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PubMed2004

Self-affine fronts in self-affine fractures: large and small-scale structure.

The evolution and spatial structure of displacement fronts in fractures with self-affine rough walls are studied by numerical simulations. The fractures are open and the two faces are identical but shifted along their mean plane, either parallel or perpendicular to the flow. An initially flat front advected by the flow is progressively distorted into a self-affine front with a Hurst exponent equal to that of the fracture walls. The lower cutoff of the self-affine regime depends only on the aperture, while the upper cutoff grows with the lateral shift and linearly with the width of the front.

Journal Article↗

PubMed1996

Localization of a peripheral patch: the role of blur and spatial frequency.

Peripheral vision serves to direct our attention and fixation to objects of interest. This requires that the visual system be capable of accurately localizing peripherally presented targets having different spatial structures. The question we address is "to what extent does stimulus spatial structure influence the precision of peripheral localization?" To address this issue, we measured the precision of spatial localization (with reference to a foveal target) for a single Gaussian or Gabor patch briefly presented in the periphery. For both stimuli, we find that when the standard deviation of the stimulus envelope (SD) is less than 1/5 the stimulus eccentricity, localization thresholds are independent of SD and are approximately 1/50 of eccentricity. For larger values of SD, localization thresholds increase linearly with increasing SD, and are approximately 1/5 of SD. The results hold over a range of eccentricities (from 2.5 to 10 deg) and stimulus contrasts (from near detection threshold to 80%). In addition, for Gabor patches, the results are independent of frequency, phase and orientation of the carrier.

Humans↗

PubMed2001

Spatial effects and rare outcrossing events in Medicago truncatula (Fabaceae).

In order to elucidate the mechanisms underlying the large amount of RAPD polymorphism found in 1990 in a population of the selfing annual Medicago truncatula GAERTN. (Fabaceae), we have analysed most of the individuals (n = 363) from the same population 6 years later using microsatellite loci. We confirm the result of the earlier study, namely that this population is very polymorphic and highly subdivided, with approximately 37% of the variance distributed among subpopulations, only 50 m apart one from another. We use standard F-statistics analyses, linkage disequilibria, minimum spanning network, multilocus assignment tests and spatial autocorrelation analyses to test the hypotheses that spatial structure and outcrossing events are involved in maintaining the large amount of genetic diversity at the level of each subpopulation. Interestingly, fine-scale spatial structure could be observed in only one subpopulation suggesting that other mechanisms are acting elsewhere. To the best of our knowledge, this is the first study of fine spatial genetic structure in a predominantly selfing species.

Crosses, Genetic↗

PubMed2006

Effect of gene flow on spatial genetic structure in the riparian canopy tree Cercidiphyllum japonicum revealed by microsatellite analysis.

Few studies have analyzed pollen and seed movements at local scale, and genetic differentiation among populations covering the geographic distribution range of a species. We carried out such a study on Cercidiphyllum japonicum; a dioecious broad-leaved tree of cool-temperate riparian forest in Japan. We made direct measurement of pollen and seed movements in a site, genetic structure at the local scale, and genetic differentiation between populations covering the Japanese Archipelago. Parentage analysis of seedlings within a 20-ha study site indicated that at least 28.8% of seedlings were fertilized by pollen from trees outside the study site. The average pollination distance within the study site was 129 m, with a maximum of 666 m. The genotypes of 30% of seedlings were incompatible with those of the nearest female tree, and the maximum seed dispersal distance within the study site was over 300 m. Thus, long-distance gene dispersal is common in this species. The correlation between genetic relatedness and spatial distance among adult trees within the population was not significant, indicating an absence of fine-scale genetic structure perhaps caused by high levels of pollen flow and overlapping seed shadows. Six populations sampled throughout the distribution of C. japonicum in Japan showed significant isolation-by-distance but low levels of genetic differentiation (F(ST) = 0.043), also indicating long-distance gene flow in C. japonicum. Long-distance gene flow had a strong influence on the genetic structure at different spatial scales, and contributes to the maintenance of genetic diversity in C. japonicum.

Gene Flow↗

PubMed2006

Spatial hydration structures and dynamics of phenol in sub- and supercritical water.

