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PubMed2006

Population genetic structuring in Acanthopagrus butcheri (Pisces: Sparidae): does low gene flow among estuaries apply to both sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (theta = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (theta = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (theta = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.

Animals↗

PubMed2001

Predator migration in response to prey density: what are the consequences?

A predator-prey metapopulation model with two identical patches and only migration of the predator is investigated. Local predator-prey interaction is described by the so-called Rosenzweig-MacArthur model, while the migration term of the predator is put in a nonlinear form, which is derived by extending the Holling time budget argument to migration. In particular, a dimensionless parameter theta is introduced to quantify the migration tendency of predators while they are handling their prey, which gives rise to a family of models connecting two extremes: predators have no inclination to migrate while handling prey (theta = 0) and standard diffusion (theta = 1). Various aspects of the model, including changes in the number and the stability of equilibria and limit cycles, are investigated. We then focus on the key question: "Does spatial structure lead to a substantial damping of the violent oscillations exhibited by many predator-prey models?". It is known that the answer is "yes" if one adopts standard diffusion (theta = 1). However, we present substantial evidence that the answer is "no" if one takes theta = 0. We conclude that the migration submodel is an important constituent of a spatial predator-prey model and that the issue deserves scrutiny, both experimentally and theoretically.

Animals↗

PubMed1995

Genealogies and geography.

Any sample of genes traces back to a single common ancestor. Each gene also has other properties: its sequence, its geographic location and the phenotype and fitness of the organism that carries it. With sexual reproduction, different genes have different genealogies, which gives us much more information, but also greatly complicates population genetic analysis. We review the close relation between the distribution of genealogies and the classic theory of identity by descent in spatially structured populations, and develop a simple diffusion approximation to the distribution of coalescence times in a homogeneous two-dimensional habitat. This shows that when neighbourhood size is large (as in most populations) only a small fraction of pairs of genes are closely related, and only this fraction gives information about current rates of gene flow. The increase of spatial dispersion with lineage age is thus a poor estimator of gene flow. The bulk of the genealogy depends on the long-term history of the population; we discuss ways of inferring this history from the concordance between genealogies across loci.

Gene Frequency↗

PubMed2001

Structure of new porous compounds after annealing in vacuum.

Dehydration process in recently synthesized porous inorganic salts formed by large cluster anions [Re6X8(CN)6]4- (X= S, Se), transition metal cations and water molecules has been investigated. Desolvation process of the complex Co(DMF)6[Mo6Br8(NCS)6], where DMF dimethylformamide. has been studied. CoK, MoK and ReL3 XAFS measurements of these new complicated compounds before and after annealing in vacuum at temperature up to 250 degrees C were performed. Changes of electronic and spatial structure of these compounds under the heating process have been established and adequate structural models of the amorphous compounds obtained are suggested and discussed.

Journal Article↗

PubMed1998

[Urban growth and socio-spatial dynamics: Cairo from 1950 to 1990].

Urban growth patterns in Cairo, Egypt, are analyzed over the period 1950-1990. "In the last 40 years, Cairo's population growth has been accompanied by a major shift in socio-demographic distribution. By using social area analysis models to measure the spatial structuring of social disparities, we can see how Cairo society has moved from sectoral segmentation reflecting a socio-professional hierarchy to a concentric pattern based increasingly on age differences and family structures."

Africa↗

PubMed2000

[Study of solid-phase catalytic isotopic exchange of hydrogen in alpha-conotoxin G1 under the effect of spillover-tritium].

