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At least 217 records · Page 12Linked to original sources
PubMed1998

Neurodegeneration induced by reversed microdialysis of NMDA; a quantitative model for excitotoxicity in vivo.

This study characterizes a quantifiable in vivo model of excitotoxicity. In halothane anesthetized rats, microdialysis probe was implanted into somatosensory cortex/striatum and perfused by various concentrations (1, 10, 50 and 100 mmol/l) of N-methyl-d-aspartate (NMDA) for 20 min. After 24 h, histological quantification confirmed that NMDA produced a concentration-dependent excitotoxic lesion. With 10 mmol/l NMDA, coadministration of magnesium reduced significantly, and 2-amino-5-phosphonovalerate blocked completely the development of excitotoxic injury.

2-Amino-5-phosphonovalerate↗
PubMed1998

Quantitative model for the cooperative interaction of the bacteriorhodopsin molecules in purple membranes.

The trimeric, asymmetric and sequential model for the cooperative interaction of the bacteriorhodopsin molecules in purple membranes [Zs. Tokaji, Biophys. J. 65 (1993) 1130-11341 is being extended in the paper. Analyses of data from absorption kinetic measurements with preexcitation and green background illumination, and photoselection measurements on oriented samples confirm the main features of this cooperative interaction and support the validity of the extended model. This model includes the observed heterogeneity of the non-excited state of the bacteriorhodopsin molecules in purple membranes, and the agreement with the data suggests that molecules in any other state than the bacteriorhodopsin ground state can alter the photocycle of their neighbors. The presented results seem to contradict other models for the cooperation of the bacteriorhodopsin molecules.

Bacteriorhodopsins↗
PubMed1991

A quantitative model suggests immune memory involves the colocalization of B and Th cells.

A prominent and essential feature of the humoral immune response of vertebrates is immunologic memory: the ability to recall previous exposure to antigen. We present a mathematical model of the growth and interactions of the major cell populations involved in the humoral immune response. Our analysis of this model predicts that the formation of a dynamic association between small numbers of antigen-specific B and Th cells, "colocalization", is sufficient to account for memory and the kinetics of the secondary response--neither specifically differentiated Th or B memory cells nor networks of antigen and anti-idiotypes are required. The colocalization hypothesis explains a number of existing experimental observations and can be tested by straightforward experiments which we describe.

Animals↗
PubMed2003

Quantitative model of small molecules uptake after in vitro cell electropermeabilization.

Electropermeabilization of the cell membrane is a phenomenon caused by exposure of the cell to electric pulses. Permeabilization depends on pulse duration, pulse amplitude, the number of pulses delivered, and also on other experimental conditions. With these parameters properly chosen, the process of permeabilization is reversible and cells return to their normal physiological state. This article describes the development of a model of diffusion-driven transmembrane transport of small molecules caused by electropermeabilization. The process of permeabilization is divided into a short permeabilizing phase that takes place during the pulse, and a longer resealing phase that begins after the end of the pulse. Because both phases of permeabilization are important for uptake of molecules into cells, most of the effort is focused on the optimization of parameters that influence the flow between intracellular and extracellular space. The model describes well the transmembrane transport caused by electropermeabilization, allowing to study the uptake of molecules as a function of elapsed time, voltage and pulse duration. In addition, our results show that the shapes of the curves of cell permeabilization and survival as functions of pulse amplitude can to a large extent be explained by cell size distribution.

Animals↗
PubMed1980

Quantitative modelling and prediction of development times of the free-living stages of Ostertagia ostertagi under controlled and field conditions.

The development of the free-living stages of Ostertagia ostertagi incubated at constant temperatures from 5 to 27 degrees C and in dung pats in the field was observed. The death rates were adequately described by a single exponential functional and the distribution of times for development by a delayed gamma density function. The times of appearance of selected development stages such as maximum numbers of embryonated eggs and half the maximum number of infective larvae, were highly dependent on temperature. The relationships between these times and temperature were adequately described by the Arrhenius equation. The parameters of this equation and mean hourly temperature recorded in dung pats in the field were used to predict development times in the field. A comparison of predicted and observed times showed that an initial delay accounted for a large proportion of the time required for development in dung pats, particularly the embryonation of eggs. This delay was attributed to lack of aeration associated with high moisture content of the dung pat.

Animals↗
PubMed1991

Spontaneous phospholipid transfer: development of a quantitative model.

The effects of lipid structure on the kinetics of spontaneous transfer of a series of phosphatidylcholines have been determined. Donors, which were model-reassembled high-density lipoproteins composed of apo A-I, 1-palmitoyl-2-oleoylphosphatidylcholine, and a trace of a radiolabeled lipid, were mixed with acceptors, which were human low-density lipoproteins. Within a series of phosphatidylcholines, the addition of double bonds and methylene units, respectively, increased and decreased the rate of transfer in a predictable way. An equation that predicts the rates of transfer of a large number of diacylglycerides and phosphoglycerides from any lipoprotein has been empirically derived from these data. The transfers of phosphatidylcholines that contain superpolyunsaturated fatty acids (four or more double bonds) do not obey the derived equation, probably due to limitations on the number of conformational degrees of freedom in these lipids. The range of measured transfer halftimes extends from less than 2 h to more than 12 days. Thus, the spontaneous transfer halftimes of some (but not all) lipids are short compared to the lifetime of lipoproteins in plasma. These results suggest that some lipids transfer among lipoproteins and cells via a spontaneous mechanism while others require specific transfer factors or hydrolysis to achieve this within a physiologically significant time frame.

