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PubMed1985

[Study of the spatial structure of a cyclic analog of bradykinin in solution by two-dimensional NMR spectroscopy].

H NMR resonances of [cyclo (9----18) Lys1, Gly6]bradykinin (CBK) in (CD3)2SO and H2O solution have been assigned by combined analysis of two-dimensional COSY and NOESY spectra. The presence of two slowly interchangeable conformers of CBK in (CD3)2SO is established, the minor conformer not exceeding 15% in the population. The minor conformer is absent from the aqueous solution, chemical shifts of the CBK and bradykinin NH and C alpha H protons differ insignificantly. The major CBK conformer contains at least two X-Pro trans-peptide groups and three amide protons NH Phe5, NH Arg9 and N zeta H Lys1 protected from solvent. A system of cross-peaks from the NOESY spectra of CBK in (CD3)2SO has been analysed and the maximum distance between backbone protons and neighbouring amino acid residues evaluated. The experimental data agree well with the assumed type II beta-bend in the sequence Pro2-Pro3-Gly4-Phe5. Spatial structure models for the backbone fragment 6-9 of CBK containing two intramolecular hydrogen bonds that involve the NH Arg9 and N zeta H Lys1 protons and the carbonyl groups of Phe5 and Gly4 are proposed.

Amino Acid Sequence↗

PubMed1984

[NMR study of the spatial structure of the Naja naja siamensis toxin 3].

The 300 and 500 MHz 1H NMR spectra of a long-chain neurotoxin, toxin 3 Naja naja siamensis (S-T3), its derivatives and close homolog, toxin 3 Naja naja naja (N-T3), have been analyzed. A combination of double resonance, difference spectroscopy and usage of a series of toxin S-T3 derivatives acetylated or trifluoroacetylated at lysine residues allowed to assign the signals from all aromatic protons and a number of signals in the aliphatic region, and to elucidate the microenvironment of certain functionally important residues. Analysis of chemical shifts pH-dependences in the 1H and 19F NMR spectra of toxin S-T3 and its trifluoroacetylated congeners delineated a considerable region of the neurotoxin molecule affected by the conformational transition, with the midpoint at pH 5,4, between two states. This conformational transition is induced by protonation of His22 and is accompanied by a change in the accessibility of its imidazole ring for the solvent, along with the alteration of the distance between the side chains of functionally important Lys27 and Lys53 residues. According to EPR data (-196 degrees) for the respective S-T3 derivative having spin labels at Lys27 and Lys53 epsilon-amino groups, the inter-label distance increases from 18 A at pH 7,5 to 23 A at pH 3,5. Notwithstanding this conformational change, the totality of the obtained results evidences in favor of considerable similarity of the toxin S-T3 spatial structure in the solution and crystalline state.

Acetylation↗

PubMed1996

Structural characterization of extracellular ribonuclease of Bacillus polymyxa: amino acid sequence determination and spatial structure prediction.

The primary structure of extracellular Bacillus polymyxa ribonuclease (RNase Bpo) was established by mass spectroscopy analysis and automatic Edman degradation of the individual peptides obtained from protein digestion with Glu-specific protease V8. RNase Bpo consists of 111 amino acid residues, with a relative molecular weight of 12 607. RNase Bpo is a close structural homolog of RNases of B. amyloliquefaciens (RNase Ba) and B. intermedius (RNase Bi), the similarity of their primary structures being 68%. Molecular modelling of the structure of the complex of RNase Bpo with substrate analog d(CGAC) was performed and a spatial model based on the known crystal structure of RNase Ba complex with the corresponding nucleotide was constructed using the methods of interactive computer graphics and energy minimization. The differences in the primary and tertiary structures of the enzymes were analyzed in order to understand the substrate specificity of Bacillus RNases.

Amino Acid Sequence↗

PubMed2005

Generalized spatial structural equation models.

It is common in public health research to have high-dimensional, multivariate, spatially referenced data representing summaries of geographic regions. Often, it is desirable to examine relationships among these variables both within and across regions. An existing modeling technique called spatial factor analysis has been used and assumes that a common spatial factor underlies all the variables and causes them to be related to one another. An extension of this technique considers that there may be more than one underlying factor, and that relationships among the underlying latent variables are of primary interest. However, due to the complicated nature of the covariance structure of this type of data, existing methods are not satisfactory. We thus propose a generalized spatial structural equation model. In the first level of the model, we assume that the observed variables are related to particular underlying factors. In the second level of the model, we use the structural equation method to model the relationship among the underlying factors and use parametric spatial distributions on the covariance structure of the underlying factors. We apply the model to county-level cancer mortality and census summary data for Minnesota, including socioeconomic status and access to public utilities.

