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PubMed1986

The DNA scanning mechanism of T4 endonuclease V. Effect of NaCl concentration on processive nicking activity.

T4 endonuclease V is a pyrimidine dimer-specific endonuclease which generates incisions in DNA at the sites of pyrimidine dimers by a processive reaction mechanism. A model is presented in which the degree of processivity is directly related to the efficacy of the one-dimensional diffusion of endonuclease V on DNA by which the enzyme locates pyrimidine dimers. The modulation of the processive nicking activity of T4 endonuclease V on superhelical covalently closed circular DNA (form I) which contains pyrimidine dimers has been investigated as a function of the ionic strength of the reaction. Agarose gel electrophoresis was used to separate the three topological forms of the DNA which were generated in time course reactions of endonuclease V with dimer-containing form I DNA in the absence of NaCl, and in 25, 50, and 100 mM NaCl. The degree of processivity was evaluated in terms of the mass fraction of form III (linear) DNA which was produced as a function of the fraction of form I DNA remaining. Processivity is maximal in the absence of NaCl and decreases as the NaCl concentration is increased. At 100 mM NaCl, processivity is abolished and endonuclease V generates incisions in DNA at the site of dimers by a distributive reaction mechanism. The change from the distributive to a processive reaction mechanism occurs at NaCl concentrations slightly below 50 mM. The high degree of processivity which is observed in the absence of NaCl is reversible to the distributive mechanism, as demonstrated by experiments in which the NaCl concentration was increased during the time course reaction. In addition, unirradiated DNA inhibited the incision of irradiated DNA only at NaCl concentrations at which processivity was observed.

DNA↗
PubMed1984

A model for the distribution and clearance of inert substances in subcutaneous tissue.

The subcutaneous space has received attention in recent years as a route for the continuous administration of drugs and implantation of drug delivery systems. Yet little work has been devoted to an examination of the mass transport (distribution) of drugs in the subcutaneous space and the factors that influence their rate of clearance. A mathematical model is developed to describe the spreading and resorption of substances infused into the subcutaneous space. It simulates radial diffusion and flow in the direction of spreading as well as lateral convection into the systemic circulation. An analytic solution is obtained for the distribution of the substance as a function of time and position in the subcutaneous space. Two independent parameters, v (Péclét no.) and H (generalized Biot no.), are found to control the transport. Examples are presented to illustrate the effects of these parameters on the distribution of substances in the subcutaneous space.

Absorption↗
PubMed1996

A physiologically based toxicokinetic model for dermal absorption of organic chemicals by fish.

A physiologically based toxicokinetic model was developed to describe dermal absorption of waterborne organic chemicals by fish. The skin was modeled as a discrete compartment into which compounds diffuse as a function of chemical permeability and the concentration gradient. The model includes a countercurrent description of chemical flux at fish gills and was used to simulate dermal-only exposures, during which the gills act as a route of elimination. The model was evaluated by exposing adult rainbow trout and channel catfish to hexachloroethane (HCE), pentachloroethane (PCE), and 1,1,2,2-tetrachloroethane (TCE). Skin permeability coefficients were obtained by fitting model simulations to measured arterial blood data. Permeability coefficients increased with the number of chlorine substituent groups, but not in the manner expected from a directly proportional relationship between dermal permeability and skin:water chemical partitioning. An evaluation of rate limitations on dermal flux in both trout and catfish suggested that chemical absorption was limited more by diffusion across the skin than by blood flow to the skin. Modeling results from a hypothetical combined dermal and branchial exposure indicate that dermal uptake could contribute from 1.6% (TCE) to 3.5% (HCE) of initial uptake in trout. Dermal uptake rates in catfish are even higher than those in trout and could contribute from 7.1% (TCE) to 8.3% (PCE) of initial uptake in a combined exposure.

Animals↗
PubMed2005

Direct stochastic simulation of Ca2+ motion in Xenopus eggs.

