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Results for “Spatial pattern formation”

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PubMed1979

Cell differentiation during fruiting body formation in polysphondylium pallidum.

The spatial pattern of cellular differentiation was studied during fruiting body formation in Polysphondylium pallidum using 3 different staining methods: Calcofluor fluorescence (cellulose accumulation), neutral red (prestalk cells) and immunofluorescence (prespore cells). Neutral-red staining revealed the existence of a clear prestalk region which becomes evident during aggregation and continues throughout culmination. Immunofluorescent staining demonstrated that cells in the prestalk region gradually lose their presporeness (fluorescence) as they are transformed into differentiated stalk cells. Calcofluor staining revealed that stalk cell differentiation begins during the mid-aggregation phase and that the mode of formation of the main stalk and the side branches differs slightly in morphology. Calcofluor staining also demonstrated the development, during aggregation, of a thick cellulosic girdle with lateral tubular extensions which surround the aggregation streams. The above results are discussed in terms of our present knowledge about differentiation and morphogenesis in cellular slime moulds.

Dictyostelium↗

PubMed2005

Intrinsic and extrinsic regulators of developmental timing: from miRNAs to nutritional cues.

A fundamental challenge in biology is to understand the reproducibility of developmental programs between individuals of the same metazoan species. This developmental precision reflects the meticulous integration of temporal control mechanisms with those that specify other aspects of pattern formation, such as spatial and sexual information. The cues that guide these developmental events are largely intrinsic to the organism but can also include extrinsic inputs, such as nutrition or temperature. This review discusses the well-characterized developmental timing mechanism that patterns the C. elegans epidermis. Components of this pathway are conserved, and their links to developmental time control in other species are considered, including the temporal patterning of the fly nervous system. Particular attention is given to the roles of miRNAs in developmental timing and to the emerging mechanisms that link developmental programs to nutritional cues.

Animals↗

PubMed2000

Sinorhizobium meliloti nfe (nodulation formation efficiency) genes exhibit temporal and spatial expression patterns similar to those of genes involved in symbiotic nitrogen fixation.

The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of the Sinorhizobium meliloti strain GR4 on alfalfa roots. The nfeA and nfeB genes are preceded by functional nif consensus sequences and NifA binding motifs. Here, we determined the temporal and spatial expression patterns of the nfe genes in symbiosis with alfalfa. Translational fusions of the nfe promoters with the gusA gene and reverse transcription-polymerase chain reaction analyses indicate that they are expressed and translated within mature nitrogen-fixing nodules and not during early steps of nodule development. Within the nodules the three nfe genes exhibit a spatial expression pattern similar to that of genes involved in symbiotic nitrogen fixation. We show that nfeB and nfeD genes are expressed not only from their own promoters but also from the upstream nfe promoter sequences. Furthermore, with the use of specific antibodies the NfeB and NfeD proteins were detected within the root nodule bacteroid fraction. Finally, NfeB was inmunolocalized in the bacteroid cell membrane whereas NfeD was detected in the bacteroid cytoplasm.

Bacterial Proteins↗

PubMed1983

Bithorax phenocopy and pattern formation. II. A model of prepattern formation.

Phenocopy maps are constructed from the spatial pattern of the phenocopy spots using a distance function defined on the frequencies with which two compartments transform separately and jointly. The temporal changes in distances between different compartments in turn enable us to make inferences concerning the diffusion-like processes involved in prepattern formation of the metathorax. A model is presented which accounts for the data in terms of the propagation of two wavefronts in sequence and in approximately orthogonal directions. Sensitivity to transformation by ether is limited in time to the interval between the passing of the two wavefronts. Changes caused by 13 successive generations of ether treatment can be interpreted in terms of alterations in the timing and rates of wave propagation. A comparison of phenocopy and fate maps suggests that the prepatterning processes affect primarily the blastoderm cytoplasm or surface membrane.

Animals↗

PubMed2000

Tumor patterning: analogies of neoplastic morphogenesis with embryogenesis.