The hydration structures and dynamics of phenol in aqueous solution at infinite dilution are investigated using molecular-dynamics simulation technique. The simulations are performed at several temperatures along the coexistence curve of water up to the critical point, and above the critical point with density fixed at 0.3 g/cm3. The hydration structures of phenol are characterized using the radial, cylindrical, and spatial distribution functions. In particular, full spatial maps of local atomic (solvent) density around a solute molecule are presented. It is demonstrated that in addition to normal H bonds with hydroxyl group of phenol, water forms pi-type complexes with the center of the benzene ring, in which H2O molecules act as H-bond donor. At ambient conditions phenol is solvated by 38 water molecules, which make up a large hydrophobic cavity, and forms on average 2.39 H bonds (1.55 of which are due to the hydroxyl group-water interactions and 0.84 are due to the pi complex) with its hydration shell. As temperature increases, the hydration structure of phenol undergoes significant changes. The disappearance of the pi-type H bonding is observed near the critical point. Self-diffusion coefficients of water and phenol are also calculated. Dramatic increase in the diffusivity of phenol in aqueous solution is observed near the critical point of simple point-charge-extended water and is related to the changes in water structure at these conditions.

Journal Article↗

PubMed1995

Mapping the spin-density and lineshape distribution of free radicals using 4D spectral-spatial EPR imaging.

The development and application of four-dimensional spectral-spatial electron paramagnetic resonance imaging (EPRI) techniques for unambiguous determination of spectral shape and spin distribution of paramagnetic samples are described. Strategies for optimizing acquisition and computation times, image resolution, and data presentation are described. The feasibility of studying small linewidth differences of approximately 0.1 G in samples of up to 25 mm in size was tested by computer simulations and by measurements on phantoms containing 0.5 mM nitroxide spin label. One thousand projections were used to reconstruct 32 x 32 x 32 x 32 pixel images. Similar 4D imaging experiments were performed on an isolated rat heart infused with a suspension of glucose char. The 4D image of the rat heart clearly showed the three-dimensional spatial structure of the heart and the spectral shape at each spatial point. Thus, we have demonstrated, for the first time, that 4D spectral-spatial EPRI could be performed on lossy biological samples or tissues at L-band frequencies, enabling the mapping of spectral information over the entire three-dimensional spatial structure of the object.

Animals↗

PubMed1989

Conformational aspects of antiviral activity of deoxyguanosine acyclic analogues.

Conformational possibilities of a series of deoxyguanosine analogues possessing or lacking antiviral activity were evaluated using methods of the molecular mechanics. Comparison of the spatial structures of acyclic analogues with one another and with the spatial structures of deoxyguanosine demonstrates restricted conformational mobility for compounds devoid of activity. The level of sterically allowed superposition of functional groups from the acyclic moieties of analogues and the corresponding atomic centres of deoxyribose could serve as a criterion of activity. The superposition could be performed in two different ways through either of the nonhydrogen substituents at the C1' atom in the five-membered ring.

Algorithms↗

PubMedDate not supplied

[Self-similarity in the structure of DNA: why are introns needed?].

Consequences of the hypothesis are analyzed that native spatial structure of DNA is the so-called crumpled globule, which is statistically free of knots. Since crumpled globule is self-similar fractal object in space, fixation of more or less unique chain fold, that is the case for eukaryotes, requires some self-similarity of the sequence. On this basis we explain quantitatively long-range power-law correlations in intron containing genes which have been discovered recently, predict some more detailed properties of correlations, which partly convinced already in experiment, and formulate a few more general hypotheses on the statistical properties of presently unassigned parts of DNA, on the role of intron as the instrument of fixation of DNA spatial structure and on the possible way of creation of such an apparatus in the evolution.

DNA↗

PubMed1999

Global and local structural properties of the principal neutralizing determinant of the HIV-1 envelope protein gp120.

The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24, and 12 residues is carried out. The modeling of the molecular spatial structures is performed by a new approach to research of conformationally mobile peptides using the algorithms of the restrained molecular mechanics method developed earlier. The following major conclusions are made based on the analysis of the simulated peptide conformations: i) there is not unique PND structure in solution, ii) there are seven different PND structures each of which agrees with the experimental data and stereochemical criteria used in computing its spatial model, iii) the PND is characterized by irregular conformation containing a number of reverse turns, iv) all of the selected conformations are conserved in the Gly-Pro-Gly-Arg-Ala-Phe stretch, the most probable viral immunodominant epitope. These data allow to suppose that binding properties of this site are determined by the structural motif which forms the conformation of a double beta-turn and appears common for all hexapeptide structures.

HIV Envelope Protein gp120↗

PubMed2003

Structural information in two-dimensional patterns: entropy convergence and excess entropy.

We develop information-theoretic measures of spatial structure and pattern in more than one dimension. As is well known, the entropy density of a two-dimensional configuration can be efficiently and accurately estimated via a converging sequence of conditional entropies. We show that the manner in which these conditional entropies converge to their asymptotic value serves as a measure of global correlation and structure for spatial systems in any dimension. We compare and contrast entropy convergence with mutual-information and structure-factor techniques for quantifying and detecting spatial structure.

