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Results for “spatial structure”

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At least 19 recordsLinked to original sources

PubMed1999

Evolution of cooperation in spatially structured populations

Using a spatial lattice model of the Iterated Prisoner's Dilemma we studied the evolution of cooperation within the strategy space of all stochastic strategies with a memory of one round. Comparing the spatial model with a randomly mixed model showed that (1) there is more cooperative behaviour in a spatially structured population, (2) PAVLOV and generous variants of it are very successful strategies in the spatial context and (3) in spatially structured populations evolution is much less chaotic than in unstructured populations. In spatially structured populations, generous variants of PAVLOV are found to be very successful strategies in playing the Iterated Prisoner's Dilemma. The main weakness of PAVLOV is that it is exploitable by defective strategies. In a spatial context this disadvantage is much less important than the good error correction of PAVLOV, and especially of generous PAVLOV, because in a spatially structured population successful strategies always build clusters. Copyright 1999 Academic Press.

Journal Article↗

PubMed1999

Detection of temporal structure depends on spatial structure.

Observers can more easily detect correlated patterns of temporal contrast modulation within hybrid visual images composed of two components when those components are drawn from the same original picture (Blake, R., & Yang, Y. (1997). Proceedings of the National Academy of Science, 94, 7115-7119). To learn whether spatial phase is a mediating variable, we measured thresholds for detection of contrast modulation over time among component gratings while manipulating spatial phase among those components. In Experiment 1, observers more easily detected correlated contrast modulation when two component gratings were aligned in peaks-subtract phase. Experiment 2 showed that this phase-dependent detectability of synchronized contrast modulation is mediated by the phase-dependent, non-linear interaction among spatial frequency channels. The rigorous evaluation of several a priori reasonable hypotheses indicates that the phase-dependent detectability is not based on local spatial features such as local luminance, contrast or luminance gradient. Taken together, our results indicate that the spatial phase relationship and the temporal correlation of contrast modulation of two component gratings are both important for triggering facilitatory interaction between neural analyzers tuned to those gratings.

Contrast Sensitivity↗

PubMedDate not supplied

[Model of the spatial structure of peptide T].

The spatial structure model of peptide T (AIDS reproduction inhibitor, the amino acid sequence of which corresponds to the fragment into the binding site of the virus protein gp120 with T4 receptor) is proposed. Peptide structure modelling has been carried out by the previously developed method based on joint usage of the molecular mechanics algorithms and NMR spectroscopy data. To build the model, two-dimensional nuclear Overhauser effect spectroscopy data for RNase A homologous fragment 22-26 were taken from the literature. The result of the presented work was a set consisting of six types of low-energy structures with different spatial packing of the peptide main chain. All structural types have been shown to be characterized by the lack of strict determination of the side chain conformations of the amino acid residues that can be realized in a few states providing approximately equal (within the given type) stabilization of one main chain form. At the same time, despite the definite differences, all of the selected structures were characterized by the presence of two consecutive reverse polypeptide chain turns at the C-terminal pentapeptide fragment. This site is supposed to be responsible for the peptide binding with T4 receptor and the antiviral effect.

Algorithms↗

PubMed1998

Spatial structure, environmental heterogeneity, and population dynamics: analysis of the coupled logistic map.

