The effects of discrete gap junction coupling on propagation in myocardium

A modified cable theory for a bi-domain model of myocardium that incorporates the effect of gap junctions as discrete objects coupling cardiac cells is derived. The theory is shown to be in agreement with a number of experiments that cannot be explained using standard continuous cable theory, and resolves some apparent contradictions on failure of propagation in two-dimensional anisotropic tissue. In addition, some as yet untested predictions of the theory are mentioned.     

Effects of diminished expression of connexin43 on gap junction number and size in ventricular myocardium

Gap junction number and size vary widely in cardiac tissues with disparate conduction properties. Little is known about how tissue-specific patterns of intercellular junctions are established and regulated. To elucidate the relationship between gap junction channel protein expression and the structure of gap junctions, we analyzed Cx43 +/- mice, which have a genetic deficiency in expression of the major ventricular gap junction protein, connexin43 (Cx43). Quantitative confocal immunofluorescence microscopy revealed that diminished Cx43 signal in Cx43 +/- mice was due almost entirely to a reduction in the number of individual gap junctions (226 +/- 52 vs. 150 +/- 32 individual gap junctions/field in Cx43 +/+ and +/- ventricles, respectively; P < 0.05). The mean size of an individual gap junction was the same in both groups. Immunofluorescence results were confirmed with electron microscopic morphometry. Thus when connexin expression is diminished, ventricular myocytes become interconnected by a reduced number of large, normally sized gap junctions, rather than a normal number of smaller junctions. Maintenance of large gap junctions may be an adaptive response supporting safe ventricular conduction.     

Flocculation in brewing yeasts: a computer simulation study

A new simulator, INDISIM-FLOC, based on the individual-based simulator INDISIM, is used to examine the predictions of two different models of yeast flocculation. The first, proposed by Calleja is known as the "addition" model. The second, proposed by Stratford is known as the "cascade" model. The simulations show that the latter exhibits a better qualitative agreement with available experimental data.     

Action potential shape change in an electrically coupled network during propagation: a computer simulation

We applied compartmental computer modeling to test a model of spike shape change in the jellyfish, Polyorchis penicillatus, to determine whether adaptive spike shortening can be attributed to the inactivation properties of a potassium channel. We modeled the jellyfish outer nerve-ring as a continuous linear segment, using ion channel and membrane properties derived in earlier studies. The model supported action potentials that shortened as they propagated away from the site of initiation and this was found to be largely independent of potassium channel inactivation. Spike broadening near the site of initiation was found to be due to a depolarization plateau that collapsed as two spikes spread from the point of initiation. The lifetime of this plateau was found to depend critically on the inward current flux and the space constant of the membrane. These data suggest that the spike shape changes may be due not only to potassium channel inactivation, but also to the passive properties of the membrane.     

Bridges linking gap junction particles extracellularly: a freeze-etching rotary-shadowing study of split junctions

The nature of the interaction between neighboring gap junction particles and the mechanism involved in particle crystallization are still unclear. We describe here interparticle bridge-like structures which could participate in the mechanism of gap junction particle aggregation and pattern determination. Gap junction membranes of rat liver, pulled apart by vascular perfusion with hypertonic sucrose, were freeze-fractured in deionized water, etched at - 100 degrees C for 8 min and rotary-shadowed at a 32 degrees angle. At the extracellular true surface of the junctions (ES-surface), the particles appear as 7.0 to 7.5 nm rings often resolvable into six radially arranged subunits. The particles appear linked to each other by filamentous bridges 1.5 to 2.2 nm thick and approximately 1.5 nm long. Some bridges (single bridges) directly interlink neighboring particles while other bridges (multiple bridges) are joined to a particle at one end and to the other bridges at the other end. Bridges are referred to as double or triple bridges if they result from the interaction of two or three bridges respectively. In particles which can be resolved into six subunits, the bridges appear to bind to the subunit tips. Stereo images indicate that the bridges lay in planes lower than the particle summits. The bridges could be either polypeptide chains of the main gap junction protein or peripheral proteins, but the unlikely possibility that they are a shadowing artifact cannot be entirely ruled out yet.     

Wave propagation in cardiac tissue and effects of intracellular calcium dynamics (computer simulation study)

Computer simulation using Luo-Rudy I1 model of ventricular myocyte showed that intracellular calcium dynamics become irregular in case of high rate stimulation. This causes the transition from stationary to nonstationary spiral wave and its breakup in 2D model of cardiac tissue. Obtained results suggest how ventricular fibrillation may occur due to the abnormalities of intracellular calcium dynamics. The short review of existing cardiac cell models with calcium dynamics is presented.     

