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PubMed1993

Molecular Turing structures in the biochemistry of the cell.

Reactive lattice gas automata simulations show that Turing structure can form on a mesoscopic scale and are stable to molecular fluctuations in this domain. Calculations on the Sel'kov model suggest that Turing instabilities can give rise to global spatial symmetry breaking in ATP concentration within the cell cytoplasm with a mesoscopic Turing scale well within typical cell dimensions. This leads to a new mechanism for the global breaking of energy distribution in the cell. It also leads to reappraisal of the importance of the Turing effect on extended biochemical spatial structures and energy transport available to cell morphogenesis.

Journal Article↗

PubMed2006

Disease mapping and spatial regression with count data.

In this paper, we provide critical reviews of methods suggested for the analysis of aggregate count data in the context of disease mapping and spatial regression. We introduce a new method for picking prior distributions, and propose a number of refinements of previously used models. We also consider ecological bias, mutual standardization, and choice of both spatial model and prior specification. We analyze male lip cancer incidence data collected in Scotland over the period 1975-1980, and outline a number of problems with previous analyses of these data. In disease mapping studies, hierarchical models can provide robust estimation of area-level risk parameters, though care is required in the choice of covariate model, and it is important to assess the sensitivity of estimates to the spatial model chosen, and to the prior specifications on the variance parameters. Spatial ecological regression is a far more hazardous enterprise for two reasons. First, there is always the possibility of ecological bias, and this can only be alleviated by the inclusion of individual-level data. For the Scottish data, we show that the previously used mean model has limited interpretation from an individual perspective. Second, when residual spatial dependence is modeled, and if the exposure has spatial structure, then estimates of exposure association parameters will change when compared with those obtained from the independence across space model, and the data alone cannot choose the form and extent of spatial correlation that is appropriate.

Epidemiologic Methods↗

PubMed1999

[Geographic differences of bronchopulmonary cancer mortality in France and spatial scales of analysis: significance of scale change in health geography].

BACKGROUND: It is important to choose a valid spatial scale to study health differences in a geographical perspective. Many scales can be valid and a combination is required to understand the spatial distribution of a given health problem. Geographic distribution of lung cancer was studied in France using different scales to illustrate the importance of changing scales in health geography. METHODS: Standardized rates (direct method) for lung cancer were calculated for the period 1988-92 and mapped at different scales. RESULTS: Original spatial structure was observed for each scale. This proved that different interactions occur at each scale between environmental and social factors. Changing the scale allowed a better understanding of variations in the spatial distribution of lung cancer. CONCLUSIONS: The validity of a regional scale to study health geographical distributions is questioned. Changing the scale would allow proposing action to improve health promotion.

Bronchial Neoplasms↗

PubMed1995

MMDB: an ASN.1 specification for macromolecular structure.

We present an exchange specification for data describing the three-dimensional structure of biological macromolecules. The specification was designed for MMDB, a Molecular Modeling Database supported by the National Center for Biotechnology Information (NCBI), based on information from the Protein Data Bank (PDB). In the MMDB specification, the chemical structures of molecules are described hierarchically as connectivity graphs, to directly support comparison by subgraph isomorphism or assignment algorithms. Three-dimensional coordinates are linked unambiguously to nodes in the chemical graph, so that homology-derived structures may be generated directly from alignment of chemically similar groups. In conversion to this form, data from PDB are extensively validated, so as to provide a description of chemical and spatial structure that is as accurate as possible. These changes in format and content of the known structure data are intended to support development of intelligent molecular modeling applications that make use of this invaluable information resource.

Amino Acid Sequence↗

PubMed2004

Large shifts in pathogen virulence relate to host population structure.

Theory on the evolution of virulence generally predicts selection for an optimal level of virulence determined by trade-offs with transmission and/or recovery. Here we consider the evolution of pathogen virulence in hosts who acquire long-lived immunity and live in a spatially structured population. We show theoretically that large shifts in virulence may occur in pathogen populations as a result of a bistability in evolutionary dynamics caused by the local contact or social population structure of the host. This model provides an explanation for the rapid emergence of the highly virulent strains of rabbit hemorrhagic disease virus.