Spatial extent can have two important consequences for population dynamics: It can generate spatial structure, in which individuals interact more intensely with neighbors than with more distant conspecifics, and it allows for environmental heterogeneity, in which habitat quality varies spatially. Studies of these features are difficult to interpret because the models are complex and sometimes idiosyncratic. Here we analyze one of the simplest possible spatial population models, to understand the mathematical basis for the observed patterns: two patches coupled by dispersal, with dynamics in each patch governed by the logistic map. With suitable choices of parameters, this model can represent spatial structure, environmental heterogeneity, or both in combination. We synthesize previous work and new analyses on this model, with two goals: to provide a comprehensive baseline to aid our understanding of more complex spatial models, and to generate predictions about the effects of spatial structure and environmental heterogeneity on population dynamics. Spatial structure alone can generate positive, negative, or zero spatial correlations between patches when dispersal rates are high, medium, or low relative to the complexity of the local dynamics. It can also lead to quasiperiodicity and hyperchaos, which are not present in the nonspatial model. With density-independent dispersal, spatial structure cannot destabilize equilibria or periodic orbits that would be stable in the absence of space. When densities in the two patches are uncorrelated, the probability that the population in a patch reaches extreme low densities is reduced relative to the same patch in isolation; this "rescue effect" would reduce the probability of metapopulation extinction beyond the simple effect of spreading of risk. Pure environmental heterogeneity always produces positive spatial correlations. The dynamics of the entire population is approximated by a nonspatial model with mean patch characteristics. This approximation worsens as the difference between the patches increases and the dispersal rate decreases: Under extreme conditions, destabilization of equilibria and periodic orbits occurs at mean parameter values lower than those predicted by the mean parameters. Apparent within-patch dynamics are distorted: The local population appears to have the wrong growth parameter and a constant number of immigrants (or emigrants) per generation. Adding environmental heterogeneity to spatial structure increases the occurrence of spatially correlated population dynamics, but the resulting temporal dynamics are more complex than would be predicted by the mean parameter values. The three classes of spatial pattern (positive, negative, and zero correlation), while still mathematically distinct, become increasingly similar phenomenologically.

Animals↗

PubMed1996

Cyclo(-GLY-DSIP), A cyclic analog of the delta-sleep-inducing peptide: computer simulation of spatial structure involving NMR data.

The spatial structure of cyclo(-Gly-DSIP-), a physiologically active analog of the delta sleep-inducing peptide, was determined by computer modelling using 1H NMR data. An interesting feature of the spatial structure in DMSO was detected. One side of almost planar resulting conformation is formed by the side chains of the Asp5, Ser7 and Glu9 residues, the side chain of the Trp1 residue forming the other part of the outer surface. This feature may be associated with the functional properties of the peptide.

Amino Acid Sequence↗

PubMed1992

[Refinement of the spatial structure of the gramicidin A ion channel].

The spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cross-peak volumes with those calculated for low-energy GA conformations, dynamic averaging of the low-energy conformation set and restrained energy minimization. Accuracy of the spatial structure determination was estimated by the penalty function Fr defined as a root mean square deviation of interproton distances corresponding to the calculated and experimental cross-peak volumes. As the initial conformation we used the right-handed pi 6,3 LD pi 6,3 LD helix established on the base of NMR data regardless of the cross-peak volumes. The conformation is in a good agreement with NOE cross-peak volumes (Fr 0.2 to 0.5 A depending on NOESY spectrum). For a number of NOEs formed by the side chain protons, distances errors were found as much as 0.5-2.0 A. Restrained energy minimization procedure had little further success. However some of these errors were eliminated by the change in torsional angle chi 2 of D-Leu12 and dynamic averaging of the Val7 side chain conformations. Apparently, majority of deviations of the calculated and experimental cross-peak volumes are due to the intramolecular mobility of GA and cannot be eliminated within the framework of rigid globule model. In summary the spatial structure of GA ion-channel can be thought as a set of low-energy conformations, differing by the side chain torsion angles chi 1 Val7 and chi 2 D-Leu4 and D-Leu10 and the orientation of the C-terminal ethanolamine group. Root mean square differences between the atomic coordinates of conformations are in the range of 0.3-0.8 A.

Cell Membrane↗

PubMed2000

Conditions for noise reduction and stable encoding of spatial structure by cortical neural networks.

