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PubMedDate not supplied

[The dynamics of the spatial organization of communities of small mammals (exemplified by rodents of the trans-Altai Gobi of Mongolia)].

Between-year variation of rodent population densities was studied in the central part of trans-Altai Gobi, Mongolia, in summers of a nine year period. Variation in spatial structure of the desert rodent community in 1982-84 and in 1992 was examined by the use of discriminant function analysis. Although population densities, breadth and positions of niches of many species tended to vary independently, the positive conjunct variation was found for the most ecologically distinctive species. This can be explained by limitations of the climate. Although a guild structure of the community was pronounced each year, there were significant between year shifts in niche breadth and niche centres along certain axes of ecological space. Within year nearest neighbours in niche overlap (high seasonal overlap) differed in between year variation in abundance. It is supposed that interspecific competition could contribute to development of community structure.

Animals↗

PubMed1992

Perception of structured phantom targets in the echolocating bat, Megaderma lyra.

Bats can discriminate among objects with different texture using echolocation. The mechanisms involved in texture discrimination are unknown. In real echoes reflected from three-dimensional objects, the spatial structure of the target creates a specific temporal and spectral pattern. In the experiments described here, simply structured phantom targets mimicking echoes reflected from an object with two parallel planes were generated by adding two differentially delayed copies of the bat's vocalizations. The discrimination performance of Megaderma lyra was studied in a two-alternative, forced-choice experiment using phantom targets with different internal delays and relative amplitudes of the two copies. When the reference target to which the bats were trained was presented, targets differing in internal delay by about 1 microseconds were discriminated. However, discrimination performance was not a globally monotonic function of the internal delay of the unrewarded target. When both targets presented in a trial differed from the reference, the bats still preferred one of them. Changes in overall level of the phantom target echo had little effect on performance; however, performance dropped considerably if only one of the two copies in an echo was attenuated. A model framework is introduced to account for these results. Models based on frequency processing yield better approximations than does a model based on time differences. The model based on spectral correlation gives a unified description of all the data. Although time domain models for texture discrimination cannot be generally refuted, the results presented here show that the discrimination of target surface structure can be explained as a discrimination of echo spectra.

Animals↗

PubMed1998

A phosphoglycerate kinase mutant (PGK Herlev; D285V) in a Danish patient with isolated chronic hemolytic anemia: mechanism of mutation and structure-function relationships.

Phosphoglycerate kinase (PGK) is a X-linked enzyme that plays a key role in the glycolytic pathway. Twelve different variants have already been reported. We describe a new PGK variant, PGK Herlev (Asp 285-->Val), in a 69-year-old Danish patient with isolated chronic hemolysis but who had no neurological or muscular disorders. The description of the mutation is based upon PCR amplification of specific regions of the PGK gene, followed by direct sequencing. Although observed in a male patient, this mutated X-linked gene is expressed partially, i.e., both normal and substituted nucleotides are present at the same position in a ratio of approximately 1:9. The most likely explanation for this observation is based on the occurrence of a somatic mutation of the PGK gene. The relationship of structure to function in PGK Herlev, as well as in all known variants, was examined by the use of a computer model based on the known spatial structure of the yeast and horse enzymes. Such an approach can be generalized to any other protein that has been crystallized and for which x-ray diffraction data are available in a species closely related to man.

Aged↗

PubMed1996

Imagining projective transformations: aligned orientations in spatial organization.

Four experiments were conducted to investigate whether variations in orientation that profoundly affect the ability to imagine rotations also affect the ability to imagine projective transformations. For a basic rectilinear object and the three simpler Platonic Solids, imagining projective transformations (e.g., the casting of a shadow) was quite successful when the objects were aligned with the direction of projection. For the solids, this alignment occurred when the objects were generalized cylinders about axes aligned with the projection. As the objects were made more oblique to the projection, performance deteriorated markedly. When the objects were moderately aligned with the projection, performance depended on the orientation of the object and the orientation of the projection to the environment. We suggest that the imagination of projection and of rotation is a type of problem solving in which spatial structures are organized in relation to initially given properties of the objects and transformations. When there is alignment among the various structural components, this process of imagination works efficiently. Without such alignment, nonexperts often fail. We suggest that aligned (i.e., parallel and perpendicular) orientations are effective in spatial imagination because they are categorically distinct and singular, and they provide a critical form of redundancy.

Adult↗

PubMed1977

Visualization of centriole-bodies using silver stain.

Duplicate staining of human metaphase chromosomes, first with Giemsa followed by silver, revealed the presence of two small silver-stained bodies not seen in the Giemsa stained metaphases. Similar bodies were subsequently found in the metaphases of several animal groups. The size, structure, spatial relationships to the nucleus, behavior throughout the cell cycle, and apparent universal presence of these bodies suggest that they are either centrioles or associated centriolar structures. These centriole-bodies can be seen throughout the cell cycle, even in hypotonically spread C-metaphase chromosome plates. The silver stain procedure allows enough resolution to distinguish parent and daughter centriole-bodies at interphase, thus permitting visualization of the replication, maturation and separation stages of these bodies with the light microscope.

