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At least 451 records · Page 25Linked to original sources

PubMed2006

Spatial network structure and amphibian persistence in stochastic environments.

In the past few years, the framework of complex networks has provided new insight into the organization and function of biological systems. However, in spite of its potential, spatial ecology has not yet fully incorporated tools and concepts from network theory. In the present study, we identify a large spatial network of temporary ponds, which are used as breeding sites by several amphibian species. We investigate how the structural properties of the spatial network change as a function of the amphibian dispersal distance and the hydric conditions. Our measures of network topology suggest that the observed spatial structure of ponds is robust to drought (compared with similar random structures), allowing the movement of amphibians to and between flooded ponds, and hence, increasing the probability of reproduction even in dry seasons.

Amphibians↗

PubMedDate not supplied

Fold change in evolution of protein structures.

Typically, protein spatial structures are more conserved in evolution than amino acid sequences. However, the recent explosion of sequence and structure information accompanied by the development of powerful computational methods led to the accumulation of examples of homologous proteins with globally distinct structures. Significant sequence conservation, local structural resemblance, and functional similarity strongly indicate evolutionary relationships between these proteins despite pronounced structural differences at the fold level. Several mechanisms such as insertions/deletions/substitutions, circular permutations, and rearrangements in beta-sheet topologies account for the majority of detected structural irregularities. The existence of evolutionarily related proteins that possess different folds brings new challenges to the homology modeling techniques and the structure classification strategies and offers new opportunities for protein design in experimental studies.

Amino Acid Sequence↗

PubMed2001

Habitat structure and population persistence in an experimental community.

Understanding spatial population dynamics is fundamental for many questions in ecology and conservation. Many theoretical mechanisms have been proposed whereby spatial structure can promote population persistence, in particular for exploiter-victim systems (host-parasite/pathogen, predator-prey) whose interactions are inherently oscillatory and therefore prone to extinction of local populations. Experiments have confirmed that spatial structure can extend persistence, but it has rarely been possible to identify the specific mechanisms involved. Here we use a model-based approach to identify the effects of spatial population processes in experimental systems of bean plants (Phaseolus lunatus), herbivorous mites (Tetranychus urticae) and predatory mites (Phytoseiulus persimilis). On isolated plants, and in a spatially undivided experimental system of 90 plants, prey and predator populations collapsed; however, introducing habitat structure allowed long-term persistence. Using mechanistic models, we determine that spatial population structure did not contribute to persistence, and spatially explicit models are not needed. Rather, habitat structure reduced the success of predators at locating prey outbreaks, allowing between-plant asynchrony of local population cycles due to random colonization events.

Animals↗

PubMed1986

Oscillating dissipative structures in mitochondrial suspensions.

The occurrence of spatial structures in the unstirred layer of an oscillating mitochondrial suspension is reported. The structures are detected by photo camera by light scattering in the unstirred layer of suspension. The spatial structures observed are shown to oscillate with the same period as that of mitochondrial oscillations in the bulk phase. Patterning is not affected by the layer depth within the range 0.3-3.0 mm. Various types of oscillatory states of mitochondria are characterized by the corresponding patterns. Patterning is effectively suppressed by the inhibitors of the respiratory chain (antimycin A or CN-).

Acetates↗

PubMed2003

Appearance of the frequency doubling stimulus in normal subjects and patients with glaucoma.

PURPOSE: To determine whether the spatial structure of the frequency doubling technology (FDT) perimetry stimulus is visible at detection-contrast threshold in normal observers and those with glaucoma and to assess its perceived spatial frequency at threshold and suprathreshold contrast. METHODS: Three subject groups were assessed: 10 young normal observers (aged <40 years), 10 older normal observers (aged >50 years), and 10 subjects with glaucoma. Detection thresholds for centrally and eccentrically presented 10 degrees squares, 0.25-cyc/deg, 25-Hz counterphase flicker sine-wave gratings were obtained by using a yes-no staircase procedure. Eccentric locations were in areas of loss of FDT sensitivity (< or =21 degrees ) in subjects with glaucoma, or at 7 degrees or 21 degrees inferonasally in normal observers. Resolution-contrast thresholds were determined by a two-alternative, forced-choice staircase procedure in which subjects selected the orientation of the grating stimulus tilted at +/-45 degrees. Perceived spatial frequency was determined by having subjects alter the spatial frequency of a temporally interleaved stationary sine-wave grating to match the FDT stimulus. RESULTS: No significant difference was found between detection- and resolution-contrast thresholds, implying that spatial structure was visible at detection threshold. In general, subjects perceived the spatial structure to have a spatial frequency closer to doubled than to veridical, although the young normal subjects reported a lower apparent spatial frequency than older individuals. CONCLUSIONS: When instructed as for clinical testing, subjects respond to the presence of the structure of the grating, and perceive the FDT stimulus to have a spatial frequency greater than its true spatial frequency. These findings were consistent across both normal observers and those with glaucoma, at both central and eccentric test locations.