Bayes Theorem↗

PubMed1992

Hierarchical geometric constraint networks as a representation for spatial structural knowledge.

A representation is proposed for capturing generic spatial knowledge about classes of objects in a structural hierarchy of biology. The basic premise is that spatial properties such as shape and relative relationships can be expressed as networks of interacting constraints. The representation is defined, partial implementations that demonstrate practical utility are described for model based organ and protein structure determination, and research issues are presented that must be solved before the representation can be implemented in its entirety. As these issues are resolved the representation will find increasing utility as the foundation for a spatial knowledge base of structural biology.

Computer Simulation↗

PubMedDate not supplied

[The functional organization of the spatial structures of the neuronal receptive fields in field 21 of the cat cerebral cortex].

In result study of structural organization of neural receptive fields (RFs) and their different zones on the prestriate cortex level was shown that neural RFs in this area have hypercomplex structure and consist of some spatial different excitatory zones. Orientation and velocity selectivity and spatial-frequency characteristics of the excitatory zones of the same RF may differ between zones. The number of zones in RFs correlate with RF sizes: the more RF size the more zones number in them (r = 0.05, P < 0.02). About 66% of zones in RFs have approximately identical sizes (12-16 deg) and sizes those zones an dependence as from their number in RFs (r = 0.03, P > 0.05) as from the eccentricity (r = 0.3, P > 0.05). Zones in RF were distributed so that distance their centres was between 56-65 degrees (an average across all 60 degrees). If two or three zones were tested simultaneously the neuron changed own frequency and orientation tuning. Consequently the functional organization of neural RFs of prestriate cortex depend upon number simultaneously tested zones in spatial information processing. Was shown that important properties of prestriate cortex neurons is their ability to integrate and complex processing of spatial information across wide area of the visual field; in the prestriate cortex thus violate of straight retinotopical representation principle of visual field, characteristics of all investigated areas of visual system. The results represented in this review allow suppose that the structural and functional unit of cortex which make integration of spatial information from different compose this information is prestriate cortex neurons and not is no striate cortex modules. Consequently combined of neurons which make images description from different parts of visual field out of dependence of cortical area in turn integrate in neuron networks. Is known that neurons of any level have characteristics different of (from) characteristics of other levels visual system. The interaction of different elements of visual system form ultrastructure of RFs and their different zones in prestriate cortex, and ensure function of networks. So just on prestriate cortex neurons level appear whole system of surrounding world universe system of connections from different cortical areas which is morphological and functional base in process of spatial information integration RFs which have the central and peripheral representation.

Animals↗

PubMedDate not supplied

[From determination of amino acid residue conformation to reconstruction of the spatial structure of proteins (from the data of nuclear Overhauser enhancement spectroscopy].

A new approach to the calculation of the spatial protein structure based on the joint utilization of the theoretical conformational analysis method and nuclear Overhauser enhancement (NOE) spectroscopy data is proposed and verified. The quality in determining various molecule structural parameters is estimated in terms of the expected NOE spectral parameters derived from the X-ray analysis data of the avian pancreatic polypeptide. The proposed approach is shown to correctly determine such structural parameters of protein molecules as local amino acid residue conformations, reciprocal spatial orientation of the C alpha atoms neighbouring along amino acid sequence and reapproached segments of the polypeptide chain. Spatially remote molecule fragments are mainly responsible for the error in determining structural parameters.

Amino Acids↗

PubMed1988

Mathematical modelling of intercellular regulation causing the formation of spatial structures in bacterial colonies.

Bacterial colonies may grow forming stable spatial, particularly circular, structures. For instance, motile bacteria Proteus vulgaris or Escherichia coli grown on agar under certain conditions may form concentric rings with the centre in the inoculation point (Rüss-Münzer, 1935, Bact. Parasit Kde (Abt 1) 7, 214; Budriené, 1985, Dokl. Acad. Nauk SSR, 283, 470). A similar picture can be observed in a different situation, i.e. when a lawn of non-motile Salmonella typhimurium bacteria is cultivated on a solid agar with the locally introduced substrate (Hoppensteadt & Jäger, 1980, Lecture Notes in Biomath. 38, 68). This paper describes a mechanism of bacterial interactions through a hypothetical mediator released by the organisms. A mathematical model has been built. Its analysis has shown that the selected laws of secretion and reception of the mediator can adequately account for the formation of circular structures in the case of both motile and non-motile bacteria.

