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PubMed1993

Exploring parameter space in detailed single neuron models: simulations of the mitral and granule cells of the olfactory bulb.

1. Detailed compartmental computer simulations of single mitral and granule cells of the vertebrate olfactory bulb were constructed using previously published geometric data. Electrophysiological properties were determined by comparing model output to previously published experimental data, mainly current-clamp recordings. 2. The passive electrical properties of each model were explored by comparing model output with intracellular potential data from hyperpolarizing current injection experiments. The results suggest that membrane resistivity in both cells is nonuniform, with somatas having a substantially lower resistivity than the dendrites. 3. The active properties of these cells were explored by incorporating active ion channels into modeled compartments. On the basis of evidence from the literature, the mitral cell model included six channel types: fast sodium, fast delayed rectifier (Kfast), slow delayed rectifier (K), transient outward potassium current (KA), voltage- and calcium-dependent potassium current (KCa), and L-type calcium current. The granule cell model included four channel types: rat brain sodium, K, KA, and the non-inactivating muscarinic potassium current (KM). Modeled channels were based on the Hodgkin-Huxley formalism. 4. Representative kinetics for each of the channel classes above were obtained from the literature. The experimentally unknown spatial distributions of each included channel were obtained by systematic parameter searches. These were conducted in two ways: large-scale simulation series, in which each parameter was varied in turn, and an adaptation of a multidimensional conjugate gradient method. In each case, the simulated results were compared wtih experimental data using a curve-matching function evaluating mean squared differences of several aspects of the simulated and experimental voltage waveforms. 5. Systematic parameter variations revealed a single distinct region of parameter space in which the mitral cell model best fit the data. This region of parameter space was also very robust to parameter variations. Specifically, optimum performance was obtained when calcium and slow K channels were concentrated in the glomeruli, with a lower density in the soma and proximal secondary dendrites. The distribution of sodium and fast potassium channels, on the other hand, was highest at the soma and axon, with a much lighter distribution throughout the secondary dendrites. The KA and KCa channels were also concentrated near the soma. 6. The parameter search of the granule cell model was much less restrained by experimental data. Several parameter regimes were found that gave a good match to the data.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2005

Cell cavities increase tortuosity in brain extracellular space.

Brain extracellular space (ECS) forms hindered pathways for molecular diffusion in chemical signaling and drug delivery. Hindrance is quantified by the tortuosity lambda; the tortuosity obtained from simulations using uniformly spaced convex cells is significantly lower than that measured experimentally. To attempt to account for the difference in results, this study employed a variety of ECS models based on an array of cubic cells containing open rectangular cavities that provided the ECS with dead-space microdomains. Monte Carlo simulations demonstrated that, in such ECS models, lambda can equal or exceed the typical experimental value of about 1.6. The simulations further revealed that lambda is relatively independent of cavity shape and the number of cavities per cell. It mainly depends on the total ECS volume fraction alpha, the cavity volume fraction alpha(c), and whether the cavity is located at the center of a cell face or formed at the junction of multiple cells. To describe the results from the different ECS models, an expression was obtained that related lambda to alpha, alpha(c), and an empirical exit factor beta that correlated with the ease with which a molecule could leave a cavity and its vicinity.

Biological Transport↗

PubMed2005

Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment.

MOTIVATION: The topology and function of gene regulation networks are commonly inferred from time series of gene expression levels in cell populations. This strategy is usually invalid if the gene expression in different cells of the population is not synchronous. A promising, though technically more demanding alternative is therefore to measure the gene expression levels in single cells individually. The inference of a gene regulation network requires knowledge of the gene expression levels at successive time points, at least before and after a network transition. However, owing to experimental limitations a complete determination of the precursor state is not possible. RESULTS: We investigate a strategy for the inference of gene regulatory networks from incomplete expression data based on dynamic Bayesian networks. This permits prediction of the number of experiments necessary for network inference depending on parameters including noise in the data, prior knowledge and limited attainability of initial states. Our strategy combines a gradual 'Partial Learning' approach based solely on true experimental observations for the network topology with expectation maximization for the network parameters. We illustrate our strategy by extensive computer simulations in a high-dimensional parameter space in a simulated single-cell-based example of hematopoietic stem cell commitment and in random networks of different sizes. We find that the feasibility of network inferences increases significantly with the experimental ability to force the system into different initial network states, with prior knowledge and with noise reduction. AVAILABILITY: Source code is available under: www.izbi.uni-leipzig.de/services/NetwPartLearn.html SUPPLEMENTARY INFORMATION: Supplementary Data are available at Bioinformatics online.

