Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
PubMed2000

Spatial structuring and frequency distribution of the nematode Steinernema feltiae Filipjev.

The frequency distribution of first generation, Steinernema feltiae Filipjev parasitic stages was over-dispersed with the majority of hosts containing few or no parasitic stages, whilst a few hosts contained a great many. Because of high extraction efficiency, the frequency distributions of the parasitic stages and the infective stages in the soil were assumed to be directly related. To explain the frequency distribution of the parasites it was therefore necessary to account for the frequency distribution of the S. feltiae infective stages in the soil. The infective stages were spatially aggregated into 30 cm diameter patches at the site of host death. These patches were randomly distributed approximately 1 m apart. At the 1 m scale, the pooled counts of infective stages were randomly distributed. Thus, in contrast to the frequency distributions, the spatial structuring of S. feltiae changed with the spatial scale of the interaction. This dynamic spatial structuring means that the majority of samples taken would contain few or no infective stages, whilst a few soil samples would contain a great many. Thus, the spatial structuring of the infective stages generates the over-dispersed frequency distribution of the S. feltiae in the soil. Hosts, encountering infective stages from this spatial distribution will, therefore, show an over-dispersed frequency distribution of S. feltiae parasitic stages.

Animals↗
PubMed2004

[Spatial structure of populations Myzus persicae and its predatory natural enemy Erigonidium graminicola].

In this paper, the spatial construction models of populations M. persicae and its predatory natural enemy E. graminicola during different periods were simulated by geostatistics, and their spatial relationships were analyzed. The spatial structure of M. persicae population was described by spherical model, showing an aggregated spatial arrangement. Its spatial dependence was 2.0252-4.1495 m, heterogeneity degree was 10,281.36-300,216.30, and sample variance was 12,176.81-303,433.70. The spatial structure of E . graminicola population was also simulated by spherical model, showing an aggregated spatial arrangement. Its spatial dependence was 3.7328-4.8983 m, heterogeneity degree was 1.4482-4.4134, and sample variance was 1.6941-5.8167. The results and methods could be applied to monitor the temporal and spatial dynamics of target insect pest population in tobacco field, and provide scientific basis for ecological control.

Animals↗
PubMed1995

[NMR spectroscopy in the study of the spatial structure of membrane peptides and proteins].

The review covers the field of the spatial structure determination of membrane-associated peptides and proteins by the High-Resolution NMR Spectroscopy. The membrane-bound conformations of several hormones, neuropeptides, lipopeptides, peptide antibiotics, bacteriophage coat proteins, transmembrane domains of receptors and others are considered. To mimic the biomembrane environment the appropriate artificial media (organic solvents, micelles of detergents of lipid vesicles) must be adjusted. In that case NMR spectroscopy is a powerful tool for the spatial structure and dynamics investigations of membrane associated peptides and proteins constituting the bases for unraveling of their structure-function relationships.

Magnetic Resonance Spectroscopy↗
PubMed2005

Asymptotically exact analysis of stochastic metapopulation dynamics with explicit spatial structure.

We describe a mathematically exact method for the analysis of spatially structured Markov processes. The method is based on a systematic perturbation expansion around the deterministic, non-spatial mean-field theory, using the theory of distributions to account for space and the underlying stochastic differential equations to account for stochasticity. As an example, we consider a spatial version of the Levins metapopulation model, in which the habitat patches are distributed in the d-dimensional landscape Rd in a random (but possibly correlated) manner. Assuming that the dispersal kernel is characterized by a length scale L, we examine how the behavior of the metapopulation deviates from the mean-field model for a finite but large L. For example, we show that the equilibrium fraction of occupied patches is given by p(0)+c/L(d)+O(L(-3d/2)), where p(0) is the equilibrium state of the Levins model and the constant c depends on p(0), the dispersal kernel, and the structure of the landscape. We show that patch occupancy can be increased or decreased by spatial structure, but is always decreased by stochasticity. Comparison with simulations show that the analytical results are not only asymptotically exact (as L-->infinity), but a good approximation also when L is relatively small.

Animals↗
PubMed2001

Spatial structure of cone inputs to color cells in alert macaque primary visual cortex (V-1).