Animals↗

PubMed2004

Intracellular domains of the delta-subunits of Torpedo and rat acetylcholine receptors--expression, purification, and characterization.

There are quite detailed structural data on the extracellular ligand-binding domain and the intramembrane channel-forming domain of the nicotinic acetylcholine receptors (nAChR). However, the structure of the intracellular domain, which has variable amino acid sequences in different nAChR subunits, remains unknown. We expressed in Escherichia coli the intracellular loops (between transmembrane fragments TM3 and TM4) of the delta-subunits from the Torpedo californica and Rattus norvegicus muscle nAChRs. To facilitate purification, (His)6-tags were attached with or without linkers, and the effects of protein truncations at C- or N-termini were examined. The proteins were purified from inclusion bodies under denaturing conditions by Ni-NTA-chromatography. Molecular weight and peptide mass fingerprint was determined by MALDI mass spectrometry. Size-exclusion chromatography revealed that the Torpedo intracellular delta-loop refolded in an aqueous buffer was present in solution as a dimer. Phosphorylation of this protein with protein kinase A and tyrosine kinase (Abl) occurred at the same serine and tyrosine residues as in the native receptor. According to CD spectra, the secondary structure was not sensitive to phosphorylation. The rat intracellular loops could be solubilized only in the presence of non-ionic detergents or lipids. CD spectra indicate that the Torpedo and rat proteins have differences in their secondary structure. In the presence of dodecylphosphocholine, high concentrations (up to 6 mg/ml) of the Torpedo and rat intracellular loops were achieved. The results suggest that the spatial structure of the intracellular loops is dependent on environment and species, but is not changed significantly upon enzymatic phosphorylation.

Animals↗

PubMed1999

Physicochemical and immunological studies of the N-terminal domain of the Torpedo acetylcholine receptor alpha-subunit expressed in Escherichia coli.

The nicotinic acetylcholine receptor (AChR) from the electric organ of Torpedo species is an oligomeric protein composed of alpha2 beta gamma delta subunits. Although much is known about its tertiary and quaternary structure, the conformation of the large extracellular domains of each of the subunits has not been analysed in detail. In order to obtain information about the spatial structure of the extracellular domain, we have expressed the N-terminal fragment 1-209 of the Torpedo californica AChR alpha-subunit in Escherichia coli. Two vectors coding for a (His)6 tag, either preceding or following the 1-209 sequence, were used and the recombinant proteins obtained (designated alpha1-209pET and alpha1-209pQE, respectively) were purified by affinity chromatography on a Ni2+-agarose column. The chemical structure of both proteins was verified by Edman degradation and mass spectrometry. The proteins were soluble in aqueous buffers but to make possible a comparison with the whole AChR or its isolated subunits, the recombinant proteins were analyzed both in aqueous solution and with the addition of detergents. The two proteins bound [125I]alpha-bungarotoxin with equal potency (KD approximately 130 nm, Bmax approximately 10 nmol.mg-1). Both were shown to interact with several monoclonal antibodies raised against purified Torpedo AChR. The circular dichroism (CD) spectra of the two proteins in aqueous solution revealed predominantly beta-structure (50-56%), the fraction of alpha-helices amounting to 32-35%. Nonionic (beta-octylglucoside) and zwitterionic (CHAPS) detergents did not appreciably change the CD spectra, while the addition of SDS or trifluoroethanol decreased the percentage of beta-structure or increased the alpha-helicity, respectively. The predominance of beta-structure is in accord with recent data on the N-terminal domain of the mouse muscle AChR alpha-subunit expressed in the mammalian cells [West et al. (1997) J. Biol. Chem. 272, 25 468]. Thus, expression in E. coli provides milligram amounts of the protein that retains several structural characteristics of the N-terminal domain of the Torpedo AChR alpha-subunit and appears to share with the latter a similar secondary structure. The expression of recombinant polypeptides representing functional domains of the AChR provides an essential first step towards a more detailed structural analysis.

Amino Acid Sequence↗

PubMed1999

Multicomponent photorefractive cnoidal waves: stability, localization, and soliton asymptotics.

An algorithm of building up a different class of stable self-consistent multicomponent periodical solutions of the nonlinear Schrödinger equation--multicomponent cnoidal waves--has been formulated by the example of a nonlinear wave propagating through a photorefractive crystal with a drift nonlinear response. Exact analytical expressions, describing distribution of light field in the components, have been obtained for solutions, which include up to three mutually incoherent components. It has been shown that such cnoidal waves are stable and their spatial structure is robust to collisions with the same cnoidal waves and to stochastic perturbations of the components' intensity distributions in a sufficiently wide range of changing spatial period.

