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PubMed2002

Spatial structure of shell polychromatism in populations of Cepaea nemoralis: new techniques for an old debate.

A conspicuous shell polychromatism is observed in colonies of Cepaea nemoralis from western France (Brittany). The present study is intended to search for a spatial structure of shell features at this scale and to infer evolutionary processes from the observed patterns. We used a database of morph frequencies (six composite phenotypes were retained) measured on 213 samples regularly distributed on the whole studied area. Data analysis was based on two distinct multivariate methods leading to the following steps: (i) to search for a structure without reference to environmental conditions with a method (global principal components analysis: GPCA) which takes into account the spatial information by means of a neighbouring relationship between sampling points (Delaunay triangulation); (ii) to test the structuring power of environmental conditions by means of two explanatory factors (distance from the sea, altitude) involved in a redundancy analysis (RDA); (iii) to search for a spatial structure using residuals of the previous analysis, ie, after removing effects of environmental conditions. Global covariance accounted for 26.4% of the total variance, leading to a highly significant autocorrelation for each phenotype (step 1). Geographical mapping of factorial scores resulting from global analysis showed a well structured littoral zone and a strong southern-northern inland differentiation. Sixteen percent of the total variance was expressed in RDA but all morphs were not equally concerned. After removing environmental effects, a significant spatial structure still remains but was essentially caused by random processes. We argue for the importance of these last phenomena.

Animals↗
PubMed1995

Spatial structure of two-locus genotypes under isolation by distance.

Extensive Monte Carlo simulations are conducted of spatial distributions of two-locus genotypes in large, continuous populations under isolation by distance models. The results show that substantial patches of double homozygotes are present in the spatial structures, even when loci are unlinked. The stochastic spread of identical two-locus genotypes largely outpowers the tendency for recombination to decouple patterns for separate loci. A spatial patch is a large area containing mostly one double homozygous genotype in a highly contiguous constellation. This patch structure is reflected in high positive spatial autocorrelations and large excesses of pairs, or joins, of identical double homozygotes at short-to-intermediate distances of spatial separation. Although spatial patches of double homozygotes are the dominant spatial feature, and the major contributors to overall high levels of autocorrelations among two-locus genotypes, other substantial features include areas of concentrations of identical genotypes heterozygous at only one locus. One implication of the patch structure is the presence of high levels of linkage disequilibrium, caused by isolation by distance even for unlinked loci, at some spatial scales; yet the disequilibrium in the large total populations is near 0. Thus linkage disequilibrium produced by isolation by distance is highly dependent on spatial scale. Another implication is that high degrees of spatial structuring and autocorrelations are produced for genetic variation controlling quantitative traits, at least when the number of loci is relatively small, under a wide range of situations, even if the trait is selectively neutral. The significance of the results to field studies is also examined.

Diploidy↗
PubMed1988

Two-dimensional spatial structure of receptive fields in monkey striate cortex.

Measurements of the spatial contrast sensitivity function and orientation selectivity of visual neurons in the foveal striate cortex (V1) of primates were interpreted within the context of a model of the two-dimensional spatial structure of their receptive fields. Estimates of the spatial dimensions of the receptive fields along the axis of preferred orientation were derived from the application of the model and were compared with estimates of the smallest spatial subunit in the dimension orthogonal to the preferred orientation. Some measure of agreement was found with corresponding estimates of parameters for psychophysical channels in human foveal vision.

Animals↗
PubMed2000

Does evolution of iteroparous and semelparous reproduction call for spatially structured systems?

A persistent question in the evolution of life histories is the fitness trade-off between reproducing only once (semelparity) in a lifetime or reproducing repeated times in different seasons (iteroparity). The problem can be formulated into a research agenda by assuming that one reproductive strategy is resident (has already evolved) and by asking whether invasion (evolution) of an alternative reproductive strategy is possible. For a spatially nonstructured system, Bulmer (1994) derived the relationship v + PA < 1 (PA is adult survival; vbS and bS are offspring numbers for iteroparous and semelparous breeding strategies, respectively) at which semelparous population cannot be invaded by an iteroparous mutant. When the inequality is changed to v + PA > 1, invasion of a semelparous mutant is not possible. From the inequalities, it is easy to see that possibilities for evolutionary establishment of a novel reproductive strategy are rather narrow. We extended the evolutionary scenario into a spatially structured system with dispersal linkage among the subunits. In this domain, a rare reproductive strategy can easily invade a population dominated by a resident reproductive strategy. The parameter space enabling invasion is far more generous with spatially structured evolutionary scenarios than in a spatially nonstructured system.

