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At least 199 records · Page 11Linked to original sources
PubMed1991

[Determination of the spatial structure of insectotoxin 15A from Buthus erpeus by (1)H-NMR spectroscopy data].

The solution structure of insectotoxin 15A (35 residues) from scorpion Buthus eupeus was determined on the basis of 386 interproton distance restraints 12 hydrogen-bonding restraints and 113 dihedral angle restraints derived from 1H NMR experiments. A group of 20 structures was calculated with the distance geometry program DIANA followed by the restrained energy minimization with the program CHARMM. The atomic RMS distribution about the mean coordinate position is 0.64 +/- 0.11 A for the backbone atoms and 1.35 +/- 0.20 A for all atoms. The structure contains an alpha-helix (residues 10-20) and a three-stranded antiparallel beta-sheet (residues 2-5, 24-28 and 29-33). A pairing of the eight cysteine residues of insectotoxin 15A was established basing on NMR data. Three disulfide bridges (residues 2-19, 16-31 and 20-33) connect the alpha-helix with the beta-sheet, and the fourth one (5-26) joins beta-strands together. The spatial fold of secondary structure elements (the alpha-helix and the beta-sheet) of the insectotoxin 15A is very similar to those of the other short and long scorpion toxins in spite of a low (about 20%) sequence homology.

Amino Acid Sequence↗
PubMed1994

Various vectorial behaviours of a spatially structured substrate cycle.

The dynamic properties of the glucose/glucose-6-phosphate cycle are studied under conditions where the phosphatase and kinase interconverting enzymes are spatially distributed. A semi-artificial membrane made of compacted plant cell walls bearing active phosphatase in its natural state, separates two compartments, one of these compartments containing soluble hexokinase. Depending only upon the two enzyme activity levels and the initial distribution of the substrates, numerous asymmetrical and vectorial behaviours can be observed, such as facilitated glucose 6-phosphate diffusion, active transport of either glucose or glucose 6-phosphate and sequential (alternative) transport between glucose and glucose 6-phosphate. A diffusion-partition reaction coupling can account for these oriented mass transfers. The possibility of such a coupling in this model system is clearly dictated by the global analog of the Curie principle. These results may provide new insight on (a) the still obscure role played by the cell-wall phosphatase activities, particularly their involvement in the transport of exogenous phosphomonoesters, and (b) the actual in vivo operation of substrate and protein cycles in view of the heterogeneity and anisotropy of the cellular milieu.

Biological Transport↗
PubMed2001

Spatially structured metapopulation models: global and local assessment of metapopulation capacity.

We model metapopulation dynamics in finite networks of discrete habitat patches with given areas and spatial locations. We define and analyze two simple and ecologically intuitive measures of the capacity of the habitat patch network to support a viable metapopulation. Metapopulation persistence capacity lambda(M) defines the threshold condition for long-term metapopulation persistence as lambda(M)>delta, where delta is defined by the extinction and colonization rate parameters of the focal species. Metapopulation invasion capacity lambda(I) sets the condition for successful invasion of an empty network from one small local population as lambda(I)>delta. The metapopulation capacities lambda(M) and lambda(I) are defined as the leading eigenvalue or a comparable quantity of an appropriate "landscape" matrix. Based on these definitions, we present a classification of a very general class of deterministic, continuous-time and discrete-time metapopulation models. Two specific models are analyzed in greater detail: a spatially realistic version of the continuous-time Levins model and the discrete-time incidence function model with propagule size-dependent colonization rate and a rescue effect. In both models we assume that the extinction rate increases with decreasing patch area and that the colonization rate increases with patch connectivity. In the spatially realistic Levins model, the two types of metapopulation capacities coincide, whereas the incidence function model possesses a strong Allee effect characterized by lambda(I)=0. For these two models, we show that the metapopulation capacities can be considered as simple sums of contributions from individual habitat patches, given by the elements of the leading eigenvector or comparable quantities. We may therefore assess the significance of particular habitat patches, including new patches that might be added to the network, for the metapopulation capacities of the network as a whole. We derive useful approximations for both the threshold conditions and the equilibrium states in the two models. The metapopulation capacities and the measures of the dynamic significance of particular patches can be calculated for real patch networks for applications in metapopulation ecology, landscape ecology, and conservation biology.