Journal Article↗

PubMed1999

Influence of crystal orientation on oxygen analysis in NiO with energy dispersive X-ray analysis

Characteristic X-ray spectra of stoichiometric NiO were investigated by EDX. Peak intensities of Ni-Kalpha and O-Kalpha are determined for several zone axes and also off-axis specimen orientations. The intensity ratios depend strongly on specimen orientation, resulting in errors of up to 30% in concentration analysis. Based on Bloch wave calculations, the dependence on the zone axis is explained qualitatively by the ordered structure of NiO, assuming the atoms to be ideal point scatterers. However, in order to get a quantitative description this simple model is not sufficient: the spatial structure of the electron shells must also be considered.

Journal Article↗

PubMed2000

Active site interactions in oligomeric structures of inorganic pyrophosphatases.

Recent progress in studies of the mode of action of cytoplasmic inorganic pyrophosphatases is mainly due to the analysis of a dozen and a half structures of the apoenzyme, its complexes, and mutants. However, despite considerable research on the mechanism of action of these enzymes, many important problems remain unclear. Among them is the problem of active site interactions in oligomeric structures and their role in catalysis; this review focuses on this problem. The abundant experimental data requires generalization and comprehensive analysis. A characteristic feature of the spatial structure of inorganic pyrophosphatases is a flexible system of noncovalent interactions between protein groups penetrating the whole molecule of the oligomeric enzyme. Binding of metal ions, sulfate (an analog of the product of the enzymatic reaction), and affinity phosphorus-containing inhibitors at the active site or site-directed mutagenesis induce rearrangements in the set of hydrogen and ionic interactions, which change active site properties and in some instances, cause molecule asymmetry. In the trimeric form of Escherichia coli pyrophosphatase obtained by dissociation of a hexamer, active sites also interact with each other, which is manifested by negative cooperativity upon substrate binding. The association of trimers into the hexamer leads to perfect organization of active sites and to their coordinated functioning, probably due to the restoration of communication channels between the trimers.

Binding Sites↗

PubMed2002

[Spatial pattern of Tetranychus urticae population in apple tree garden].

Spatial pattern of insect population is an important aspect of insect ecology. It reveals the spatial structure characteristics of populations, and provides a basis for relevant sampling techniques and data transformation. Tetranychus urticae Koch is a serious pest of apple tree. Its spatial pattern and time-series dynamics were analyzed by calculating four indices of aggregation, and parameters of Iwao model. The results showed that the spatial pattern of T. urticae in apple tree garden belonged to an aggregated distribution pattern. The aggregation intensity was the highest in upper and southern part of crown, and the lowest in its lower and inner part. The aggregation was due to the biological habits of T. urticae and environmental heterogeneity. No matter T. urticae was in the upper, middle, or lower crown of apple tree, its aggregation intensity was higher before first ten days of June, and then gradually decreased after the middle ten days of June.

Acari↗

PubMed1992

[Physico-chemical and immunochemical characteristics of molecular forms of carcinoembryonic antigen (CEA) not bound with concanavalin A].

A molecular form of CEA non-binding Con A (CEAnC) was isolated from colon adenocarcinoma metastases in liver as a fraction of CEA having no affinity to Con-A-Sepharose. CEAnC was shown to be immunochemically identical to CEA, but to differ substantially with regard to the amino acid and sugar composition, and structure of the sugar moiety, possibly containing non only N-, but also O-glycosyl carbohydrate chains. The antigens studied were also found to possess different spatial structures. The differences between CEA and CEAnC suggest CEAnC to be a new molecular form of CEA.

Adenocarcinoma↗

PubMed2003

Manipulation and removal of defects in spontaneous optical patterns.

Defects play an important role in a number of fields dealing with ordered structures. We demonstrate theoretically and experimentally the possibility of an active manipulation of defects in terms of an externally induced motion. We focus on the spontaneous formation of two-dimensional spatial structures in a nonlinear-optical system, a liquid crystal light valve under single optical feedback. For a particular parameter setting, a spontaneously formed hexagonal intensity pattern contains several dislocation-type defects. A scheme based on Fourier filtering allows us to restore spatial order in a selectable part of the pattern. Starting without control, the controlled area is progressively expanded, such that defects are swept out of the pattern.

Journal Article↗

PubMed1984

Spatial-temporal dissipative structures arising in open reactive systems with a negative feedback loop.

A systematic way of finding the possible spatial-temporal structures that may emerge in open reactive systems coupled with diffusive transport and containing one inhibitory (negative feedback) loop is presented. The method is illustrated on two kinetic models, one used by L. Glass, another by Higgins et al. which we coupled with diffusion. The ranges of cooperativity index and Fick transport coefficients we find for the occurrence of a spatially non-uniform time periodicity are consistent with in vitro experiments.