Tritium-labeled alpha-conotoxin G1 with a molar radioactivity of 35 Ci/mmol and full biological activity (according to the binding to nicotinic acetylcholine receptor) was obtained by the high-temperature solid-state catalytic isotope exchange (HSCIE). The tritium distribution in the molecule of alpha-conotoxin G1 was revealed by 3H NMR spectroscopy. Tritium was found in all amino acid residues except for the Asn4-Pro5-Ala6 fragment. The data on the comparative reactivity of C-H bonds, the ab initio quantum-chemical calculation of the hydrogen exchange reaction, and the information on the spatial structures of alpha-conotoxin G1 in solution and in crystal state allowed us to establish that the reactivity of H atoms may be increased by their interaction with the electron donor O and N atoms at the transition state of the HSCIE reaction. A decrease in the rate of the HSCIE reaction could be caused by both a poor spatial accessibility of C-H bonds and a limited mobility of the peptide fragment containing these bonds.

Amino Acid Sequence↗

PubMed2002

Excitability transitions and wave dynamics under spatiotemporal structured noise.

We present an analytic and numerical study of the effects of external fluctuations in active media. Our analytical methodology transforms the initial stochastic partial differential equations into an effective set of deterministic reaction-diffusion equations. As a result we are able to explain and make quantitative predictions on the systematic and constructive effects of the noise, for example, target patterns created out of noise and traveling or spiral waves sustained by noise. Our study includes the case of realistic noises with temporal and spatial structures.

Journal Article↗

PubMed2026

Wastewater viromics reveals host-structured viral signals and non-human pathogens.

Wastewater represents a powerful platform for human virus surveillance. However, the entry of animal- and plant-associated viruses into sewage is heterogeneous and incompletely understood, creating uncertainty about how reliably wastewater reflects non-human virus circulation. Here, we address this by analysing monthly wastewater metagenomic data from two distinct periods (2020-2021 and 2024-2025) across five major Finnish wastewater treatment plant catchments using a targeted hybrid-capture approach to characterise the composition, host range, and spatial distribution of the non-human wastewater virome. Nearly half of the detected viral accessions were non-human, indicating substantial diversity, despite human-associated viruses accounting for 83% of normalised viral reads. Rodent-, livestock-, and bird-associated viruses showed spatial structuring consistent with regional host populations. The wastewater viromics also detected four EU-regulated plant pathogens, including tomato brown rugose fruit virus, which was highly prevalent in wastewater two years before its first official detection in Finland. Together, these results show that wastewater contains structured, host-linked viral signals, supporting its use as an ecological proxy for non-human virus circulation.

Wastewater↗

PubMed2005

Velocity constancy and models for wide-field visual motion detection in insects.

The tangential neurons in the lobula plate region of the flies are known to respond to visual motion across broad receptive fields in visual space. When intracellular recordings are made from tangential neurons while the intact animal is stimulated visually with moving natural imagery,we find that neural response depends upon speed of motion but is nearly invariant with respect to variations in natural scenery. We refer to this invariance as velocity constancy. It is remarkable because natural scenes, in spite of similarities in spatial structure, vary considerably in contrast, and contrast dependence is a feature of neurons in the early visual pathway as well as of most models for the elementary operations of visual motion detection. Thus, we expect that operations must be present in the processing pathway that reduce contrast dependence in order to approximate velocity constancy. We consider models for such operations, including spatial filtering, motion adaptation, saturating nonlinearities, and nonlinear spatial integration by the tangential neurons themselves, and evaluate their effects in simulations of a tangential neuron and precursor processing in response to animated natural imagery. We conclude that all such features reduce interscene variance in response, but that the model system does not approach velocity constancy as closely as the biological tangential cell.

Animals↗

PubMed2004

Population genetic structure of the polypore Datronia caperata in fragmented mangrove forests.

Datronia caperata, a basidiomycete fungus, is one of the dominant polypore species found in neotropical mangrove forest fragments, where it is locally specialized on Laguncularia racemosa. We examined the genetic structure of D. caperata populations from four Panamanian mangrove forests using AFLP markers. Using five primer pair combinations, 145 loci were detected, 98.6% of which were polymorphic. Each of the populations showed a high degree of genetic diversity (Nei's h ranging from 0.146 to 0.223). Results from minimum spanning trees and Mantel tests showed little evidence for small-scale spatial structure within sites. A significant amount of total genetic variation was partitioned among populations (phi(ST) = 0.21) separated by 10s to 100s of km, a considerably greater amount than has been detected in other mushroom and wood-decaying fungi sampled at equal or greater geographic distances. These results suggest that despite production of copious basidiospores capable of long distance dispersal, some homobasidiomycete fungi may be susceptible to genetic isolation due to habitat fragmentation.