Animals↗
PubMed1990

The two-dimensional spatial structure of nonlinear subunits in the receptive fields of complex cells.

We have estimated the second-order response properties of complex cells in two spatial dimensions by cross-correlating their spike trains with a binary approximation of a Gaussian white noise stimulus ensemble. Wiener-like kernels were computed and generally consisted of two or three parallel, elongated subregions alternating between augmented and suppressed response. These subunits were scattered across the receptive fields of complex cells and their axes of elongation agreed with the optimal orientation determined with drifting gratings.

Animals↗
PubMed1999

Selection for intermediate mortality and reproduction rates in a spatially structured population.

How local interactions influence both population and evolutionary dynamics is currently a key topic in theoretical ecology. We use a 'well-mixed' analytical model and spatially explicit individual-based models to investigate a system where a population is subject to rare disturbance events. The disturbance can only propagate through regions of the population where the density of individuals is sufficiently high and individuals affected by the disturbance die shortly after. We find that populations where individuals are sessile often exhibit very different dynamic behaviour when compared to populations where individuals are mobile and spatially well mixed. When mutations are allowed which affect either offspring birth rates or mortality rates, the well-mixed populations always evolve to a state where a single disturbance event leads to extinction. Populations often persist substantially longer if individuals are sessile and they disperse their offspring locally. We also find that for sessile populations selection may favour short-lived individuals with limited offspring production. Population dynamics are found to be strongly influenced by the host characters that are evolving and the rate at which host variation is introduced into the system.

Animals↗
PubMed2000

Spatial pooling in the second-order spatial structure of cortical complex cells.

We investigate what computational mechanisms give rise to the nonlinearity of complex cell responses in the primary visual cortex. Complex cells are characterized by their nonlinear spatial properties such as spatial phase invariance and nonlinear spatial additivity. We carried out network simulations to estimate the second-order Wiener-like kernels for several different models. Models with nonlinear spatial pooling of simple-cell-like linear subunits reproduce the second-order kernels in good agreement with physiologically estimated kernels, while models without the pooling mechanism fail to reproduce the kernel. The results support the cascade mechanism consisting of simple cells' local feature extraction followed by spatial pooling.

Humans↗
PubMed1999

The effects of local spatial structure on epidemiological invasions.

Predicting the likely success of invasions is vitally important in ecology and especially epidemiology. Whether an organism can successfully invade and persist in the short-term is highly dependent on the spatial correlations that develop in the early stages of invasion. By modelling the correlations between individuals, we are able to understand the role of spatial heterogeneity in invasion dynamics without the need for large-scale computer simulations. Here, a natural methodology is developed for modelling the behaviour of individuals in a fixed network. This formulation is applied to the spread of a disease through a structured network to determine invasion thresholds and some statistical properties of a single epidemic.

Communicable Disease Control↗
PubMed1981

The 1H nuclear-magnetic-resonance spectra and spatial structure of the Naja mossambica mossambica neurotoxin III.

The proton NMR spectra at 300 MHz of neurotoxin III from venom of Naja mossambica mossambica are reported. By the use of double resonance techniques, pH dependence chemical shifts, isotope labeling technique, and comparison with homologous neurotoxins all proton signals in the aromatic and methyl regions as well as epsilon-CH2 proton signals of some lysine residues have been assigned to individual amino acid residues and their spatial microenvironment has been determined. The results deduced on the solution structure of neurotoxin III are in complete agreement with the crystal structure of sea snake erabutoxins as well as with the previously established backbone folding and inter-residue interactions for the Naja naja oxiana short-chain neurotoxin in solution. In addition evidence has been obtained (a) that the conformation of the beta turn in the 31-34 segment depends on the ionization state of Asp-31 and His-32 side chain groups and (b) that an intricate electrostatic interaction exists in a system of ionogenic groups of the invariant Lys-27, Lys-47, Asp-31, Arg-33, Glu-38 and His-32 residues. These aspects of dynamic conformation are related to an interaction mechanism of a neurotoxin molecule and a nicotinic acetylcholine receptor.

Amino Acids↗
PubMed2005

Spatial structure of complex cell receptive fields measured with natural images.

