A von Willebrand factor-derived heparin-binding peptide regulates cell--substrate adhesive strength and chemokinesis behavior

The ability of a soluble heparin-binding oligopeptide sequence derived from the von Willebrand factor (vWF) to modulate the adhesion and chemokinetic migration behavior of arterial smooth muscle cells was assessed using a novel glass microsphere centrifugation assay and automated time-lapse fluorescence videomicroscopy, respectively. Treatment of cells grown on fibronectin-coated substrates with the heparin-binding peptide resulted in the disassembly of focal adhesions, as assessed by immunohistochemical staining. These observations were consistent with six-fold decrease in cell--substrate adhesive strength (P<0.001), a biphasic effect on migration speed (P<0.05), as well as a dose-dependent reduction in the percentage of motile cells and the cell dispersion coefficient (mu=S(2)T/2). The specificity of this response to the vWF-derived heparin-binding peptide was supported by the absence of an observed effect in the presence of either a scrambled peptide or a consensus heparin-binding peptide sequence of similar heparin affinity. These data support the notion that competitive interactions between cell surface heparan sulfates with heparin-binding peptide domains located in soluble peptide fragments may modulate chemokinetic cell migration behavior and other adhesion-related processes.     

Swimming behavior regulation by GABAB receptors in Paramecium

In Paramecium, internal Ca(2+) concentration increase coupled to membrane depolarization induces a reversal in the direction of ciliary beating and, consequently, a reversal in swimming direction. The ciliary reversal (CR) duration is correlated to Ca(2+) influx, and the addition of drugs that block the Ca(2+) current leads to a reduction in the backward swimming duration. In this study we have examined the possible function of GABA(B) receptors in P. primaurelia swimming control. The presence of GABA(B) immunoanalogue in Paramecium was evidenced using SDS-PAGE, Western blotting, and confocal laser scanning microscopy. By applying the specific GABA(B) receptor agonist baclofen, a dose-dependent inhibition of the membrane depolarization-induced CR duration was observed. This inhibition was antagonized by phaclofen, persisted when K(+) channel blockers were applied, and disappeared after treatment with nifedipine and verapamil. Moreover, the action of baclofen on depolarization-induced CR was suppressed by treatment with pertussis toxin. Therefore, these experiments suggest that baclofen modulates CR by a G protein (G(0) or G(1)) mediated inhibition of dihydropyridine-sensible calcium channels. Finally, synthesis and release of GABA in the environment by Paramecium have been demonstrated by HPLC. Possible correlations between GABA(B) receptor activation and the regulation of intracellular Ca(2+) levels are discussed.     

Computer simulation of Clostridium botulinum strain 56A behavior at low spore concentrations

It is generally assumed that spore behavior is independent of spore concentration, but recently published mathematical models indicate that this is not the case. A Monte Carlo simulation was employed in this study to further examine the independence assumption by evaluating the inherent variance in spore germination data. All simulations were carried out with @Risk software. A total of 500 to 4,000 iterations were needed for each simulation to reach convergence. Lag time and doubling time from a higher inoculum concentration were used to simulate the time to detection (TTD) at a lower inoculum concentration under otherwise identical environmental conditions. The point summaries of the simulated and observed TTDs were recorded for the 26 simulations, with kinetic data at the target inoculum concentration. The ratios of the median (R(m) = median(obs)/median(sim)) and 90% range (R(r) = 90% range(obs)/90% range(sim)) were calculated. Most R(m) and R(r) values were greater than one, indicating that the simulated TTDs were smaller and more homogeneous than the observed ones. R(r) values departed farther from one than R(m) values. Ratios obtained when simulating 1 spore with 10,000 spores deviated the farthest from one. Neither ratio was significantly different from the other when simulating 1 spore with 100 spores or simulating 100 spores with 10,000 spores. When kinetic data were not available, the percent positive observed at the 95th percentile of the simulated TTDs was obtained. These simulation results confirmed that the assumption of independence between spores is not valid.     

