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At least 361 records · Page 20Linked to original sources
PubMed1990

A modified algorithm of the single pool urea kinetic model.

Urea Kt/V, calculated according to the variable volume single pool urea kinetic model (UKM), has been accepted as the yardstick reflecting the adequacy of haemodialysis therapy. However, the classical algorithm of UKM requires great care in dialyser urea clearance (K) measurement in order to avoid major inaccuracies in estimating the urea distribution volume (V). Thus, we suggest a modified algorithm of UKM which avoids the measurement of K. It assumes an arbitrary V value and then calculates kinetically K as a function of the assumed V value. The rationale of the modified algorithm can be derived from the knowledge that the classical algorithm imposes a proportionality ration between K and V: given a particular set of data, a change in the attributed value of K leads to a proportional change in the calculated V value, so that the ratio K/V remains nearly constant. Aims of the study were (1) to validate the modified algorithm by comparing the resulting Kt/V and normalised protein catabolic rate (NPCR) values with the homologous ones obtained using the classical algorithm in a group of 33 patients on thrice-weekly haemodialysis; plasma water urea concentrations were used with the classical algorithm (CApw) and the modified algorithm (MApw); and (2) to verify the possibility of using plasma urea concentrations with the modified algorithm (MAp) instead of the more rigorous plasma water concentrations. NPCR (g/kg per day) was 1.33 +/- 0.05 in CApw, 1.29 +/- 0.05 in MApw and 1.28 +/- 0.04 in MAp. Kt/V was 1.27 +/- 0.03 in CApw, 1.25 +/- 0.03 in MApw and 1.26 +/- 0.03 in MAp.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1999

Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic.

Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.

Bacterial Proteins↗
PubMed1994

Kinetic modeling of exciton migration in photosynthetic systems. 2. Simulations of excitation dynamics in two-dimensional photosystem I core antenna/reaction center complexes.

Kinetic modeling of the exciton migration in the cyanobacterial photosystem I core complex from Synechococcus sp. was performed by an exact solution of the Pauli master equation for exciton motion. A square two-dimensional 10 x 10 pigment lattice and a Förster dipole-dipole coupling between chromophores was assumed. We calculated decay-associated spectra and lifetimes and compared them to the corresponding experimental data from picosecond fluorescence and transient absorption obtained by global analysis. Seven spectral chlorophyll(Chl) forms, identical in shape but shifted in their absorption maximums, were used to describe the non-homogeneous broadening of the PS I-100 particle absorption spectrum. The optimized Chl lattice arrangement best reproducing the experimental decay-associated spectra as well as the steady-state fluorescence spectrum indicated the long-wavelength-absorbing Chls forming a cluster in the corner of the lattice with the reaction center (RC) placed apart at a distance of two lattice constants. The variable parameters, i.e., the charge separation rate in the RC and the lattice constant a, were found to be optimal at kRC = 2.3 ps-1 and a = 1.14 nm, respectively. The surprising conclusions of the simulations is that Chls with absorption maxima as long a 724 nm have to be taken into account to describe the time-resolved spectra of this PS I particle properly. The dependencies of the exciton decay in the model PS I particle on the excitation wavelength and on the temperature are discussed. We also show that the excited state decay of similar PS I particles that lack the long-wavelength absorbing Chls is nearly mono-exponential. Various critical factors that limit the general reliability of the conclusions of such simulations are discussed in detail.

Biophysical Phenomena↗
PubMed2006

Assessment of formal and low structured kinetic modeling of polyhydroxyalkanoate synthesis from complex substrates.

A formal kinetic mathematical model for poly-(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) [P(3HB-co-3HV-co-4HB)] terpolyester synthesis from glucose and galactose derived from whey permeate supplemented with gamma-butyrolactone by the archaeon Haloferax mediterranei was created. Further, a low structured mathematical model for poly-3-hydroxybutyrate synthesis from whey permeate by Pseudomonas hydrogenovora was developed. In both cases, biosyntheses for obtaining the experimental data used for compiling the models were performed via fed-batch cultivations. The model developed for H. mediterranei consists of 10 differential and 11 algebraic equations, including 27 kinetic constants. The model compiled for P. hydrogenovora encompasses 10 differential and 3 algebraic equations, including 36 kinetic constants. Both models were solved by Runge-Kuta variable step numerical integration with Monte Carlo parameter optimization procedure. Difficulties arising from the modeling of redirection of metabolic fluxes from biomass growth toward polyhydroxyalkanoate synthesis and byproducts are discussed.

Computer Simulation↗
PubMed1992

A kinetic model of CD4+ lymphocytes with the human immunodeficiency virus (HIV).