Animals↗

PubMed2002

Spectral reflectance and directional properties of structural coloration in bird plumage.

Bird plumage is coloured both by pigments and by spectrally selective interference in the light reflected from feather barbs. These barbs are composites of high- and low-refractive-index materials, and light is reflected at refractive index boundaries. The spatial structure determines the wavelengths where constructive interference occurs and, hence, the spectral tuning. The spectral tuning of interference colours often varies with angles of illumination and reflection, which produces iridescence. Iridescence and other optical effects mean that interference coloration looks different from pigmentation and is visually striking. To study the optical and visual properties of structural plumage colours, we recorded the reflectance spectra of feathers and in particular their directional properties. A fixed spot on a feather was viewed from a fixed position, whilst the feather orientation and the angle of illumination were varied. We recognise two main types of coloration, 'directional' and 'diffuse'. Within these types, there is considerable variation, and five examples illustrate some features of structural plumage colours and suggest how their optical and visual properties can be measured and described.

Animals↗

PubMed1990

Spatial and temporal analysis by neurons in the representation of the central visual field in the cat's lateral suprasylvian visual cortex.

We studied quantitatively the receptive-field properties of 74 units recorded from the representation of the central visual fields in the cat's lateral suprasylvian (LS) visual cortex. In agreement with previous workers, we found that LS receptive fields tended to be large and to lack discernible spatial structure. They resembled the complex receptive fields of areas 17 and 18 in their general organization. We examined the responses of these neurons to moving optimally oriented sinusoidal gratings that varied in spatial and temporal frequency of drift. Most LS neurons were selective for the spatial frequency of sinusoidal gratings; 7% responded to all spatial frequencies below a cutoff value. In agreement with previous reports, the optimal spatial frequencies for LS neurons covered a wider range than is seen in either area 17 or 18 alone (0.05-1 cycle/deg), but are certainly included in the range covered by both these afferent areas. Individual neurons in LS responded to a range of spatial frequencies broader than is typical for neurons in areas 17 and 18. The effect of varying the drift rate of otherwise optimal gratings was similar in LS to that reported for areas 17 and 18. Most neurons were optimally responsive to drift rates between 0.5 and 4 Hz, and resolved frequencies as high as 10-30 Hz. A few neurons had optima higher than 6 Hz and resolved frequencies in excess of 30 Hz. We conclude that the receptive fields of LS neurons reflect rather closely the properties of their afferents from areas 17 and 18.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

The cellular basis for parallel neural transmission of a high-frequency stimulus and its low-frequency envelope.

Sensory stimuli often have rich temporal and spatial structure. One class of stimuli that are common to visual and auditory systems and, as we show, the electrosensory system are signals that contain power in a narrow range of temporal (or spatial) frequencies. Characteristic of this class of signals is a slower variation in their amplitude, otherwise known as an envelope. There is evidence suggesting that, in the visual cortex, both narrowband stimuli and their envelopes are coded for in separate and parallel streams. The implementation of this parallel transmission is not well understood at the cellular level. We have identified the cellular basis for the parallel transmission of signal and envelope in the electrosensory system: a two-cell network consisting of an interneuron connected to a pyramidal cell by means of a slow synapse. This circuit could, in principle, be implemented in the auditory or visual cortex by the previously identified biophysics of cortical interneurons.

Animals↗

PubMed2000

Dispersal, Environmental Correlation, and Spatial Synchrony in Population Dynamics.

