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PubMed1998

Spatial structure determination of antiarrhythmic peptide using nuclear magnetic resonance spectroscopy.

The peptide AAP10 was synthesized according to the Merrifield technique following the Fmoc-strategy and its spatial structure in aqueous solution studied with NMR principles. It is known from previous studies that the peptide has antiarrhythmic activity and inhibits cardiac ischemia induced alterations of the activation pattern, decreases the activation-recovery interval (ARI) dispersion and improves cellular coupling via enhancement of gap junction conductance (2, 2, 3, 4). The peptide was synthesized as a peptide amide. Two different semi cyclic conformations were characterized.

Anti-Arrhythmia Agents↗
PubMed2000

Towards the integration of social dominance and spatial structure.

My aim was to show how individual-oriented (or artificial life) models may provide an integrative background for the development of theories about dominance by including effects of spatial structure. Dominance interactions are thought to serve two different, contrasting functions: acquisition of high rank and reduction of aggression. The model I present consists of a homogeneous virtual world inhabited by artificial agents whose actions are restricted to grouping and dominance interactions in which the effects of winning and losing are self-reinforcing. The two functions are implemented as strategies to initiate dominance interactions and the intensity of aggression and dominance perception (direct or memory based) are varied experimentally. Behaviour is studied by recording the same behavioural units as in real animals. Ranks appear to differentiate more clearly at high than at low intensity of aggression and also more in the case of direct than of memory-based rank perception. Strong differentiation of rank produces a cascade of unexpected effects that differ depending on which function is implemented: for instance, a decline in aggression, spatial centrality of dominants and a correlation between rank and aggression. Insight into the origination of these self-organized patterns leads to new hypotheses for the study of the social behaviour of real animals. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMedDate not supplied

Spatial structures in a model substrate-inhibition reaction diffusion system.

An important new model universal oscillator proposed by Seelig which depends on substrate inhibition is considered. In a finite spatial domain with zero flux boundary conditions and in which the substrates can diffuse it is shown that diffusion-driven instability is possible and can result in finite amplitude spatial structures. Illustrative numerical results are presented which exhibit this behaviour.

Catalysis↗
PubMed1984

The spatial structure of the axially bound methionine in solution conformations of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c551 by 1H NMR.

A generally applicable method for the determination of the spatial structure of the heme iron-bound methionine in c-type ferrocytochromes at atomic resolution is presented. It relies primarily on measurements of nuclear Overhauser effects between the individual hydrogen atoms of the axial methionine, and between individual hydrogens of the methionine and the heme group. Four different methionine conformers, corresponding to the four possible stereospecific assignments for the methionine methylene proton resonances, are generated by a structural interpretation of the nuclear Overhauser effects with the use of an interactive computer graphics technique. A unique structure and unique stereospecific resonance assignments are then obtained by discriminating between these four conformers on the basis of van der Waals' constraints and heme ring current effects on the chemical shifts. The use of the method is illustrated with studies of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551. Comparison with the crystal structures shows close coincidence between the methionine conformations in solution and in single crystals of these proteins.

Animals↗
PubMed1979

A colour-dependent abnormality in human visual detection of stimulus motion and spatial structure.

We have studied the wavelength dependence of visual responses in a single human subject, M.W., who has an unusual visual defect. It is shown that for red stimuli, both spatial resolution for grating patterns and detection of target movement are grossly abnormal. On the basis of these and other [8] experimental data, we argue that M.W.'s response pattern implies interdependent central visual processing of colour, movement and spatial structure. We examine this conclusion in relation to recent anatomical and electrophysiological findings.

Color Perception↗
PubMed1988

Incorporating the effects of spatial structure in discrete choice models of migration.

Discrete-choice theory and logit models are evaluated for their usefulness in analyzing migration patterns in a zonal system. The authors "argue that spatial effects and more specifically the relative location of zones are not taken into account in such analyses. We, therefore, introduce a measure of spatial structure and advocate its usage as a predictor of migration in such models. In an example of intrametropolitan migration in Toronto [Canada], we demonstrate that this variable is not only significant but also it improves the performance of all the other variables with the greatest impact on the distance between zones. In addition, inclusion of this variable improves the overall performance of the model in terms of residuals."

