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PubMed2005

Determining the spectral signature of spatial coherent structures in an open cavity flow.

We applied to an open flow a proper orthogonal decomposition (POD) technique, on two-dimensional (2D) snapshots of the instantaneous velocity field, to reveal the spatial coherent structures responsible for the self-sustained oscillations observed in the spectral distribution of time series. We applied the technique to 2D planes out of three-dimensional (3D) direct numerical simulations on an open cavity flow. The process can easily be implemented on usual personal computers, and might bring deep insights regarding the relation between spatial events and temporal signature in (both numerical or experimental) open flows.

Journal Article↗

PubMed1995

[Homogeneity of the spatial distribution of cancers of the female reproductive tract in Quebec].

Risk factors associated with women's reproductive life and sexual growth do not adequately predict cancer incidence of the breast, uterus and ovary. The heterogeneous worldwide distribution of these cancers could imply that some environmental and cultural risk factors are involved in their cancerogenesis. The few attempts made so far to unravel their spatial structures at a geographic scale facilitating the search for exogenous risk factors have proved inconclusive. This study reports the results of a spatial analysis of the cancer incidence rates for breast, cervix, endometrium and ovary among Community Health Departments (CHD) in Quebec using a spatial autocorrelation method. Correlograms built according to four definitions of the inter-CHDs distance indicate that breast and ovary incidence rates follow quite similar spatial gradients attesting to their etiologic affinity. They also suggest that the spatial distribution of endometrial cancer follows a gradient divergent from that of breast and ovary cancers, and that the CHDs' spatial scale does not suitably describe the distribution of cervical cancer. The demonstration of a structured spatial distribution for breast, endometrium and ovary cancers in Québec strengthen the hypothesis that cultural or environmental risk factors are involved in their etiology. But, the observed disparities in the spatial structure of these cancers imply that their etiologic specificity may be greater than their biologic bond would suggest.

Adolescent↗

PubMedDate not supplied

[Structure and function of pore-forming proteins from bacteria of the genus Yersinia: I. Isolation and a comparison of physicochemical properties and functional activity of Yersinia porins].

The molecular organization and functional activity of porins isolated from the outer membrane (OM) of the Yersinia enterocolitica and three phylogenetically close nonpathogenic Yersinia species (Y. intermedia, Y. kristensenii, and Y. frederiksenii) cultured at 6-8 degrees C were comparatively studied for the first time. The proteins were isolated in two molecular forms (trimeric and monomeric), and their spatial structures were characterized by the methods of optical spectroscopy, CD and intrinsic protein fluorescence. The studied porins were shown to belong to the beta-structural proteins (they have 59-96% total beta structures and 0-17% alpha helices). The spatial structures of the proteins were demonstrated to depend on the nature of the detergent used for solubilization. Unlike the enterobacterial pore-forming proteins, the porin trimers are less stable to sodium dodecyl sulfate (SDS). The spatial structures of the porins become more compact after the substitution of octyl beta-D-glucoside for SDS: the content of beta structures increases and the accessibility of Trp residues to solvent decreases. It was established with the use of the technique of bilayer lipid membranes that the functional properties of the porins are similar to those of the OmpF proteins of Gram-negative bacteria. Trimers are functionally active forms of the porins. Special features of the pore-forming activity of the Yersinia porins were revealed to depend on the microorganism species and the value of the membrane potential.

Bacterial Outer Membrane Proteins↗

PubMed2005

Spatial genetic structure of Simarouba amara Aubl. (Simaroubaceae), a dioecious, animal-dispersed Neotropical tree, on Barro Colorado Island, Panama.

Simarouba amara (Simaroubaceae) is a vertebrate-dispersed, insect-pollinated Neotropical tree found in lowland moist forest from upper Mesoamerica to the Amazon basin. We assessed the spatial genetic structure of S. amara within the 50-ha Forest Dynamics Plot on Barro Colorado Island in the Republic of Panama. A total of 300 individuals were genotyped using five microsatellite loci, representing 100 individuals with a dbh>or=10 cm, 100 individuals of 1-10 cm dbh, and 100 individuals of <1 cm dbh. The 200 individuals in the two larger size classes were also genotyped with 155 AFLP loci. Spatial autocorrelation analysis using Moran's Index detected significant genotypic association at the smallest distance classes for 1-10 cm dbh (0-20 m) and >10 cm dbh (0-40 m) size categories. Significant spatial autocorrelations were detected over larger scales (0-140 m) in <1 cm dbh individuals. The relatively weak genetic structure of S. amara, in comparison to other recent studies, may be explained by pollen and seed dispersal over the 50 ha plot, overlapping seed shadows, and postrecruitment mortality.

