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At least 595 records · Page 33Linked to original sources
PubMed1988

A pattern formation mechanism to control spatial organization in the embryo of Drosophila melanogaster.

It is known that cells are already committed to a particular segment at the cellular blastoderm stage during embryogenesis of Drosophila melanogaster. Recently, several segmentation genes have been observed to be expressed in a sequence of banded spatial patterns in the syncytial blastoderm, prior to the formation of the cellular blastoderm. It is demonstrated in this paper that a two component reaction-diffusion (RD) system with net production functions which are antisymmetric with respect to the uniform steady-state values, is capable of producing a sequence of seven spatial patterns in the syncytial blastoderm. The sequence of patterns obtained exhibit a strong preference for banded or striped patterns. The first pattern is a simple anteroposterior gradient while the second is a gradient in the dorsoventral direction. The next five patterns are a sequence of banded patterns which exhibit frequency doubling, i.e. the number of bands in each pattern tend to be double the number in the previous pattern. The predicted pattern sequence is comparable to that observed in the expression of some segmentation genes. It is suggested that a pattern formation mechanism based on such an RD system may exist in the embryo where it produces a sequence of prepatterns to regulate the expression of various segmentation genes leading ultimately to a segmented embryo. There is sufficient spatial information in the sequence of banded prepatterns for the segments to be unique.

Animals↗
PubMed1979

Spatial firing patterns of auditory neuron network modelling by computer simulation.

This communication examines, in digital computer simulated network, input signals and response patterns established at excitatory neurons' level i.e. the membrane potential of neuron soma. It is restricted to spatial patterns of the auditory neuron networks and time factor for nervous conduction and transmission is neglected compared with long maintained membrane potentials of neuron somas. The model analyzes the change in the spatial patterns of the membrane potential in the two dimensional networks of the auditory system. In order to evaluate the contribution of the various parameters, it is started that the simplest model has only one parameter, lateral inhibition. The other parameters are then added, one at a time, to successive models. The lateral inhibition is a necessary condition in the auditory nervous system if any sharpening of the response areas in the single neurons is to occur. A necessary condition for the validity of the model is that is should be applicable to the other senses such as vision and chemical patterns, taste. The threshold feature of auditory neurons aids in producing a sharpening in the neuron of the auditory relay nuclei. It does this clipping the spatial response patterns in one dimensional arrays of excitatory neurons. Recurrent inhibition seems a necessary condition in the sensory nervous system that any kinds of input signals are to be preserved over a wide range of stimulus intensity. In other words, this network has a wide dynamic range against any kinds of input signals. A simple self-recurrent negative feedback does not contribute to the sharpening, but more complex socalled averaged type does. A neuron network is capable of responding stably to stimuli with a wide range of intensity and with any kind of spatial patterns if there is a simple negative feedback mechanism. When there is no negative feedback, input signals soon disappear or saturate in the neuron network. Therefore, recurrent inhibition is the most important mechanism. Spontaneous activity appears to aid in the sharpening by providing a kind of contrast, that is by reducting the amount of activity in neurons adjacent to the excitatory area. Moreover, the effect of spontaneous activity in the model seems to make repples around the excitatory area and suggests that an introduction of activity at any stage of the networks, from whatever source for example reticulum formation and thalamus, might appreciably alter the response patterns at subsequent neuron network. This suggests that the mechanism of the consciousness that might be controlled by the thalamus and or reticular formation. These two dimensional neuron networks may be expanded to three dimensional neuron networks. The former might simulate the auditory nervous system while the latter might simulate the visual system.

Animals↗
PubMed2000

Selecting relevant electrode positions for classification tasks based on the electro-encephalogram.

The aim is to describe a general approach to determining important electrode positions when measured electro-encephalogram signals are used for classification. The approach is exemplified in the frame of the brain-computer interface, which crucially depends on the classification of different brain states. To classify two brain states, e.g. planning of movement of right and left index fingers, three different approaches are compared: classification using a physiologically motivated set of four electrodes, a set determined by principal component analysis and electrodes determined by spatial pattern analysis. Spatial pattern analysis enhances the classification rate significantly from 61.3 +/- 1.8% (with four electrodes) to 71.8 +/- 1.4%, whereas the classification rate using principal component analysis is significantly lower (65.2 +/- 1.4%). Most of the 61 electrodes used have no influence on the classification rate, so that, in future experiments, the setup can be simplified drastically to six to eight electrodes without loss of information.