Cortical circuits have been proposed to encode information by forming stable spatially structured attractors. Experimentally in the primary somatosensory cortex of the monkey, temporally invariant stimuli lead to spatially structured activity patterns. The purpose of this work is to study a recurrent cortical neural network model with lateral inhibition and examine what effect additive random noise has on the networks' ability to form stable spatially structured representations of the stimulus pattern. We show numerically that this network performs edge enhancement and forms statistically stationary, spatially structured responses when the lateral inhibition is of moderate strength. We then derive analytical conditions on the connectivity matrix that ensure stochasticly stable encoding of the stimulus spatial structure by the network. For stimuli whose strength falls in the near linear region of the sigmoid, we are able to give explicit conditions on the eigenvalues of the connection matrix. Finally, we prove that a network with a connection matrix, where the total excitation and inhibition impinging upon a neural unit are nearly balanced, will yield stable spatial attractor responses.

Animals↗

PubMed1997

Contrast adaptation and the spatial structure of natural images.

Natural images have a characteristic spatial structure, with amplitude spectra that decrease with frequency roughly as 1/f. We have examined how contrast (pattern-selective) adaptation to this structure influences the spatial sensitivity of the visual system. Contrast thresholds and suprathreshold contrast and frequency matches were measured after adaptation to random samples from an ensemble of images of outdoor scenes or of synthetic images formed by filtering the amplitude spectra of noise over a range of spectral slopes. Adaptation selectively reduced sensitivity at low-to-medium frequencies, biasing contrast sensitivity toward higher frequencies. The pattern of aftereffects was similar for different natural image ensembles but varied with large changes in the slope of the noise spectra. Our results suggest that adaptation to the spatial structure in natural scenes may exert strong and selective influences on perception that are important in characterizing the normal operating states of the visual system.

Adaptation, Physiological↗

PubMedDate not supplied

[Spatial structure of angiotensin in an aqueous solution].

The spatial structure of spin-labeled angiotensin in aqueous solution wa investigated with the combined use of NMR, fluorescence spectroscopy and energy calculation including Monte-Carlo techniques. The calculated mean values of molecular parameters were compared with the experimental ones. The calculated and experimental mean values were regarded as statistically indistinguishable when the corresponding mean values occurred within the 95% confidence limit. The experimental parameters were shown to be adequately described by calculated conformers only with the assumption of the existence of dynamic equilibrium of conformers in solution. The mean values of statistical weights and their limits providing the agreement between the calculated and experimental data were determined. Two geometrically different forms of backbone structure for C-terminal hexapeptide in aqueous solution were revealed using the discussed approach; the N-terminal part of the molecule appeared to be much more conformationally labile. The model of molecule spatial structure is consistent with available literature data upon angiotensin titration experiments, its complexing with heavy metal ions etc.

Angiotensins↗

PubMedDate not supplied

[How does environment modify the spatial structure of Dictyostelium discoideum population].

The transformation of the spatial structure of a Dictyostelium discoideum population in response to environmental changes induced by this population was investigated. A comparative analysis of the spatial and temporal characteristics of the D. discoideum colony is given for two cases: (a) when the colony is cultivated on a bacterial lawn, i.e. under conditions close to natural, and (b) in the absence of the bacterial lawn when the colony grows on the nutrient substrate enriched with folic acid. It is shown that the environmental changes induced by cell metabolism modify the spatial structure of the D. discoideum population first, the rate of population propagation falls drastically, which correlates with a decrease in the substrate pH; second, the spatial redistribution of the D. discoideum cell density correlates with the redistribution of folic acid in the substrate. The mechanism of the environment impact on the D. discoideum colony transformation is discussed.

Agar↗

PubMed2000

Evolution of nitrogen fixation in spatially structured populations of Rhizobium.