Computer simulation of mutagenesis

A FORTRAN program is described which simulates point-substitution mutations in the DNA strands of typical organisms. Its objective is to help students to understand the significance and structure of the genetic code, and the mechanisms and effects of mutagenesis. The program is intended to be used as part of an elementary course in genetics at degree level.     

Computer simulation of calcium-induced myotonia

Summary In an extensive research project on myotonia, the ionic mechanisms which are at the basis of the phenomenon of calcium-induced myotonia have been taken into consideration. A mathematical model of a muscle fibre was constructed to demonstrate the possibility that anomalous values of the membrane permeability to Calcium ions have an active part in the genesis of myotonia. This work was in great part supported by Grant of Muscular Dystrophy Assoc. Inc. and by CNR, Rome.     

Computer simulation of biological systems

The current status of mathematical models of biological systems is reviewed. Advances in supercomputer hardware allows more complex models to be constructed. The new generation of microcomputers are quite adequate for many computer simulations of biological systems. A theory of modeling is being developed to improve the relationship between the real biological system and the model. Deterministic models, stochastic models and applications of control theory and optimization methods are discussed. Examples given include models of molecular structure, of experimental techniques, and of biochemical reactions. It is recommended that experimental biologists consider the use of microcomputers to model the system under study as a part of their research program.     

Computer simulation of DNA supercoiling

We treat supercoiled DNA within a wormlike model with excluded volume. A modified Monte Carlo approach has been used, which allowed computer statistical-mechanical simulations of moderately and highly supercoiled DNA molecules. Even highly supercoiled molecules do not have a regular shape, though with an increase in writhing the chains look more and more like branched interwound helixes. The averaged writhing (Wr) approximately 0.7 delta Lk. The superhelical free energy F is calculated as a function of the linking number. Lk. The calculations have shown that the generally accepted quadratic dependence of F on Lk is valid for a variety of conditions, though it is by no means universal. Significant deviations from the quadratic dependence are expected at high superhelical density under ionic conditions where the effective diameter of DNA is small. The results are compared with the available experimental data.     

Computer simulation of purine metabolism

A computer model of purine metabolism, including catabolism, salvage pathways and interconversion among nucleotides, is given. Steady-state rate equations corresponding to metabolic enzymes are written based on information from the literature about their kinetic behaviour. Numerical integration of this set of equations is performed employing selected parameters taken from the literature. After stabilization of purine compound concentrations is reached, simulation of enzyme deficit and enzyme overproduction is carried out. The latter is calculated by varying specified maximum velocities in the numerical integration. A pattern of intermediate metabolite concentrations is found. These results form a basis for the comparison of normal patterns or patterns reflecting the effects of inborn errors of metabolism. The aim of this paper is to demonstrate the usefulness of this computer simulation method in complex metabolism pathways.     

Computer simulation of introductory neurophysiology

A computer-assisted learning (CAL) package, NeuroLab, developed for use by first-year university students undertaking professional programs in the health area, is described and evaluated. NeuroLab is a simulation of a laboratory, in which students are able to impale neurons to measure resting membrane potentials and subsequently undertake experiments including measuring resting membrane potentials, determining threshold potentials, measuring refractory periods, and examining effects on membrane potential through altering the membrane permeability to sodium and potassium ions. Students find the package to be a worthwhile learning experience, with 81 +/- 2.2% reporting the package increased their understanding of neuron function, and 78 +/- 2.5% expressing a desire for more CAL packages. Exposure to the package resulted in significantly higher mean scores in a multiple-choice question test on measuring neuron membrane potentials compared with those who were not exposed (mean scores out of 4 of 2.42 and 2.02, respectively, P < 0.001).     

Computer simulation of single-file transport

A stochastic model of single-file transport was developed as the Markov process in continuous time technique. The model was constructed using an EC-1060 computer. Unidirectional fluxes were investigated and populations of channels were correlated with flux fluctuations. The profiles of channel populations were shown to have nonlinear shapes even with the transport of nonelectrolyte (the classical diffusion approach gives linear profiles). The relationship between the paired correlation function F(AB) and the concentration of transported particles was examined. The F(AB) profile was shown to become flattened (or exponential for asymmetrical cases) at high concentrations. The concentration dependence jA/jA0 ratio were analyzed, where jA is a single-file unidirectional flux, jA0 is unidirectional flux for the case of free diffusion. An interesting "stack" phenomenon was observed for abnormal time correlations of single-file fluxes.     