This report describes a kinetic model of in vitro cytopathology involving interactions of human immunodeficiency virus (HIV) with CD4+ helper T lymphocytes. The model uses nonlinearly coupled, ordinary differential equations to simulate the dynamics of infected and uninfected cells and free virions. It is assumed that resting cells are more readily infected than activated cells, but once infected, only activated cells produce more virus. Resting cells can be activated by some appropriate stimulus (e.g. phytohemagglutinin, soluble antigen). The model predicts that the initial inoculum of virus is taken up by resting cells and without stimulation the system comes to a steady state of two populations, namely infected and uninfected cells. Stimulation of this system produces two additional populations, namely infected and uninfected activated cells which, along with the previous populations, exhibit cyclic behavior of growth, viral expression/release, and death. Additional stimuli enhance or diminish the cyclic behavior depending upon their occurrence in time. These simulations suggest a similar dynamics in human HIV infection and may explain a major factor responsible for the widely varying depletion rate of (CD4+) helper T cells in AIDS patients.

CD4-Positive T-Lymphocytes↗
PubMed2005

Toward a kinetic model for acrylamide formation in a glucose-asparagine reaction system.

A kinetic model for the formation of acrylamide in a glucose-asparagine reaction system is pro-posed. Equimolar solutions (0.2 M) of glucose and asparagine were heated at different temperatures (120-200 degrees C) at pH 6.8. Besides the reactants, acrylamide, fructose, and melanoidins were quantified after predetermined heating times (0-45 min). Multiresponse modeling by use of nonlinear regression with the determinant criterion was used to estimate model parameters. The proposed model resulted in a reasonable estimation for the formation of acrylamide in an aqueous model system, although the behavior of glucose, fructose, and asparagine was slightly underestimated. The formation of acrylamide reached its maximum when the concentration of sugars was reduced to about 0. This supported previous research, showing that a carbonyl source is needed for the formation of acrylamide from asparagine. Furthermore, it is observed that acrylamide is an intermediate of the Maillard reaction rather than an end product, which implies that it is also subject to a degradation reaction.

Acrylamide↗
PubMed1992

Reaction kinetic model of a proposed plasma membrane two-cycle H(+)-transport system of Chara corallina.

Biophysical and numerical analysis methods were used to characterize and model the transport protein that gives rise to the acid and alkaline regions of Chara. A measuring system that permits the detection of area-specific current-voltage curves was used. These current-voltage curves, obtained from the inward current regions of Chara, underwent a parallel shift when the alkaline region was inverted by means of an acid pH treatment. In this situation the reversal potential of this area shifted from -120 mV to -340 mV. Together with data obtained from experiments using a divided chamber system, these results suggest that a common transport protein generates inward and outward current regions of Chara. On the basis of these experimental findings, a reaction kinetic model is proposed that assigns two operational modes to the proposed transport protein. Switching between these modes generates either acid or alkaline behavior. Since the observed pH dependence of the postulated transporter is rather complex, a reaction kinetic saturation mechanism had to be incorporated into the model. This final 10-state reaction kinetic model provides an appropriate set of mathematical relations to fit the measured current-voltage curves by computer.

Carrier Proteins↗
PubMed2001

Relaxation in kinetic models on alternating linear chains.

A restricted dynamics, previously introduced in a kinetic model for relaxation phenomena in linear polymer chains, is used to study the dynamic critical exponent of one-dimensional Ising models. Both an alternating isotopic chain and an alternating-bond chain are considered. In contrast with what occurs for Glauber dynamics, in these two models the dynamic critical exponent turns out to be the same. The alternating isotopic chain with the restricted dynamics is shown to lead to Nagel scaling for temperatures above some critical value. Further support is given relating the Nagel scaling to the existence of multiple (simultaneous) relaxation processes, the dynamics apparently not playing the most important role in determining such scaling.

Journal Article↗
PubMed1984

Kinetic model for isometric contraction in smooth muscle on the basis of myosin phosphorylation hypothesis.

A kinetic model was proposed to simulate an isometric contraction curve in smooth muscle on the basis of the myosin phosphorylation hypothesis. The Ca2+-calmodulin-dependent activation of myosin light-chain kinase and the phosphorylation-dephosphorylation reaction of myosin were mathematically treated. Solving the kinetic equations at a steady state, we could calculate the relationship between the Ca2+ concentration and the myosin phosphorylation. Assuming that two-head-phosphorylated myosin has an actin-activated Mg2+-ATPase activity and that this state corresponds to an active state, we computed the time courses of the myosin phosphorylation and the active state for various Ca2+ transients. The time course of the active state was converted into that of isometric tension by use of Sandow's model composed of a contractile element and a series elastic component. The model could simulate not only the isometric contraction curves for any given Ca2+ transient but also the following experimental results: the calmodulin-dependent shift of the Ca2+ sensitivity of isometric tension observed in skinned muscle fibers, the disagreement between the Ca2+ sensitivity of myosin phosphorylation and that of isometric tension at a steady state, and the disagreement between the time course of myosin phosphorylation and that of isometric tension development.