Neuronal receptive fields (RFs) play crucial roles in visual processing. While the linear RFs of early neurons have been well studied, RFs of cortical complex cells are nonlinear and therefore difficult to characterize, especially in the context of natural stimuli. In this study, we used a nonlinear technique to compute the RFs of complex cells from their responses to natural images. We found that each RF is well described by a small number of subunits, which are oriented, localized, and bandpass. These subunits contribute to neuronal responses in a contrast-dependent, polarity-invariant manner, and they can largely predict the orientation and spatial frequency tuning of the cell. Although the RF structures measured with natural images were similar to those measured with random stimuli, natural images were more effective for driving complex cells, thus facilitating rapid identification of the subunits. The subunit RF model provides a useful basis for understanding cortical processing of natural stimuli.

Action Potentials↗
PubMed2003

Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs. molecular traits.

Understanding the origin, maintenance and significance of phenotypic variation is one of the central issues in evolutionary biology. An ongoing discussion focuses on the relative roles of isolation and selection as being at the heart of genetically based spatial variation. We address this issue in a representative of a taxon group in which isolation is unlikely: a marine broadcast spawning invertebrate. During the free-swimming larval phase, dispersal is potentially very large. For such taxa, small-scale population genetic structuring in neutral molecular markers tends to be limited, conform expectations. Small-scale differentiation of selective traits is expected to be hindered by the putatively high gene flow. We determined the geographical distribution of molecular markers and of variation in a shell shape measure, globosity, for the bivalve Macoma balthica (L.) in the western Dutch Wadden Sea and adjacent North Sea in three subsequent years, and found that shells of this clam are more globose in the Wadden Sea. By rearing clams in a common garden in the laboratory starting from the gamete phase, we show that the ecotypes are genetically different; heritability is estimated at 23%. The proportion of total genetic variation that is between sites is much larger for the morphological additive genetic variation (QST = 0.416) than for allozyme (FST = 0.000-0.022) and mitochondrial DNA cytochrome-c-oxidase-1 sequence variation (phiST = 0.017). Divergent selection must be involved and intraspecific spatial genetic differentiation in marine broadcast spawners is apparently not constrained by low levels of isolation.

Analysis of Variance↗
PubMed2006

Stochasticity, complex spatial structure, and the feasibility of the shifting balance theory.

Sewall Wright's shifting balance theory of evolution posits a mechanism by which a structured population may escape local fitness optima and find a global optimum. We examine a one-locus, two-allele model of underdominance in populations with differing spatial arrangements of demes, both analytically and with Monte Carlo simulations. We find that inclusion of variance in interpatch connectivities can significantly reduce the number of generations required for fixation of the more favorable allele relative to island and stepping-stone models. Although time to fixation increases with migration rate in all cases, the presence of one or two relatively isolated demes may reduce the number of generations by 80% or more. These results suggest that the shifting balance process may operate under less restrictive conditions than those found with a simple spatial arrangement of demes.

Biological Evolution↗
PubMedDate not supplied

[Likeness: a system for rapid retrieval of similar conformation of proteins and their spatial structures].

We report a method for estimating the conformational likeness between any two proteins. Likeness is handled in terms of stochastic geometry, fuzzy logic and decision making theories. Using the method, a computer system LIKENESS was developed. The system does "real time" searching and spatial alignment of any PDB-available proteins. LIKENESS is accessible at URL: "http:@cl.sdsc.edu/".

Amino Acid Sequence↗
PubMed1983

A new spatial structure for the axial methionine observed in cytochrome c5 from Pseudomonas mendocina. Correlations with the electronic structure of heme c.

Cytochrome c5 from Pseudomonas mendocina has been isolated and the coordination geometry at the heme iron was investigated by 1H nuclear magnetic resonance and circular dichroism spectroscopy. Individual assignments were obtained for heme c and the axial ligands. From studies of nuclear Overhauser enhancements the axial histidine imidazole ring orientation relative to the heme group was found to coincide with that of other c-type cytochromes. In contrast, a new structure was observed for the axial methionine. This includes S chirality at the iron-bound sulfur atom, but compared to cytochromes c-551 from Pseudomonads and Rhodopseudomonas gelatinosa, which also contain S-chiral methionine, the spatial arrangement of the gamma- and beta-methylene groups and the alpha carbon of methionine is markedly different. Analysis of the electron spin density distribution in ferricytochrome c5 in the light of this new coordination geometry provides additional support for the hypothesis that the electronic structure of heme c is primarily governed by the orientation of the sp3 lone-pair orbital of the axial sulfur atom with respect to the heme plane.

