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At least 235 records · Page 13Linked to original sources
PubMed1992

A truncated laminin chain homologous to the B2 chain: structure, spatial expression, and chromosomal assignment.

We describe the identification of a novel laminin chain. Overlapping clones were isolated from a human fibrosarcoma HT1080 cell cDNA library spanning a total of 5,200 bp. A second set of clones contained an alternative 3' end sequence giving a total of 4,316 bp. The longer sequence contained an open reading frame for a 1,193-residue-long polypeptide. The alternative sequence was shortened at the carboxyl-terminal end coding for a 1,111-residue-long polypeptide. The amino acid sequence contained 21 amino acids of a putative signal peptide and 1,172 residues or alternatively 1,090 residues of a sequence with five distinct domains homologous to domains I-V in laminin chains. Comparison of the amino acid sequences showed that the novel laminin chain is homologous to the laminin B2 chain. However, the structure of the novel laminin chain isolated here differs significantly from that of the B2 chain in that it has no domain VI and domains V, IV, and III are shorter, resulting in a truncated laminin chain. The alternative sequence had a shortened domain I/II. In accordance with the current nomenclature, the chain characterized here is termed B2t. Calculation of possible chain interactions of laminin chains with the B2t chain domain I/II indicated that the B2t chain can replace the B2 chain in some laminin molecules. The gene for the laminin B2t chain (LAMB2T) was localized to chromosome 1q25-q31 in close proximity to the laminin B2 chain gene. Northern analysis showed that the B2t chain is expressed in several human fetal tissues but differently from the laminin B1 and B2 chains. By in situ hybridization expression of the B2t chain was localized to specific epithelial cells in skin, lung, and kidney as opposed to a general epithelial and endothelial cell expression of the laminin B2 chain in the same tissues.

Amino Acid Sequence↗
PubMed2001

Spatial structure and habitat variation in a grasshopper hybrid zone.

A hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae) in northern Spain has been analyzed for variation in morphology and ecology. These species are readily distinguished by the number of stridulatory pegs on the hind femur. Both sexes are fully winged and inhabit disturbed habitats throughout the study area. We develop a maximum-likelihood approach to fitting a two-dimensional cline to geographical variation in quantitative traits and for estimating associations of population mean with local habitat. This method reveals a cline in peg number approximately 30 km south of the Picos de Europa Mountains that shows substantial deviations in population mean compared with the expectations of simple tension zone models. The inclusion of variation in local vegetation in the model explains a significant proportion of the residual variation in peg number, indicating that habitat-genotype associations contribute to the observed spatial pattern. However, this association is weak, and a number of populations continue to show strong deviations in mean even after habitat is included in the final model. These outliers may be the result of long-distance colonization of sites distant from the cline center or may be due to a patchy pattern of initial contact during postglacial expansion. As well as contrasting with the smooth hybrid zones described for Chorthippus parallelus, this situation also contrasts with the mosaic hybrid zones observed in Gryllus crickets and in parts of the hybrid zone between Bombina toad species, where habitat-genotype associations account for substantial amounts of among-site variation.

Animals↗
PubMed2004

Spatial structure of quantitative representation of numbers: evidence from the SNARC effect.

Dehaene, Bossini, and Giraux (1993) revealed that subjects responded to large numbers faster with the choice on the right than with the choice on the left, whereas the reverse held true for small numbers (SNARC effect). According to Dehaene et al. (1993), the SNARC effect depends on the quantitative representation of number, such as a left-to-right-oriented analog number line. The main goal of the present study was twofold: first, to investigate whether the vertical SNARC effect could be observed, and, second, to verify whether Dehaene et al.'s (1993) explanation of the SNARC effect is correct. Experiments 2A and 2B showed the vertical SNARC effect in a parity judgment task. Subjects responded to large numbers faster with the top choice than with the bottom choice, whereas the reverse held true for small numbers. However, Experiment 3 failed to show the SNARC effect in a number magnitude judgment task, suggesting that the quantitative representation could be dissociated from the spatial code that produces the SNARC effect.