The release of important intracellular ions has been widely modeled using two approaches, namely, (1) Fickian diffusion, in which sometimes tensorial diffusion coefficients are used to fit observed temporally varying concentrations of calcium, and (2) cellular automata, which produce a set of localized finite difference equations that result in complex global behavior. Here, we take a different approach, employing some assumed, a priori, distribution of ion-binding proteins in the cell, and some assumed biochemical capture and release characteristics to explain ionic motion, and ultimately, distribution. We study several scenarios for ion distribution, based on differences in binder action and distribution. The numbers and strengths of ion binders, spatial variation in inositol 1,4,5-triphosphate concentration, together with the escalating distribution of ionic diffusion speed, are found to be key factors leading to concavity in the Ca2+ wave shape. We also offer an explanation for geometrical effects on previously observed ion diffusion speeds in the cellular cortex of the Xenopus laevis egg during fertilization, based on an angle-of-view correction.

Animals↗
PubMed2005

Kokua Mau: a statewide effort to improve end-of-life care.

BACKGROUND: Many Americans die in pain, without hospice, and without regard to advance directives, suggesting a need to improve end-of-life (EOL) awareness and services. OBJECTIVE: This paper describes Kokua Mau, a community-state partnership to improve EOL in Hawaii funded by The Robert Wood Johnson Foundation (RWJF). Coalition activities were guided by innovation-diffusion theory, targeting "innovators" and "change agents" within communities and organizations willing to learn about and facilitate improvements to EOL care. DESIGN: Evaluation of a community-wide intervention to improve EOL care. SETTING/SUBJECTS: Honolulu, Hawaii. MEASUREMENTS: We tracked dissemination of campaign messages by counting numbers of coalition members (including innovators and change agents to carry on the work), individuals reached through awareness and educational offerings, and new EOL projects initiated during and after the initial 3-year RWJF funding. To measure change, we counted the number of legislative policies that were modified by the coalition as well as indicators of hospice utilization, advance directive (AD) completion, support for physician-assisted death, and place of death. RESULTS: In the first 3 years of the project: coalition membership grew to 350 members; EOL care curricula were developed and offered to various target audiences; 17,000 individuals attended educational events; policy changes were facilitated; decreases were seen in proportions of residents supporting physician-assisted suicide; and increases were seen in advance directive completion rates and hospice utilization. Most importantly, after the grant period, coalition members went on to develop and implement new programs to improve care to the dying. CONCLUSIONS: Although it will take several years to effect comprehensive and sustained changes in the way death is perceived and the dying process is facilitated, findings suggest that programs based on innovation-diffusion theory can increase EOL awareness and help develop the change agents and role models needed to affect community-wide change over the long term.

Adolescent↗
PubMed1984

Weak acid-induced release of liposome-encapsulated carboxyfluorescein.

Leakage of the entrapped anionic fluorophore carboxyfluorescein was used as a measure of the permeability of liposomes to several different acids. Carboxyfluorescein leakage increased with increasing buffer concentration at a given pH and depended on its chemical nature: apolar weak acids such as acetic or pyruvic acids induced fast leakage at relatively high pH (4 to 5), while glycine, aspartic, citric and hydrochloric acids induced leakage only at lower pH. Fluorescence leakage measurements reflected the acidification of the liposomes' aqueous spaces, which was primarily caused by the diffusion of undissociated acid molecules across the lipid bilayer. A simple mathematical model in accord with this hypothesis and assuming that carboxyfluorescein leakage was directly related to the proportion of its neutral lactone form, described satisfactorily the carboxyfluorescein leakage kinetics and allowed rough estimation of permeability coefficients for carboxyfluorescein (neutral lactone form: 9 X 10(-9) cm X s-1), acetic acid (greater than 1 X 10(-7) cm X s-1) and glycine (cation: 6 X 10(-9) cm X s-1). These results are consistent with low effective proton permeability of liposomes (less than 5 X 10(-12) cm X s-1) and with the permeability coefficient of HCl (3 X 10(-3) cm X s-1) reported by Nozaki and Tanford ( (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 4324-4328). Diffusion of weak acid molecules across lipid membranes has implications for drug encapsulation and delivery, and may be of biological significance.