Demography↗

PubMed2004

Filamentous-actins in human hepatocarcinoma cells with CLSM.

AIM: To establish a method for optical sections of HepG2 human hepatoblastoma cells with confocal laser scanning microscope (CLSM) and to study the spatial structure of filamentous actin (F-actin) in HepG2 cells. METHODS: HepG2 cells were stained with FITC-phalloidin that specifically binds F-actin, with propidium iodide (PI) to the nucleus, and scanned with a CLSM to generate optically sectioned images. A series of optical sections taken successively at different focal levels in steps of 0.7 microm were reconstructed with the CLSM reconstruction program. RESULTS: CLSM images showed that the FITC-stained F-actin was abundant microfilament bundles parallel or netted through the whole cell and its processes. Most F-actin microfilaments extended through the cell from one part toward the other or run through the process. Some microfilaments were attached to the plasma membrane, or formed a structural bridge connecting to the neighboring cells. CONCLUSION: A method for double labeling HepG2 human hepatoblastoma cells and CLSM imaging F-actin microfilaments and nuclei by image thin optical sections and spatial structure was developed. It provides a very useful way to study the spatial structure of F-actin.

Actin Cytoskeleton↗

PubMed2000

[Structure and spatial pattern dynamics of dominant populations in a natural forest in north Guangdong Province].

Five 1000-m2 plots were set up in a forest dominated by Schima superba, Castanopsis fargesii and Pinus massoniana in Luoba Nature Reserve, Shixing County, north Guangdong Province. Field data were obtained by tally with contiguous grid quadrat method. The analysis of population structure and spatial distribution patterns of the dominant species in the forest shows that S. superba and C. fargesii had a large reserve of seedlings, with up to 1538 and 9763 seedlings per hm2, respectively, showing a pyramid shape of population structure. Both populations had a high mortality for seedlings of classes I and II in the process of development to saplings. The population structure of P. massoniana was an inverse pyramid type, with no seedlings and only 4 saplings per hm2, but 44 large trees per hm2. The spatial distribution patterns of P. massoniana and C. fargesii in coniferous broadleaved mixed community chiefly dominated by broadleaved trees were uniform, and in those chiefly dominated by P. massoniana were aggregated, but there were different causes of pattern dynamics for P. massoniana and C. fargesii. S. superba in both communities showed an aggregated distribution pattern. The aggregation intensity was different, with K values from 0.4280 to 0.9750. Regarding the distribution patterns in different development stages, S. superba was aggregated in different stages, while C. fargesii varied with uniform distribution pattern for the large trees and aggregated distribution pattern for the saplings and median trees. As for P. massoniana, its median trees showed an aggregated distribution pattern, while both the saplings and large trees were uniform. The variations in spatial distribution patterns of populations in different development stages were closely related to the biological and ecological characteristics of the species, but different block size had an impact on the outcome of spatial distribution patterns.

China↗

PubMed2002

Spatial genetic structure and clonal diversity of island populations of lady's slipper (Cypripedium calceolus) from the Biebrza National Park (northeast Poland).

Three populations of the rare and endangered plant species Cypripedium calceolus were included in a study of genetic diversity and spatial genetic structure in the Biebrza National Park, northeast Poland. Analysis of 11 allozyme loci indicate that the populations of this species contained high genetic variability (P = 45.5%, A= 1.73). On the other hand, the genetic differentiation (FST = 0.014, P < 0.05) among C. calceolus populations was very low when compared to other species with similar life history characteristics. The observed high rate of gene flow (Nm = 18) may suggest that the populations studied derived from each other in the recent past. Five polymorphic allozyme markers identified 109 multilocus genotypes in three populations and the majority of them (67%) were population-specific. One of the populations studied, characterized by particularly extensive vegetative reproduction, showed the lowest clonal diversity (G/N = 0.15) and heterozygosity (HO = 0.111) values and the highest FIS(0.380), when compared to other two populations (G/N = 0.26-0.27, HO= 0.166-178, FIS = 0.024-0.055). This may indicate that clonal reproduction has an important influence on the genetic structure of C. calceolus populations. The longevity of genets, the out-crossing breeding system and the presence of recruitment from seeds are factors maintaining genetic diversity in C. calceolus.