Algorithms↗

PubMed2004

Simulating protein evolution in sequence and structure space.

Naturally occurring proteins comprise a special subset of all plausible sequences and structures selected through evolution. Simulating protein evolution with simplified and all-atom models has shed light on the evolutionary dynamics of protein populations, the nature of evolved sequences and structures, and the extent to which today's proteins are shaped by selection pressures on folding, structure and function. Extensive mapping of the native structure, stability and folding rate in sequence space using lattice proteins has revealed organizational principles of the sequence/structure map important for evolutionary dynamics. Evolutionary simulations with lattice proteins have highlighted the importance of fitness landscapes, evolutionary mechanisms, population dynamics and sequence space entropy in shaping the generic properties of proteins. Finally, evolutionary-like simulations with all-atom models, in particular computational protein design, have helped identify the dominant selection pressures on naturally occurring protein sequences and structures.

Algorithms↗

PubMed2004

Comparative study of multipoint methods for genotype error detection.

Several programs are currently available for the detection of genotyping error that may or may not be Mendelianly inconsistent. However, no systematic study exists that evaluates their performance under varying pedigree structures and sizes, marker spacing, and allele frequencies. Our simulation study compares four multipoint methods: Merlin, Mendel4, SimWalk2, and Sibmed. We look at empirical thresholds, power, and false-positive rates on 7 small pedigree structures that included sibships with and without genotyped parents, and a three-generation pedigree, using 11 microsatellite markers with 3 different map spacings. Simulated data includes 5,000 replicates of each pedigree structure and marker map, with random genotyping errors in about 4% of the middle marker's genotypes. We found that the default thresholds used by these programs provide low power (47-72%). Power is improved more by adding genotyped siblings than by using more closely spaced markers. Some mistyping methods are sensitive to the frequencies of the observed alleles. Siblings of mistyped individuals have elevated false-positive rates, as do markers close to the mistyped marker. We conclude that thresholds should be decided based on the pedigree and marker data and that greater focus should be placed on modeling genotyping error when computing likelihoods, rather than on detecting and eliminating genotyping errors.

Alleles↗

PubMedDate not supplied

Adaptational changes in the neural control of cardiorespiratory function in a confined environment: the CNEC#3 experiment.

The goal of the study was to characterize the changes in neurovegetative control of the circulation, attending the presumed physiological and psychological stress originated by the isolation and confinement typical of the living condition of space stations, as simulated in a ground based unit, using time and frequency domain analysis. As a secondary goal we sought to verify the implementation of real time data acquisition, for off line spectral analysis of R-R interval, systolic arterial pressure (by Finapres) and respiration (by PVF2 piezoelectric sensors). We addressed the cardiorespiratory and neurovegetative responses to standardized, simple stressors (active standing, dynamic and static handgrip) on the EXEMSI 92 crew, before, during and after the isolation period. On average the appropriate excitatory responses (to stand, dynamic and static handgrip) were elicited also in isolation and confinement. Active standing and small masses muscular exercises are easy to be performed in a confined and isolated environment and provide a valuable tool for investigating the adaptational changes in neural control mechanisms. The possibility there exists of using this time and frequency domain approach to monitor the level of performance and well being of the space crew in (quasi) real time.

Adaptation, Physiological↗

PubMed2001

[Effect of microgravity simulation with clinostat on different strains in Anabaena oryza].