Adult↗
PubMed2005

Spatial structure of genetic variation and primary succession in the pioneer tree species Antirhea borbonica on La Réunion.

In habitats where colonization and extinction are recurrent, the distribution of gene frequencies among patches of suitable habitat may reflect the age structure of different populations. In this study, we quantify population genetic structure for a pioneer tree species, Antirhea borbonica, in a chrono-sequence of primary succession on the lava flows of the Piton de La Fournaise volcano (La Réunion). Using microsatellite loci and amplified fragment length polymorphism (AFLP) markers, we quantified genetic variation within and among populations for early- and late-succession populations in a landscape where extinction and recolonization are recurrent (the 'Grand Brûlé') and for late-succession populations in a more stable landscape. This study produced three main results. First, we detected no evidence that founder events increase genetic differentiation among colonizing populations; F(ST) values among early- and among late-succession populations were similar. Second, we found no evidence for isolation by distance; genetic distance was not correlated with spatial distance within and among populations. Third, F(IS) values are consistently high in all populations, despite the fact that A. borbonica populations are functionally close to dioecy and thus expected to have an outcrossing mating system. Multiple colonization events from different sources may limit differentiation among young populations and spatial isolation may enhance differentiation among late-succession populations. Ecological processes acting during colonization may create the conditions for spatial aggregation within pioneer populations, and thus contribute to the high F(IS) values.

DNA Primers↗
PubMed1987

The receptive-field spatial structure of cat retinal Y cells.

1. Y-type ganglion cells in the cat's retina were stimulated with bars of light and grating patterns at photopic luminances. Stimuli were stationary, and luminance at each point was varied sinusoidally in time at 2 Hz. Impulse rates were recorded from single cells. 2. When the stimulus was a narrow bar of light, the impulse rate approached a sinusoidal function of time as contrast was reduced. The linear behaviour of each cell was therefore characterized by taking the limit of response parameters as contrast approached zero. 3. The ratio of surround strength to centre strength varied widely between cells but the two strengths were approximately equal on average. The difference between surround phase and centre phase averaged 168 deg. 4. As contrast increased, responses became rectified. Rectifier output was well described by a power law of stimulus amplitude, where the power was usually 1.4 or 1.5. 5. Response phase advanced with increasing contrast, and at high response amplitudes grew less than proportionally with contrast. These effects were assumed due to the contrast gain control described by Shapley & Victor (1978). 6. Gratings in which luminance varied sinusoidally with distance were used to determine Y cell spatial resolution. The second-harmonic amplitude of the response diminished rapidly with increasing spatial frequency: the radius of the best-fitting Gaussian mechanism was about 0.25 deg for a cell at 10 deg eccentricity. 7. This spatial resolution is close to the linear resolution of X cells as determined by Linsenmeier, Frishman, Jakiela & Enroth-Cugell (1982). 8. A receptive field model incorporating both linear and non-linear elements is described. The model consists of an array of subunit pathways, each of which has a centre-surround organization followed by a rectifier; a pool weights and sums subunit outputs, and signals are then passed through a contrast gain control. 9. The model accounts qualitatively for the over-all centre-surround organization of Y cell linear responses, the dependence of frequency-doubled responses on spatial frequency, and impulse rate as a function of time for a variety of bar and grating stimuli.

Animals↗
PubMed1983

The impact of migration on the spatial structure of rural settlement.

"Changes in the system of settlement in Staraya Russa Rayon, Novgorod Oblast [USSR], are traced. Migration from peripheral areas of the rayon to the suburban zone of Staraya Russa and to larger inhabited places along highways has transformed the historical pattern of settlement focused on river valleys into a new pattern focused on the central city of Staraya Russa, i.e., from the traditional dendritic configuration into a monocentric pattern. The impact of the migration process on land use is discussed, and it is suggested that abandoned peripheral villages be converted to recreation uses."

Agriculture↗
PubMedDate not supplied

Spatial structure of chromatically opponent receptive fields in the human visual system.

