance rate constants were those found by fitting the pharmacokinetics of the third compartment to the QSAR data. This result validated the magnitude and mechanistic significance of the rate constants used to model the QSAR data. The PDT response to dose theory was applied to the kinetic behavior of the target compartment drug concentration. This produced a pharmacokinetic-based function connecting PDT response to dose as a function of time postinjection. This mechanistic dose-response function was fitted to published, single time point QSAR data for the pheophorbides. As a result, the PDT target threshold dose together with the predicted QSAR as a function of time postinjection was found.

Animals↗

PubMedDate not supplied

Design, operation, and modeling of a membrane photobioreactor to study the growth of the Cyanobacterium Arthrospira platensis in space conditions.

A membrane photobioreactor was designed, implemented and used to grow the cyanobacterium Arthrospira platensis PCC 8005 in batch mode. Growth was followed directly by monitoring optical density and indirectly by measuring pressure increase due to the oxygen produced and separated from the liquid phase by diffusion through a hydrophobic membrane, and pH increase due to carbon consumption. When the pressure attained an upper limit, valves opened automatically, and the oxygen in the gas chamber was flushed out with nitrogen. As expected, two growth phases were observed, a short exponential phase followed by a linear phase, indicating limitation by light transfer. Growth rate during the second phase was measured easily and accurately, and consistency of optical density, pressure and pH data values was checked using a model of the system. Pressure measurement was found best suited to monitoring and measuring growth rate in space in terms of accuracy, precision and reliability.

Bioreactors↗

PubMed2001

Intra-particle oxygen diffusion limitation in solid-state fermentation.

Oxygen limitation in solid-state fermentation (SSF) has been the topic of modeling studies, but thus far, there has been no experimental elucidation on oxygen-transfer limitation at the particle level. Therefore, intra-particle oxygen transfer was experimentally studied in cultures of Rhizopus oligosporus grown on the surface of solid, nutritionally defined, glucose and starch media. The fungal mat consisted of two layers--an upper layer with sparse aerial hyphae and gas-filled interstitial pores, and a dense bottom layer with liquid-filled pores. During the course of cultivation ethanol was detected in the medium indicating that oxygen was depleted in part of the fungal mat. Direct measurement of the oxygen concentrations in the fungal mat during cultivation, using oxygen microelectrodes, showed no oxygen depletion in the upper aerial layer, but revealed development of steep oxygen concentration gradients in the wet bottom layer. Initially, the fungal mat was fully oxygenated, but after 36.5 hours oxygen was undetectable at 100 microm below the gas-liquid interface. This was consistent with the calculated oxygen penetration depth using a reaction-diffusion model. Comparison of the overall oxygen consumption rate from the gas phase to the oxygen flux at the gas-liquid interface showed that oxygen consumption of the microorganisms occurred mainly in the wet part of the fungal mat. The contribution of the aerial hyphae to overall oxygen consumption was negligible. It can be concluded that optimal oxygen transfer in SSF depends on the available interfacial gas-liquid surface area and the thickness of the wet fungal layer. It is suggested that the moisture content of the matrix affects both parameters and, therefore, plays an important role in optimizing oxygen transfer in SSF cultures.

Aerobiosis↗

PubMed1981

Permeability characteristics of complement-damaged membranes: evaluation of the membrane leak generated by the complement proteins C5b-9.

Permeability characteristics of the membrane lesion generated by the terminal complement proteins are considered in light of recent observations that the measured diffusion of solute across complement-damaged membranes does not conform to the "doughnut hole" model of a discrete transmembrane pore formed by the inserted C5b-9 complex. By using the measured kinetics of steady-state tracer isotope diffusion of nonelectrolytes across resealed erythrocyte ghost membranes treated with C5b-9, a new transport model is developed. This model considers the apparent membrane lesion strictly in terms of the operational criteria of a functional conducting pathway for the observed diffusing solute, independent of a priori assumptions about the geometry or molecular properties of the membrane lesion. With this definition of the unit membrane lesion and the assumption that the exclusion size of the conducting pathway varies directly with the multiplicity of bound C5b-9 (as suggested by previous measurements under conditions of varying input of C5b-9), numerical estimates of te apparent permeability of the complement-damaged membrane to four diffusing nonelectrolytes are derived. These results suggest that the pathway for a particle diffusing across the complement lesion cannot be a pore and is functionally equivalent to an aqueous leak pathway, free of pore constraints. Implications of these results are discussed in terms of current molecular models for the mechanism of membrane damage by the complement proteins.

Biological Transport↗

PubMed2004

Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center.

Electrostatic interactions strongly enhance the electron transfer reaction between cytochrome (Cyt) c(2) and reaction center (RC) from photosynthetic bacteria, yielding a second-order rate constant, k(2) approximately 10(9) s(-1).M(-1), close to the diffusion limit. The proposed mechanism involves an encounter complex (EC) stabilized by electrostatic interactions, followed by a transition state (TS), leading to the bound complex active in electron transfer. The effect of electrostatic interactions was previously studied by Tetreault et al. [Tetreault, M., Cusanovich, M., Meyer, T., Axelrod, H. & Okamura, M. Y. (2002) Biochemistry 41, 5807-5815] by measuring k(2) for RC and Cyt molecules with modified charged residues at the binding interface. The present work is a computational analysis of this kinetic study to determine the ensemble of configurations of the TS and EC. Changes in the TS energies due to different mutations were compared with differences in the calculated electrostatic energies for a wide range of Cyt/RC configurations. The TS ensemble, obtained from structures having the highest correlation coefficients in the comparison with experimental data, has the Cyt displaced by approximately 10 A from its position in x-ray crystal structure, close to the average position of the EC ensemble, with strong electrostatic interactions between Cyt on the M subunit side of the RC surface. The heme of the Cyt is oriented toward Tyr L162 on the RC, the tunneling contact in the bound final state on the RC. The similarity between the structures of the EC, TS, and bound state can account for the rapid rate of association responsible for fast diffusion-controlled electron transfer.

Cytochromes c2↗