Animals↗
PubMedDate not supplied

[Changes in the spatial structure of the destruction process under the conditions of atmospheric pollution of forest ecosystems].

Contamination of the southern taiga forests (Middle Urals) by discharges from cooper smelters (heavy metals combined with SO2) not only decreases the mean rate of decomposition of pure cellulose, but also radically changes the spatial structure of the destruction process. Heterogeneity of distribution of the destruction rate is sharply increased near the source of discharge due to differentiation of the space into microregions with high and low destruction rates. The characteristic size of spatial heterogeneity amounts to several tens of centimeters and the distribution of microregions with a high rate is accidental within several tens of meters. A hypothesis has been put forward that the described changes in the spatial structure of the destruction process are related, above all, to disturbed colonization of the substrate by soil myxomycetes.

Air Pollutants↗
PubMedDate not supplied

[Spatial structure of apamin in solution].

The calculation of the complete spatial structure of the bee venom peptide neurotoxin apamin has been carried out by means of a method elaborated earlier. It is based on the joint utilization of the molecular mechanics algorithms and NMR spectroscopy data. It was established that the molecule backbone conformation in solution may be represented as the combination of the beta-turn III (residues 2-5) and alpha-helical segment (9-18) both separated by the non-standard bend IV (5-8). The most probable system of the intramolecular hydrogen bonds in the apamin polypeptide backbone was proposed. Certain amino acid residues have been shown to be characterized by the lack of strict determination of the conformations of their side chains which may be realized in a few states providing approximately equal stabilization of the same form of the main chain. The conformational parameters of the proposed apamin structural model are appropriate to the NMR spectroscopy data derived from the literature and used in the calculations and are not contradictory to other experimental information.

Amino Acid Sequence↗
PubMed1998

Dynamics of a feline retrovirus (FeLV) in host populations with variable spatial structure.

The predictions of epidemic models are remarkably affected by the underlying assumptions concerning host population dynamics and the relation between host density and disease transmission. Furthermore, hypotheses underlying distinct models are rarely tested. Domestic cats (Felis catus) can be used to compare models and test their predictions, because cat populations show variable spatial structure that probably results in variability in the relation between density and disease transmission. Cat populations also exhibit various dynamics. We compare four epidemiological models of Feline Leukaemia Virus (FeLV). We use two different incidence terms, i.e. proportionate mixing and pseudo-mass action. Population dynamics are modelled as logistic or exponential growth. Compared with proportionate mixing, mass action incidence with logistic growth results in a threshold population size under which the virus cannot persist in the population. Exponential growth of host populations results in systems where FeLV persistence at a steady prevalence and depression of host population growth are biologically unlikely to occur. Predictions of our models account for presently available data on FeLV dynamics in various populations of cats. Thus, host population dynamics and spatial structure can be determinant parameters in parasite transmission, host population depression, and disease control.

Animals↗
PubMed2000

Role of commensal relationships on the spatial structure of a surface-attached microbial consortium.

A flow cell-grown model consortium consisting of two organisms, Burkholderia sp. LB400 and Pseudomonas sp. B13(FR1), was studied. These bacteria have the potential to interact metabolically because Pseudomonas sp. B13(FR1) can metabolize chlorobenzoate produced by Burkholderia sp. LB400 when grown on chlorobiphenyl. The expected metabolic interactions in the consortium were demonstrated by high performance liquid chromatography (HPLC) analysis. The spatial structure of the consortium was studied by fluorescent in situ rRNA hybridization and scanning confocal laser microscopy. When the consortium was fed with medium containing a low concentration of chlorobiphenyl, microcolonies consisting of associated Burkholderia sp. LB400 and Pseudomonas sp. B13(FR1) bacteria were formed, and separate Pseudomonas sp. B13(FR1) microcolonies were evidently not formed. When the consortium was fed citrate, which can be metabolized by both species, the two species formed separate microcolonies. The structure development In the consortium was studied online using a gfp-tagged Pseudomonas sp. B13(FR1) derivative. After a shift In carbon source from citrate to a low concentration of chlorobiphenyl, movement of the Pseudomonas sp. B13(FR1) bacteria led to a change in the spatial structure of the consortium from the unassociated form towards the associated form within a few days. Experiments Involving a gfp-based Pseudomonas sp. B13(FR1) growth activity reporter strain Indicated that chlorobenzoate supporting growth of Pseudomonas sp. B13(FR1) is located close to the Burkholderia sp. LB400 microcolonies in chlorobiphenyl-grown consortia.