This study investigates the receptive-field structure of mechanisms operating in human color vision, by recording visual evoked potentials (VEPs) to multiharmonic gratings modulated either in luminance or color (red-green). Varying the Fourier phase of the harmonics from 0 deg to 90 deg produced a family of stimulus profiles that varied from lines to edges. The stimuli were contrast reversed to elicit steady-state VEPS, and also randomly jittered (at a higher temporal frequency than the contrast reversal) to ensure that the evoked response resulted from the polarity reversal, rather than from local variation of luminance or color. Reliable VEPs were recorded from both luminance and chromatic stimuli at all phases, suggesting that the mechanisms sensitive to chromatic contrast and those sensitive to luminance contrast have both symmetric and asymmetric receptive fields. Contrast thresholds estimated by extrapolation of the contrast response curves were very similar to psychophysical thresholds for phase discrimination, suggesting that the VEP response is generated by mechanisms mediating phase discrimination. The results support the idea that human color mechanisms have receptive fields with a variety of spatial symmetries (including odd- and even-symmetric fields) and that these mechanisms may contribute to phase discrimination of chromatic stimuli in a similar way to what has been suggested for luminance vision.

Color Perception↗
PubMed1981

The spatial structure of Latin American cities.

"Using published census data, metropolitan area population and employment statistics are constructed for several large Latin American cities in 1950, 1960, and 1970, and compared to similar statistics from selected North American cities. The Latin cities are experiencing decentralization of population and some decentralization of employment. Overall population density patterns of large Latin cities resemble those in older North American cities; newer North American cities have lower densities and are much more decentralized than Latin cities. High-status groups are somewhat concentrated in the central cities of Latin American metropolitan areas, but their concentrations there are declining."

Americas↗
PubMed2004

A parametric model for estimation of dispersal patterns applied to five passerine spatially structured populations.

Natal dispersal capture-recapture data from five fragmented populations of house sparrows, great tits, and blue tits were analyzed using maximum likelihood methods. A new two-parametric distribution was constructed that includes four distributions previously used as special cases in the literature. Dispersal standard deviations were estimated at 22.9 km for the house sparrows and ranged from 0.66 to 4.4 km for the tits. Female great tits and blue tits dispersed consistently further than males. Estimates of the shape parameter of the dispersal distribution ranged from 0.66 to 2.27, indicating strong to moderately leptokurtic dispersal displacements. There were significant effects of density on local immigration rates and a consistent tendency for immigration rates to depend underproportionally on local densities. Potential implications of the shape of the dispersal distribution for the spread of invading organisms were investigated and compared with previous results. It is shown that the wave speed, for a given dispersal standard deviation, depends only to some extent on leptokurtosis, provided that the intrinsic growth rate of the population is moderate or small. In estimating the dispersal standard deviation, however, incorrect assumptions about the degree of leptokurtosis can lead to a large bias in estimation and predictions.

Animal Migration↗
PubMed1995

Modeling of the spatial structure of eukaryotic ornithine decarboxylases.

We used sequence and structural comparisons to determine the fold for eukaryotic ornithine decarboxylase, which we found is related to alanine racemase. These enzymes have no detectable sequence identity with any protein of known structure, including three pyridoxal phosphate-utilizing enzymes. Our studies suggest that the N-terminal domain of ornithine decarboxylase folds into a beta/alpha-barrel. Through the analysis of known barrel structures we developed a topographic model of the pyridoxal phosphate-binding domain of ornithine decarboxylase, which predicts that the Schiff base lysine and a conserved glycine-rich sequence both map to the C-termini of the beta-strands. Other residues in this domain that are likely to have essential roles in catalysis, substrate, and cofactor binding were also identified, suggesting that this model will be a suitable guide to mutagenic analysis of the enzyme mechanism.

Amino Acid Sequence↗
PubMed1998

Extinction times and phase transitions for spatially structured closed epidemics.