The structure of percolated polymer systems: a computer simulation study

We studied the percolation process in a system consisting of long flexible polymer chains and solvent molecules. The polymer chains were approximated by linear sequences of beads on a two-dimensional triangular lattice. The system was athermal and the excluded volume was the only potential. The properties of the model system across the entire range of polymer concentrations were determined by Monte Carlo simulations employing a cooperative motion algorithm (CMA). The scaling behavior and the structure of the percolation clusters are presented and discussed.     

Sudden loading during a dynamic lifting task: a simulation study

It is believed that nurses risk the development of back pain as a consequence of sudden loadings during tasks in which they are handling patients. Forward dynamics simulations of sudden loads (applied to the arms) during dynamic lifting tasks were performed on a two-dimensional whole-body model. Loads were in the range of -80 kg to 80 kg, with the initial load being 20 kg. Loading the arm downwards with less than that which equals a mass of 20 kg did not change the compressive forces on the spine when compared to a normal lifting motion with a 20 kg mass in the hands. However when larger loads (40 kg to 80 kg extra in the hands) were simulated, the compressive forces exceeded 13,000 N (above 3400 N is generally considered a risk factor). Loading upwards led to a decrease in the compressive forces but to a larger backwards velocity at the end of the movement. In the present study, it was possible to simulate a fast lifting motion. The results showed that when loading the arms downwards with a force that equals 40 kg or more, the spine was severely compressed. When loading in the opposite direction (unloading), the spine was not compressed more than during a normal lifting motion. In practical terms, this indicates that if a nursing aide tries to catch a patient who is falling, large compressive forces are applied to the spine.     

Transcription regulation by steroid hormones: a computer simulation study.

Three-dimensional structures of complexes of 66 amino acid-DNA binding domains of human progesterone (hPR), estrogen (hER) and glucocorticoid (hGR) receptors (proteins), with ten base pair DNA duplexes: d(AGGTCATGCT).d(AGCATGACCT) and d(AGAACATGCT).d(AGCATGTTCT) were obtained using computer modeling and molecular mechanics techniques. Cartesian coordinates for the proteins were obtained from: 1) structural data of hER and hGR by NMR spectroscopy; 2) steric constraints imposed by tetrahedral coordination of the zinc ion to Cys residues, and 3) energy minimization in torsional and cartesian space. The proteins were made to interact with DNA (in B-form) in major groove through alpha-helical linker between the two zinc fingers. The geometry of the complexes was obtained by allowing them to slide, glide, penetrate in to and out of the groove, and to rotate about the helical axis. The complexes were energy minimized. Also maximized was the number of H-bonds between proteins and DNA. The complex structures were refined by molecular mechanics using AMBER 3.0. Structural parameters of DNA were analyzed in each complex and compared with those of native DNA optimized separately. The stereochemical differences of the complexes are discussed.     

Dynamical effects of diffusive cell coupling on cardiac excitation and propagation: a simulation study

Cell coupling is considered to be important for cardiac action potential propagation and arrhythmogenesis. We carried out computer simulations to investigate the effects of stimulation strength and cell-to-cell coupling on action potential duration (APD) restitution, APD alternans, and stability of reentry in models of isolated cell, one-dimensional cable, and two-dimensional tissue. Phase I formulation of the Luo and Rudy action potential model was used. We found that stronger stimulation resulted in a shallower APD restitution curve and onset of APD alternans at a faster pacing rate. Reducing diffusive coupling between cells prolonged APD. Weaker diffusive currents along the direction of propagation steepened APD restitution and caused APD alternans to occur at a slower pacing rate in tissue. Diffusive current due to curvature changed APD but had little effect on APD restitution slope and onset of instability. Heterogeneous cell coupling caused APD inhomogeneities in space. Reduction in coupling strength either uniformly or randomly had little effect on the rotation period and stability of a reentry, but random cell decoupling slowed the rotation period and, thus, stabilized the reentry, preventing it from breaking up into multiple waves. Therefore, in addition to its effects on action potential conduction velocity, diffusive cell coupling also affects APD in a rate-dependent manner, causes electrophysiological heterogeneities, and thus modulates the dynamics of cardiac excitation. These effects are brought about by the modulation of ionic current activation and inactivation.     