Acids↗
PubMed1994

Lipid domains and lipid/protein interactions in biological membranes.

In the fluid mosaic model of membranes, lipids are organized in the form of a bilayer supporting peripheral and integral proteins. This model considers the lipid bilayer as a two-dimensional fluid in which lipids and proteins are free to diffuse. As a direct consequence, both types of molecules would be expected to be randomly distributed within the membrane. In fact, evidences are accumulating to indicate the occurrence of both a transverse and lateral regionalization of membranes which can be described in terms of micro- and macrodomains, including the two leaflets of the lipid bilayer. The nature of the interactions responsible for the formation of domains, the way they develop and the time- and space-scale over which they exist represent today as many challenging problems in membranology. In this report, we will first consider some of the basic observations which point to the role of proteins in the transverse and lateral regionalization of membranes. Then, we will discuss some of the possible mechanisms which, in particular in terms of lipid/protein interactions, can explain lateral heterogenities in membranes and which have the merit of providing a thermodynamic support to the existence of lipid domains in membranes.

Animals↗
PubMed2005

Modelling of the uptake rate of the nitrogen dioxide Palmes diffusive sampler based on the effect of environmental factors.

The influence of environmental parameters on the uptake rate of the nitrogen dioxide (NO(2)) Palmes diffusive sampler was investigated. The main factors affecting the uptake rate were found to be wind speed, the preponderant factor, followed by relative humidity and temperature. The NO(2) concentration and exposure time, as well as the interactions among the factors were not found to have a significant influence on the uptake rate of the Palmes sampler. As a result, a model able to predict the uptake rate of the Palmes sampler was established. In addition, by using the model-predicted uptake rate, the agreement between chemiluminescence and the Palmes sampler during the field tests was improved. The NO(2) Palmes diffusive sampler was shown to comply with the requirement on accuracy defined by the European Directive for the indicative methods of measurements.

Air Movements↗
PubMed2006

Water diffusion heterogeneity index in the human brain is insensitive to the orientation of applied magnetic field gradients.

The alpha diffusion-weighted imaging (DWI) method was developed to study heterogeneous water diffusion in the human brain using magnetic resonance imaging (MRI). An advantage of this model is that it does not require an assumption about the shape of the intravoxel distribution of apparent diffusion rates, and it has a calculable relationship to this distribution. The alpha-DWI technique is useful for detecting microstructural tissue changes associated with brain tumor invasion, and may be useful for directing therapy to invading tumor cells. In previous work, alpha-DWI was performed with magnetic field gradients applied along a single direction in order to avoid artificially introducing a source of heterogeneity to the decay. However, it is known that restricted diffusion is anisotropic in the brain, and the alpha-DWI method must take this into account to be complete. In this work the relationship between the applied magnetic field gradients and the fitted stretched-exponential model parameters was studied in the human brain. It was found the distributed diffusion coefficient (DDC) varies with the direction of applied gradients, while the heterogeneity index alpha is relatively direction-insensitive. It is proposed that in clinical use, maps of alpha can be created using diffusion-weighting gradients applied in a single direction that reflect the tissue heterogeneity.

Algorithms↗
PubMed2006

Diffusion kernel-based logistic regression models for protein function prediction.