Adult↗

PubMed1997

Representation of amino acid sequences in terms of interaction energy in protein globules.

We suggest a new simple approach for comparing the primary structure of proteins and their spatial structure. It relies on the one-to-one correspondence between each residue of the polypeptide chain and the energy of van der Waals interactions between the regions of the native globule flanking this residue. The method obviates the sophisticated geometrical criteria for estimating similarity between spatial structures. Besides, it permits one to analyze structural units of different scale.

Amino Acid Sequence↗

PubMed1973

Psychophysical evidence for sustained and transient detectors in human vision.

1. The sensitivity to temporally modulated sinusoidal gratings was determined. Two thresholds could be distinguished for the modulated gratings: the contrast at which flicker could be perceived and the contrast at which the spatial structure became distinct.2. The flicker detection thresholds and pattern recognition threshold varied independently as functions of the spatial and temporal frequencies, suggesting that the two thresholds represent the activity of two independent systems of channels.3. The channels detecting flicker prefer low and medium spatial frequencies. They have a pronounced decline in sensitivity at low temporal frequencies of sinusoidal modulation. They respond twice as well to gratings whose phase is alternated repetitively as to gratings turned on and off at the same rate.4. The channels responsible for the discrimination of spatial structure are most responsive at high and medium spatial frequencies. There is no decline in sensitivity at low temporal frequencies. These channels respond equally well to alternating and on/off gratings up to about 8 Hz.5. The temporal properties as revealed with sinusoidal modulation, suggest that the flicker-detecting channels would give transient responses to prolonged presentation of stimuli: the channels responsible for analysing the spatial structure would give sustained responses. The responses of the two types of channel to alternating and on/off gratings confirm this suggestion.

Flicker Fusion↗

PubMed2006

Demographic spatial genetic structure of the Neotropical tree, Jacaranda copaia.

We used genotypes from six microsatellite loci and demographic data from a large mapped forest plot to study changes in spatial genetic structure across demographic stages, from seed rain to seedlings, juveniles, and adult diameter classes in the Neotropical tree, Jacaranda copaia. In pairwise comparisons of genetic differentiation among demographic classes, only seedlings were significantly differentiated from the other diameter classes; F(ST) values ranged from 0.006 to 0.009. Furthermore, only seedlings showed homozygote excess suggesting biparental inbreeding in the large diameter reproductive adults. We found very low levels of relatedness in the first distance class of trees, 1-26 cm diameter (F(ij) = 0.011). However, there was a 5- to 10-fold rise in relatedness in the smallest distance class, from the smallest to the largest tree diameter classes (F(ij) = 0.110 for individuals > 56 cm diameter). A variety of non-mutually exclusive mechanisms have been invoked perviously to explain such a pattern, including natural selection, history, or nonequilibrium population dynamics. The long-term demographic data available for this species allow us to evaluate these mechanisms. Jacaranda is a fast-growing, light-demanding species with low recruitment rates and high mortality rates in the smaller diameter classes. It successfully regenerates only in large light gaps, which occur infrequently and stochastically in space and time. These factors contribute to the nonequilibrium population dynamics and observed low genetic structure in the small size classes. We conclude that the pattern of spatial genetic transitions in Jacaranda is consistent with overlapping related generations and strong but infrequent periods of high recruitment, followed by long periods of population decline.

Bignoniaceae↗

PubMed2006

Analysis of spatial genetic structure in an expanding Pinus halepensis population reveals development of fine-scale genetic clustering over time.

