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At least 433 records · Page 24Linked 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↗
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↗
PubMed2002

Temporal and spatial expression pattern of the OSVP1 and OSEM genes during seed development in rice.

The spatial and temporal expression patterns of the rice VP1 (OSVP1) gene, as well as the OSEM gene which it controls, were studied during seed development by in situ hybridization and immuno-localization techniques. The expression of OSVP1 could be detected in embryos as early as 2-3 d after pollination (DAP) and thereafter became preferentially localized to shoot, radicle and vascular tissues during the embryo development at both the mRNA and protein levels. In the aleurone layers, OSVP1 mRNA and protein were detected after 6 DAP. OSEM mRNA was detectable after 6 DAP in the embryo and aleurone tissue. The spatial distribution within the embryo of OSEM mRNA and OSVP1 mRNA/protein was very similar after 6 DAP. Transgenic rice carrying a beta-glucuronidase (GUS) gene transcribed from a chimeric promoter consisting of the CaMV 35S minimal promoter (-46) and the 55-bp promoter fragment of OSEM, minimally required for ABA and VP1 regulation, also exhibited a spatial pattern of GUS expression similar to that of OSEM and OSVP1. These results suggest that (OS)VP1 is a major determinant not only of the seed specificity but also of the spatial pattern of OSEM expression in the developing seed.

Abscisic Acid↗
PubMed1995

Spatial distribution patterns of the sporocyst infrapopulation of Schistosoma mansoni within its mollusc host (Biomphalaria glabrata): an unusual phenotype of aggregation.

A study carried out on the intramolluscan development of the larval stages of Schistosoma mansoni from Venezuela in its intermediate host Biomphalaria glabrata shows the existence of 2 patterns for the spatial distribution of daughter sporocysts within the digestive gland of the snail. Besides the normal pattern, which is a random distribution of daughter sporocysts within the gland, 11% of the infected snails harbored an infection phenotype with daughter sporocysts strongly aggregated in only the posterior half of the digestive gland. These data suggest a possible strategy allowing a better nutritional efficiency of the infected digestive gland, a process to block the supply of hemolymph toward the gonad, resulting in castration or both.

Animals↗
PubMed1984

Generation of spatially periodic patterns by a mechanical instability: a mechanical alternative to the Turing model.

We have studied the generation of spatial patterns created by mechanical (rather than chemical) instabilities. When dissociated fibroblasts are suspended in a gel of reprecipitated collagen, and the contraction of the gel as a whole is physically restrained by attachment of its margin to a glass fibre meshwork, then the effect of the fibroblasts' traction is to break up the cell-matrix mixture into a series of clumps or aggregations of cells and compressed matrix. These aggregations are interconnected by linear tracts of collagen fibres aligned under the tensile stress exerted by fibroblast traction. The patterns generated by this mechanical instability vary depending upon cell population density and other factors. Over a certain range of cell concentrations, this mechanical instability yields geometric patterns which resemble but are usually much less regular than the patterns which develop normally in the dermis of developing bird skin. We propose that an equivalent mechanical instability, occurring during the embryonic development of this skin, could be the cause not only of the clumping of dermal fibroblasts to form the feather papillae, but also of the alignment of collagen fibres into the characteristic polygonal network of fibre bundles - which interconnect these papillae and which presage the subsequent pattern of the dermal muscles serving to control feather movements. More generally, we suggest that this type of mechanical instability can serve the morphogenetic functions for which Turing's chemical instability and other reaction-diffusion systems have been proposed. Mechanical instabilities can create physical structures directly, in one step, in contrast to the two or more steps which would be required if positional information first had to be specified by chemical gradients and then only secondarily implemented in physical form. In addition, physical forces can act more quickly and at much longer range than can diffusing chemicals and can generate a greater range of possible geometries than is possible using gradients of scalar properties. In cases (such as chondrogenesis) where cell differentiation is influenced by the local population density of cells and extracellular matrix, the physical patterns of force and distortion within this extracellular matrix should even be able to accomplish the spatial control of differentiation, usually attributed to diffusible 'morphogens'.