Many species exhibit widespread spatial synchrony in population fluctuations. This pattern is of great ecological interest and can be a source of concern when the species is rare or endangered. Both dispersal and spatial correlations in the environment have been implicated as possible causes of this pattern, but these two factors have rarely been studied in combination. We develop a spatially structured population model, simple enough to obtain analytic solutions for the population correlation, that incorporates both dispersal and environmental correlation. We ask whether these two synchronizing factors contribute additively to the total spatial population covariance. We find that there is always an interaction between these two factors and that this interaction is small only when one or both of the environmental correlation and the dispersal rate are small. The interaction is opposite in sign to the environmental correlation; so, in the normal case of positive environmental correlation across sites, the population synchrony will be lower than predicted by simply adding the effects of dispersal and environmental correlation. We also find that population synchrony declines as the strength of population regulation increases. These results indicate that dispersal and environmental correlation need to be considered in combination as explanations for observed patterns of population synchrony.

Moran effect↗

PubMed2004

Solution structure of conformationally restricted vasopressin analogues.

In recent years, a massive effort has been directed towards designing potent and selective antagonists of neurohypophyseal hormones substituted at position 3. Modification of vasopressin at position 3 with 4,4'-biphenylalanine results in pharmacologically inactive analogues. Chemically, this substitution appears to vary only slightly from those previously made by us (1-Nal or 2-Nal), which afforded potent agonists of V(2) receptors. In this situation, it seemed worthwhile to study the structure of the analogues with 4,4'-biphenylalanine (BPhe) at position 3 in aqueous solution using NMR spectroscopy and total conformational analysis. This contribution is part of extensive studies aimed at understanding spatial structures of 3-substituted [Arg(8)]vasopressin analogues of different pharmacological properties. NMR data were used to calculate 3D structures for all the analogues using two methods, EDMC with the ECEPP/3 force field, and molecular dynamic with the simulated annealing (SA) algorithm. The structures obtained by the first method show a better fit between the NMR spectral evidence and the calculation for all the peptides.

Algorithms↗

PubMed2005

Large-scale structural analysis of the core promoter in mammalian and plant genomes.

DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.

Animals↗

PubMed1992

A new approach to the design of a sequence with the highest affinity for a molecular surface.

We describe an algorithm to design the primary structures for peptides which must have the strongest binding to a given molecular surface. This problem cannot be solved by a direct combinatorial sorting, because of an enormous number of possible primary and spatial structures. The approach to solve this problem is to describe a state of each residue by two variables: (i) amino acid type and (ii) 3-D coordinate, and to minimize binding energy over all these variables simultaneously. For short chains which have no long-range interactions within themselves, this minimization can be done easily and efficiently by dynamic programming. We also discuss the problem of how to estimate specificity of binding and how to deduce a sequence with maximal specificity for a given surface. We show that this sequence can be deduced by the same algorithm after some modification of energetic parameters.

Algorithms↗

PubMedDate not supplied

[A peptide inhibitor of the binding site of oncoproteins of the p21ras family].

The method of theoretical conformational analysis was used to study the inverse structural problem to determine the amino acid sequence of the peptide molecule capable of inhibiting the site of binding of p21 to cell receptors. At the first stage of the computational experiment, the spatial structure and the conformational possibilities of the binding sites of protein p21 and its cellular receptors were determined. Then the three-dimensional structures of several peptides containing the Arg-Ala-Ala-Glu-Asp site were studied. By varying the number of alanine residues in the adjacent regions of the molecule, the sequence H-Asp1-Ala2-Ala3-Ala4-Arg5-Ala6-Ala7-Glu8-Asp9-Ala10-Ala11--Lys12-QH was chosen, which most adequately simulates the conformational properties of the address fragments of oncoprotein receptors. The peptide-molecule having this primary structure is capable of forming a complex with p21, i.e., blocking the binding site of the oncoprotein by preventing the signal transduction from the oncoprotein to the cell, thereby breaking the cycle of the carcinogenic process.

Amino Acid Sequence↗

PubMedDate not supplied

[Determination of energetically significant parts of globulins and hierarchy of domain structure in macromolecules of proteins].