Symbiosis between legumes and nitrogen-fixing bacteria is thought to bring mutual benefit to each participant. However, it is not known how rhizobia benefit from nodulation of legume hosts because they fix nitrogen only after differentiating into bacteroids, terminally differentiated cells that cannot reproduce. Because free-living rhizobia can reproduce, and may benefit from the increase of plant root exudates stimulated by nodulation, evolution of symbiotic nitrogen fixation may depend upon kin selection. However, unrelated nonmutualists may also benefit from increased plant exudates and nitrogen-fixing populations are therefore vulnerable to invasion by nonfixing, saprophytic Rhizobium. The access of nonfixing Rhizobium to the plant exudates associated with nodules depends upon the spatial structure of the Rhizobium populations within the soil. We investigate the influence of spatial structure on the evolution of N-fixation within a Rhizobium population using a mathematical model. Our model demonstrates that spatial structure is necessary for the evolution of N-fixation and that N-fixation is more likely to evolve with increasing degrees of spatial structure. In fact, we identify three dynamic outcomes that depend upon the relative strength of the costs of N-fixation relative to the degree of spatial structure and benefits resulting from nodulations. If the costs are relatively high, N-fixation will not evolve; if the costs are relatively low, N-fixing genes will fix in the population, but at intermediate conditions, a stable mixture of N-fixing bacteria and nonfixing bacteria will be maintained. The conditions for coexistence of N-fixing bacteria and nonfixing bacteria expand under a saturating relationship between nodule numbers and N-fixing genotype frequency.

Biological Evolution↗

PubMed1993

Two-dimensional 1H-NMR study of the spatial structure of neurotoxin II from Naja naja oxiana.

The spatial structure of neurotoxin II from the venom of the central Asian cobra Naja naja oxiana was determined by two-dimensional 1H-NMR techniques and computational analysis. Nearly complete proton resonance assignments for 61 amino acid residues have been made using two-dimensional (2D) homonuclear total correlated spectroscopy, 2D homonuclear double-quantum-filtered correlated spectroscopy and 2D homonuclear NOE spectroscopy (NOESY) experiments. The cross-peak volumes in NOESY spectra spin-spin coupling constants of vicinal protons NH-C alpha H and C alpha H-C beta H and the observation of slow deuterium exchange of amide protons were used to define local structure and a set of constraints for distance geometry program DIANA. The average root-mean-square deviations are 53 pm for backbone heavy atoms and 118 pm for all heavy atoms of 19 final neurotoxin II conformations. The spatial structure is characterized by a short double-stranded (residues 1-5 and 13-17) and a triple-stranded (residues 22-30, 33-41 and 50-54) antiparallel beta-sheets.

Amino Acid Sequence↗

PubMed1987

[Relation between the spatial structure and antigenic activity of trophoblast-specific beta1-glycoprotein].

Temperature- and pH-dependence of spatial structure of a native trophoblast-specific beta-glycoprotein (TSG), its desialated and deglycosylated derivatives, as well as of a fragment obtained by partial acid hydrolysis on the temperature and pH variations has been studied using CD and UV spectroscopy. Within the range 45-50 degrees C a conformational transition of the protein moiety of TSG, leading to partially reversible alterations in tertiary and secondary structures of this glycoprotein after cooling the solution to 20 degrees C has been found out. The results of spectral studies of the spatial structure of the TSG protein component have been compared with the data on antigen activity of native, temperature- and pH-denaturated, desialated, and deglycosilated TSG. It has been concluded that the protein moiety of TSG consists mainly of beta-structures; the greater part of antigen determinants of TSG is topographic and belongs to the protein component of TSG, and only 15% of antigen determinants are not connected with TSG's spatial structure.

Circular Dichroism↗

PubMedDate not supplied

Hierarchy of regions of amino acid sequence with respect to their role in the protein spatial structure.

The method of the representation of amino acid sequence by graph of the interactions energy between parts of spatial structure has been elaborated. Our method provides the possibility to establish the compatibility between each point of a polypeptide chain and the Van der Waals interactions energy of regions of a native globule adjacent to this amino acid residue. We have undertaken an exhaustive analysis of a set of proteins. Boundaries of domain and module structures have been found. Nonequivalence of different parts of sequences in respect to their contribution to stabilization of the spatial structure of the protein macromolecules has been revealed. On the basis of the number of energetic levels which are necessary to identify all independent parts of the globule, the contribution from each part of the sequence to stabilization of the spatial structure of the globule is defined. Thus, it has been found that the sequence of amino acid residues coincides with the sequence of the numerical values which can be used in turn in formal procedures, such as an alignment, a search of consensus, the recognition of composition peculiarities, etc. An example of the comparison of proteins with various sequence identities is considered to demonstrate the scheme of an alignment procedure.