Diffusion↗

PubMed2007

Local structure and thermodynamics of a core-softened potential fluid: theory and simulation.

Phase behavior and structural properties of homogeneous and inhomogeneous core-softened (CS) fluid consisting of particles interacting via the potential, which combines the hard-core repulsion and double attractive well interaction, are investigated. The vapour-liquid coexistence curves and critical points for various interaction ranges of the potential are determined by discrete molecular dynamics simulations to provide guidance for the choice of the bulk density and potential parameters for the study of homogeneous and inhomogeneous structures. Spatial correlations in the homogeneous CS system are studied by the Ornstein-Zernike integral equation in combination with the modified hypernetted chain (MHNC) approximation. The local structure of CS fluid subjected to diverse external fields maintaining the equilibrium with the bulk CS fluid are studied on the basis of a recently proposed third order+second order perturbation density functional approximation (DFA). The accuracy of DFA predictions is tested against the results of a grand canonical ensemble Monte Carlo simulation. Reasonable agreement between the results of both methods proves that the DFA theory applied in this work is a convenient theoretical tool for the investigation of the CS fluid, which is practically applicable for modeling numerous real systems.

Journal Article↗

PubMed1986

Structural relationships in the adenylate kinase family.

The sequences of five distantly related adenylate kinases have been aligned. The local conservation of amino acids is discussed in the light of the known three-dimensional structure of one of the enzymes, the cytosolic isoenzyme 1 (AK1) from porcine muscle. The similarity profile outlines clearly the active site in the cleft of the spatial structure of AK1. The alignment reveals further that the enzyme family can be subdivided into small and large variants according to the presence or absence of a particular segment of about 30 residues in the middle of the chain. The extra segments of the large variants are strongly conserved.

Adenylate Kinase↗

PubMed1997

Spatial Patterns of Rhizoplane Populations of Pseudomonas fluorescens.

Geostatistical analysis was used to compare rhizoplane colonization patterns of an antibiotic-producing biological control bacterium versus a non-antibiotic-producing mutant strain. Pea seeds were inoculated with Pseudomonas fluorescens 2-79RN(inf10) or P. fluorescens 2-79-B46 (a phenazine-deficient Tn5 mutant of P. fluorescens 2-79RN(inf10)) (10(sup8) CFU/pea), planted in sterile sand, and incubated at 20(deg)C. After 3 days, seedlings were prepared for scanning electron microscopy. Photomicrographs (x1,000) of the root surface were taken at the seed-root junction and at 0.5-cm intervals to the root tip. Bacterial counts on the root surface were made in 5- by 5-(mu)m sample units over an area which was 105 by 80 (mu)m. Coordinates and number of bacteria were recorded for each sample unit. Spatial statistics were calculated by covariance for the following directions: omnidirectional, 0, 45, 90, and 135(deg). The ranges of spatial influence and nugget (estimator of spatially dependent variation) were determined. For both P. fluorescens 2-79RN(inf10) and P. fluorescens 2-79-B46, spatial structure was evident along the entire root, particularly in the 0(deg) direction (along the root length) (e.g., range = 24 (mu)m, nugget = 0.52). The degree of spatial dependence observed indicated aggregation of bacterial cells. No differences were detected in the spatial patterns of colonies of P. fluorescens 2-79RN(inf10) and P. fluorescens 2-79-B46, indicating that the lack of phenazine production did not influence spatial patterns on the rhizoplane.

Journal Article↗

PubMed2005

Temporal factors in tactile spatial acuity: evidence for RA interference in fine spatial processing.

We investigated the extent to which subjects' ability to perceive the fine spatial structure of a stimulus depends on its temporal properties (namely the frequency at which it vibrates). Subjects were presented with static or vibrating gratings that varied in spatial period (1-8 mm) and vibratory frequency (5-80 Hz) and judged the orientation of the gratings, presented either parallel or perpendicular to the long axis of the finger. We found that the grating orientation threshold (GOT)-the spatial period at which subjects can reliably discriminate the orientation of the grating-increased as the vibratory frequency of the gratings increased. As the spatial modulation of SA1 and RA afferent fibers has been found to be independent of vibratory frequency, the frequency dependence of spatial acuity cannot be attributed to changes in the quality of the peripheral signal. Furthermore, we found GOTs to be relatively independent of stimulus amplitude, so the low spatial acuity at high flutter frequencies does not appear to be due to an inadequacy in the strength of the afferent response at those frequencies. We hypothesized that the RA signal, the strength of which increases with vibratory frequency, interfered with the spatially modulated signal conveyed by SA1 fibers. Consistent with this hypothesis, we found that adapting RA afferent fibers improved spatial acuity, as gauged by GOTs, at the high flutter frequencies.

Afferent Pathways↗