Journal Article↗

PubMed1989

Thermostability of cytochrome c-552 from the thermophilic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus.

The denaturation of the c-type cytochrome of the thermophilic bacterium Hydrogenobacter thermophilus cytochrome c-552 by heat and guanidine hydrochloride was studied by measuring the change in circular dichroic spectra. The melting temperature (T1/2) of cytochrome c-552 in the presence of 1.5 M guanidine hydrochloride was 34 degrees C higher than that of the c-type cytochrome of Pseudomonas aeruginosa cytochrome c-551. Hydrogenobacter cytochrome c-552 is a much more stable protein than cytochrome c-551 of the mesophilic bacterium P. aeruginosa, even though their amino acid sequences are 56% identical and they have numerous other similarities. However, notwithstanding these similarities between the sequences of the cytochromes c-552 and c-551 that were compared, it is very likely that these differences in stability could be due to some heretofore undefined differences in their spatial structures. It has been suggested that alpha-helix structure and electrostatic interaction could be the source of the stable spatial structure of cytochrome c-552.

Amino Acid Sequence↗

PubMed1999

Molecular surface sequence analysis of several E. coli enzymes and implications for existence of casein kinase-2 bacterial predecessor.

Casein kinase-2 (CK2) is known as pleiotropic eukaryotic protein kinase that phosphorylates significant number of cellular proteins. Not all functions of the protein were registered up to the present time. However, it is known that this Ser/Thr-specific kinase is involved in the cell cycle progression and is essentially required for the eukaryotic cell viability. Fully automated molecular surface analysis procedure for identification of functionally significant surface residues and sequences on the base of protein spatial structure was elaborated. Using the elaborated procedure, several E. coli enzymes spatial structures and sequences were investigated. It was found that most of the casein kinase 2 potential sites found in sequences of enzymes are accessible for modification. Four of the 5 structures studied have CK2 consensus sites that may definitely influence the activity of the enzyme upon phosphorylation. Some of the potential "CK2-sites" has amino acid contents characteristic for physiological substrates of casein kinase 2 in eukaryotes. The main point of the elaborated method and the structural evidence for existence of a putative casein kinase E. coli predecessor or a protein with similar kinase activity are discussed. Physiological, biochemical, structural and evolutionary aspects of the existence of the putative predecessor are considered.

Adenylate Kinase↗

PubMedDate not supplied

[Continuity and discontinuity of the geomerida: the bionomic and biotic aspects].

The view of the spatial structure of the geomerida (Earth's life cover) as a continuum that prevails in modern phytocoenology is mostly determined by a physiognomic (landscape-bionomic) discrimination of vegetation components. In this connection, geography of life forms appears as subject of the landscapebionomic biogeography. In zoocoenology there is a tendency of synthesis of alternative concepts based on the assumption that there are no absolute continuum and absolute discontinuum in the organic nature. The problem of continuum and discontinuum of living cover being problem of scale aries from fractal structure of geomerida. This problem arises from fractal nature of the spatial structure of geomerida. The continuum mainly belongs to regularities of topological order. At regional and subregional scale the continuum of biochores is rather rare. The objective evidences of relative discontinuity of the living cover are determined by significant alterations of species diversity at the regional, subregional and even topological scale Alternatively to conventionally discriminated units in physionomically continuous vegetation, the same biotic complexes, represented as operational units of biogeographical and biocenological zoning, are distinguished repeatedly and independently by different researchers. An area occupied by certain flora (fauna, biota) could be considered as elementary unit of biotic diversity (elementary biotic complex).

Animals↗

PubMed2000

Genetic relationships and spatial genetic structure among clonal stocks of Trypanosoma cruzi in Colombia.

Genetic variability in the protozoan causative agent of Chagas' disease, Trypanosoma cruzi, has been analysed in some Latin American countries; Brazil, Bolivia, Chile and Paraguay. Although Colombia is a country displaying enormous biological diversity, few studies have been conducted from the perspective of the population genetics of Trypanosoma cruzi. This study was carried out using 23 Colombian stocks of this protozoan, analysed for 13 isoenzyme loci. The main population genetic results were: (1) Colombia is one of the distribution areas where T. cruzi appears to have the highest genetic variability and heterogeneity in Latin America; (2) the Pgm locus was found in fixed heterozygosis, supporting the presence of diploidy in this organism; (3) the absence of segregating genotypes and the absence of Hardy-Weinberg equilibrium support the view of the existence of a clonal structure as claimed by Tibayrenc and Ayala. Nevertheless, one characteristic of clonal structure, that of over-representation of some identical zymodemes in vast areas of varying environmental conditions, was not found in Colombia. In this country, a strong spatial autocorrelation, with a classic structure of regional patches, was observed.