Americas↗
PubMed2003

Ecological and genetic spatial structuring in the Canadian lynx.

The Canadian lynx, distributed all across the northern part of North America, is well known for its regular population cycles-cycles that have different underlying structures in different parts of Canada. Using both nuclear and mitochondrial DNA markers, we report here a close resemblance between the earlier observed spatial ecological structuring of the Canadian lynx and its spatial genetic structuring. Specifically, we demonstrate that the Rocky Mountains represent a barrier to gene flow in western Canada, and, somewhat surprisingly, we detect the presence of a geographically invisible barrier south of Hudson Bay (coinciding with the separation between the ecological Continental and Atlantic regions). No evidence for isolation in different glacial refugia within North America was found. We suggest that ecological factors underlying the spatial dynamic structuring also strongly influence the genetic structuring of the Canadian lynx.

Animals↗
PubMed2005

Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters.

AIMS: To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air. METHODS AND RESULTS: A microbiological study and a measurement of biodegradation activities were simultaneously carried out on two identical peat-packed columns, seeded with two different inocula, treating polluted air containing 11 VOCs. For both reactors, the spatial structure of the microbial communities was investigated by means of single-strand conformation polymorphism (SSCP) analysis. For both reactors, stratification of degradation activities in function of depth was observed. Oxygenated compounds were removed at the top of the column and aromatics at the bottom. Comparison of SSCP patterns clearly showed a shift in community structure in function of depth inside both biofilters. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. Although the operating conditions of both reactors were identical and the biodegradation activities similar, the composition of microflora differed for biofilters A and B. Subdivision of biofilter B into two independent parts supplied with polluted air containing the complex VOC mixture showed that the microflora having colonized the bottom of biofilter B retained their potential for degrading oxygenated compounds. CONCLUSIONS: This work highlights the spatialization of biodegradation functions in a biofilter treating a complex mixture of VOCs. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: This vertical structure of microbial communities must be taken into consideration when dealing with the malfunctioning of bioreactors. These results are also useful information about changes in microbial communities following natural or anthropogenic alterations in different ecosystems (soils and sediments) where structuring of microbial communities according to depth has been observed.

Air Microbiology↗
PubMed2006

Detection of irregular spatial structures.

Wilson et al.'s (1997) study on Glass patterns suggested that the integration of stimulus features into a linear shape occurs quite locally, whereas curved structures--such as circular--require global summation. Their conclusion was based on experiments in which they varied the size of the signal area containing a spatial structure. In the present study, we tested the integration of constant-sized linear and curved Glass patterns by varying their global irregularity. If the mechanisms underlying the detection of a Glass pattern pool features globally throughout the stimulus, the irregularity should have a strong effect on detection performance. The irregular Glass patterns were composed of a variable number of sub-areas, each of which contained its own linear or curved structure. The structural irregularity impaired the detection of the curved patterns, whereas the thresholds for the linear patterns were not affected. Thus, our results are in line with the notion that the integration of curved Glass patterns occurs more globally than the integration of linear patterns.

Humans↗
PubMed1992

[Study of the spatial structure of the duplex (Phn-NH(CH2)NH)pd(CCAAACA).pd(TGTTTGGC) with covalently bound 10-(2-hydroxyethyl)phenazine by in aqueous solution by 2D-(1)H-NMR and by limited molecular mechanics].

Detailed investigation of the spatial structure of duplex (Phn-NH(CH2)2NH) x pd(CCAAACA).pd(TGTTTGGC) having a covalently linked N-(2-hydroxyethyl)-phenazine in aqueous solution was continued by means of one- and two-dimensional 1H-NMR spectroscopy. Distances between the protons of the oligonucleotides as well as distances between the phenazinium and the nearest nucleotide groups protons were determined from the series of one-dimensional NOE experiments. The effective correlation time tau c determined for some proton pairs shows the phenazinium fragment to have greater internal motion than the heterocyclic bases. The deoxyribose protons coupling constants show the sugars to be in 2'-endo-conformation. The restrained molecular mechanics have yielded a possible structure of duplex in the aqueous solution fitting the experimental set of interproton distances.