We analysed the change of spatial genetic structure (SGS) of reproductive individuals over time in an expanding Pinus halepensis population. To our knowledge, this is the first empirical study to analyse the temporal component of SGS by following the dynamics of successive cohorts of the same population over time, rather than analysing different age cohorts at a single time. SGS is influenced by various factors including restricted gene dispersal, microenvironmental selection, mating patterns and the spatial pattern of reproductive individuals. Several factors that affect SGS are expected to vary over time and as adult density increases. Using air photo analysis, tree-ring dating and molecular marker analysis we reconstructed the spread of reproductive individuals over 30 years beginning from five initial individuals. In the early stages, genotypes were distributed randomly in space. Over time and with increasing density, fine-scale (< 20 m) SGS developed and the magnitude of genetic clustering increased. The SGS was strongly affected by the initial spatial distribution and genetic variation of the founding individuals. The development of SGS may be explained by fine-scale environmental heterogeneity and possibly microenvironmental selection. Inbreeding and variation in reproductive success may have enhanced SGS magnitude over time.

Biomarkers↗

PubMed2000

Stabilization of the kerr effect by self-induced ionization: formation of optical light spatially localized structures

The nonlinear propagation of ultrashort laser pulses launched into the air is investigated. The formation of optical light "bullets," or spatially localized structures, has been experimentally observed recently. Their stability is shown as due to the occurrence of a dynamical balance between two opposite nonlinear effects: an optical focusing Kerr effect balanced by a defocusing self-induced multiphoton partial ionization of the neutral gas. Characteristics of the "bullets" are predicted analytically and confirmed numerically. They are found to be in agreement with observations.

Journal Article↗

PubMed1990

[Structural and spatial organization of epithelial components of the palatine glands in newborn infants and adults].

By means of plastic reconstruction peculiarities in structure and spatial organization of the palatal glands have been revealed in newborns and mature persons. Morphometrical analysis has been performed in serial semithin sections stained with toluidine++ blue. The palatal gland ducts in the newborn are presented as a system of epithelial tubules with a gradually enlarged external and internal diameters and wall thickness towards direction of saliva flow. In the excretory ducts of the newborn sharp dilatations, facilitating to delay and accumulation of the secretion are not revealed. In the excretory ducts system in the mature person certain changes in the wall thickness are revealed and a number of narrowed and dilated areas have been found; they probably effect the secretion rate. This, in its turn, should produce some effect on the definite composition of saliva.

Adult↗

PubMed1997

Sex-related spatial kin structure in a spring population of grey-sided voles Clethrionomys rufocanus as revealed by mitochondrial and microsatellite DNA analyses.

Polymerase chain reaction-directed mitochondria (mt) and microsatellite DNA analyses were performed to examine the kin structure in a spring population of grey-sided voles Clethrionomys rufocanus in Hokkaido, Japan. The spatial distribution of 81 voles in a trapping grid (about 1 ha) was estimated by using the catch-mark-release method. DNA samples were extracted from the toes clipped for individual identification. Maternal lineages of voles were unequivocally determined by the mtDNA haplotypes, as identified by nucleotide sequencing of the control region. Relatedness between individuals was estimated based on the genotype and allele frequencies at several microsatellite loci. Although the distribution of voles was uniform within the grid, neighbouring females were frequently from the same maternal lineage. Relatedness values between females correlated negatively with geographical distances. Combination of the two molecular markers revealed four clusters of closely related, matrilineal females in the population, whereas no such cluster was apparent in males. The present study first demonstrated a sex-related spatial kin structure in a natural population of the grey-sided vole.

Animals↗

PubMed2005

Spatial analysis and eutrophication assessment for chlorophyll a in Taihu Lake.

Spatial structure analysis and kriging analysis have been identified to be useful tools in illustrating the spatial patterns of variables. Taihu Lake is one of the largest fresh water lakes in China, and has suffered serious eutrophication in recent years due to the rapid economic development and growing environmental pollution in the Taihu Catchment. In this paper, spatial structural analysis, kriging interpolation and eutrophication assessment were carried out for chlorophyll a in the lake. Studies show that spherical model could be applied to fit all experimental variograms. Positive nuggets were observed for three directions except NE-SW direction. The variograms show some anisotropy with anisotropic ratio falling within 1.76. The spatial structural patterns of chlorophyll a in the lake were affected by factors such as distribution of pollution sources, water flow and wind. Two-dimensional ordinary block kriging was applied for interpolation process. An eutrophication assessment map was also made based on a water-quality evaluation standard. Results show that the content of chlorophyll a in Taihu Lake was quite high. The whole lake has suffered serious eutrophication. However, the eutrophic situation varied in space. Higher contents of chlorophyll a appeared mainly in the northern part of the lake.

China↗

PubMed1998

Spatial genetic structure of human populations in Japan.