Circular Dichroism↗
PubMedDate not supplied

[The spatial structure of the alpha rhythm in the healthy human being studied by EEG mapping].

EEG study was conducted in the state of relative rest in 15 healthy subjects with predominance of the alpha rhythm. Data processing was performed on neuromapper ("Neuroscience", Great Britain). Principal attention was paid to the dynamics of spatial-temporal relations of the alpha rhythm. Cyclic changes were shown of the alpha-rhythm amplitude, proceeding with change of high and low amplitudes during seconds, varying in time in various individuals. Three types of spatial distribution of the alpha rhythm over the cortex at the relative rest were obtained: 1) generalized distribution over the cortex with the wavy shift of the frequency fields; 2) formation of delimited local zones of the alpha rhythm, differing by the frequency from the rhythm in other cortical areas; 3) local zone of the low-frequency alpha rhythm in the visual projection zone (18 and 19 fields). Change of the distribution types of the alpha rhythm in the state of rest takes place in the seconds of time intervals, corresponding, according to the literature data, to the proceeding of elementary mental processes.

Adult↗
PubMed2002

The evolution of reproductive isolation in spatially structured populations.

Recent models of speciation have incorporated population structure and migration into the classic model of speciation in which reproductive isolation arises as a by-product of divergence. In this paper, we expanded these models to explore the joint effects of migration and population subdivision on speciation in a spatially explicit context. The results of our simulation support previous results concerning the influence of population subdivision on the accumulation of reproductive isolation. The simulation also shows that speciation in subdivided populations occurs most rapidly when subpopulations are not strictly allopatric. These results counter the widespread notion that speciation is most likely to occur in allopatric populations and suggest that there are useful insights to be gained by incorporating increasingly realistic types of population structure into models of speciation.

Biological Evolution↗
PubMed1991

Structure, spatial, and temporal expression of two sea urchin metallothionein genes, SpMTB1 and SpMTA.

The metallothionein-B genes of the sea urchin Strongylocentrotus purpuratus encode a metallothionein (MT) isoform distinguishable from the MTA isoform. The MTB subfamily consists of at least two genes, MTB1 and MTB2, and possibly two to three others. The unique MTB1 and MTA genes have a high degree of identity but diverge in structural detail and expression. Transcripts of the MTA, MTB1, troponin C Spec 1, and CyIIIa actin genes begin simultaneously to accumulate at an early blastula stage. MTB1 mRNA becomes localized in the embryonic gut and oral ectoderm, whereas MTA, Spec 1, and CyIIIa actin mRNAs are spatially restricted to the aboral ectoderm. Several DNA elements are localized at the same positions in the MTB1 and MTA genes: these include respective CATA and TATA boxes, two metal response elements, and three distinct upstream DNA elements that are also present, and in the same order, in the Spec 1 gene promoter. A heptameric sequence, element A, is present at two sites each in the Spec 1 and CyIIIa actin genes, five sites in MTA, but only one site in MTB1. Most strikingly, the first intron of MTA contains elements not found in the MTB1 introns, including a consensus metal response element, an element A, and the P3A site demonstrated in the CyIIIa actin gene to be linked to the regulation of spatial expression.

Amino Acid Sequence↗
PubMed1989

BioGraf 3D: an algorithm for optimization and graphical representation of nuclear structure spatial distributions.

BioGraf 3D is a computer algorithm for rapid three dimensional visualization and analysis of digitized three dimensional biological data to aid in the subsequent generation of models of nuclei or cells. This graphically oriented program permits unlimited three dimensional perspective viewpoints of data in onscreen single frame, zoom or stereo forms. Analysis of data is enhanced by an optimization problem solution which determines viewpoint coordinates whereby maximum clustering of preselected structures is achieved. Mathematical representation of the transformations and optimization is presented in detail. Biograf 3D is written in the C programming language for IBM and compatible personal computers. In this study BioGraf 3D is utilized to examine the infrastructure of the nucleus and the spatial distribution of meiotic chromosomes in the hermaphroditic nematode Caenorhabditis elegans.

Algorithms↗