The spatial structure of color cell receptive fields is controversial. Here, spots of light that selectively modulate one class of cones (L, M, or S, or loosely red, green, or blue) were flashed in and around the receptive fields of V-1 color cells to map the spatial structure of the cone inputs. The maps generated using these cone-isolating stimuli and an eye-position-corrected reverse correlation technique produced four findings. First, the receptive fields were Double-Opponent, an organization of spatial and chromatic opponency critical for color constancy and color contrast. Optimally stimulating both center and surround subregions with adjacent red and green spots excited the cells more than stimulating a single subregion. Second, red-green cells responded in a luminance-invariant way. For example, red-on-center cells were excited equally by a stimulus that increased L-cone activity (appearing bright red) and by a stimulus that decreased M-cone activity (appearing dark red). This implies that the opponency between L and M is balanced and argues that these cells are encoding a single chromatic axis. Third, most color cells responded to stimuli of all orientations and had circularly symmetric receptive fields. Some cells, however, showed a coarse orientation preference. This was reflected in the receptive fields as oriented Double-Opponent subregions. Fourth, red-green cells often responded to S-cone stimuli. Responses to M- and S-cone stimuli usually aligned, suggesting that these cells might be red-cyan. In summary, red-green (or red-cyan) cells, along with blue-yellow and black-white cells, establish three chromatic axes that are sufficient to describe all of color space.

Animals↗
PubMed1989

Analysis of spatial structure in eccentric vision.

The analysis of spatial structure, ie, the encoding of relative positions between pattern elements, was studied in central and eccentric vision. In a two-alternative forced-choice task the observer had to discriminate between two patterns consisting of short line segments. At each trial the two patterns were flashed for 140 msec and the observer indicated whether the patterns were identical or mirror symmetric. Psychometric functions were measured by changing pattern size at each eccentricity in order to find the threshold size allowing 75% of correct responses. The scaling factor, required for discriminating between mirror symmetric and identical patterns independent of eccentricity, was found to be similar to the size-scaling proposed by Levi et al (Vision Res 25:963, 1985) for vernier acuity tasks.

Differential Threshold↗
PubMedDate not supplied

[Spatial structure of the rp142 peptide containing the immunodominant epitope of the HIV-1 gp120 protein. A theoretical study].

A model of spatial structure of the synthetic peptide rp142 (24 amino acid residues) containing the immunodominant epitope of the HIV-1 protein gp120 in the region Gly-10-Phe-15 was constructed by the method of "constrained" molecular mechanics, which uses the algorithms of theoretical conformational analysis, based on NMR spectroscopy data. A comparative analysis of calculated conformations revealed that the spatial structure of rp142 in solution can be described by a family of conformations to which nine different structural clusters involving the sets of topologically close conformers correspond. It is shown that the main chain of the peptide forms irregular but "structured" conformations in which the main portion of amino acid residues is incorporated into beta-turns and helix-like fragments, while Pro-11 and Gly-12 form in some structures inverse gamma-turns, which rarely occur in protein-peptide molecules. It was found that the spatial packing of the Gly-10-Phe-15 hexapeptide in different clusters is realized at different internal rotation angles, to which topologically close structures correspond. It is assumed that this invariant structural element describes the "conformation of complex formation" that is complementary to the antigen-binding center of antibodies and is responsible for their binding to the peptide.

Amino Acid Sequence↗
PubMed1983

[Conformation NMR analysis of the spatial structure of Buthus eupeus insectotoxin I5A].

1H NMR spectroscopy has been used to collect data related to the spatial structure of insectotoxin I5A Buthus eupeus: pH-dependence of the chemical shifts, deuterium exchange rates of individual amide hydrogens, spin-spin coupling of the H-N-C alpha-H and H-C alpha-C beta-H protons, and nuclear Overhauser effect between distinct protons belonging to amino acid residues remote in the sequence. Molecular conformation in the regions from Asp9 to Cys19 (beta-turn 9-12 and right-hand alpha-helix 12-19) and from Asn23 to Asn34 (antiparallel beta-sheet with the beta-turn 27-30) directly follows from the observed parameters. Pseudoatomic approach of distance geometry algorithm was used to solve the overall folding of the molecule and propose the most probable set of disulfide bridges: Cys2-Cys19, Cys5-Cys31, Cys16-Cys26 and Cys20-Cys33. The spatial structure of insectotoxin I5A B. eupeus demonstrates remarkable similarity with that of a "long" type scorpion neurotoxin V-3 Centruroides sculpturatus.