Animals↗
PubMed2004

Reduced kinetic models of facilitative transport.

In spite of the highly complex structural dynamics of globular proteins, the processes mediated by them can usually be described in terms of relatively simple kinetic diagrams. How do complex proteins, characterized by undergoing transitions among a possibly very large number of intermediate states, exhibit functional properties that can be interpreted in terms of kinetic diagrams consisting of only a small number of states? One possible way of explaining this apparent contradiction is that, under some conditions, a reduction of the actual complete kinetic diagram that describes all of the macromolecular states and transitions takes place. In this work, we contribute with a formal basis to this interpretation, by generalizing the procedure of diagram reduction to the case of multicyclic kinetic diagrams. As an example, we apply the procedure to a complex kinetic model of facilitative transport. We develop Monte Carlo simulations to obtain the kinetic parameters of the complex model and we compare them with the ones analytically obtained from the reduced model. We confirm that, under some conditions, the kinetic behavior of the complex transporter is indistinguishable from the one of a four-state simple carrier model, derived from the former by diagram reduction. Besides introducing some novel methodological aspects, this work further contributes to the idea that, under many physiological and experimental conditions, a reduction occurs of the complete kinetic diagram that describes the dynamics of a globular protein.

Carrier Proteins↗
PubMed1995

[Kinetic model of micro-organism growth: the case of Xanthomonas campestris].

Microbial growth is studied and kinetic models to describe the process rate useful in the scale-up are proposed. The growth of Xanthomonas campestris NRRL B-1459, a bacterium producing xanthan, a major industrial gum, is studied. Experimental data are arranged by means of different methods, and linear and non-linear regression techniques are applied in several ways (i.e. fixing or not fixing the values of certain parameters) and they are compared. To obtain parameter values with statistical meaning, two parameters must be calculated (namely, the maximum specific growth rate and the maximum biomass concentration available) by means of a non-linear regression technique employing the logistic equation. The maximum specific growth rate is related to temperature by means of different equations, but that of Ratkowsky et al. is the most suitable for X. campestris growth. Studied variables present no tendency to error and the reproduction of experimental data is very good.

Bacteriological Techniques↗
PubMed1990

Kinetic modelling and continuous on-line blood volume measurement during dialysis therapy.

Changes of relative blood volume during haemodialysis therapy have been investigated using kinetic modelling and on-line blood volume registration by continuous haemoglobinometry. An exponential relation has been found between blood volume reduction per litre of ultrafiltrate and the amount of fluid overload. Between the amount of refilling and ultrafiltration rate there was also an exponential dependence. There was a linear relation between the change in plasma sodium concentration and blood volume. An acceptable correspondence was found between calculated and measured data.

Blood Volume↗
PubMed2001

Kinetic model of ionization waves in a positive column at intermediate pressures in inert gases.

A kinetic model of ionization waves in the inert gas discharge is constructed, which is based on the simultaneous solution of the kinetic equation for electrons and the continuity equations for ions and excited atoms. The model corresponds to a range of intermediate pressures and small currents, when elastic collisions dominate in the electron energy balance and electron-electron collisions are negligibly small. A linear theory of ionization waves is constructed, growth rates and frequencies of wave disturbances able to propagate in plasma are found. It is shown that there is an upper bound to the existence of striations by pressure, as well as the lower bound by current. The self-consistent solution of the source system of equations is obtained, which describes a nonlinear wave. The profile of electric field and the electron distribution function in this field are calculated. The results of calculations are compared with the experimental data. The wavelengths obtained are essentially larger than the electron energy relaxation length. Such waves cannot be described within the limits of fluid models.

Journal Article↗
PubMed1993

Application of kinetic models to estimate transit time through cell cycle compartments.

Models of the carcinogenesis process emphasize the importance of understanding cell cycle-specific effects of a chemical exposure. Development of mathematical models describing the kinetics of individual cell movements within the growth cycle are applied to a cultured cell system. Treatment with 100 micrograms/ml trichloroacetic acid is shown to retard transit through the synthesis phase of the cycle. The models are compared with standard relative movement calculations and are found to be more sensitive. In addition, the DNA compartments are modeled over time to detect possible development of aneuploidy during treatment.

Animals↗
PubMed2002

Mucin core O-glycosylation is modulated by neighboring residue glycosylation status. Kinetic modeling of the site-specific glycosylation of the apo-porcine submaxillary mucin tandem repeat by UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases T1 and T2.