Animals↗

PubMed2005

Genetic spatial structure of European common hamsters (Cricetus cricetus)--a result of repeated range expansion and demographic bottlenecks.

The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15,000-10,000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85,000-147,000 bp. Expansion times fall during the last glaciation (115,000-10,000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50,000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains--core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary.

Animals↗

PubMed1984

[Dominant and reciprocal relationships in the organization of the spatial structure of the biopotential correlations of the brain].

The factor analysis of correlation coefficients of brain potentials spatial-temporal structure revealed the "leading constellations" of neural centers in the coordination system for activity of the human brain hemispheres in resting as well as in functional loads; the reciprocity in organization of potential oscillations in the frontal and occipital brain areas, the reciprocal interrelationships being more obvious in the dominant hemisphere. This factor was shown to depend on the level of activation of the subjects even in a functional state unaltered in respect to other EEG indices. When expecting stimuli demanding a left-hand response, a rearrangement of spontaneous dominant interrelationships to the advantage of the right hemisphere occurs in the EEG.

Adult↗

PubMed1990

Spatial structures in microtubular solutions requiring a sustained energy source.

Microtubules are believed to be the principal organizers of the cell interior. Cells respond to a variety of stimuli by modifying the spatial distribution of the microtubules. These effects are central to cell division and morphogenesis, and embryo development. During embryo development, macroscopic patterns are frequently observed. Here we report that microtubular solutions spontaneously form alternating white and dark stripes about 1 mm wide and 1 cm long. Small-angle neutron scattering measurements show that in each segment the microtubules are aligned obliquely to the direction of the stripe, and that the white and dark stripes differ in having mutually orthogonal orientations. The formation of these structures requires an initial reservoir of organic phosphate. Phosphorus NMR measurements show that the process is accompanied by the energy-liberating conversion of organic to inorganic phosphate. These observations, together with similarities to the dissipative spatial structure formed by the Belousov-Zhabotinski reaction, provide strong evidence that the observed structures are energy-dissipative in nature. Dissipative structures are thought to be critical to the appearance of complex living organisms. Our results strongly suggest that microtubules are capable of forming such structures. Microtubular dissipative structures may occur during mitosis and embryo morphogenesis.

Animals↗

PubMed1999

Measures of spatial structure in samples of genotypes for multiallelic loci.

Various spatial autocorrelation statistics have been widely used both in theoretical population genetics and to study the spatial distribution of diploid genotypes in many plant and animal populations. However, previous simulation studies have considered only diallelic loci. In this paper, we use a large number of space-time simulations to characterize for the first time the parametric and statistical values of Moran's I-statistics for converted individual genotypes as well as for join-count statistics. A wide range of levels of dispersal and numbers of alleles and allele frequencies are modelled and the results reveal the different general effects of each of these factors on these statistics. We also examine the range of appropriate sampling designs and sizes for which predicted values can be interpolated for specific sampling schemes for any given population genetic field survey. Numbers of alleles and allele frequencies each affect some statistics but not others. The results indicate generally low standard deviations. The results also develop precise and efficient methods of estimating gene dispersal, based on the various autocorrelation measures of standing spatial patterns of genetic variation within populations. The results also extend these methods to loci with multiple alleles, typical of those studied through modern molecular methods.

Alleles↗

PubMed2005

Physical limits to spatial resolution of optical recording: clarifying the spatial structure of cortical hypercolumns.

Neurons in macaque primary visual cortex are spatially arranged by their global topographic position and in at least three overlapping local modular systems: ocular dominance columns, orientation pinwheels, and cytochrome oxidase (CO) blobs. Individual neurons in the blobs are not tuned to orientation, and populations of neurons in the pinwheel center regions show weak orientation tuning, suggesting a close relation between pinwheel centers and CO blobs. However, this hypothesis has been challenged by a series of optical recording experiments. In this report, we show that the statistical error associated with photon scatter and absorption in brain tissue combined with the blurring introduced by the optics of the imaging system has typically been in the range of 250 microm. These physical limitations cause a systematic error in the location of pinwheel centers because of the vectorial nature of these patterns, such that the apparent location of a pinwheel center measured by optical recording is never (on average) in the correct in vivo location. The systematic positional offset is approximately 116 microm, which is large enough to account for the claimed misalignment of CO blobs and pinwheel centers. Thus, optical recording, as it has been used to date, has insufficient spatial resolution to accurately locate pinwheel centers. The earlier hypothesis that CO blobs and pinwheel centers are coterminous remains the only hypothesis currently supported by reliable observation.