Electrodes↗
PubMed1988

A multipurpose vertical holeboard with automated recording of spatial and temporal response patterns for rodents.

A method is presented for manual or automated recording of rats' spontaneous nose-poking ('visit') behaviors to a vertical holeboard with a matrix of 45 or 54 holes. Several behavior parameters are presented: visit frequency, visit duration, temporal visit pattern, spatial visit pattern, stereotype of visits, diversity of visits and variability of visit patterns. The paper describes the development of the apparatus and some methods of analyzing and presenting the multi-parametric data. The use of the apparatus is illustrated with a one-trial appetitive conditioning task. After 5 min in a single 10-min session, a food pellet is presented, only once in a given hole, to provide reinforcement of a spontaneous visit to that hole. The behavior parameters are compared before and after reinforcement. When the one-trial conditioning effect was challenged with d-amphetamine, the behavior parameters changed in a graded manner depending upon the dose (0.25-6.0 mg/kg). The apparatus has also proven useful for studies of exploratory behavior without using food reinforcement following lesion or drug interventions.

Animals↗
PubMed2001

Two types of pea leghemoglobin genes showing different O2-binding affinities and distinct patterns of spatial expression in nodules.

Five distinct cDNA clones for leghemoglobin (Lb) were isolated from pea (Pisum sativum) nodules. They were classified into two groups designated PsLbA and PsLbB according to sequence homology, O(2)-binding affinities of the recombinant proteins, and in situ localization of the mRNAs. The PsLbB group was comprised of four cDNA clones: PsLb120-1, -8, -29, and -34. They showed a high similarity of deduced amino acid sequences and O(2)-binding affinities of their recombinant proteins. Among them, the spatial expression pattern of PsLb120-1 was investigated in great detail, indicating that its transcripts were localized in the region from infection zone II to the distal part of nitrogen fixation zone III in effective nodules. PsLb5-10, which is the only cDNA clone of the PsLbA type, differed considerably from the PsLbB type in amino acid sequence, and the recombinant protein had a higher O(2)-binding affinity than those of the PsLbB type. The transcripts of PsLb5-10 were detected throughout the central tissue of effective nodules. However, in ineffective nodules on the pea mutant E135 (sym13), transcripts of PsLb5-10 were restricted to the distal portion of the central tissue as well as those of PsLb120-1. These findings indicate that the pea genome contains two types of Lb genes and suggest that they have different roles in the development of nitrogen-fixing symbiosis in pea nodules.

Amino Acid Sequence↗
PubMed1981

Positional information and pattern formation.

Spatial patterns of cellular differentiation may arise from cells first being assigned a position, as in a coordinate system, and then interpreting the positional value that they have acquired. This interpretation will depend on their genetic constitution and developmental history. Different patterns may thus arise from similar positional fields. The specification of positional value may involve a positional signal, such as the concentration of a diffusible morphogen, but can also depend on how long the cells remain in a particular region, such as a progress zone. Positional values may also be acquired by direct transfer from one cell layer to another, as in directed embryonic induction. Positional value, unlike a positional signal, involves long-term memory, and can be regarded as a type of cell determination. Cells of the same differentiation class may have different positional values and may thus be non-equivalent. Evidence is presented for a signal providing positional information along the antero-posterior axis during chick limb development. This signal has properties similar to those of a diffusible morphogen.

Animals↗
PubMed1997

Subicular cells generate similar spatial firing patterns in two geometrically and visually distinctive environments: comparison with hippocampal place cells.