Effect of nonuniform interstitial space properties on impulse propagation: a discrete multidomain model

This work presents a discrete multidomain model that describes ionic diffusion pathways between connected cells and within the interstitium. Unlike classical models of impulse propagation, the intracellular and extracellular spaces are represented as spatially distinct volumes with dynamic/static boundary conditions that electrically couple neighboring spaces. The model is used to investigate the impact of nonuniform geometrical and electrical properties of the interstitial space surrounding a fiber on conduction velocity and action potential waveshape. Comparison of the multidomain and bidomain models shows that although the conduction velocity is relatively insensitive to cases that confine 50% of the membrane surface by narrow extracellular depths (≥2 nm), the action potential morphology varies greatly around the fiber perimeter, resulting in changes in the magnitude of extracellular potential in the tight spaces. Results also show that when the conductivity of the tight spaces is sufficiently reduced, the membrane adjacent to the tight space is eliminated from participating in propagation, and the conduction velocity increases. Owing to its ability to describe the spatial discontinuity of cardiac microstructure, the discrete multidomain can be used to determine appropriate tissue properties for use in classical macroscopic models such as the bidomain during normal and pathophysiological conditions.     

Accuracy analysis for RSA: a computer simulation study on 3D marker reconstruction

In this paper, error analysis of three-dimensional marker coordinates reconstructed from noisy two-dimensional measurement in RSA was performed. Mathematical models to predict error propagation of focus position and object points were derived and computer simulations were performed to validate these models. Two clinical calibration cages were compared by testing the error propagation at each RSA step. The results revealed that errors of reconstructed object points were related to the focus position error, two-dimensional measurement error, position of focus and positions of object points, while errors of reconstructed focus position were determined by the two-dimensional measurement error, number of control points and location of the focus. The maximum difference between the mathematical model and the simulation for the assessment of errors of focus position was 14 microm and the maximum difference of object point positions was 1.1 microm. These differences were small and judged irrelevant, hence the simulations indicated that our models were accurate.     

Differential growth and plant tropisms: a study assisted by computer simulation

Tropisms and other movements of a plant organ result from alterations in local rates of cell elongation and a consequent development of a growth differential between its opposite sides. Relative elemental rates of elongation (RELELs) are useful to characterize the pattern of growth along and round an organ. We assume that the value of the RELEL at a given point is dependent on distance from the tip and that the distribution of values along the organ surface can be characterized in terms of the spread and the position of the maximum value. A computer model is described which accommodates these parameters and simulates tropic curvatures due to differential growth. Additional regulatory functions help to return the simulated organ to its original orientation. Particular attention is given to the simulation of root gravitropism because here not only do each of the various growth and regulatory parameters have a known biological counterpart, but some can also be given an actual quantitative value. The growth characteristics relate to the biophysical properties of cells in the elongation zone of the root, while the regulatory functions relate to aspects of the graviperception and transmission systems. We believe that, given a suitably flexible model, computer simulation is a powerful means of characterizing, in a quantitative way, the contribution of each parameter to the elongation of plant organs in general and their tropisms in particular.     

双歧杆菌的完整肽聚糖对小鼠腹腔巨噬细胞缝隙链接的影响

目的探讨双歧杆菌的完整肽聚糖（WPG）对巨噬细胞缝隙连接介导的细胞间通讯（GJIC）的影响。方法首先分离培养昆明小鼠腹腔巨噬细胞,然后以WPG刺激巨噬细胞,再用脂荧光探针标记细胞,最后采用激光共聚焦显微镜结合激光漂白后荧光恢复技术检测反映GJIC变化的荧光恢复程度。结果和对照组相比,以WPG刺激巨噬细胞后,其GJIC的平均荧光恢复率明显增加（P〈0.01）。结论双歧杆菌的WPG可提高巨噬细胞的缝隙连接介导的细胞间通讯。     

Direct calculation and computer simulation of the enantiomerization barrier of oxazepam in dynamic HPLC experiments--a comparative study

Dynamic chromatographic methods constitute a versatile approach to the rapid and precise determination of enantiomerization barriers of stereolabile drugs. In the present study enantioselective dynamic high-performance liquid chromatography (DHPLC) was employed to determine the enantiomerization barrier of oxazepam. Dynamic elution profiles, exhibiting plateau formation and/or peak broadening between 20 and 60 degrees C at pH 2.6 and pH 8 were obtained in the presence of the chiral stationary phase (CSP) Nucleodex-beta-PM (permethylated beta-cyclodextrin chemically bonded to silica) using a 6:4 mixture of phosphate buffer and methanol as mobile phase. Evaluation of the experimental chromatograms was performed by the novel approximation function (AF) (without computer simulation), and by the stochastic model implemented in the ChromWin simulation software (with computer simulation) furnishing the respective apparent forward rate constants, k(1)(app)(T). From the rate constants, k(1)(app)(T), measured at variable temperatures, the kinetic Eyring activation parameters, deltaG(T)(#), deltaH(#) and deltaS(#), of the enantiomerization of oxazepam were obtained. By variation of the flow rate of the mobile phase, the expected independence of the enantiomerization barrier from the chromatographic time scale was demonstrated for the first time.     