Energy Transfer↗
PubMedDate not supplied

Quantitative model for Gal4p-mediated expression of the galactose/melibiose regulon in Saccharomyces cerevisiae.

A mathematical model based on equilibrium binding between Gal4p and its specific DNA binding site has been developed. A model for GAL gene expression solely due to cooperativity, as a function of Gal4p concentration, has been developed for a gal80 mutant. The above model was extended to include other known regulatory molecules, namely Gal80p and Gal3p. Parameters determined from the above simulation were then used to represent a physiological status of gene expression in response to glucose (in terms of Gal4p concentration) and galactose in a wild-type strain. We demonstrate that in a wild-type strain glucose repression is more stringent due to cooperativity and autogenous regulation, while the induction response to galactose is only through autogenous regulation. The biological significance of autogenous regulation in Saccharomyces cerevisiae is discussed vis-a-vis the lactose operon of Escherichia coli.

DNA-Binding Proteins↗
PubMed1998

Quantitative Model Studies on the Effectiveness of Different Precursor Systems in the Formation of the Intense Food Odorants 2-Furfurylthiol and 2-Methyl-3-furanthiol.

The yields of the two intense food odorants 2-furfurylthiol (FFT) and 2-methyl-3-furanthiol (MFT) obtained by heating mixtures of possible precursors in model systems varying in temperature, pH value, or water content were determined by using stable isotope dilution assays. Although pentoses generated much higher amounts of FFT and MFT than hexoses when heated in the presence of cysteine, glucose and rhamnose also gave significant yields. Studies on several intermediates indicated the highest yields for MFT (1.4 mol %) when hydroxyacetaldehyde and mercapto-2-propanone were reacted for 6 min at 180 degrees C in the absence of water. Both intermediates also generated significant amounts of FFT (0.05 mol %). However, the system furan-2-aldehyde/H(2)S showed a 10 times higher efficiency in generating FFT. Thiamin and norfuraneol/cysteine were less effective precursors of MFT. The results imply that different formation pathways may run in parallel during food processing and may account for the different amounts of the two odorants present in the respective food.

Journal Article↗
PubMed1983

Structure-activity correlations for a series of antiallergy agents. 3. Development of a quantitative model.

A nonlinear regression model has been employed to investigate the activity of a series of 51 drugs in the rat passive cutaneous anaphylaxis assay. Although several classes of molecules are represented in the sample, there are certain common structural features that enable detailed geometric and electronic comparisons to be made. Ab initio Hartree-Fock SCF calculations were performed by using the molecular fragment approach to characterize the electronic structure and preferred conformations of the molecules. The statistical results establish the importance of nine structural factors in determining the potency as inhibitors of histamine release. Both the conformation of a drug and its capacity to act effectively as an electron acceptor in charge-transfer interactions are shown to be critical for high activity.

Animals↗
PubMed2006

Quantitative model of electrochemical Ostwald ripening and its application to the time-dependent electrode potential of nanocrystalline metals.

The contact of a metastable nanocrystalline metal ensemble with a metal ion electrolyte leads to an electrochemical Ostwald ripening. The kinetics is modeled on the level of irreversible thermodynamics for the case that the rate is controlled by the electrode/electrolyte transfer resistance. In particular, the kinetic behavior of medium-sized particles and the time dependence of the electromotive force is investigated. Even though it is expressed in electrochemical terms (mixed potential), the modeling is also applicable to chemical Ostwald ripening as long as it is interfacially controlled. Under these conditions, the kinetics exhibits, even though not self-accelerating, strong similarities to selection dynamics, with the competition stemming from the cannibalistic nature of the process.

Journal Article↗
PubMed2002

Quantitative modelling of crude oil toxicity using the approach of cybernetics and structured mechanisms of microbial processes.

Cybernetics and structured approach to biochemical processes in microbial cells offer the status of using various cell components of Azotobacter as molecular markers in toxicity assay of environmental toxicants. The intra-linked dynamic physicochemical reactions of the basic macromolecules--DNA, protein and membrane lipids--with respect to the crude oil in the growth environment, results in an 'impulse transfer function'. The structured effects are reduction in both DNA and protein levels, and an elevated level of lipid peroxidation products. Toxicity index (Ti) of the crude oil, at a given concentration, is the percent ratio of the summation of the products of these effect parameters' and their respective weightings, relative to control. The EC50 is the effective percent (w/v) concentration of the crude oil at which a toxicity index of 50% was recorded, and this corresponded with about 44% loss in nitrogen fixation of the diazotrophic bacterium.