Adaptation, Physiological↗
PubMed1998

Spatial structure model of the CD4 receptor-binding site of the HIV envelope protein gp120.

In this study we have undertaken attempt to predict 3D structure of the CD4 receptor-binding site of the HIV envelope protein gp120. The structure of this site has been constructed by the analysis of low-energy conformers of peptide T, an HIV reproduction inhibitor with amino acid sequence corresponding to the fragment Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr of protein gp120, ensuring the interaction of virus with T4 lymphocytes. To do this, the following researches have been carried out: i) the spatial structure models of peptide T and similar fragment 4-11 of an analogues of vasoactive intestinal peptide have been modeled by the restrained molecular mechanics method developed earlier, ii) conformational parameters of these models have been compared to geometrical characteristics of homologous segments of unrelated proteins with known spatial structures. The following major conclusions have been made based on the comparative analysis: i) the conformation of C-terminal fragment Thr-Thr-Asn-Tyr-Thr of peptide T, responsible for the biological activity of the molecule, does not undergo the essential distortions while embedding into the peptide chains of unrelated proteins; ii) this conformation, that is realized in isolated molecule and includes two consecutive reverse turns of the polypeptide chain, adequately describes the main conformational features of an appropriate site of the HIV protein gp120; iii) the fragment Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr of protein gp120 accepts one of six spatial forms which are characteristic for peptide T.

Binding Sites↗
PubMed1997

The spatial structure of lipids in human leukocytes: studies by nonradiative energy transfer.

The spatial structure of lipids in living human lymphocytes and granulocytes has been studied using the energy transfer between lipophilic fluorescent probes. One of the probes, an energy donor (DMC), was localized in the lipid interior, whereas another donor (K-68) and an energy acceptor (DSP-12) were near the lipid/water interface. The energy transfer in lymphocytes was the same as in artificial lipid membranes (liposomes). Obviously, in lymphocytes as in liposomes, both donors are localized near the lipid surface (the distance from the donors to the lipid surface is less than Forster's radius R0, i.e., 3.4-5 nm). On the contrary, in granulocytes, the energy transfer from K-68 was 2.2 times more efficient than from the lipid-immersed DMC. It was suggested that a fraction of DMC molecules was immersed into some lipid particles, and the distance from the molecules to the surface of the particles was greater than R0. The positions of the DMC fluorescence spectrum maxima in lymphocytes and in liposomes were the same, but in granulocytes the spectrum was blue-shifted (as in the case of lipoproteins). After subcellular fractionation the DMC fluorescence intensity correlated only with phospholipid concentration in different fractions but not with protein or nucleic acid concentrations. It was suggested that lipid organelles are the main source of the DMC fluorescence. The studies of cell-lipoprotein model mixtures support the suggestion that lipids in lymphocytes are mainly present as lamellar structures (membranes); the presence of lipoprotein-like particles of rather small radius can not be excluded either. On the other hand, in addition to membrane lipids, granulocytes have lipid-containing particles similar to large serum very low density lipoproteins.

Chalcone↗
PubMed1990

Carcinoembryonic antigen, its spatial structure and localization of antigenic determinants.

The effects of temperature and pH on the spatial structure of carcinoembryonic antigen (CEA) and its various derivatives are studied by circular dichroic spectroscopy and differential UV spectroscopy. The spatial organization of the protein portion of CEA and its derivatives as revealed by spectroscopic evidence is discussed with respect to the antigenic activity of the species studied. We conclude that the protein portion of CEA consists mainly of a beta-structural type. Using the various modifications of the sugar moiety and the protein portion, antigenic determinants of CEA are shown to possess the main conformational character of the molecule while participation of the sugars in the formation and orientation of the carbohydrate chains relative to the protein core of the antigen appear to be important.