Animals↗
PubMed1988

Solution spatial structure of 'long' neurotoxin M9 from the scorpion Buthus eupeus by 1H-NMR spectroscopy.

1H-NMR spectra of Buthus eupeus neurotoxin M9 (66 amino acid residues, four disulfide bonds) reveal two slowly exchangeable conformations at acidic pH. The spatial structure of the conformer prevailing under physiologically relevant conditions has been determined from two-dimensional 1H-NMR data treated by means of a distance geometry algorithm and refined by molecular modelling. Interrelation between the structure and function of mammalian neurotoxin M9 is discussed by comparing its conformation with those of the scorpion insectotoxins which exhibit different biological specificity (insectotoxins v-2, v-3 and I5A).

Amino Acid Sequence↗
PubMed2002

Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating.

Zervamicin IIB is a 16-amino acid peptaibol that forms voltage-dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. The spatial structure of zervamicin IIB bound to dodecylphosphocholine micelles was studied by nuclear magnetic resonance spectroscopy. The set of 20 structures obtained has a bent helical conformation with a mean backbone root mean square deviation value of approximately 0.2 A and resembles the structure in isotropic solvents (Balashova et al., 2000. NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466:333-336). The N-terminus represents an alpha-helix, whereas the C-terminal part has a mixed 3(10)/alpha(R) hydrogen-bond pattern. In the anisotropic micelle environment, the bending angle on Hyp10 (23 degrees) is smaller than that (47 degrees) in isotropic solvents. In the NOESY (Nuclear Overhauser Effect Spectroscopy) spectra, the characteristic attenuation of the peptide signals by 5- and 16-doxylstearate relaxation probes indicates a peripheral mode of the peptaibol binding to the micelle with the N-terminus immersed slightly deeper into micelle interior. Analysis of the surface hydrophobicity reveals that the zervamicin IIB helix is amphiphilic and well suited to formation of a tetrameric transmembrane bundle, according to the barrel-stave mechanism. The results are discussed in a context of voltage-driven peptaibol insertion into membrane.

Anisotropy↗
PubMed2004

[Temporal and spatial structure of carabid community in agricultural landscape of Dongbeiwang, Beijing].

From May to October 2000, the carabid beetles in the habitats of woodland, field margin and crop field in Dong-beiwang agroecosystem in Beijing were investigated by pitfall traps, and the temporal and spatial structure of carabid community was analyzed. The results indicated that the numbers of both carabid species and individuals were much higher in the field margin and woodland than in the crop field. Both dominant species and rare species tended to live in field margin and/or woodland. Field margins had a positive effect on the diversity and richness of carabid community in their adjacent crop fields. The modest disturbance (plowing in autumn) in the field margin was beneficial for the increase of the individual number of carabid community, and the treatments of irrigation, fertilization and straw return in field had no effects on both the individual and species number of carabid community. Furthermore, the threatening condition to some carabid species was discussed, based on the analysis of the temporal and spatial dynamics of carabid community.

Agriculture↗
PubMed1996

Metapopulations and equilibrium stability: the effects of spatial structure.

Recently, there has been a great deal of interest in the dynamics of metapopulations, where a number of local populations are coupled via dispersal. The importance of movement for the persistence of an ensemble of locally unstable patches has been established in many studies. In this paper, we present analytical and simulation results concerning the effects of spatial structure on the equilibrium stability of individual populations. We conclude that for general single-species and two-species competition models, the introduction of the spatial dimension in a biologically sensible way has no effect on the overall stability properties. In host-parasitoid models, however, strong host or parasitoid over-dispersal may be destabilizing.

Animals↗
PubMed1999

NMR spatial structure of alpha-conotoxin ImI reveals a common scaffold in snail and snake toxins recognizing neuronal nicotinic acetylcholine receptors.