Assigning functions to unknown proteins is one of the most important problems in proteomics. Several approaches have used protein-protein interaction data to predict protein functions. We previously developed a Markov random field (MRF) based method to infer a protein's functions using protein-protein interaction data and the functional annotations of its protein interaction partners. In the original model, only direct interactions were considered and each function was considered separately. In this study, we develop a new model which extends direct interactions to all neighboring proteins, and one function to multiple functions. The goal is to understand a protein's function based on information on all the neighboring proteins in the interaction network. We first developed a novel kernel logistic regression (KLR) method based on diffusion kernels for protein interaction networks. The diffusion kernels provide means to incorporate all neighbors of proteins in the network. Second, we identified a set of functions that are highly correlated with the function of interest, referred to as the correlated functions, using the chi-square test. Third, the correlated functions were incorporated into our new KLR model. Fourth, we extended our model by incorporating multiple biological data sources such as protein domains, protein complexes, and gene expressions by converting them into networks. We showed that the KLR approach of incorporating all protein neighbors significantly improved the accuracy of protein function predictions over the MRF model. The incorporation of multiple data sets also improved prediction accuracy. The prediction accuracy is comparable to another protein function classifier based on the support vector machine (SVM), using a diffusion kernel. The advantages of the KLR model include its simplicity as well as its ability to explore the contribution of neighbors to the functions of proteins of interest.

Databases, Protein↗
PubMed1999

Accumulation of intracellular amyloid-beta peptide (A beta 1-40) in mucopolysaccharidosis brains.

To evaluate whether in vivo accumulations of heparan sulfate caused by inborn errors in the metabolism of glycosaminoglycans lead to the formation of neurofibrillary tangles and/or senile plaques, as seen in Alzheimer disease (AD), we studied postmortem brains from 9 patients, ages 1 to 42 years, with mucopolysaccharidosis (MPS). The brains of patients with Hurler's syndrome (MPS I: n = 5) and Sanfilippo's syndrome (MPS III; n = 4) as well as from caprine MPS IIID and murine MPS VII models were evaluated by thioflavine-S staining and by immunohistochemistry using antibodies directed against heparan sulfate proteoglycans, hyperphosphorylated tau, amyloid-beta peptide precursor proteins (APP), and amyloid-beta peptides (A beta [1-40], and A beta [1-42]). A two-site sandwich enzyme-linked immunosorbent assay (ELISA) was also utilized to compare levels of total soluble and insoluble A beta (1-40) and A beta (1-42) obtained from temporal cortex of MPS patients. Although no neurofibrillary tangles, senile plaques, or tau-positive lesions were detected in any of the MPS brains studied here, antibodies directed against A beta (1-40) intensely and diffusely stained the cytoplasm of cells throughout the brains of the MPS patients and the caprine MPS model. The ELISA assay also demonstrated a significant 3-fold increase in the level of soluble A beta (1-40) in the MPS brains compared with normal control brains. Thus, at least some of the metabolic defects that lead to accumulations of glycosaminoglycans in MPS also are associated with an increase in immunoreactive A beta (1-40) within the cytoplasmic compartment where they could contribute to the dysfunction and death of affected cells in these disorders, but not induce the formation of plaques and tangles. Models of MPS may enable mechanistic studies of the role A beta and glycosaminoglycans play in the amyloidosis that is a neuropathological feature of AD.

Adolescent↗
PubMed2006

Brownian diffusion and surface kinetics of liposome and viral particle uptake by human lung cancer cells in-vitro.