Cells in both the hippocampus and the subiculum show location related firing patterns, so that the momentary firing rate of a cell is related to the spatial location of a freely moving rat as it navigates in an environment. Since the subiculum receives a strong anatomical projection from the hippocampus, it seems possible that the subicular cell spatial patterns are simply driven by the spatial signals from hippocampal place cells. Data presented here, however, suggest that the two areas code space in fundamentally different ways. Here, spatial firing patterns of individual hippocampal and subicular cells were studied as rats navigated in two different environments. The two chambers were a cylinder and a square, of equal area. For some rats the two chambers were painted to have similar visual stimulus characteristics, while for others, the two were very different. The subicular cells showed very similar firing patterns in the two chambers, regardless of whether they were visually similar or different. In contrast, as predicted based on the findings of earlier studies, hippocampal place cells showed different patterns in the two (again, regardless of their visual similarity). These results suggest that the subicular cells have the ability to transfer a single, abstract spatial representation from one environment to another. This pattern is stretched to fit within the boundaries of the current environment. Thus, the subicular cells seem to provide a generic representation of the geometric relationships between different locations in an environment. It seems possible that this representation may contribute to some navigational abilities exhibited by animals, such as dead reckoning, and novel route generation in unfamiliar environments. In contrast, it appears that hippocampal place cells provide a spatial representation-which is unique for each environment and which is strongly influenced by the exact details and overall context of the situation.

Animals↗
PubMed1999

Subicular place cells expand or contract their spatial firing pattern to fit the size of the environment in an open field but not in the presence of barriers: comparison with hippocampal place cells.

Cells in the hippocampus and subiculum signal spatial location in fundamentally different ways. Specifically, hippocampal cells show environment-specific spatial patterns, whereas subicular cells show the same pattern in each environment. In this study, cell firing patterns were recorded in both a large square and in a smaller square located within the large square. For some groups, portions of the small square were left in place during exposure to the large square, thus forming partial barriers. Subicular cell patterns during exposure to the large square were expanded versions of those in the small square. Hippocampal cells were likely to change their pattern completely ("remap") during exposure. However, when the barriers were left in place, cells in both areas retained the same pattern while rats were in the small square, regardless of whether they also had access to the entire large square area. Thus, subicular cells can change the size of their spatial pattern to fit the environment but will not do so across barriers.

Action Potentials↗
PubMed1999

Multitype spatial point patterns with hierarchical interactions.

Multitype spatial point patterns with hierarchical interactions are considered. Here hierarchical interaction means directionality: points on a higher level of hierarchy affect the locations of points on the lower levels, but not vice versa. Such relations are common, for example, in ecological communities. Interacting point patterns are often modeled by Gibbs processes with pairwise interactions. However, these models are inherently symmetric, and the hierarchy can be acknowledged only when interpreting the results. We suggest the following in allowing the inclusion of the hierarchical structure in the model. Instead of regarding the pattern as a realization of a stationary multivariate point process, we build the pattern one type at a time according to the order of the hierarchy by using nonstationary univariate processes. As interactions connected to points x on a certain level are considered, the effect of the higher levels is interpreted as heterogeneity of the pattern x, and the points on the lower levels are neglected because of the hierarchical structure.

Animals↗
PubMed2005

Change in spatial distribution patterns of a biennial plant between growth stages and generations in a patchy habitat.

BACKGROUND AND AIMS: The aim of the study was to evaluate factors causing change in spatial distribution patterns of plants between growth stages and generations for a monocarpic biennial plant, Lysimachia rubida. It was assumed that habitat heterogeneity was a primary factor determining spatial patterns of plants, and a randomization procedure was developed for testing the null hypothesis that only spatial association with ground surface conditions determined spatial patterns of plants. METHODS: A 5-year demographic census was conducted on an open dry habitat that was heterogeneous with regard to the ground surface conditions. KEY RESULTS: There was significant habitat association in that plants at vegetative and reproductive stages were denser in areas with smaller gravel than with larger gravel. Point process analyses rejected the null hypothesis of the spatial association with ground surface conditions. CONCLUSIONS: The results suggest that other factors, such as patchy seed dispersal, secondary dispersal of the seeds and life-history variation at various spatial scales, also affected spatial patterns of individuals in a population of L. rubida. Spatial structures and dynamics of a local population in a patchy habitat represent various performances of plants within patches and seed dispersal within a patch and beyond the patch.