Base Sequence↗

PubMed2005

Recovery of image blocks using the method of alternating projections.

A technique for block-loss restoration in block-based image and video coding, dubbed recovery of image blocks using the method of alternating projections (RIBMAP), is developed. The algorithm is based on orthogonal projections onto constraint sets in a Hilbert space. For the recovery of a linear dimension N size block, a total of 8N vectors are extracted from the surrounding area of an N x N missing block. These vectors form a library from which the best matching spatial information for the missing block is extracted. Recovery vectors, including both undamaged and restored damaged pixels, are introduced. The vectors are used to find highly correlated information relating to the lost pixels. To assure continuity with the surrounding undamaged area, three additional convex constraints are formulated. Adherance to these sets is imposed using alternating projections. Simulation results using orthogonal projections demonstrate that RIBMAP recovers spatial structure faithfully. Simulation comparisons with other procedures are presented: Ancis and Giusto's hybrid edge-based average-median interpolation technique, Sun and Kwok's projections onto convex sets-based method, Hemami and Meng's interblock correlation interpolation approach, Shirani et al.'s modified interblock correlation interpolation scheme, and Alkachouh and Bellanger's fast discrete cosine transformation-based spatial domain interpolation algorithm. Characteristic of the results are those of the "Lena" JPEG image when one fourth of periodically spaced blocks in the image have errors. The peak signal-to-noise ratio of the restored image is 28.68, 29.99, 31.86, 31.69, 31.57, and 34.65 dB using that of Ancis and Giusto, Sun and Kwok, Hemami and Meng, Shirani et al., Alkachouh and Bellanger, and RIPMAP, respectively.

Algorithms↗

PubMed2006

Evolving metacommunities: toward an evolutionary perspective on metacommunities.

The metacommunity framework predicts that local coexistence depends on the outcome of local species interactions and regional migration. In analogous fashion, spatial structure among populations can shape species interactions through evolutionary mechanisms. Yet, most metacommunity theories assume that populations do not evolve. Here, we evaluate how evolution shapes local species coexistence and exclusion within the multiscale and multispecies context embodied by the metacommunity framework. In general, coexistence in joint ecological-evolutionary models requires low to intermediate dispersal rates that can promote maintenance of both regional species and genetic diversity. These conditions support a set of key mechanisms that modify patterns of species coexistence including local adaptation, gene storage effects, genetic rescue effects, spatial genetic subsidies, and metacommunity evolution. Multispecies extensions indicate that correlated selection can further alter the outcome of interspecific interactions depending on the magnitude and direction of correlations and shape of fitness trade-offs. We suggest that an evolving metacommunity perspective has the potential to generate novel predictions about community structure and function by incorporating the genetic and species diversity that characterize natural communities. In adopting such a perspective, we seek to facilitate understanding about the interactions between evolutionary and metacommunity dynamics.

Biological Evolution↗

PubMed2007

SEM and 3D synchrotron radiation micro-tomography in the study of bioceramic scaffolds for tissue-engineering applications.