Reconstitution of cardiac gap junction channeling activity into liposomes: a functional assay for gap junctions

Cardiac gap junctions were reconstituted into liposomes. To determine if reconstitution resulted in membrane channel formation, we developed an assay for channel function that used a liposome-entrapped peroxidase to detect entry of a substrate into the liposome. The data demonstrate, for the first time, that reconstituted gap junctions from heart are capable of channel-forming activity in artificial membranes.     

Delta-opioid receptor activation before ischemia reduces gap junction permeability in ischemic myocardium by PKC-epsilon-mediated phosphorylation of connexin 43

The aim of this study was to examine the hypothesis that delta-opioid receptor activation before ischemia suppresses gap junction (GJ) permeability by PKC-mediated connexin 43 (Cx43) modulation, which contributes to infarct size limitation afforded by the delta-opioid receptor activation. A delta-opioid receptor agonist, [D-Ala(2),D-Leu(5)]-enkephalin acetate (DADLE, 300 nM), was used in place of preconditioning (PC) ischemia to trigger PC mechanisms in rat hearts. GJ permeability during ischemia, which was assessed by Lucifer yellow, was reduced by DADLE to 47% of the control level, and this effect of DADLE was almost abolished by a PKC-epsilon inhibitor [PKC-epsilon translocation inhibitory peptide (PKC-epsilon-TIP)] but was not affected by a PKC-delta inhibitor (rottlerin). After DADLE infusion, PKC-epsilon, but not PKC-delta, was coimmunoprecipitated with Cx43, and the level of phosphorylation of Cx43 at a PKC-dependent site (Ser(368)) was significantly elevated during ischemia. DADLE reduced infarct size after 35 min of ischemia followed by 2 h of reperfusion by 69%, and PKC-epsilon-TIP and rottlerin eliminated 48% and 63%, respectively, of the infarct size-limiting effect of DADLE. Infusion of a GJ blocker, heptanol, before reperfusion reduced infarct size by 36%, and this protection was not enhanced by preischemic infusion of rottlerin + DADLE, which allows PKC-epsilon activation by DADLE. These results suggest that phosphorylation of Cx43 by PKC-epsilon plays a crucial role in delta-opioid-induced suppression of GJ permeability in ischemic myocardium and that this modulation of the GJ is possibly an adjunct mechanism of infarct size limitation afforded by preischemic delta-opioid receptor activation.     

Study of DNA base-Li doped SiC nanotubes in aqueous solutions: a computer simulation study

Due to the importance of soluble nanotubes in biological systems, computational research on DNA base functionalized nanotubes is of interest. This study presents the quantitative results of Monte Carlo simulations of Li-doped silicon carbide nanotubes and its nucleic acid base complexes in water. Each species was first modeled by quantum mechanical calculations and then Monte Carlo simulations were applied to study their properties in aqueous solution. Solvation free energies were computed to indicate the solvation behavior of these compounds. The computations show that solvation free energies of the complexes of DNA bases with Li-doped SiC nanotubes are in the order: thymine > cytosine > adenine > guanine. The results of complexation free energies were also used to study the stability of related structures, which indicate that thymine-Li-doped SiC nanotubes produce the most stable compound among the four DNA base complexes.     

Estimating the power of a proposed linkage study: a practical computer simulation approach.

I describe a simulation method to estimate the power to detect linkage given a set of pedigrees of known structure and for which family history data may be available. This method can be applied to autosomal and X-linked dominant diseases; depending on the pedigrees under consideration, it will often be applicable for autosomal and X-linked recessive diseases. This power calculation can most usefully be undertaken after family history data are gathered, but prior to examination and testing of pedigree members to obtain marker information. Of key importance, the power calculation is straightforward to carry out and not too time-consuming; it is practical even on a microcomputer. The result of the power calculation is an objective answer to the question: Will my families be sufficient to demonstrate linkage?