The influence of peptide sequence and environment on the initiation and elongation of mucin O-glycosylation is not well understood. The in vivo glycosylation pattern of the porcine submaxillary gland mucin (PSM) tandem repeat containing 31 O-glycosylation sites (Gerken, T. A., Gilmore, M., and Zhang, J. (2002) J. Biol. Chem. 277, 7736-7751) reveals a weak inverse correlation with hydroxyamino acid density (and by inference the density of glycosylation) with the extent of GalNAc glycosylation and core-1 substitution. We now report the time course of the in vitro glycosylation of the apoPSM tandem repeat by recombinant UDP-GalNAc:polypeptide alpha-GalNAc transferases (ppGalNAc transferase) T1 and T2 that confirm these findings. A wide range of glycosylation rates are found, with several residues showing apparent plateaus in glycosylation. An adjustable kinetic model that reduces the first-order rate constants proportional to neighboring glycosylation status, plus or minus three residues of the site of glycosylation, was found to reasonably reproduce the experimental rate data for both transferases, including apparent plateaus in glycosylation. The unique, transferase-specific, positional weighting constants reveal information on the peptide/glycopeptide recognition site for each transferase. Both transferases displayed high sensitivities to neighboring Ser/Thr glycosylation, whereas ppGalNAc T2 displayed additional high sensitivities to the presence of nonglycosylated Ser/Thr residues. This is the first demonstration of the ability to model mucin O-glycosylation kinetics, confirming that under the appropriate conditions neighboring glycosylation status can be a significant factor modulating the first step of mucin O-glycan biosynthesis.

Amino Acid Sequence↗
PubMed1999

Oscillatory behavior of a simple kinetic model for proteolysis during cell invasion.

Extracellular proteolysis during cell invasion is thought to be tightly organized, both temporally and spatially. This work presents a simple kinetic model that describes the interactions between extracellular matrix (ECM) proteins, proteinases, proteolytic fragments, and integrins. Nonmonotonous behavior arises from enzyme de novo synthesis consecutive to integrin binding to fragments or entire proteins. The model has been simulated using realistic values for kinetic constants and protein concentrations, with fibronectin as the ECM protein. The simulations show damped oscillations of integrin-complex concentrations, indicating alternation of maximal adhesion periods with maximal mobility periods. Comparisons with experimental data from the literature confirm the similarity between this system behavior and cell invasion. The influences on the system of cryptic functions of ECM proteins, proteinase inhibitors, and soluble antiadhesive peptides were examined. The first critical parameter for oscillation is the discrepancy between integrin affinity for intact ECM proteins and the respective proteolytic fragments, thus emphasizing the importance of cryptic functions of ECM proteins in cell invasion. Another critical parameter is the ratio between proteinase and the initial ECM protein concentration. These results suggest new insights into the organization of the ECM degradation during cell invasion.

Activity Cycles↗
PubMedDate not supplied

[Simple kinetic models explaining critical phenomena in enzymatic reactions with isomerization of the enzyme and substrate].

Kinetic models for enzyme reactions are considered which take into account enzyme and substrate isomerization. Application of graph-theoretic methods allows to reveal fragments in schemes which may induce multiple stead-states or concentrational selfoscillations. The role of substrate isomers in the inhibition of enzyme isomers to produce critical phenomena is considered. The boundaries of parameter domains for critical phenomena are estimated. It is shown that the controlled change in concentrations of substrate and enzyme isomers may be important in regulation of enzyme systems, if different enzyme isomers are inhibited mainly by different substrate isomers. The models are used for interpretation of possible critical phenomena in the open reaction catalyzed by lactate dehydrogenase. It is shown that lactate dehydrogenase may act as a trigger in carbohydrate metabolism by changing "critically" its activity in relation to changes in pH and pyruvate fluxes. Slow enzyme inhibition by enolpyruvate is suggested as a possible reason for glycolytic oscillations.

Enzymes↗
PubMed1999

Kinetic modeling of oligosaccharide synthesis catalyzed by leuconostoc mesenteroides NRRL B-1299 dextransucrase

The kinetic behavior of soluble and insoluble forms of dextransucrase from Leuconostoc mesenteroides NRRL B-1299 was investigated with sucrose as substrate and maltose as acceptor. To study the parameters involved, a kinetic model was applied that was previously developed for L. mesenteroides NRRL B-512F dextransucrase. There are significant correlations between the parameters of the soluble form of B-1299 dextransucrase and those calculated for the B-512F enzyme; that is, their properties are comparable and differ from those of the insoluble form of B-1299 dextransucrase. Whereas the calculated parameters for high maltose concentrations describe the kinetic behavior very well, the time curves for low maltose concentrations were not described correctly. Therefore, the parameters were calculated separately for the two ranges. Copyright 1999 John Wiley & Sons, Inc.

Journal Article↗