Different biomaterials have been proposed as scaffolds for the delivery of cells and/or biological molecules to repair or regenerate damaged or diseased bone tissues. Particular attention is being given to porous bioceramics that mimic trabecular bone chemistry and structure. Chemical composition, density, pore shape, pore size, and pore interconnection are elements that have to be considered to improve the efficiency of these biomaterials. Commonly, two-dimensional (2D) systems of analysis such as scanning electron microscope (SEM) are used for the characterization and comparison of the scaffolds. Unfortunately, these systems do not allow a complete investigation of the three-dimensional (3D) spatial structure of the scaffold. In this study, we have considered two different techniques, that is, SEM and 3D synchrotron radiation (SR) micro-CT to extract information on the geometry of two hydroxyapatite (HA) bioceramics with identical chemical composition but different micro-porosity, pore size distribution, and pore interconnection pathway. The two scaffolds were obtained with two different procedures: (a) sponge matrix embedding (scaffold FB), and (b) foaming (scaffold EP). Both scaffolds showed structures suitable for tissue-engineering applications, but scaffold EP appeared superior with regard to interconnection of pores, surface on which the new bone could be deposited, and percentage of volume available to bone deposition.

Bone Substitutes↗

PubMed2001

Evolutionary self-organization of cell-free genetic coding.

Genetic encoding provides a generic construction scheme for biomolecular functions. This paper addresses the key problem of coevolution and exploitation of the multiple components necessary to implement a replicable genetic encoding scheme. Extending earlier results on multicomponent replication, the necessity of spatial structure for the evolutionary stabilization of the genetic coding system is established. An individual-based stochastic model of interacting molecules in three-dimensional space is presented that allows the evolution of genetic coding to be analyzed explicitly. A massively parallel configurable computer (NGEN) is used to implement the model, on the time scale of millions of generations, directly in electronic hardware. The spatial correlations between components of the genetic coding system are analyzed and found to be essential for evolutionary stability.

Animals↗

PubMed2006

Free volume of an epoxy resin and its relation to structural relaxation: evidence from positron lifetime and pressure-volume-temperature experiments.

The microstructure of the free volume and its temperature dependence in the epoxy resin diglycidyl ether of bisphenol-A (DGEBA) have been examined using positron annihilation lifetime spectroscopy (PALS, 80-350K, 10(-5) Pa) and pressure-volume-temperature (PVT, 293-470 K, 0.1-200MPa) experiments. Employing the Simha-Somcynsky lattice-hole theory (S-S eos), the excess (hole) free volume fraction h and the specific free and occupied volumes, Vf=hV and Vocc=(1-h)V, were estimated. From the PALS spectra analyzed with the new routine LT9.0 the hole size distribution, its mean, , and mean dispersion, sigma h, were calculated. varies from 35 130 A3. From a comparison of with V and Vf, the specific hole number N'h was estimated to be independent of the temperature [Nh(300 K)=N'h/V=0.65 nm-3]. From comparison with reported dielectric and viscosity measurements, we found that the structural relaxation slows down faster than the shrinkage of the hole free volume Vf would predict on the basis of the free volume theory. Our results indicate that the structural relaxation in DGEBA operates via the free-volume mechanism only when liquidlike clusters of cells of the S-S lattice appear which contain a local free volume of approximately 1.5 or more empty S-S cells. The same conclusion follows from the pressure dependency of the structural relaxation and Vf. It is shown that PALS mirrors thermal volume fluctuations on a subnanometer scale via the dispersion in the ortho-positronium lifetimes. Using a fluctuation approach, the temperature dependency of the characteristic length of dynamic heterogeneity, xi, is estimated to vary from xi=1.9 nm at Tg to 1.0 nm at T/Tg>1.2. A model was proposed which relates the spatial structure of the free volume as concluded from PALS to the known mobility pattern of the dynamic glass transition at low (cooperative alpha-relaxation) and high (alpha-relaxation) temperatures. We discuss possible reasons for the differences between the results of our method and the conclusion from dynamic heat capacity.

Journal Article↗

PubMed1990

[The current role of lymphoscintigraphy in the study of lymphedema of the limbs].