Ecosystem↗
PubMed2006

Measuring the spatial arrangement patterns of pathological lesions in histological sections of brain tissue.

The development of abnormal protein aggregates in the form of extracellular plaques and intracellular inclusions is a characteristic feature of many neurodegenerative diseases such as Alzheimer's disease (AD), Creutzfeldt-Jakob disease (CJD) and the fronto-temporal dementias (FTD). An important aspect of a pathological protein aggregate is its spatial topography in the tissue. Lesions may not be randomly distributed within a histological section but exhibit spatial pattern, a departure from randomness either towards regularity or clustering. Information on the spatial pattern of a lesion may be useful in elucidating its pathogenesis and in studying the relationships between different lesions. This article reviews the methods that have been used to study the spatial topography of lesions. These include simple tests of whether the distribution of a lesion departs significantly from random using randomized points or sample fields, and more complex methods that employ grids or transects of contiguous fields and which can detect the intensity of aggregation and the sizes, distribution and spacing of the clusters. The usefulness of these methods in elucidating the pathogenesis of protein aggregates in neurodegenerative disease is discussed.

Brain↗
PubMed2004

Spatial distribution patterns of malaria vectors and sample size determination in spatially heterogeneous environments: a case study in the west Kenyan highland.

The current study examined temporal and spatial distribution patterns of anopheline malaria vectors in a highland site and determined the number of houses to be sampled to achieve the targeted precision level. Adult mosquito sampling was conducted seasonally in May and August 2002 in a 3 by 3-km2 area, and in November 2002 and February 2003 in an expanded 4 by 4-km2 area in Kakamega District, western Kenya. Anopheles gambiae Giles was the predominant malaria vector species, constituting 84.6% of the specimens, whereas Anopheles funestus Giles constituted 15.4% of the vector populations. An. gambiae abundance increased by six- to eight-fold in the long rainy season over the dry seasons, but An. funestus abundance peaked 3 mo after the long rainy season. For both species, the coefficient of variation was larger than 1, suggesting that the distribution of mosquito adults was aggregated. Mosquito clustering occurred in houses <400 m from a valley bottom. The negative binomial distribution was accepted in one sample period (August 2002) for An. gambiae and in two sampling periods (May and August 2002) for An. funestus. Taylor's power law analyses indicated that An. gambiae distribution was more aggregated in the wet seasons than in the dry seasons, whereas the degree of aggregation of An. funestus was similar in all four seasons. The minimum number of houses required to estimate anopheline female abundance within the commonly acceptable precision level (0.2) should be 17 houses per km2 for An. gambiae and 42 houses per km2 for An. funestus. The potential factors causing aggregated anopheline mosquito distribution are discussed.

Animals↗
PubMedDate not supplied

Evolution of spatial expression pattern.

How can complex patterns of gene expression evolve? Understanding the near-precise repeatability of morphology created by animal development, through the interactions between morphogens and networks of transcription factors, is one of the most difficult outstanding problems in developmental biology. Spatial patterns are created in part by interactions between transcription factors and their DNA targets. Here we simulate the evolution of such interactions to compare the success and the evolvability of simple and complex gene networks in reaching a desired spatial pattern of expression along an embryo. We find that adding more genes to a network makes only a slight difference to evolvability. Expression patterns can evolve within a few hundred mutational events, and some simulations show partial redundancy. However, there is wide variation between simulations, with both simple and complex networks being liable to reach evolutionary "dead ends" that can only be escaped by means of an advantageous combination of individually deleterious mutations.

Biological Evolution↗
PubMed2004

Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels.

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.

Age Factors↗
PubMed1999

Oscillatory models of the hippocampus: a study of spatio-temporal patterns of neural activity.