Biological Evolution↗

PubMed2005

Rapidly declining fine-scale spatial genetic structure in female red deer.

A growing literature now documents the presence of fine-scale genetic structure in wild vertebrate populations. Breeding population size, levels of dispersal and polygyny--all hypothesized to affect population genetic structure--are known to be influenced by ecological conditions experienced by populations. However the possibility of temporal or spatial variation in fine-scale genetic structure as a result of ecological change is rarely considered or explored. Here we investigate temporal variation in fine-scale genetic structure in a red deer population on the Isle or Rum, Scotland. We document extremely fine-scale spatial genetic structure (< 100 m) amongst females but not males across a 24-year study period during which resource competition has intensified and the population has reached habitat carrying capacity. Based on census data, adult deer were allocated to one of three subpopulations in each year of the study. Global F(ST) estimates for females generated using these subpopulations decreased over the study period, indicating a rapid decline in fine-scale genetic structure of the population. Global F(ST) estimates for males were not different from zero across the study period. Using census and genetic data, we illustrate that, as a consequence of a release from culling early in the study period, the number of breeding females has increased while levels of polygyny have decreased in this population. We found little evidence for increasing dispersal between subpopulations over time in either sex. We argue that both increasing female population size and decreasing polygyny could explain the decline in female population genetic structure.

Animals↗

PubMed2006

[Preparation and spectral analysis of a new type of blue light-emitting material delta-Alq3].

In the present article, delta-Alq3, a new type of blue light-emitting material, was synthesized and investigated by IR spectra, XRD spectra, UV-Vis absorption spectra, photoluminescence (PL) spectra, and electroluminescence (EL) spectra. The relationship between molecular spatial structure and spectral characteristics was studied by the spectral analysis of delta-Alq3 and alpha-Alq3. Results show that a new phase of Alq3 (delta-Alq3) can be obtained by vacuum heating alpha-Alq3, and the molecular spatial structure of alpha-Alq3 changes during the vacuum heating. The molecular spatial structure of delta-Alq3 lacks symmetry compared to alpha-Alq3. This transformation can reduce the electron cloud density on phenoxide of Alq3 and weaken the intermolecular conjugated interaction between adjacent Alq3 molecules. Hence, the pi--pi* electron transition absorption peak of delta-Alq3 shifts toward short wavelength in UV-Vis absorption spectra, and the maximum emission peak of delta-Alq3 (lamda max = 480 nm) blue-shifts by 35 nm compared with that of alpha-Alq3 (lamda max = 515 nm) in PL spectra. The maximum emission peaks of delta-Alq3 and alpha-Alq3 are all at 520 nm in EL spectra.

English Abstract↗

PubMed1982

[Maturation of evoked potentials to patterned stimuli, and sensitivity of the visual system to deprivation].

A study was made of age peculiarities of EPs to spatially structurized stimuli in the shape of chess fields with different dimensions of their cells in children and juveniles with normal vision, aged from seven to seventeen. Heterochroneity has been established in maturation of EPs to a homogeneous and a spatially structurized stimuli. In accordance with the criterion of "maturity" of the EP to a spatially structurized stimulus, an enhanced probability of "mature" EPs appearance was observed with age, from 0.23 in seven year old to 0.75 in 11 to 17 years old. Correspondence was shown of age EP dynamics to age changes of the visual system sensitivity to deprivation.

Adolescent↗

PubMed2000

Competition by allelopathy proceeds in traveling waves: colicin-immune strain aids colicin-sensitive strain.

Producing toxic chemicals to suppress both the growth and survivorship of local competitors is called allelopathy; some strains of the bacteria Escherichia coli produce a toxin (named colicin) which may kill colicin-sensitive neighbors while they themselves are immune. In a previous paper, the competitive outcome between colicin-producing and colicin-sensitive strains was shown to differ between a spatially structured and a completely mixed population. In this paper, we analyze the role of a third, "colicin-immune," strain, which does not produce colicin but is immune to it. Without spatial structure, the colicin-immune strain suppresses the colicin-producing strain and enables the colicin-sensitive strain to win. In a spatially structured population, modeled as a reaction-diffusion system, we examine the speed of boundaries between areas dominated by different strains in traveling waves and the events after the collision of two such boundaries. The colicin-immune strain passes through the area dominated by the colicin-sensitive strain and drives the colicin-producing strain to extinction. Subsequently the colicin-sensitive strain occupies the whole population.