The Biological responses of Anabana oryza (different strains) to microgravity simulation with clinostat were analyzed. The simulation of growth rate was observed under clinoration all the strains, especially in flight strains (AoR16 and AoSR16-17). Anabana oryza HB23 showed higher activity than flight strains in photosynthesis and respiration. The nitrogen which flight strains with high nitrogrnase activity fixed under culturing in ground was used to accumulate phycobiliprotein in cell and excrete ammonium out of cell after meeting the normal metabolism, however, it was mainly used to simulate growth rate under culturing with clinostat. menwhile, it was different from space flight that microgravity simulation with clinostat was not able to induced the phenotype segregation in Anabana oryzae.

Anabaena↗

PubMed1977

Laboratory apparatus for studying visual space perception of the pilot in simulated night approaches to landing.

The device provides a relatively inexpensive means of assessing a number of perceptual and human factors parameters in the night approach to landing situation. A technique for modeling airport runway lighting is described along with electromechanical and optical systems for precise control of simulated approach speed, model slant, and direction in the visual field of the simulated radial approach axis. The realism of this display is enhanced by preservation of the natural relations of size and brightness of simulated runway lights to distance.

Aerospace Medicine↗

PubMed1993

Characterization of tissue microstructure scatterer distribution with spectral correlation.

Characterization of tissue microstructure from the backscattered ultrasound signal using the spectral autocorrelation (SAC) function provides information about the scatterer distribution in biological tissue. This paper demonstrates SAC capabilities in characterizing periodicities in A-scans due to regularity in the scatterer distribution. The A-scan is modelled as a cyclostationary signal, where the statistical parameters of the signal vary in time with single or multiple periodicities. This periodicity manifests itself as spectral peaks both in the power spectral density (PSD) and in the SAC. Periodicity in the PSD will produce a well defined dominant peak in the cepstrum, which has been used to determine the scatterer spacing. The relationship between the scatterer spacing and the spacing of the spectral peaks is established using a stochastic model of the echo-formation process from biological tissue. The distribution of the scatterers within the microstructure is modelled using a Gamma function, which offers a flexible method of simulating parametric regularity in the scatterer spacing. Simulations of the tissue microstructure for lower orders of regularity indicate that the SAC components reveal information about the scatterer spacing that are not seen in the PSD and the cepstrum. The echoformation process is tested by simulating microstructure of varying regularity and analyzing their effect on the SAC, PSD and cepstrum. Experimental validation of the simulation results are provided using in vivo scans of the breast and liver tissue that show the presence of significant spectral correlation components in the SAC.

Computer Simulation↗

PubMed2005

Effects of lung time constant, gas analyser delay and rise time on measurements of respiratory dead-space.

This study evaluated effects of mechanical time constants (tau(m)) of the respiratory system, delays between flow and CO(2) partial pressure (P(CO)(2)) signals and rise time of the CO(2) analyser on dead-space measurements. A computer model simulated low alveolar dead-space, high alveolar dead-space, 0.2 <or= tau(m) <or= 3.6 s and varying ventilation-perfusion ratios (V/Q). CO(2) expirograms were recorded from the model under each condition and from 22 anaesthetized intubated patients. P(CO)(2) signals were shifted with respect to flow to produce varying time delays and anatomic and physiological dead-spaces were calculated. The CO(2) analyser was simulated as a critically damped second-order system with 10-90% rise times of 25-400 ms. The error in measured dead-space increases approximately 2.5% per 10 ms signal delay for normal lungs (tau(m) = 1 s), but has low sensitivity (0.58% per 10 ms) to the rise time of the CO(2) analyser. Sensitivity of physiological dead-space, but not anatomic dead-space to delay is decreased in high alveolar dead-space and abnormal V/Q distribution. Shorter tau(m) increase the error sensitivity of both physiological and anatomic dead-spaces to both delay and rise time. P(CO)(2) and flow should be well synchronized, particularly when tau(m) are short, to avoid dead-space errors.

Aged↗

PubMed1999

Teaching of space life sciences.