Azotobacter↗
PubMed2002

Electrokinetic control of a chemical reaction in a lab-on-a-chip micro-reactor: measurement and quantitative modelling.

We have investigated the complex formation/dissociation reaction between Ni(2+) ions and the ligand pyridine-2-azo-p-dimethylaniline (PADA) in a glass micro-reactor operating under electrokinetic control. An in situ, microscope-imaging technique was used to determine the spatial and temporal evolution of the reaction within the channel network of the micro-reactor. Using appropriately controlled voltage sequences, a 'slug' of PADA was injected into a stream of Ni(2+) solution. Under the experimental reaction conditions used, Ni(2+) ions are mixed with the PADA as a consequence of the species' different electrokinetic mobilities allowing the complex formation to occur at the trailing edge of the PADA slug. Following complex formation, reversal of the flow results in the partial re-formation of free PADA by dissociation of the complex, demonstrating that voltage control can be used to drive the reaction either forwards or backwards. We discuss the methods whereby all the parameters required to predict the spatial and temporal evolution of the reaction in the micro-reactor can be either measured or estimated. Based on the estimated parameters, model calculations of the concentration profiles as a function of time show good agreement with the measured data.

Journal Article↗
PubMed2004

Expression of GAL genes in a mutant strain of Saccharomyces cerevisiae lacking GAL80: quantitative model and experimental verification.

The regulatory network of GAL genes is a model system for the production of foreign proteins. A mathematical model based on steady state was developed for the expression of GAL (galactosidase) genes in a mutant strain of Saccharomyces cerevisiae lacking GAL80. The transcriptional and translational responses of the GAL switch were predicted at various steady-state glucose concentrations. The model predicted ultrasensitive transcriptional response with a Hill coefficient ( h ) of 1.9 and 3.2 for genes with one and two binding sites respectively. Further, a lesser degree of ultrasensitivity was predicted for translational response with an h value of 1.3 for genes with one binding site and 2.1 for genes with two binding sites. The ultrasensitivity was due to dimerization of regulatory protein Gal4p and co-operative binding of Gal4p to DNA. The steady-state predictions were experimentally verified through measurements of alpha-galactosidase (for one binding site) and beta-galactosidase (for two binding sites). The steady state model was further extended to represent the dynamic expression profile and the same was verified experimentally. The growth phase and the synthesis of foreign protein could be distinctly separated using a mutant strain of Saccharomyces cerevisiae (baker's yeast).

Binding Sites↗
PubMed2003

A quantitative model of the generation of N(epsilon)-(carboxymethyl)lysine in the Maillard reaction between collagen and glucose.

The Maillard reaction between reducing sugars and amino groups of biomolecules generates complex structures known as AGEs (advanced glycation endproducts). These have been linked to protein modifications found during aging, diabetes and various amyloidoses. To investigate the contribution of alternative routes to the formation of AGEs, we developed a mathematical model that describes the generation of CML [ N(epsilon)-(carboxymethyl)lysine] in the Maillard reaction between glucose and collagen. Parameter values were obtained by fitting published data from kinetic experiments of Amadori compound decomposition and glycoxidation of collagen by glucose. These raw parameter values were subsequently fine-tuned with adjustment factors that were deduced from dynamic experiments taking into account the glucose and phosphate buffer concentrations. The fine-tuned model was used to assess the relative contributions of the reaction between glyoxal and lysine, the Namiki pathway, and Amadori compound degradation to the generation of CML. The model suggests that the glyoxal route dominates, except at low phosphate and high glucose concentrations. The contribution of Amadori oxidation is generally the least significant at low glucose concentrations. Simulations of the inhibition of CML generation by aminoguanidine show that this compound effectively blocks the glyoxal route at low glucose concentrations (5 mM). Model results are compared with literature estimates of the contributions to CML generation by the three pathways. The significance of the dominance of the glyoxal route is discussed in the context of possible natural defensive mechanisms and pharmacological interventions with the goal of inhibiting the Maillard reaction in vivo.

Collagen↗
PubMed2000

A quantitative model for differential motility of gliomas in grey and white matter.

We have extended a mathematical model of gliomas based on proliferation and diffusion rates to incorporate the effects of augmented cell motility in white matter as compared to grey matter. Using a detailed mapping of the white and grey matter in the brain developed for a MRI simulator, we have been able to simulate model tumours on an anatomically accurate brain domain. Our simulations show good agreement with clinically observed tumour geometries and suggest paths of submicroscopic tumour invasion not detectable on CT or MRI images. We expect this model to give insight into microscopic and submicroscopic invasion of the human brain by glioma cells. This method gives insight in microscopic and submicroscopic invasion of the human brain by glioma cells. Additionally, the model can be useful in defining expected pathways of invasion by glioma cells and thereby identify regions of the brain on which to focus treatments.

Brain Neoplasms↗