Alleles↗

PubMed2004

Spatial analysis of the distribution of intestinal nematode infections in Uganda.

The spatial epidemiology of intestinal nematodes in Uganda was investigated using generalized additive models and geostatistical methods. The prevalence of Ascaris lumbricoides and Trichuris trichiura was unevenly distributed in the country with prevalence greatest in southwest Uganda whereas hookworm was more homogeneously distributed. A. lumbricoides and T. Trichiura prevalence were nonlinearly related to satellite sensor-based estimates of land surface temperature; hookworm was nonlinearly associated with rainfall. Semivariogram analysis indicated that T. trichiura prevalence exhibited no spatial structure and that A. lumbricoides exhibited some spatial dependency at small spatial distances, once large-scale, mainly environmental, trends had been removed. In contrast, there was much more spatial structure in hookworm prevalence although the underlying factors are at present unclear. The implications of the results are discussed in relation to parasite spatial epidemiology and the prediction of infection distributions.

Adolescent↗

PubMed2003

Sensorimotor coordination and the structure of space.

Embedded in neural and behavioral organization is a structure of sensorimotor space. Both this embedded spatial structure and the structure of physical space inform sensorimotor control. This paper reviews studies in which the gravitational vertical and horizontal are crucial. The mathematical expressions of spatial geometry in these studies indicate methods for investigating sensorimotor control in freefall. In freefall, the spatial structure introduced by gravitation - the distinction between vertical and horizontal - does not exist. However, an astronaut arriving in space carries the physiologically-embedded distinction between horizontal and vertical learned on earth. The physiological organization based on this distinction collapses when the strong otolith activity and other gravitational cues for sensorimotor behavior become unavailable. The mathematical methods in this review are applicable in understanding the changes in physiological organization as an astronaut adapts to sensorimotor control in freefall. Many mathematical languages are available for characterizing the logical structures in physiological organization. Here, group theory is used to characterize basic structure of physical and physiological spaces. Dynamics and topology allow the grouping of trajectory ranges according to the outcomes or attractors. The mathematics of ordered structures express complex orderings, such as in multiphase movements in which different parts of the body are moving in different phase sequences. Conditional dynamics, which combines dynamics with the mathematics of ordered structures, accommodates the parsing of movement sequences into trajectories and transitions. Studies reviewed include those of the sit-to-stand movement and early locomotion, because of the salience of gravitation in those behaviors. Sensorimotor transitions and the conditions leading to them are characterized in conditional dynamic control structures that do not require thinking of an organism as an input-output device. Conditions leading to sensorimotor transitions on earth assume the presence of a gravitational vertical which is lacking in space. Thus, conditions used on earth for sensorimotor transitions may become ambiguous in space. A platform study in which sensorimotor transition conditions are ambiguous and are related to motion sickness is reviewed.

Gravitation↗

PubMed2004

Simulation of the interaction between ScyTx and small conductance calcium-activated potassium channel by docking and MM-PBSA.

Computational methods are employed to simulate interaction of scorpion toxin ScyTx in complex with the small conductance calcium-activated potassium channel rsk2. All of available 25 structures of ScyTx in the Protein Data Bank determined by NMR were considered for improving performance of rigid protein docking of ZDOCK. Four main binding modes were found among a large number of predicted complexes by using clustering analysis, screening with expert knowledge, energy minimization, and molecular dynamics simulations. The quality and validity of the resulting complexes were further evaluated by molecular dynamics simulations with the generalized Born solvation model and by calculation of relative binding free energies with the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) in the AMBER 7 suit of programs. The complex formed by the 22nd structure of the ScyTx and rsk2 channel was identified as the most favorable complex by using a combination of computational methods, which contain further introduction of flexibility without restraining residue side chain. From the resulted spatial structure of the ScyTx and rsk2 channel, ScyTx associates the mouth of the rsk2 channel with alpha-helix rather than beta-sheet. Structural analysis first revealed that Arg(13) played a novel and vital role of blocking the pore of the rsk2 channel, whose role is remarkably different from that of highly homologous scorpion toxin P05. Between the interfaces in the ScyTx-rsk2 complex, strong electrostatic interaction and hydrogen bonds exist between Arg(13) of ScyTx and Gly-Tyr-Gly-Asp sequential residues located in the four symmetrical chains of the pore region. Simultaneously, five hydrogen bonds between Arg(6) of ScyTx and Asp(341)(C), Val(366)(C), and Pro(367)(C), and electrostatic interaction between Arg(6) of ScyTx and Asp(364)(B) and Asp(341)(C) are also found by structural analysis. In addition, His(31) located at the C-terminal of ScyTx is surrounded by Val(342)(A), Asp(364)(A), Met(365)(A), Pro(367)(B), and Asn(366)(B) within a contact distance of 4.0 A. These simulation results are in good agreement with experimental data and can effectively explain the binding phenomena between ScyTx and the potassium channel at the level of molecular spatial structure. The consistency between results of molecular modeling and experimental data strongly suggests that our spatial structure model of the ScyTx-rsk2 complex is reasonable. Therefore, molecular docking combined with molecular dynamics simulations followed by molecular mechanics Poisson-Boltzmann surface area analysis is an attractive approach for modeling scorpion toxin-potassium channel complexes a priori for further biological studies.