After a brief review of the classical methodology and results of lymphoscintigraphy, the technique is considered in terms of an original kinetic study approach. Immediately after distal subcutaneous injection of a technetium colloid (rhenium sulfocolloid), 40 1-min serial images of the limbs are recorded followed 4 h after injection by recording of static images. The main abnormalities detected by scintigraphy concern the lymphatic vessels, nodes and interstitium. They reveal the presence of lymphedema and provide information about its mechanism, indicating, particularly in the case of primary lymphedema, whether there is predominant hyperplasia or hypoplasia in vessels or nodes. Synoptic study of the initial dynamic recording based on simple examination of serial images is difficult. Complementary data provided by activity curves determined from manually selected regions of interest (ROI'S) are of limited value since the ROI'S correspond to superimposed spatial structures. Two data-processing techniques--the condensed image (CI) and factorial analysis (FA)--were therefore applied to dynamic scintigraphic recordings in order to study lymphatic progress of the radiotracer in the legs. A complete dynamic series is described in two IC, one for each leg. The CI, obtained by mounting the 40 serial images in vertical strips 1 pixel in width, describes the spatial distribution of radioactivity along the leg during recording. Factorial analysis provides automatic extraction of pure kinetic components or factors from the dynamic series despite their spatial superposition. The factors are described by factorial curves and factorial images representing the spatial identity of the factor. Three-factor FA was applied successively to each leg.(ABSTRACT TRUNCATED AT 250 WORDS)

Arm↗

PubMed1989

[Antipeptide antibodies to the porcine lactate dehydrogenase isoenzyme M4 active center fragment as a probe for the structural analysis of active centers of human lactate dehydrogenase isoforms].

Antipeptide antibodies (AB) to the fragment of the active center of porcine lactate dehydrogenase M4 isoform were used for the analysis of antigenic properties and structural comparison of active centers of human lactate dehydrogenase isoforms. Selective precipitation of the M-subunit-containing isoforms using an immunoadsorbent based on antipeptide AB as well as selective inhibition of the enzymic activity of the M4 isoform by antipeptide AB testify to the specific binding of isoforms to antipeptide AB. The experimental results confirm the literary data on conformational changes in the structure of the active centers of corresponding human lactate dehydrogenase isoforms. The specific interaction of antipeptide AB with human lactate dehydrogenase isoforms suggests that the site of the amino acid sequence (residues 180-214) in both human and porcine M4 isoenzymes is immunochemically identical. The data obtained suggest that antipeptide AB are convenient probes for detecting differences (including minor ones) in the primary and spatial structure of enzymes.

Animals↗

PubMed2004

Folding and stability of chimeric immunofusion VL-barstar.

A chimeric protein VL-barstar that comprises the VL domain of anti-human ferritin monoclonal antibody F11 and barstar, the naturally occurring inhibitor of bacterial RNase barnase, has been constructed for study of structure-function characteristics of chimeric immunoglobulin fused proteins. Such chimeric constructs may be potentially employed for development of bivalent/bispecific antibodies on the basis of the high affinity interaction between barstar and barnase (the association constant is about 10(14) M(-1)). We have developed a protocol for VL-barstar expression in E. coli and purification and refolding from inclusion bodies that yields a homogeneous and soluble form of this protein. Differential scanning calorimetry in combination with fluorescence and CD spectroscopy revealed that the VL-barstar formed well-resolved ordered secondary and compact tertiary structures. However, partial loss of tertiary interactions resulted in low stability of the recombinant protein and the lack of functional activity of the two constituent modules. These conformational features suggest that the protein might be referred to the class of native molten globules, which comprises partially unfolded conformations stabilized under physiological conditions. Since individually expressed VL domain and barstar retain completely folded conformation and stable spatial structure, the incomplete folding of the chimeric protein may be attributed to interaction between heterologous domains, which appears at the folding stage preceding formation of a system of tertiary interactions in both structural modules. The results provide evidence for non-native interactions between heterologous modules that may occur in chimeric proteins composed of taxonomically distinct fusion partners.

Amino Acid Sequence↗