Amino Acid Sequence↗
PubMed1988

Trophoblast-specific beta 1-glycoprotein: its spatial structure and localization of antigenic determinants.

Effects of temperature and pH on the spatial structures of trophoblast-specific beta 1-glycoprotein (TSG) and its various derivatives and fragments have been studied by circular dichroic spectroscopy. The spatial organization of the protein portion of TSG derivatives, as revealed by the spectroscopic evidence, has been discussed with respect to the antigenic activity of the species studied. We concluded that the TSG protein portion consists mainly of a beta-structural type. The antigenic determinants were shown to be topographic, and are preferentially localized in the protein portion; only about 15% of the TSG antigenic activity failed to bear a direct relation to the spatial structure. The antigenic determinants seemed to include a tryptophan residue.

Circular Dichroism↗
PubMed1999

Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition.

An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared with available data. The method is based on entirely physical model of van der Waals interactions that reflects as illustrated in this work the distribution of electron density. Various levels of hierarchy in the protein spatial structure are discerned by analysis of the energy interaction between structural units of different scales. Thus the level of energy hierarchy plays role of sole parameter, and the method obviates the use of complicated geometrical criteria with numerous fitting parameters. The algorithm readily and accurately locates domains formed by continuous segments of the protein chain as well as those comprising non-sequential segments, sets no limit to the number of segments in a domain. We have analyzed 309 protein structures. Among 277 structures for which our results could be compared with the domain definitions made in other works, 243 showed complete or partial coincidence, and only in 34 cases the domain structures proved substantially different. The domains delineated with our approach may coincide with reference definition at different levels of the globule hierarchy. Along with defining the domain structure, our approach allows one to consider the protein spatial structure in terms of the spatial distribution of the interaction energy in order to establish the correspondence between the hierarchy of energy distribution and the hierarchy of structural elements.

Algorithms↗
PubMed1985

[Study of the spatial structure of the protein component of the carcino-embryonic antigen by circular dichroism, Raman spectroscopy and UV-spectroscopy].

The spatial structure features of intact and deglycosylated carcino-embryonic antigen (CEA) have been studied by circular dichroism. Raman and UV-spectroscopy methods in order to elucidate a pattern and localization of CEA immunodominants. The temperature-induced changes in the spatial structure of the protein moiety were compared with data on the CEA immunochemical activity estimated by EIA procedure. A conformational transition was found within the 55-75 degrees range that produced irreversible alterations in the tertiary structure, while the secondary structure could be restored after lowering the temperature to 20 degrees C. Spectral studies of intact and deglycosylated CEA demonstrated that immunochemical activity, at least partly, was associated with the tertiary structure of the CEA protein portion.

Carcinoembryonic Antigen↗
PubMed2006

Spatial structure and activity mechanism of a novel spider antimicrobial peptide.

Latarcins (Ltc), linear peptides (ca. 25 amino acid long) isolated from the venom of the Lachesana tarabaevi spider, exhibit a broad-spectrum antibacterial activity, most likely acting on the bacterial plasmatic membrane. We study the structure-activity relationships in the series of these compounds. At the first stage, we investigated the spatial structure of one of the peptides, Ltc2a, and its mode of membrane perturbation. This was done by a combination of experimental and theoretical methods. The approach includes (i) structural study of the peptide by CD spectroscopy in phospholipid liposomes and by (1)H NMR in detergent micelles, (ii) determination of the effect on the liposomes by a dye leakage fluorescent assay and (31)P NMR spectroscopy, (iii) refinement of the NMR-derived spatial structure via Monte Carlo simulations in an implicit water-octanol slab, and (iv) calculation of the molecular hydrophobicity potential. The molecule of Ltc2a was found to consist of two helical regions (residues 3-9 and 13-21) connected via a poorly ordered fragment. The effect of the peptide on the liposomes suggests the carpet mechanism of the membrane deterioration. This is also supported by the analysis of hydrophobic/hydrophilic characteristics of Ltc2a and homologous antimicrobial peptides. These peptides exhibiting a helix-hinge-helix structural motif are characterized by a distinct and feebly marked amphiphilicity of their N- and C-terminal helices, respectively, and by a hydrophobicity gradient along the peptide chain. The approach we suggested may be useful in studying not only other latarcins but also a wider class of membrane-active peptides.