This paper considers the time to extinction for a stochastic epidemic model of SEIR form without replacement of susceptibles. It first shows how previous rigorous results can be heuristically explained in terms of the more transparent dynamics of an approximating deterministic system. The model is then extended to include a host population structured into patches, with weak nearest-neighbour mixing of infection. It is shown, by considering the approximating deterministic system, that the expected time to extinction in a population of n + 1 patches each of size N is of the form a log N + bn, provided that N > Nc where Nc is a critical patch size below which transits are unlikely to occur. This corresponds to the simple decomposition of the time of an epidemic into the time it takes to spread through one patch plus the time it takes to transit to each of n successive patches. Expressions for this threshold and the coefficients of the time to extinction are given in terms of the transmission parameters of infection and the coupling strength between patches. These expressions are compared with numerical results using parameters relevant to a study of phocine distemper virus in North Sea seals, and the agreement is found to be good for large and small N. In the region when N approximately Nc, where transits may or may not occur, interesting transitional behaviour is seen, leading to a non-monotonicity of the extinction time as a function of N.

Animals↗
PubMed1993

The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli.

The three-dimensional structure of L-fuculose-1-phosphate aldolase (FucA) from Escherichia coli was determined by X-ray crystallography at a resolution of 2.13 A. The enzyme is a homotetramer with an M(r) of 23,775 per subunit. Since its activity depends on the presence of metal ions (Zn2+) the enzyme belongs to the class II aldolases. As expected from amino acid sequence comparisons, this first structure of a class II aldolase shows no similarity to the known structures of class I aldolases. It has some unusual features concerning the overall chain fold, the quaternary structure, and the co-ordination of the catalytically active zinc ion. A sequence comparison with the data bank indicated that the middle domain of the enzyme L-ribulose-5-phosphate-4-epimerase is homologous to FucA and may contain an active-center metal ion.

Aldehyde-Lyases↗
PubMed1997

On the evolution of density dependent dispersal in a spatially structured population model.

A simple metapopulation lattice model of two competing phenotypes is presented, where one phenotype reacts more sensitively to overcrowding by migrating to neighbouring local habitats. The sensitivity is formulated by means of a threshold density of the subpopulations, above which dispersal is triggered off. If this threshold density is not very far from the local carrying capacity, an increased mobility provides benefits on the metapopulation level. At a surprisingly small difference between migrational triggering thresholds, the phenotype of larger mobility (or lower threshold) squeezes out the less mobile one from the whole system in a wide parameter range. Evolutionary considerations give an optimal threshold level for our model metapopulation.

Animals↗
PubMed1980

Spatial structure of immunoglobulin molecules.

Immunoglobulin molecules of the class G (antibody molecules) consist of two heavy chains (50,000 dalton molecular weight) and two light chains (25,000 dalton). The overall shape is a Y with the arms formed by the light chains and the N-terminal half of the heavy chains in tight association. The stem is formed by the C-terminal halves of the heavy chains. The heavy and the light chains fold into globular domains of molecular weights of 12,000 dalton. There are four domains of the heavy chain and two of the light chain. All these domains show a similar fold, consisting of two B-sheets but display considerable differences in detail. The N-terminal variable domains of heavy and light chains and specifically the hypervariable polypeptide segments of the domains, located at the tips of the Y, constitute the antigen and hapten binding site. The nature of the amino acid residues of the hypervariable loops determines the shape and the specificity of the antibody. All domains pair tightly laterally, except the CH2 domains of the heavy chain. This domain has carbohydrate bound which prevents lateral association. Longitudinal interaction between the domains is loose and allows flexibility in the arrangement. Flexibility is probably of significance for antibody function. Arm (Fab) and stem (Fc) parts are linked by the hinge peptide which contains a segment with a unique conformation of two parallel poly-proline helices. Antigen binding triggers effector functions of antibodies. Antigen binding is at the tips of the Y-shaped antibody, but effector functions are displayed by the stem part. It is an open question whether conformational changes of the antibody molecule play a significant role in the trigger mechanism.

Amino Acids↗