Spatial patterns of theta-rhythm activity in oscillatory models of the hippocampus are studied here using canonical models for both Hodgkin's class-1 and class-2 excitable neuronal systems. Dynamics of these models are studied in both the frequency domain, to determine phase-locking patterns, and in the time domain, to determine the amplitude responses resulting from phase-locking patterns. Computer simulations presented here demonstrate that phase deviations (timings) between inputs from the medial septum and the entorhinal cortex can create spatial patterns of theta-rhythm phase-locking. In this way, we show that the timing of inputs (not only their frequencies alone) can encode specific patterns of theta-rhythm activity. This study suggests new experiments to determine temporal and spatial synchronization.

Animals↗
PubMed2003

Inferring functional relationships of proteins from local sequence and spatial surface patterns.

We describe a novel approach for inferring functional relationship of proteins by detecting sequence and spatial patterns of protein surfaces. Well-formed concave surface regions in the form of pockets and voids are examined to identify similarity relationship that might be directly related to protein function. We first exhaustively identify and measure analytically all 910,379 surface pockets and interior voids on 12,177 protein structures from the Protein Data Bank. The similarity of patterns of residues forming pockets and voids are then assessed in sequence, in spatial arrangement, and in orientational arrangement. Statistical significance in the form of E and p-values is then estimated for each of the three types of similarity measurements. Our method is fully automated without human intervention and can be used without input of query patterns. It does not assume any prior knowledge of functional residues of a protein, and can detect similarity based on surface patterns small and large. It also tolerates, to some extent, conformational flexibility of functional sites. We show with examples that this method can detect functional relationship with specificity for members of the same protein family and superfamily, as well as remotely related functional surfaces from proteins of different fold structures. We envision that this method can be used for discovering novel functional relationship of protein surfaces, for functional annotation of protein structures with unknown biological roles, and for further inquiries on evolutionary origins of structural elements important for protein function.

Amino Acid Sequence↗
PubMed2005

Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.

MicroRNAs (miRNAs) are an extensive class of regulatory RNA whose specific functions in animals are generally unknown. Although computational methods have identified many potential targets of miRNAs, elucidating the spatial expression patterns of miRNAs is necessary to identify the sites of miRNA action. Here, we report the spatial patterns of miRNA transcription during Drosophila embryonic development, as revealed by in situ hybridization to nascent miRNA transcripts. We detect expression of 15 "stand-alone" miRNA loci and 9 intronic miRNA loci, which collectively represent 38 miRNA genes. We observe great variety in the spatial patterns of miRNA transcription, including preblastoderm stripes, in aspects of the central and peripheral nervous systems, and in cellular subsets of the mesoderm and endoderm. We also describe an intronic miRNA (miR-7) whose expression pattern is distinct from that of its host mRNA (bancal), which demonstrates that intronic miRNAs can be subject to independent cis-regulatory control. Intriguingly, the expression patterns of several fly miRNAs are analogous to those of their vertebrate counterparts, suggesting that these miRNAs may have ancient roles in animal patterning.

Animals↗
PubMed2005

B(1) destructive interferences and spatial phase patterns at 7 T with a head transceiver array coil.

RF behavior in the human head becomes complex at ultrahigh magnetic fields. A bright center and a weak periphery are observed in images obtained with volume coils, while surface coils provide strong signal in the periphery. Intensity patterns reported with volume coils are often loosely referred to as "dielectric resonances," while modeling studies ascribe them to superposition of traveling waves greatly dampened in lossy brain tissues, raising questions regarding the usage of this term. Here we address this question experimentally, taking full advantage of a transceiver coil array that was used in volume transmit mode, multiple receiver mode, or single transmit surface coil mode. We demonstrate with an appropriately conductive sphere phantom that destructive interferences are responsible for a weak B(1) in the periphery, without a significant standing wave pattern. The relative spatial phase of receive and transmit B(1) proved remarkably similar for the different coil elements, although with opposite rotational direction. Additional simulation data closely matched our phantom results. In the human brain the phase patterns were more complex but still exhibited similarities between coil elements. Our results suggest that measuring spatial B(1) phase could help, within an MR session, to perform RF shimming in order to obtain more homogeneous B(1) in user-defined areas of the brain.

Algorithms↗