Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2006

The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments.

Spatial structure is thought to be an important factor influencing the emergence and maintenance of genetic diversity. Previous studies have demonstrated that environmental heterogeneity, provided by spatial structure, leads to adaptive radiation of populations. In the present study, we investigate not only the impact of environmental heterogeneity on adaptive radiation, but also of population fragmentation and niche construction. Replicate populations founded by a single genotype of Escherichia coli were allowed to evolve for 900 generations by serial transfer in either a homogeneous environment, or a spatially structured environment that was either kept intact or destroyed with each daily transfer. Only populations evolving in the structured environment with intact population structure diversified: clones are significantly divergent in sugar catabolism, and show frequency-dependent fitness interactions indicative of stable coexistence. These findings demonstrate an important role for population fragmentation, a consequence of population structure in spatially structured environments, on the diversification of populations.

Adaptation, Physiological↗
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↗
PubMed2003

High reproductive rates result in high predation risks: a mechanism promoting the coexistence of competing prey in spatially structured populations.

I tested the hypothesis that spatial structure provides a trade-off between reproduction and predation risk and thereby facilitates predator-mediated coexistence of competing prey species. I compared a cellular automata model to a mean-field model of two prey species and their common predator. In the mean-field model, the prey species with the higher reproductive rate (the superior competitor) always outcompeted the other species (the inferior competitor), both in the presence of and the absence of the predator. In the cellular automata model, both prey species, which differed only in their reproductive rates, coexisted for a long time in the presence of their common predator at intermediate levels of predation. At low predation rates, the superior competitor dominated, while high predation rates favored the inferior competitor. This discrepancy in the results of the different models was due to a trade-off that spontaneously emerged in spatially structured populations; that is, the more clustered distribution of the superior competitor made it more susceptible to predation. In addition, coexistence of competing prey species declined with increasing dispersal ranges of either prey or predator, which suggests that the trade-off that results from spatial structure becomes less important as either prey or predator disperse over a broader range.

Animals↗
PubMed2003

The impact of spatial structure on the accuracy of contour maps of small data sets.

Spatial analysis of insect counts provides important information about how insect species respond to the heterogeneity of a given sampling space. Contour mapping is widely used to visualize spatial pest distribution patterns in anthropogenic environments, and in this study we outlined recommendations regarding semivariogram analysis of small data sets (N < 50). Second, we examined how contour maps based upon linear kriging were affected by the spatial structure of the given data set, as error estimation of contour maps appears to have received little attention in the entomological domain. We used weekly trap catches of the warehouse beetle, Trogoderma variabile, and the accuracy assessment was based upon data sets that had either a random spatial structure or were characterized by asymptotic spatial dependence. Asymptotic spatial dependence (typically described with a semivariogram analysis) means that trap catches at locations close to each other are more similar than trap catches at locations further apart. Trap catches were poorly predicted for data sets with a random spatial structure, while there was a significant correlation between observed and predicted trap catches for the spatially rearranged data sets. Therefore, for data sets with a random spatial structure we recommend visualization of the insect counts as scale-sized dots rather than as contour maps.

Animals↗
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↗
PubMed2003

Medium scale spatial structures of Polycyclic Aromatic Hydrocarbons in the topsoil of Tianjin area.

The spatial distribution patterns of Polycyclic Aromatic Hydrocarbons (PAHs) in soil are important to regional environmental assessment. In this paper, the spatial structural features of sixteen prior PAH compounds in the topsoil of Tianjin area, as well as soil properties, were studied. Results shown that medium scale spatial autocorrelations were well revealed. Spherical models with sills could be used to fit all experimental variograms. The spatial structures of PAHs contents demonstrated significant anisotropy. Air precipitation caused by the combustion of coal was the key factor in the formation of the spatial structural patterns of PAHs in the topsoil of Tianjin area.

China↗
PubMedDate not supplied

[Residual dipolar couplings and molecular dynamic calculations as a source for refinement of protein spatial structures].

The precision of techniques and factors affecting the interpretation of residual dipolar couplings (RDCs) in analysis of spatial structures of partially aligned proteins are discussed. Experimental RDC values were obtained for pairs of 1H-15N nuclei of the protein barstar partially aligned in a liquid crystalline matrix of bicelles composed of dimiristoylphosphatidylcholine and dihexanoylphosphatidylcholine. The observed couplings agree well with the spatial structures of barstar determined earlier by X-ray and NMR methods. However, the differences between the experimental and calculated RDCs that were calculated on the basis of the known spatial structures of barstar, exceed the experimental errors three- to fourfold. These discrepancies can be explained by differences in the protein structures in solution and in crystal, a limited precision of the X-ray analysis, and the intramolecular mobility of the protein molecule. A comparison of the results of modeling of the molecular dynamics of barstar in solution, crystal structures, and the experimental RDCs showed that the methods of molecular dynamics provide for a reasonable description of the character and amplitudes of internal motions and they should be considered for the correct determination of protein spatial structures from NMR spectroscopic data.

Amino Acid Substitution↗
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↗
PubMed2004

On parts and holes: the spatial structure of the human body.

Spatial representation and reasoning is a central component of medical informatics. The spatial concepts most often used in medicine are not the quantitative, point-based concepts of classical geometry, but rather qualitative relations among extended objects such as body parts. A mereotopology is a formal theory of qualitative spatial relations, such as parthood and connection. This paper considers how an extension of mereotopology which includes also location relations can be used to represent and reason about the spatial structure of the human body.

Anatomy↗
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↗
PubMed2004

Spatial structure often inhibits the evolution of cooperation in the snowdrift game.

Understanding the emergence of cooperation is a fundamental problem in evolutionary biology. Evolutionary game theory has become a powerful framework with which to investigate this problem. Two simple games have attracted most attention in theoretical and experimental studies: the Prisoner's Dilemma and the snowdrift game (also known as the hawk-dove or chicken game). In the Prisoner's Dilemma, the non-cooperative state is evolutionarily stable, which has inspired numerous investigations of suitable extensions that enable cooperative behaviour to persist. In particular, on the basis of spatial extensions of the Prisoner's Dilemma, it is widely accepted that spatial structure promotes the evolution of cooperation. Here we show that no such general predictions can be made for the effects of spatial structure in the snowdrift game. In unstructured snowdrift games, intermediate levels of cooperation persist. Unexpectedly, spatial structure reduces the proportion of cooperators for a wide range of parameters. In particular, spatial structure eliminates cooperation if the cost-to-benefit ratio of cooperation is high. Our results caution against the common belief that spatial structure is necessarily beneficial for cooperative behaviour.

Animals↗