A 600 MHz NMR study of alpha-conotoxin ImI from Conus imperialis, targeting the alpha7 neuronal nicotinic acetylcholine receptor (nAChR), is presented. ImI backbone spatial structure is well defined basing on the NOEs, spin-spin coupling constants, and amide protons hydrogen-deuterium exchange data: rmsd of the backbone atom coordinates at the 2-12 region is 0.28 A in the 20 best structures. The structure is described as a type I beta-turn (positions 2-5) followed by a distorted helix (positions 5-11). Similar structural patterns can be found in all neuronal-specific alpha-conotoxins. Highly mobile side chains of the Asp-5, Arg-7 and Trp-10 residues form a single site for ImI binding to the alpha7 receptor. When depicted with opposite directions of the polypeptide chains, the ImI helix and the tip of the central loop of long chain snake neurotoxins demonstrate a common scaffold and similar positioning of the functional side chains, both of these structural elements appearing essential for binding to the neuronal nAChRs.

Amino Acid Sequence↗
PubMed2003

Analysis on sensitivity and landscape ecological spatial structure of site resources.

This article establishes a set of indicators and standards for landscape ecological sensitivity analysis of site resources by using the theories and approaches of landscape ecology. It uses landscape diversity index (H), evenness (E), natural degree (N), contrast degree (C) to study spatial structure and landscape heterogeneity of site resources and thus provides a qualitative-quantitative evaluation method for land planning and management of small, medium scale areas. The analysis of Yantian District, Shenzhen of China showed that Wutong Mountain belonged to high landscape ecological sensitivity area, Sanzhoutian Reservoir and Shangping Reservoir were medium landscape sensitivity and high ecological sensitivity area; Dameisha and Xiaomeisha belonged to medium sensitivity area caused by the decline of natural ecological areas. Shatoujiao, Yantian Pier belonged to low sensitivity area but urban landscape ecological development had reshaped and influenced their landscape ecological roles in a great extent. Suggestions on planning, protection goals and development intensity of each site or district were raised.

China↗
PubMed2001

Increased coupling between subpopulations in a spatially structured environment can lead to population outbreaks.

Destruction and fragmentation of habitats is widely considered as a major threat to biological diversity. A theoretical framework aimed at understanding and predicting species responses to these destructive processes is still lacking, however. In this paper, the species dynamics in a spatially structured, two-habitat, patchy environment is considered subject to changes in individual migration intensity, i.e. coupling between the habitats. The subpopulation dynamics inside each habitat is assumed to be bistable but with different parameter values. By using space-discrete/continuous metapopulation dynamic models and computer simulations, we show that there can be two principally different regimes of metapopulation dynamics. With increasing intensity in the interplay between subpopulations, the total abundance can either gradually decrease or experience a sudden burst-like increase. This result is shown to be robust to the choice of mathematical models (discrete or continuous). Particularly, both the "self-excitation" and "self-inhibition" regimes of the metapopulation system are robust to variation in habitat size; however, when one of the habitats is much smaller than the other, the "self-excitation" regime can give way to the "self-inhibition" regime and vice versa.

Animals↗
PubMed1999

Spatial structure of the human alpha rhythm: global correlation in adults and local correlation in children.

OBJECTIVE: The maturation of the neocortex during childhood and adolescence involves dramatic increases in white-matter volume. EEG recordings from children and adults were examined to determine whether there are associated changes in spatial properties of dynamic processes in the neocortex. METHODS: Spontaneous eyes-closed and eyes-open EEG were recorded at 128 electrodes in 20 children aged 6-11 years and 23 adults aged 18-23 years. The surface Laplacian algorithm was applied to improve the spatial resolution of each electrode. Power and coherence were used to characterize the spatial structure of the alpha rhythm. A stochastic field model was used to eliminate coherences that are inflated due to volume conduction. RESULTS: In adults, the alpha rhythm is characterized by very high coherence between distant electrodes. The children demonstrated reduced anterior power and coherence between anterior and posterior electrodes at the peak alpha frequency in comparison to the adults. The Laplacian alpha rhythm demonstrated much higher power in the children at both anterior and posterior electrodes, but was weakly correlated between electrodes. CONCLUSIONS: The maturation of neocortex in late childhood involves increased global correlation by long-range corticocortical connections. The local correlation that contributes power to each electrode, independent of other electrodes, is reduced as the global correlation increases.

Adolescent↗