Amino Acid Sequence↗
PubMed2001

[Spatial structure and pattern of Nilaparvata lugens population in large-scale].

Brown planthopper(BPH), Nilaparvata lugens, is a major pest of rice. Its spatial distribution of different generations in Guangdong Province was studied by using variograms. The results showed that this population distributed in a clump pattern in rice fields during the 1st rice season. 3 generations of this population had different spatial structures, with the clump range of 400 km, 200 km and 205 km respectively in the 1st rice season. The simulation distribution maps of BPH, which was interpolated by Ordinary Kriging, showed that the density of BPH populations in west Guangdong province were higher than that in the east. The effect of sampling size on the spatial structure of BPH was not significant.

Animals↗
PubMed2004

Elucidation of the deposition processes and spatial structures of alkanethiol and arylthiol molecules adsorbed on Pt111 electrodes with in situ scanning tunneling microscopy.

In situ scanning tunneling microscopy (STM) was used to examine the spatial structures of n-alkane thiols (1-hexanethiol, 1-nonanethiol, and 1-octahexanethiol) and arylthiols (benzenethiol and 4-hydroxybenzenethiol) adsorbed on well-ordered Pt111 electrodes in 0.1 M HClO4. The electrochemical potential and molecular flux were found to be the dominant factors in determining the growth mechanisms, final coverages, and spatial structures of these organic adlayers. Depending on the concentrations of the thiols, deposition of self-assembled monolayers (SAMs) followed either the nucleation-and-growth mechanism or the random fill-in mechanism. Low and high thiol concentrations respectively produced two ordered structures, (2 x 2) and (square root of 3 x square root of 3)R30 degrees , between 0.05 and 0.3 V. On average, an ordered domain spanned 500 A when the SAMs were made at 0.15 V, but this dimension shrank substantially once the potential was raised above 0.3 V. This potential-induced order-to-disorder phase transition resulted from a continuous deposition of thiols, preferentially at domain boundaries of (square root of 3 x square root of 3 x )R30 degrees arrays. All molecular adlayers were completely disordered by 0.6 V, and this restructuring event was irreversible with potential modulation. Since all thiols were arranged in a manner similar to that adopted by sulfur adatoms (Sung et al. J. Am. Chem. Soc. 1997, 119, 194), it is likely that they were adsorbed mainly through their sulfur headgroups in a tilted configuration, irrespective of the coverage. Both the sulfur and phenyl groups of benzenethiol admolecules gave rise to features with different corrugation heights in the molecular-resolution STM images. All thiols were adsorbed strongly enough that they remained intact at a potential as negative as -1.0 V in 0.1 M KOH.

Journal Article↗
PubMed1992

Visual experience, visual field size, and the development of nonvisual sensitivity to the spatial structure of outdoor neighborhoods explored by walking.

When places are explored without vision, observers go from temporally sequenced, circuitous inputs available along walks to knowledge of spatial structure (i.e., straight-line distances and directions characterizing the simultaneous arrangement of the objects passed along the way). Studies show that a life history of vision helps develop nonvisual sensitivity, but they are unspecific on the formative experiences or the underlying processes. This study compared judgments of straight-line distances and directions among landmarks in a familiar area of town by partially sighted persons who varied in types and ages of visual impairment. Those with early childhood loss of broad-field vision and those blind from birth performed significantly worse than those with early or late acuity loss and those with late field loss. Broad-field visual experience facilitates perceptual development by providing a basis for proprioceptive and efferent information from locomotion against distances and directions relative to the surrounding environment. Differences in the perception of walking, in turn, cause the observed differences in sensitivity to spatial structure.