Carbohydrate Conformation↗
PubMedDate not supplied

[Statistical criteria for evaluating the spatial structure, used in the reverse case of forming protein globules].

Statistical requirements to spatial structure representation used in the inverse folding problem have been considered. The representation by the distance from centers of side chaines to center of backbone of the molecule has been elaborated. It allows to select residue position and environmental properties and thus to improve computer methods for estimation 3D-1D compatibility.

Protein Conformation↗
PubMed2000

The evolution of parasite virulence and transmission rate in a spatially structured population.

If the transmission occurs through local contact of the individuals in a spatially structured population, the evolutionarily stable (ESS) traits of parasite might be quite different from what the classical theory with complete mixing predicts. In this paper, we theoretically study the ESS virulence and transmission rate of a parasite in a lattice-structured host population, in which the host can send progeny only to its neighboring vacant site, and the transmission occurs only in between the infected and the susceptible in the nearest-neighbor sites. Infected host is assumed to be infertile. The analysis based on the pair approximation and the Monte Carlo simulation reveal that the ESS transmission rate and virulence in a lattice-structured population are greatly reduced from those in completely mixing population. Unlike completely mixing populations, the spread of parasite can drive the host to extinction, because the local density of the susceptible next to the infected can remain high even when the global density of host becomes very low. This demographic viscosity and group selection between self-organized spatial clusters of host individuals then leads to an intermediate ESS transmission rate even if there is no tradeoff between transmission rate and virulence. The ESS transmission rate is below the region of parasite-driven extinction by a finite amount for moderately large reproductive rate of host; whereas, the evolution of transmission rate leads to the fade out of parasite for small reproductive rate, and the extinction of host for very large reproductive rate.

Animals↗
PubMed2001

Self-organized dynamics in spatially structured populations.

Self-organization and pattern formation represent the emergence of order in temporal and spatial processes. Self-organization in population ecology is gaining attention due to the recent advances concerning temporal fluctuations in the population size of dispersal-linked subunits. We shall report that spatially structured models of population renewal promote the emergence of a complex power law order in spatial population dynamics. We analyse a variety of population models showing that self-organization can be identified as a temporal match in population dynamics among local units, and how the synchrony changes in time. Our theoretical results are concordant with analyses of population data on the Canada lynx.

Animals↗
PubMed2001

High-resolution speckle-microscopy: study of the spatial structure of a bioflow.

Perspectives of velocity measurements of a random bioflow and its spatial structure by speckle-methods are studied in this paper. The mechanism of output signal formation and the optical scheme of the speckle-microscope are described. Amplitude, phase and frequency characteristics of this measuring system are investigated. The main types of signal distortions in the speckle-microscope are considered. Results of the analysis of output characteristics are applied to measurements of the spatial distribution of the refractive index of a blood flow in a small single microvessel. It is shown that the minimal size of flow inhomogeneities (with fluctuations in the optical path of the investigated object, less than 0.01 lambda) that can be resolved by the speckle-microscope is about a quarter of the waist beam diameter.

Algorithms↗
PubMed1987

Evaluating the aggregate spatial structure of Canadian metropolitan areas.

"Few attempts have been made to develop and test a conceptual framework for the comparative analysis of urban spatial structure and growth. This paper offers one aggregate approach as well as a series of empirical tests based on Canada's 27 largest urban areas. Six composite indices are introduced: population densities, rates of change, intraurban population redistribution, mobility rates, incidence of low-income populations, and degree of social polarization. Regression analyses reveal that differences among urban areas in spatial patterning and structural change are consistent with the hypothesized effects of city size, age, transport usage, social heterogeneity, production base, and physical setting. Yet immense regional and intraurban diversity remains. No single model of urban structure is sufficient to capture this diversity." (SUMMARY IN FRE)

Americas↗
PubMed2001

Evolution in a spatially structured population subject to rare epidemics.

We study a model that gives rise to spatially inhomogeneous population densities in a system of host individuals subject to rare, randomly distributed disease events. For stationary hosts that disperse offspring over short distances, evolutionary dynamics can lead to persistent populations with a variety of spatial structures. A mean-field analysis is shown to account for the behavior observed in simulations of a one-dimensional system, where the evolutionarily stable state corresponds to the solution of a straightforward optimization problem. In two dimensions, evolution drives the system to a stable critical state that is less well understood.

Animals↗