Space life sciences is not really a new life sciences discipline such as immunology was some decades ago and it may never be so. Rather it is a field that will provide each existing life sciences discipline with new and more information gathered from space research. In fact, the danger is that space research will be confined in a separate discipline, and thus it will be cut off from classical ground research. Conversely, scientists should increasingly consider spaceflight as a tool and should integrate the findings of space research into their traditional disciplines. A brief survey of topics and main findings in the various subdisciplines of space life sciences is provided. This is followed by a discussion of typical problems encountered such as access to space, controls, ground-based simulations, medical care in space, extravehicular activity, and environmental control and life support. As many space life sciences courses are initiated around the world either by space agencies or universities or jointly, there is a need to consider the international, intercultural, and interdisciplinary aspects of such programs. It is argued that the growing knowledge derived from space research should be integrated into the regular teaching of life sciences rather than leaving it confined to a separate field. Teaching of space life sciences is a prime candidate for the application of the new techniques of "cyberspace education", where interactive learning and globalization of the learning process will take a leading place. The experts and student body are dispersed over many nations, research is of necessity conducted on a basis of international cooperation. The conduct of tele-education is discussed and existing information sources and courses are listed.

Biological Science Disciplines↗

PubMed2005

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation.

Gaussian split Ewald (GSE) is a versatile Ewald mesh method that is fast and accurate when used with both real-space and k-space Poisson solvers. While real-space methods are known to be asymptotically superior to k-space methods in terms of both computational cost and parallelization efficiency, k-space methods such as smooth particle-mesh Ewald (SPME) have thus far remained dominant because they have been more efficient than existing real-space methods for simulations of typical systems in the size range of current practical interest. Real-space GSE, however, is approximately a factor of 2 faster than previously described real-space Ewald methods for the level of force accuracy typically required in biomolecular simulations, and is competitive with leading k-space methods even for systems of moderate size. Alternatively, GSE may be combined with a k-space Poisson solver, providing a conveniently tunable k-space method that performs comparably to SPME. The GSE method follows naturally from a uniform framework that we introduce to concisely describe the differences between existing Ewald mesh methods.

Journal Article↗

PubMedDate not supplied

Simulations of voltage clamping poorly space-clamped voltage-dependent conductances in a uniform cylindrical neurite.

Significant error is made by using a point voltage clamp to measure active ionic current properties in poorly space-clamped cells. This can even occur when there are no obvious signs of poor spatial control. We evaluated this error for experiments that employ an isochronal I(V) approach to analyzing clamp currents. Simulated voltage clamp experiments were run on a model neuron having a uniform distribution of a single voltage-gated inactivating ionic current channel along an elongate, but electrotonically compact, process. Isochronal Boltzmann I(V) and kinetic parameter values obtained by fitting the Hodgkin-Huxley equations to the clamp currents were compared with the values originally set in the model. Good fits were obtained for both inward and outward currents for moderate channel densities. Most parameter errors increased with conductance density. The activation rate parameters were more sensitive to poor space clamp than the I(V) parameters. Large errors can occur despite "normal"-looking clamp curves.

Action Potentials↗

PubMed2006

In vitro-cleaning efficacy of interdental brushes with different stiffness and different diameter.

PURPOSE: The aim of this study was to evaluate the cleaning efficacy of interdental brushes with different stiffnesses, e.g. soft and hard interdental brushes with identical brush diameter. MATERIALS AND METHODS: Cylindrical soft and hard interdental brushes with diameters of 2,3 and 5 mm each were tested. Sixteen extracted human molars were fixed in split cast models to simulate eight interdental spaces. After coating the teeth with a dye to simulate plaque, digital photographs were taken from the proximal surfaces in a highly standardised set-up. The teeth were repositioned and the proximal surfaces were cleaned in a standardised manner. Post-brushing digital photographs were taken as before. After digital subtraction, the cleaned area was measured by pixel count and the relative cleaning efficacy was calculated. RESULTS: The cleaning efficacy values of soft and hard interdental brushes of corresponding size in extra-small, small, medium and large interdental spaces as well as overall showed no statistically significant difference. In small, medium and large interdental spaces, increasing brush diameters resulted in higher cleaning efficacy; these differences were statistically significant. Irregular values were seen in extra-small interdental spaces. CONCLUSION: Both hard and soft interdental brushes cleaned the proximal tooth surfaces effectively. The filament stiffness had no statistically significant influence on the cleaning efficacy.