Animals↗
PubMed1992

From stripes to spots: prepatterns which can be produced in the skin by a reaction-diffusion system.

A key question in the area of spatial pattern formation in developmental biology is: how do groups of cells in a homogeneous tissue suddenly differentiate along entirely different developmental paths compared to neighbouring cells? Although experiments are now beginning to provide answers to this question, the mechanisms responsible for the development of repeated or periodic structures and spatial patterns, e.g., hair follicles and pigmentation patterns, are still unknown. Theoretical biologists and applied mathematicians have suggested various prepattern mechanisms as the primary cause of repeated or periodic spatial patterns. A class of biochemical reactions referred to here as reaction-diffusion (RD) systems, having the capacity to spontaneously generate stable stationary wavelike spatial patterns (Turing, 1952), has been suggested as a possible prepattern mechanisms, e.g., during hair follicle initiation and development (Nagorcka, 1989), and pigmentation patterns (Murray, 1989). Spatial patterns arising during development of the vertebrate skin are frequently complex. Spatial patterns in the skin can be seen to vary within an individual from one region of the skin to another. One pattern change commonly observed across the skin is from stripes to spots. An RD system is defined which is able to generate different spatial patterns depending on the value of a single parameter. The parameter varied controls the transport of the chemical components of the RD system across the basement membrane separating the epidermis and dermis. The patterns produced range from stripes to an irregular array of spots. Not only are different patterns produced, but a different time sequence of prepatterns is expected to arise in the different skin regions depending on whether the first prepattern in an array of spots or stripes. As a consequence it is possible to account for hair follicle initiation in the hair-bearing regions of the mammalian skin as well as the sequence of events required for the formation of dermatoglyphics in the volar regions.

Animals↗
PubMed2000

Visual detection of spatial contrast patterns: evaluation of five simple models.

The ModelFest Phase One dataset is a collection of luminance contrast thresholds for 43 two-dimensional monochromatic spatial patterns confined to an area of approximately two by two degrees. These data were collected by a collaboration among twelve laboratories, and were designed to provide a common database for calibration and testing of spatial vision models. Here I report fits of the ModelFest data with five models: Peak Contrast, Contrast Energy, Generalized Energy, a Gabor Channels model, and a Discrete Cosine Transform model. The Gabor Channels model provides the best fit, though the other, simpler models, with the exception of Peak Contrast, provide remarkably good fits as well. Though there are clear individual differences, regularities in the data suggest the possibility of constructing a standard observer for spatial vision.

Contrast Sensitivity↗
PubMed1997

The spatial relationship between scanning saccades and express saccades.

When monkeys interrupt their saccadic scanning of a visual scene to look at a suddenly appearing target, saccades to the target are made after an "express" latency or after a longer "regular" latency. The purpose of this study was to analyze the spatial patterns of scanning, express, and regular saccades. Scanning patterns were spatially biased. Express saccade patterns were biased, too, and were directly correlated with scanning patterns. Regular saccade patterns were more uniform and were not directly correlated with scanning patterns. Express saccades, but not regular saccades, seemed to be facilitated by preparation to scan. This study contributes to a general understanding of how monkeys examine scenes containing both unchanging and suddenly appearing stimuli.

Animals↗
PubMed1997

Multifactorial comparative study of spatial point pattern analysis methods.

A way of studying cooperative behaviour of biological entities (proteins, cells, etc.) is by using topographical analysis: the quantification of the spatial patterns formed by the entities considered as points. Five methods of topographical analysis were compared in terms of discriminant power, stability of parameters, methodological bias and algorithms. We tested five methods (nearest neighbour distribution, radial distribution, Voronoï paving, quadrat count, minimal spanning tree graph) which generated nine parameters on four simulated models (random point process, hardcore model and two cluster models) and on experimental cellular models. The method which offers the best discrimination power and stability seems to be the minimal spanning tree graph edge length distribution.

Animals↗