In this study, the simultaneous roles of transport, diffusion, and surface kinetic uptake of liposome (Lip-FD), adenoviral (AD-Cy2), and liposome-adenoviral complex (lip-FD-Ad) particles by a non-small cell human lung cancer (A549) were examined through a coupling of in vitro experimental and mathematical modeling techniques. Experimentally, quantitative fluorescence spectroscopy was used to monitor time dependent particle uptake rates including low temperature (5 degrees C) conditions where endocytosis could be inhibited. Mathematically, analytic solutions to the Brownian particle diffusion equation with Langmuir type boundary conditions for the adsoprtion, desorption, and endocytosis process, were obtained for both unsteady and steady-state (no endocytosis) conditions. By direct comparisons of experimental data to model solutions, the adsorption constants, desorption constants, and number of cell surface receptor sites were determined for all particle types considered. It was found that the particle adsorption and desorption constants were of the same order of magnitude compared to earlier studies (Singh, M., T. Ghose, G. Faulkner, and M. Mezei. Cancer Res. 49:3976-3984, 1990.) using different cell lines, particle types, and methodologies. Also in agreement with previous studies using differing cell lines and methodologies (Miller, C. R., B. Boundurant, S. D. McLeon, K. A. McGovern, and D. F. O'Brien. Biochemistry 37:12875-12883, 1998; Perry, D. G., and W. J. Martin II. J. Immunol. Methods 181:269-285, 1995; Muller, W. J., K. Zen, A. B. Fisher, and H. Shuman. Am. J. Physiol. L11-L19, 1995), the number of cell surface receptor sites was predicted to be several orders of magnitude higher for liposome and liposome-viral complex than for viral particles alone, suggesting a nonspecific or nonrestrictive binding pattern for liposomes and liposome complexes and a specific or restrictive binding pattern for viral particles. The surface kinetic constants obtained here for the A549 cells may be useful in physiological modeling or pharmacokinetic applications of chemical or genetic carrying particles in the treatment of lung cancer and other lung diseases. Furthermore, the methodologies given here are straightforward and can be applied to other particle-cell uptake systems.

Adenoviridae↗
PubMed2001

A mathematical model for chemoattractant gradient sensing based on receptor-regulated membrane phospholipid signaling dynamics.

The crawling movement of cells in response to a chemoattractant gradient is a complex process requiring the coordination of various subcellular activities. Although a complete description of the mechanisms underlying cell movement remains elusive, the very first step of directional sensing, enabling the cell to perceive the imposed gradient, is becoming more transparent. A fundamental problem of directional sensing is its exquisite sensitivity. Even in the presence of relatively shallow chemoattractant gradients, cell projections are extended precisely in the region exposed to the highest chemoattractant concentration. This reflects the existence of a mechanism for amplifying the external signal. Recent experiments have identified a potential candidate for the seat of this amplification-membrane phosphoinositides such as PI4,5P2 and PI3,4,5P3 appear to be the first components of the signal transduction pathway to be amplified. Perturbing the cell with various chemoattractant gradients reveals a rich spectrum of phosphoinositide dynamics (Parent, C. A., and P. N. Devreotes. Science 284:765, 1999). The goal of this work is to develop a mathematical model of these phosphoinositide dynamics. Specifically, we address the following questions: (a) Which signaling pathway could lead to the localized accumulation of membrane phosphoinositides? (b) Why is this accumulation independent of the slope and mean value of the chemoattractant gradient? The model is based on the phosphoinositide cycle that transfers phosphoinositides between the plasma membrane and endoplasmic reticulum. We show that a mathematical model taking due account of receptor desensitization and the reaction-diffusion processes of the phosphoinositide cycle captures many of the experimentally observed dynamics. Having shown the plausibility of the model with respect to directional sensing, we discuss its implications for lamellipod extension, the process that follows directional sensing.

Biomedical Engineering↗
PubMed1989

A simple add-on algorithm to extend one-dimensional finite difference diffusion calculations to include charge coupling.

The importance of interionic charge coupling in chemical and biological diffusion problems is discussed, and the Nernst-Planck (ionic) and Onsager-Fuoss (neutral component) methods are considered. A novel single pass charge-coupling algorithm 'Q-COUPLE' is proposed, which should be usable as a separate add-on subroutine with many one-dimensional finite difference diffusion calculations. Its mode of operation is explained with the help of elementary electrostatics and by reference to listings in BASIC. The algorithm is being applied in a finite difference model of diffusion-with-reaction in dental plaque, with 12 ions or ionizable molecules diffusing and interacting with fixed charges. It is shown to be invariant with respect to the direction of sweep, and in the simple case of coupled diffusion of a single polyvalent electrolyte is found to compare well with the analytical solution. Advantages and limitations of the proposal are discussed.

Algorithms↗
PubMed2004

Therapeutic efficacy of DTI-015 using diffusion magnetic resonance imaging as an early surrogate marker.