Adolescent↗
PubMed1996

Chloroplastic aspartate aminotransferase from Arabidopsis thaliana: an examination of the relationship between the structure of the gene and the spatial structure of the protein.

A clone encoding a plastid isoenzyme of aspartate amino-transferase (AAT5) was isolated from an Arabidopsis genomic library and its complete sequence determined. The gene for AAT5 (asp5) contains an open reading frame of 2447 bp comprising 11 exons separated by introns ranging in length from 74 to 207 bp. The upstream regulatory region contains a putative TATA box and multiple copies of two sequence motifs, CTCTT and AAAGAT, previously associated with nodule-specific gene activity in legumes. The deduced primary amino acid sequence of the protein product of asp5 was used to generate a three-dimensional structure of the AAT5 protein by using the computer program Sybyl: Biopolymer Composer and known AAT structures on the protein databases. Both the mature protein and its precursor protein containing a putative N-terminal transit peptide were modelled. The resulting structure of the precursor protein indicated that the transit peptide might also inhibit dimerization of the protein until after its translocation across the chloroplast membrane. The derived structure of the mature protein was then analysed in terms of its component elements of secondary structure, and the positions on the polypeptide back-bone corresponding to intron insertion sites were determined. It is observed that the introns tend to map to regions between structural subdomains of the protein and also map to sites on the surface of the molecule. The asp5 gene in Arabidopsis is thus consistent with Gilbert's exon-shuffling theory of gene evolution [Gilbert (1985) Science 228, 823-824]. A high degree of conservation of intron insertion sites between AAT genes from different plants and animals is observed, particularly within the part of the gene encoding a large beta-sheet structure that forms the structural and functional core of the protein. This beta-sheet structure is thus believed to compromise an ancient and very highly conserved moiety of the molecule.

Amino Acid Sequence↗
PubMed1988

The effect of exposure duration on the analysis of spatial structure in eccentric vision.

There is some evidence from grating experiments that the transient presentation of a stimulus pattern interferes with the encoding of positional relationships between pattern elements (i.e. the analysis of spatial structure) more in eccentric vision than in central vision. The present study investigated the effect of exposure duration on the analysis of spatial structure in eccentric vision using a task in which the observer discriminated between two mirror symmetric patterns consisting of short line segments. In each trial, the two patterns were flashed for 140 or 500 ms, and the observer had to decide whether the patterns were identical or mirror symmetric. Both constant-size and size-scaled patterns were used in eccentric vision. The longer exposure duration slightly increased the proportion of correct responses in eccentric vision but performance remained distinctly inferior to that in central vision.

Humans↗
PubMed1999

Two forms of cytotoxin II (cardiotoxin) from Naja naja oxiana in aqueous solution: spatial structures with tightly bound water molecules.

1H-NMR spectroscopy data, such as NOE intraprotein and (bound water)/protein contacts, 3J coupling constants and deuterium exchange rates were used to determine the in-solution spatial structure of cytotoxin II from Naja naja oxiana snake venom (CTII). Exploiting information from two 1H-NMR spectral components, shown to be due to cis/trans isomerization of the Val7-Pro8 peptide bond, spatial structures of CTII minor and major forms (1 : 6) were calculated using the torsion angle dynamics algorithm of the DYANA program and then energy refined using the FANTOM program. Each form, major and minor, is represented by 20 resulting conformers, demonstrating mean backbone rmsd values of 0.51 and 0.71 A, respectively. Two forms of CTII preserve the structural skeleton as three large loops, including two beta-sheets with bend regions, and demonstrate structural differences at loop I, where cis/trans isomerization occurs. The CTII side-chain distribution constitutes hydrophilic and hydrophobic belts around the protein, alternating in the trend of the three main loops. Because of the Omega-shaped backbone, formed in participation with two bound water molecules, the tip of loop II bridges the tips of loops I and III. This ensures the continuity of the largest hydrophobic belt, formed with the residues of these tips. Comparison revealed pronounced differences in the spatial organization of the tips of the three main loops between CTII and previous structures of homologous cytotoxins (cardiotoxins) in solution.

Animals↗