Amino Acid Sequence↗

PubMed1997

Estimation of evolutionary distances from protein spatial structures.

New equations are derived to estimate the number of amino acid substitutions per site between two homologous proteins from the root mean square (RMS) deviation between two spatial structures and from the fraction of identical residues between two sequences. The equations are based on evolutionary models, analyzing predominantly structural changes and not sequence changes. Evolution of spatial structure is treated as a diffusion in an elastic force field. Diffusion accounts for structural changes caused by amino acid substitutions, and elastic force reflects selection, which preserves protein fold. Obtained equations are supported by analysis of protein spatial structures.

Amino Acid Sequence↗

PubMed1986

Spatial structures in mitochondrial suspension induced by cation efflux.

The formation of spatial structures in a thin unstirred layer of a mitochondrial suspension has been studied. It is shown that the structure formation depends on the state of the ion-transporting systems of mitochondria and that pattern development coincides with the activation of cation efflux from preloaded mitochondria. Spatial structure formation is an energy-dependent process and is suppressed by respiratory chain inhibitors. Patterning is also inhibited by EGTA, EDTA and ruthenium red, reflecting the requirement for divalent cation translocation in mitochondria for the studied phenomenon.

Animals↗

PubMed2000

Testing local dependence of spatial structures on images

Associations between two spatial processes can be due to a real dependence between the two processes or to the dependence on common underlying variables. We propose to test the existence of a real dependence by use of local tests, leading to a global test of real dependence and a map of local interactions. We present first how classical interaction tests based on random rotations between completely observed processes such as those developed by Berman (Berman. Appl. Statist. (1986) 35, 54-62), can be integrated in local analyses. For this purpose, tests are first performed locally, and the distribution of their p-values is then compared to the corresponding value under the null hypothesis. A similar approach is proposed to test non-stationarity of a point pattern by using distance statistics popularized by Diggle (Diggle. Statistical Analysis of Spatial Point Patterns. (1983) Academic Press, New York). The problem of testing the interaction between a random field and a censoring area pattern process is discussed and an approach similar to the preceding ones is then proposed. The methods are mainly applied to agricultural examples but they can be applied to any microscopical images for which one wishes to analyse the spatial structure.

Journal Article↗

PubMed2000

Spatial structuring and frequency distribution of the nematode Steinernema feltiae Filipjev.

The frequency distribution of first generation, Steinernema feltiae Filipjev parasitic stages was over-dispersed with the majority of hosts containing few or no parasitic stages, whilst a few hosts contained a great many. Because of high extraction efficiency, the frequency distributions of the parasitic stages and the infective stages in the soil were assumed to be directly related. To explain the frequency distribution of the parasites it was therefore necessary to account for the frequency distribution of the S. feltiae infective stages in the soil. The infective stages were spatially aggregated into 30 cm diameter patches at the site of host death. These patches were randomly distributed approximately 1 m apart. At the 1 m scale, the pooled counts of infective stages were randomly distributed. Thus, in contrast to the frequency distributions, the spatial structuring of S. feltiae changed with the spatial scale of the interaction. This dynamic spatial structuring means that the majority of samples taken would contain few or no infective stages, whilst a few soil samples would contain a great many. Thus, the spatial structuring of the infective stages generates the over-dispersed frequency distribution of the S. feltiae in the soil. Hosts, encountering infective stages from this spatial distribution will, therefore, show an over-dispersed frequency distribution of S. feltiae parasitic stages.

Animals↗