To investigate diffusion weighted magnetic resonance imaging as a quantitative surrogate marker for evaluating the therapy-induced cellular changes in an orthotopic experimental glioma model, tumors were treated with direct intratumoral administration of DTI-015, a solution of 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) in 100% EtOH. Intracerebral 9L tumors were induced in Fischer 344 rats, and three treatment groups were established: DTI-015, EtOH, and sham. Two groups of rats received intratumoral injection of either 67 mg/mL BCNU in EtOH or EtOH alone at 50% of the tumor volume up to a maximum of 30 mul under stereotactic guidance. Diffusion magnetic resonance images were acquired before treatment and after treatment at 1, 24, 48, and 72 hours and then 3 times per week thereafter. Tumor cell viability was examined using multislice diffusion weighted magnetic resonance imaging with diffusion weighted transverse magnetic resonance images and histogram plots of each tumor quantified over time. Control animals (EtOH- or sham-treated animals) showed mean apparent diffusion coefficients (ADCs) that remained essentially unchanged over the experimental time course. In contrast, rats treated with DTI-015 showed a significant increase in ADC relative to the pretreatment within 24 hours, which further increased over time, followed by a significant therapeutic response as evidenced by subsequent tumor volume shrinkage, development of a cystic region, and enhanced animal survival. Finally, not only were ADC measurements predictive of differences between treatment groups, but they also yielded spatial and temporal data regarding the efficacy of treatment within individual treated animals that could be used to guide subsequent therapy.

Animals↗
PubMed1999

Multi-component apparent diffusion coefficients in human brain.

The signal decay with increasing b-factor at fixed echo time from brain tissue in vivo has been measured using a line scan Stejskal-Tanner spin echo diffusion approach in eight healthy adult volunteers. The use of a 175 ms echo time and maximum gradient strengths of 10 mT/m allowed 64 b-factors to be sampled, ranging from 5 to 6000 s/ mm2, a maximum some three times larger than that typically used for diffusion imaging. The signal decay with b-factor over this extended range showed a decidedly non-exponential behavior well-suited to biexponential modeling. Statistical analyses of the fitted biexponential parameters from over 125 brain voxels (15 x 15 x 1 mm3 volume) per volunteer yielded a mean volume fraction of 0.74 which decayed with a typical apparent diffusion coefficient around 1.4 microm2/ms. The remaining fraction had an apparent diffusion coefficient of approximately 0.25 microm2/ms. Simple models which might explain the non-exponential behavior, such as intra- and extracellular water compartmentation with slow exchange, appear inadequate for a complete description. For typical diffusion imaging with b-factors below 2000 s/mm2, the standard model of monoexponential signal decay with b-factor, apparent diffusion coefficient values around 0.7 microm2/ms, and a sensitivity to diffusion gradient direction may appear appropriate. Over a more extended but readily accessible b-factor range, however, the complexity of brain signal decay with b-factor increases, offering a greater parametrization of the water diffusion process for tissue characterization.

Adult↗
PubMed1987

Standardless EDS analysis of bulk and thin specimens.

A direct relationship between the x-ray intensity ratio and the concentration ratio for bulk and thin specimens has been established by use of a revised full-diffusion model of electron scattering. The suitable ionization cross section, the most important parameter influencing the accuracy of the calculated Cliff-Lorimer factors, has been found after comparing the experimental intensity ratio I(L)/I(K) of eight elements (from Ge to Sn) and I(M)/I(L) of six elements (from Sm to Bi) with the calculated values. The quantitative standardless EDS analysis of bulk samples obtained by this direct method is more satisfactory than the commercial indirect method which gives the composition through ZAF correction after calculating the intensity factors of pure elements. The quantitative standardless analysis of thin samples has been improved by the suitable cross section significantly. This method has been applied to the analysis of film on substrate either without any common element or with one common element (P-Si glass film on Si). It has also been used to calculate the intensity factors of pure bulk samples and the backscattering correction factor in Auger electron spectroscopy.

Electron Probe Microanalysis↗