Analysis of Variance↗

PubMed1994

Conformation of the oligosaccharide receptor for E-selectin.

A tetrasaccharide related to the blood group oligosaccharides, known as sialyl LewisX, has been proposed as the receptor for the lectin responsible for leukocyte adhesion named alternatively as E-selectin or ELAM-1. The 13C- and 1H-nmr spectra have been completely assigned for a tetrasaccharide model of this receptor, Neu5Ac alpha-(2-->3)-Gal beta-(1-->4)-[Fuc alpha-(1-->3)-]GlcNAc beta-NHAc. Quantitative nuclear Overhauser data (NOESY) have been recorded and analyzed by a complete spin matrix simulation method. Conformational space was exhaustively searched and all conformational models whose simulated NOESY spectra matched the experiment were found. Molecular mechanics and molecular dynamics calculations were carried out to test whether the experimental conformations are low energy and thus likely to represent true single conformations for the tetrasaccharide. It was concluded that while the LewisX trisaccharide portion of the compound adopts a single conformation, there is likely to be some flexibility about the Neu5Ac alpha-(2-->3)-linkage. A model featuring fast exchange between two different conformations of this linkage is found to be consistent with both the nmr experiments and the molecular dynamics simulations.

Carbohydrate Conformation↗

PubMed2004

Limited conformational space for early-stage protein folding simulation.

MOTIVATION: The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the early-stage structure for simulation of protein folding. The proposed conformational sub-space was developed on the basis of the backbone conformation, with side-chain interactions excluded. RESULTS: The ellipse-path-limited conformation of BPTI was created using the criterion of shortest distance between Phi, Psi angles in native form of protein and the Phi, Psi angles belonging to the ellipse. No knots were observed in the structure created according to ellipse-path conformational sub-space. The energy minimization procedure applied to ellipse-path derived conformation directed structural changes toward the native form of the protein with SS-bonds system introduced to the procedure. AVAILABILITY: Program 'Ellipse' to create the ellipse-path derived structure available on request: myroterm@cyf-kr.edu.pl

Algorithms↗

PubMed2003

A central partition of molecular conformational space. I. Basic structures.

On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a 3x(N-1)-dimensional polytope. Conformations can be precisely located within the face hierarchy of the polytope, whose 1-skeleton provides the framework for determining paths between selected conformations.

HIV Integrase↗

PubMed1990

Actin filaments responsible for the location of the nucleus in the lentil statocyte are sensitive to gravity.

The location of the nucleus in statocytes or lentil roots grown: 1), at 1 g on the ground, 2), on a 1 g centrifuge in space, 3), in simulated microgravity on a slowly rotating clinostat (0.9 rmp) 4), in microgravity in space was investigated and statistically evaluated. In cells differentiated at 1 g on the ground, the nuclear membrane was almost in contact with the plasmalemma lining the proximal cell wall, whereas in statocytes of roots crown on the clinostat there was a distance of 0.47 micrometers (horizontal clinorotation) and or 0.76 micrometers (vertical clinorotation) between these membranes. However, in microgravity the nucleus was the most displaced, 0.87 micrometers from the proximal cell wall. Centrifugation of vertically grown roots in the root-tip direction showed that the threshold of centrifugal force to detach all nuclei from the proximal cell wall was about 40 g. In statocytes developed in the presence of cytochalasin B at 1 g the nuclei were sedimented on the amyloplasts at the distal cell pole, demonstrating that the location of the nucleus depends on actin filaments. The results obtained are in agreement with the hypothesis that gravity causes a tension of actin filaments and that this part of the cytoskeleton undergoes a relaxation in microgravity.

Actins↗