Computer simulation of aqueous biomolecular systems

Computer simulation techniques are increasingly being used to predict structural and thermodynamic properties of large heterogeneous macromolecule and solvent assemblies. We discuss, with examples from our own studies, some problems we and others have experienced in using these techniques, which were originally devised for simple liquids. In particular, we consider the problems which arise from the large size and heterogeneity of macromolecule water systems, comparisons with experimental data and equilibrium and sampling procedures.     

Computer simulation of diffusely-connected neuronal populations

This paper describes computer simulations of diffusely-connected neuronal populations. Main findings are that diffuse monosynaptic linkages between populations are selectively sensitive to synchronized clusters of action potentials in the pre-synaptic population; that diffusely-connected excitatory recurrent collaterals tend to produce rhythmic series of synchronized clusters; and that diffusely-connected inhibition (both recurrent and afferent) tend to reduce the number of cells participating in a given synchronized cluster and thereby the overall transfer rate. However, recurrent inhibition tends to increase the rate at which synchronized clusters are produced by recurrent excitation. These results suggest the speculation that diffusely connected neuronal populations are particularly prone to deal with synchronized clusters of action potentials.This work has been supported by Grant GB 33687 of the National Science Foundation, Grant 1-R01-NS-10781-01 COM of the National Institutes of Health, and by a fellowship from Zonta, International     

Computer simulation of antibody binding specificity

A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives⁸) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form. © 1993 Wiley-Liss, Inc.     

Computer simulation of renal countercurrent systems

The history of mathematical modeling of renal countercurrent systems is briefly outlined. Several examples are cited and discussed. These include efforts at parameter estimation and experimental design with models. The goal of this work was the evaluation of hypotheses of hypertonic urine formation. The argument is made that computer simulation with reasonably isomorphic models can be used in a variety of ways, but that one indispensable role for this approach is to provide a test of the quantitative sufficiency of hypotheses. Hypotheses of hypertonic urine formation that do not consider active transport in thin ascending limbs do not pass this test. A new proposal is suggested in which the energy for NaCl reabsorption from thin ascending limbs is derived from dissipation of a urea gradient via an antiport.     

Computer simulation of movement-generating cross-bridges.

A stochastic computational method was developed to study properties of cross-bridge models for muscle contraction, by following the time history of individual cross-bridge model of Andrew Huxley (1957) and a modified two-state model with more realistic behavior during steady stretching are used as examples. The method can readily compute steady-state force during shortening and stretching and force-transients following rapid changes in length. Computations of velocity with a steady load and of velocity transients are more sensitive to the randomness inherent in the stochastic method.     

Computer simulation studies of self-assembling macromolecules

Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of self-assembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid self-assembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.     

Computer simulation of human body dynamics

Understanding human body dynamics is important in many situations, such as automobile and aircraft crashes, aircraft ejections, falls, and other acceleration environments. The design of automobile interiors, cockpits, and safety equipment requires knowledge of the forces and accelerations encountered during an emergency. Because of the limited information available from actual events and the various constraints in testing, computer simulations are often the only means of obtaining detailed information. The Armstrong Laboratory (AL) developed the Articulated Total Body (ATB) model to predict the human body dynamics in many of these environments. This model is a three-dimensional rigid body dynamics program in which the human body is modeled as a series of segments. Forces on the body segments are calculated based on their interaction with the surroundings including seat and cockpit surfaces. The model also calculates the internal joint resistive and constraint forces. Because of this capability to predict both internal and external forces acting on the body, the ATB model can be used in investigating injuries. It is also a valuable design tool for evaluating safety of proposed systems before prototypes are built or costly tests conducted. When testing is conducted, the model provides data that cannot be measured, such as forces within the body, and supplementing test data with parameter variation simulations. To validate the model, tests such as those conducted on the AL impact sled are simulated. Test films and instrumentation data are compared with simulation graphics and quantitative output to gain confidence in the simulation results.