Animals↗

PubMed2004

Spatial models of virus-immune dynamics.

To date, the majority of theoretical models describing the dynamics of infectious diseases in vivo are based on the assumption of well-mixed virus and cell populations. Because many infections take place in solid tissues, spatially structured models represent an important step forward in understanding what happens when the assumption of well-mixed populations is relaxed. Here, we explore models of virus and virus-immune dynamics where dispersal of virus and immune effector cells was constrained to occur locally. The stability properties of our spatial virus-immune dynamics models remained robust under almost all biologically plausible dispersal schemes, regardless of their complexity. The various spatial dynamics were compared to the basic non-spatial dynamics and important differences were identified: When space was assumed to be homogeneous, the dynamics generated by non-spatial and spatially structured models differed substantially at the peak of the infection. Thus, non-spatial models may lead to systematic errors in the estimates of parameters underlying acute infection dynamics. When space was assumed to be heterogeneous, spatial coupling not only changed the equilibrium properties of the uncoupled populations but also equalized the dynamics and thereby reduced the likelihood of dynamic elimination of the infection. In line with experimental and clinical observations, long-lasting oscillation periods were virtually absent. When source-sink dynamics were considered, the long-term outcome of the infection depended critically on the degree of spatial coupling. The infection collapsed when emigration from source sites became too large. Finally, we discuss the implications of spatially structured models on medical treatment of infectious diseases, and note that a huge gap exists in data accurately describing infection dynamics in solid tissues.

Chronic Disease↗

PubMed2006

Morphomechanical programming of morphogenesis in cnidarian embryos.

The factors governing the pattern formation process in the early morphogenesis of a marine colonial hydroid, Dynamena pumila, have been studied. Two different types of morphogenesis have been distinguished. Morphogenesis of the first type goes on via changes in cell shape and cell axis orientation, while morphogenesis of the second type is based upon the active coordinated cell movements associated with cell rearrangements. It was shown that morphogenesis of both types can be considered as cascades in which any event is a consequence of the previous one. The spatial structure of each developmental stage contains information about the direction and the initial conditions of further morphogenesis. So, an "epigenetic program" of morphogenesis gradually originates in the course of development and provides the stable reproduction of spatial structures. It is reasonable to consider the activity of epigenetic factors guiding Dynamena morphogenesis (geometry/topology of an embryo, heterogeneity of an embryo spatial structure, configuration of the field of mechanical stresses of the embryo surface) as "morphomechanical programming" of morphogenesis.

Animals↗

PubMed1978

[The antigen activity and structure of analogues and fragments of angiotensin, which contain enantiomeric forms of amino acids and aza-alpha'-homoamino acids].

The antigen activity of angiotensin, its fragments and analogues, which contain enantiomeric forms of amino acids and aza-alpha'-homoamino acids is studied by cross reactions with specific antibodies, obtained for angiotensin and its central tetrapeptide. It is found that the inclusion of additional NH-group between alpha carbon and carboxyl group of peptide chain, although in few cases radically changes spatial structure of compounds, does not deprivate their antigen activity. The replacement of NH-group to the C-end of the angiotensin molecule by affection the antigen determinant considerably decreases the antigen activity of the analogues. The important role in the determination of the antigen activity play the tyrosine residue and its specific orientation with respect to the antigen molecule. Low molecular weight fragments and analogues of the central part of angiotensin molecule, which have less "rigid" spatial structures, are capable to reorganize their spatial structure during interaction with antibodies.

Amino Acids↗

PubMed2006

Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management.

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.

Animals↗