We have justified a Van der Waals approach for the problem of domains structure in globular proteins. A method for isolation of hierarchy of Van der Waals interactions in the space of protein globule has been found out. The definition of hierarchy's levels in the spatial structure of macromolecules is effected by the position of maxima in the distribution of potential energy of interactions. Multilevels system for domain structure organization of globular proteins and method for isolation of domains on different levels of energetical hierarchy has been established. Using this method we have revealed regions of different stability in 15 proteins globule.

Globulins↗

PubMed1995

Application of the population potential model in the structural regionalisation of Poland.

"The application of population potential in the research procedure employed to arrive at Poland's structural regionalisation allows three main tasks to be solved: (1) determining the interaction in the urban system, (2) establishing macroregional nodes, and (3) delimiting peripheral zones of macroregions. The configuration of the potential surface and membership functions indicates the spatial structuring of socio-economic reality at the level of population interaction."

Demography↗

PubMed2005

Comparative analysis of the structure of sterically stabilized ferrofluids on polar carriers by small-angle neutron scattering.

Results of experiments on small-angle neutron scattering from ferrofluids on polar carriers (pentanol, water, methyl-ethyl-ketone), with double-layer sterical stabilization of magnetic nanoparticles, are reported. Several types of spatial structural organization are observed. The structure of highly stable pentanol-based samples is similar to that of stable ferrofluids based on organic non-polar carriers (e.g., benzene) with mono-layer covered magnetic nanoparticles. At the same time, the effect of the interparticle interaction on the scattering is stronger in polar ferrofluids because of the structural difference in the surfactant shell. The structure of the studied methyl-ethyl-ketone- and water-based ferrofluids essentially different from the previous case. The formation of large (>100 nm in size) elongated or fractal aggregates, respectively, is detected even in the absence of external magnetic field, which corresponds to weaker stability of these types of ferrofluids. The structure of the fractal aggregates in water-based ferrofluids does not depend on the particle concentration, but it is sensitive to temperature. A temperature increase results in a decrease in their fractal dimension reflecting destruction of the aggregates. In addition, in water-based ferrofluids these aggregates consist of small (radius approximately 10 nm) and temperature-stable primary aggregates.

Colloids↗

PubMed2006

Bacterial extracellular DNA forming a defined network-like structure.

It is generally assumed that nucleic acids are localized inside of living cells and that their primary function is the storage of information. In contrast, extracellular DNA is mainly considered as a remnant of lysed cells. Here, we report the formation of extracellular bacterial DNA as a spatial structure. An aquatic bacterium, strain F8, was isolated, which produced a stable filamentous network of extracellular DNA. Different staining and enzymatic techniques confirmed that it was DNA. We were able to amplify the 16S rRNA gene from the extracellular DNA. Restriction endonuclease cleavage and randomly amplified polymorphic DNA analysis of extracellular and genomic DNAs revealed major similarities, but also some differences in both sequences. Our data demonstrate a new function and relevance for extracellular DNA.

Bacteria↗

PubMed2001

On the need for another type of predictive model in structured foods.

Most of the models discussed up till now in predictive microbiology do not take into account the variability of microbial growth with respect to space. In structured (solid) foods, microbial growth can strongly depend on the position in the food and the assumption of homogeneity can thus not be accepted: space must be considered as an independent variable. Indeed, experimental evidence exists of bacteria competition on agar not showing the same behavior as the competition in a well-mixed liquid culture system. It is conjectured that this is due to the spatially structured habitat. Therefore, in the current paper, a prototype two species competition model proposed in previous work by the authors is extended to take space into account. The extended model describes two phenomena: (i) local evolution of biomass and (ii) transfer of biomass through the medium. The structure of the food product is taken into account by limiting the diffusion through the medium. The smaller mobility of the micro-organisms in solid foods allows spatial segregation which causes pattern formation. Evidence is given for the fact that taking space into account indeed has an influence on the behavior (coexistence/extinction) of the populations. Although the reported simulations are by no means to be interpreted as accurate predictions, the proposed model structure allows one to highlight (i) important characteristics of microbial growth in structured foods and (ii) future research trends in predictive microbiology.

Bacteria↗