Animals↗

PubMed1992

How to build a baby: II. Conceptual primitives.

A mechanism of perceptual analysis by which infants derive meaning from perceptual activity is described. Infants use this mechanism to redescribe perceptual information into image-schematic format. Image-schemas create conceptual structure from the spatial structure of objects and their movements, resulting in notions such as animacy, inanimacy, agency, and containment. These earliest meanings are nonpropositional, analogical representations grounded in the perceptual world of the infant. In contrast with most perceptual processing, which is not analyzed in this fashion, redescription into image-schematic format simplifies perceptual information and makes it potentially accessible for purposes of concept formation and thought. In addition to enabling preverbal thought, image-schemas provide a foundation for language acquisition by creating an interface between the continuous processes of perception and the discrete nature of language.

Child↗

PubMed2005

Chloroplast DNA variation of Quercus rubra L. in North America and comparison with other Fagaceae.

Quercus rubra is one of the most important timber and ornamental tree species from eastern North America. It is a widespread species growing under variable ecological conditions. Chloroplast DNA variation was studied by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) in 290 individuals from 66 populations sampled throughout the natural range. A total of 12 haplotypes were detected, with one found in 75% of the trees. Population differentiation is relatively low (G(ST) = 0.46), even when similarities between haplotypes are taken into account (N(ST) = 0.50), pointing to a weak phylogeographical structure. Furthermore, no spatial structure of genetic diversity could be detected. The genetic differentiation increased northwards, reflecting the postglacial history of Q. rubra. The unusual aspect of this study was the low level of chloroplast DNA genetic differentiation in Q. rubra compared to that typically observed in other oak species. Palynological evidence indicates that during the last glacial maximum, Q. rubra had one major distribution range with populations located relatively far to the north, resulting in only modest movement northwards when climate improved, whereas European white oaks were largely restricted to the southern European peninsulas and experienced extensive movements during the postglacial period. The contrasted geographical features and levels of tree species richness of both continents might further explain why congeneric species sharing similar life history traits have genetic structures that are so different.

DNA, Chloroplast↗

PubMedDate not supplied

Spatial and genetic structure within populations of wild American ginseng (Panax quinquefolius L., Araliaceae).

Spatial structure and fine-scale genetic structure were analyzed for the medicinal plant American ginseng (Panax quinquefolius L.) to more fully understand biological processes within wild populations. P. quinquefolius has been harvested for more than 250 years and is now considered threatened or rare throughout its range. Plants within four protected and four unprotected populations were significantly clumped based on Ripley's univariate analysis. Analysis with Ripley's bivariate test determined that juvenile plants were significantly clumped with adult plants at the shortest distance classes in all populations. Although plants were highly clumped, we found that significant fine-scale genetic structure was restricted to the shortest distance classes based on estimates of coancestry (f(ij)). In most cases, estimates of f(ij) were more significant among juveniles than among adults, especially at the shortest distance classes. The spatial structure of ginseng seems to result from the establishment and persistence of plants in favorable microhabitats coupled with limited seed dispersal around maternal individuals. There were no differences in patterns of fine-scale genetic structure between protected and unprotected populations.

Age Factors↗

PubMed2006

Scale-dependent interactions and community structure on cobble beaches.

Recent theory suggests that scale-dependent interaction between facilitation and competition can generate spatial structure in ecological communities. The application of this hypothesis, however, has been limited to systems with little underlying heterogeneity. We evaluated this prediction in a plant community along an intertidal stress gradient on cobble beaches in Rhode Island, USA. Prior studies have shown that Spartina alterniflora facilitates a forb-dominated community higher in the intertidal by modifying the shoreline environment. We tested the hypothesis that, at a smaller scale, Spartina competitively excludes forb species, explaining their marked absence within the lower Spartina zone. Transplant experiments showed forb species grow significantly better in the Spartina zone when neighbours were removed. Removal of the Spartina canopy led to a massive emergence of annual forbs, showing that competition limits local occupation. These findings indicate that interaction of large-scale facilitation and small-scale competition drives plant zonation on cobble beaches. This study is the first to provide empirical evidence of scale-dependent interactions between facilitation and competition spatially structuring communities in heterogeneous environments.

Chenopodiaceae↗