Animals↗

PubMed2003

Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

Animals↗

PubMed1996

Spatial structure and insertion capacity of immunodominant region of hepatitis B core antigen.

Spatial and immunochemical elucidation of hepatitis B core antigen suggested unique organization of its major immunodominant region (MIR) localized within the central part of molecule around amino acid residues 74-83. This superficial loop was recognized as the most prospective target for the insertion of foreign epitopes ensuring maximal antigenicity and immunogenicity of the latter. MIR allowed a substantial capacity of insertions up to about 40 amino acid residues without loss of the capsid-forming ability of core particles. Vector capacity as well as structural behavior and immunological fate of inserted epitopes were dependent on their primary structure. Special sets of display vectors with retained but cross-sectioned MIR as well as with uni- and bidirectionally shortened MIR have been investigated.

Amino Acid Sequence↗

PubMed2001

A numerical study of spatial structure during oscillatory combustion in closed vessels in microgravity.

The existence and spatial development of gas-phase, thermokinetic oscillations under the influence of mass and thermal diffusion have been investigated by numerical methods in a 1-dimensional system. The conditions correspond to those that would be experienced under microgravity. The interest arises because there have been recent experimental investigations of oscillatory reactions, involving cool flames during butane oxidation, as part of the NASA, KC135 microgravity flight programme. The Sal'nikov, thermokinetic scheme, which is a two-variable model representing an intermediate chemical species and reactant temperature (taking the form P-->A-->B), forms the basis of the present work. In this model, thermal feedback occurs through the exothermicity of the second step and the non-linearity is derived from its temperature dependence. There are no known chemical examples that satisfy Sal'nikov's formal structure but Griffiths and co-workers conceived an experimental analogue under terrestrial conditions whereby a gaseous reactant was allowed to flow from an external reservoir into a closed, heated reactor at a controlled rate via a capillary tube which fed the reactant to the centre of the vessel. The exothermic reaction that occurred in the vessel satisfied the necessary conditions for the second step and the inflow, with no temperature dependence, represented a physical analogue to the first step of the Sal'nikov scheme. Thermokinetic oscillations were observed and the range of conditions for their existences was investigated. One of the experimental systems was the exothermic reaction between hydrogen and chlorine. To represent the Sal'nikov conditions hydrogen was fed slowly into the reactor, which already contained chlorine. We have exploited this chemical system and its experimental implementation in the present paper to investigate the behaviour when no convection or bulk gas motion occurs and when heat and mass transport is driven solely by diffusion. We study the response of alternative numerical approaches to the way in which the first step of the scheme is simulated. In the first, the precursor (P) is supplied at the same rate simultaneously throughout the cells representing the reactor. This is close to the concept of the Sal'nikov model. In the second method, a fixed rate of supply is applied at the inner boundary of the axisymmetric, 1-dimensional system. This is analogous to the experimental procedure. The numerical results show how oscillatory states can be sustained as a result of heat and mass transport by diffusion. The temporal and spatial evolution of reaction in a range of circumstances is discussed.

Journal Article↗

PubMed2001

Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density.

The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.

Animals↗

PubMed2001

Hydrophobic moments of protein structures: spatially profiling the distribution.

It is generally accepted that globular proteins fold with a hydrophobic core and a hydrophilic exterior. Might the spatial distribution of amino acid hydrophobicity exhibit common features? The hydrophobic profile detailing this distribution from the protein interior to exterior has been examined for 30 relatively diverse structures obtained from the Protein Data Bank, for 3 proteins of the 30S ribosomal subunit, and for a simple set of 14 decoys. A second-order hydrophobic moment has provided a simple measure of the spatial variation. Shapes of the calculated spatial profiles of all native structures have been found to be comparable. Consequently, profile shapes as well as particular profile features should assist in validating predicted protein structures and in discriminating between different protein-folding pathways. The spatial profiles of the 14 decoys are clearly distinguished from the profiles of their native structures.

Amino Acids↗