We studied spatial patterns for 24 allele frequencies representing 15 systems (blood antigens, enzymes, serum proteins, color blindness, and cerumen) in Japan. The total number of samples over all systems and localities is 1125. We investigated patterns of genetic variation graphically as interpolated allele frequency surfaces, as one-dimensional and directional correlograms, and by testing for the direction of maximal genetic autocorrelation. We examined the allele frequency surfaces by various techniques of spatial autocorrelation analysis and found 13 allele frequency surfaces from 9 genetic systems exhibiting significant spatial patterns. Several surfaces have clinal patterns along the major axis of the Japanese archipelago; others tend toward a maximum or minimum in south-central Honshu. Yet other allele frequencies show long-distance differentiation or patchiness. We discovered seven areas of rapid genetic change by using the wombling method. These areas largely reflect maritime and montane barriers, and some are associated with dialectal boundaries in these populations. The observed patterns support the hybridization or dual structure hypothesis for the peopling of Japan.

Alleles↗

PubMed1998

Three-dimensional structure of binase in solution.

We present the spatial structure of binase, a small extracellular ribonuclease, derived from 1H-NMR* data in aqueous solution. The total of 20 structures were obtained via torsion angle dynamics using DYANA program with experimental NOE and hydrogen bond distance constraints and phi and chi1 dihedral angle constraints. The final structures were energy minimised with ECEPP/2 potential in FANTOM program. Binase consists of three alpha-helices in N-terminal part (residues 6-16, 26-32 and 41-44), five-stranded antiparallel beta-sheet in C-terminal part (residues 51-55, 70-75, 86-90, 94-99 and 104-108) and two-stranded parallel beta-sheet (residues 22-24 and 49-51). Three loops (residues 36-39, 56-67 and 76-83), which play significant role in biological functioning of binase, are flexible in solution. The differences between binase and barnase spatial structures in solution explain the differences in thermostability of binase, barnase and their hybrids.

Bacillus↗

PubMed1995

[Structural organization of rimorphin and its synthetic analogs].

The spatial structure and conformations of rimorphin were investigated using theoretical conformational analysis. The spatial organization of the peptide can be described by a set of 11 low-energy conformations of the backbone. By solving the reverse conformational problem, a number of modified amino acid sequences ([Ala2], [Ala3], [MePhe9], [MeLys10], [MeVal11], and [MeVal12]-analogs of rimorphin) were determined that have spatial structures corresponding to the set of low-energy conformations and should, therefore, possess physiological activity.

Amino Acid Sequence↗

PubMed1996

Measurement of genetic structure within populations using Moran's spatial autocorrelation statistics.

Spatial structure of genetic variation within populations, an important interacting influence on evolutionary and ecological processes, can be analyzed in detail by using spatial autocorrelation statistics. This paper characterizes the statistical properties of spatial autocorrelation statistics in this context and develops estimators of gene dispersal based on data on standing patterns of genetic variation. Large numbers of Monte Carlo simulations and a wide variety of sampling strategies are utilized. The results show that spatial autocorrelation statistics are highly predictable and informative. Thus, strong hypothesis tests for neutral theory can be formulated. Most strikingly, robust estimators of gene dispersal can be obtained with practical sample sizes. Details about optimal sampling strategies are also described.

Biological Evolution↗

PubMed2005

The effects of opposite-polarity dipoles on the detection of Glass patterns.

Glass patterns--randomly positioned coherently orientated dipoles--create a strong sensation of oriented spatial structure. On the other hand, coherently oriented dipoles comprising dots of opposite polarity ("anti-Glass" patterns) have no distinct spatial structure and are very hard to distinguish from random noise. Although anti-Glass patterns have no obvious spatial structure themselves, their presence can destroy the structure created by Glass patterns. We measured the strength of this effect for both static and dynamic Glass patterns, and showed that anti-Glass patterns can raise thresholds for Glass patterns by a factor of 2-4, increasing with density. The dependence on density suggests that the interactions occur at a local level. When the Glass and anti-Glass dipoles were confined to alternate strips (in translational and circular Glass patterns), the detrimental effect occurred for stripe widths less than about 1.5 degrees, but had little effect for larger stripe widths, reinforcing the suggestion that the interaction occurred over a limited spatial extent. The extent of spatial interaction was much less than that for spatial summation of these patterns, at least 30 degrees under matched experimental conditions. The results suggest two stages of analysis for Glass patterns, an early stage of limited spatial extent where orientation is extracted, and a later stage that sums these orientation signals.

Humans↗