Patterning or pattern formation is a spatial and temporal process, by which ordered arrangements of cells and tissue structure are attained. The term is mostly applied to the morphogenesis in developmental biology, but it can also be useful for the neomorphogenesis in tumor biology. Despite increasing data on the proliferation and differentiation of tumor cells, processes of tumor patterning are rarely studied and poorly understood. A fundamental embryonic process of patterning is the gastrulation and a basic example of neoplastic patterning is the colonic adenoma-carcinoma sequence. Both processes exhibit distinct nuclear translocations and expressions of beta-catenin, which is considered to be a decisive transcriptional regulator. Our recent studies demonstrate striking analogies of patterning and nuclear beta-catenin expressions between the colonic adenoma-carcinoma sequence and the gastrulation steps. The shared patterns are dissociation, reassembly, tubular reconstruction and branching of neoplastic cells in association with nuclear beta-catenin expressions. These new findings establish patterning as a relevant concept for tumor biology and link the neoplastic morphogenesis with embryogenesis.

Body Patterning↗

PubMed2006

Molecular signaling in feather morphogenesis.

The development and regeneration of feathers have gained much attention recently because of progress in the following areas. First, pattern formation. The exquisite spatial arrangement provides a simple model for decoding the rules of morphogenesis. Second, stem cell biology. In every molting, a few stem cells have to rebuild the entire epithelial organ, providing much to learn on how to regenerate an organ physiologically. Third, evolution and development ('Evo-Devo'). The discovery of feathered dinosaur fossils in China prompted enthusiastic inquiries about the origin and evolution of feathers. Progress has been made in elucidating feather morphogenesis in five successive phases: macro-patterning, micro-patterning, intra-bud morphogenesis, follicle morphogenesis and regenerative cycling.

Animals↗

PubMed2006

Scale-dependent inhibition drives regular tussock spacing in a freshwater marsh.

Regular spatial patterning is common in nature, and various mechanisms of self-organization have been proposed to explain regular patterning. We report on regular spatial patterning in Carex stricta in a freshwater wetland and investigate the applicability of theoretical models that explain regular patterning based on inhibition, facilitation, or interaction between the two. Spectral analysis of aerial photographs revealed that tussocks were regularly spaced at an average distance of 60 cm. Photosynthetically active radiation varied significantly with distance from the tussock and was lowest at intermediate distance from the tussock center (15-40 cm). Using transplants to assay growth conditions, we found that C. stricta grew well in all distance classes with and without natural C. stricta biomass, except at intermediate distances when buried in C. stricta wrack. Our experimental results reveal that C. stricta inhibits its growth in a scale-dependent manner: inhibition was found to peak at intermediate distance from the tussock. We compared three alternative models to examine potential mechanisms driving regularity and found that, similar to our experimental results, scale-dependent inhibition provides the best explanation for the observed regular tussock spacing. Our study underlines the importance of scale-dependent feedback in the formation of regular spatial patterning in ecosystems.

Carex Plant↗

PubMed2004

Origin, structure, and role of background EEG activity. Part 2. Analytic phase.

OBJECTIVE: To explain spontaneous EEG through measurements of spatiotemporal patterns of phase among beta-gamma oscillations. METHODS: High-density 8 x 8 intracranial arrays were fixed over sensory cortices of rabbits. EEGs were spatially low pass filtered, temporally bandpass filtered and segmented in overlapping windows stepped at 2 ms. Phase was measured with the cosine as the temporal basis function, using both Fourier and Hilbert transforms to compensate for their respective limitations. Spatial patterns in 2D phase surfaces were measured with the geometric form of the cone as the spatial basis function. RESULTS: Two fundamental state variables were measured at each digitizing step in the 64 EEGs: the rate of change in phase with time (frequency) and the rate of change in phase with distance (gradient). The parameters of location, diameter, duration, and phase velocity of the cone of phase were derived from these two state variables. Parameter distributions including recurrence intervals extending into the low theta range were fractal; the mean values varied with window duration and interelectrode distance. CONCLUSIONS: The formation of spatial amplitude patterns began with state transitions that were documented by phase discontinuities and phase cones. The multiplicity of overlapping cones indicated that sensory neocortices maintained a scale-free state of self-organized criticality (SOC) in each hemisphere as the basis for its rapid integration of sensory input with prior learning stored in cortical synaptic webs. Further evidence came from the fractal properties of the phase parameters and the self-similarity of phase patterns in the ms/mm to m/s ranges. SIGNIFICANCE: These EEG data suggest that neocortical dynamics is analogous to the dynamics of self-stabilizing systems, such as a sand pile that maintains its critical angle by avalanches, and a pan of boiling water that maintains its critical temperature by bubbles that release heat. Beta-gamma oscillations stem from the ability of neocortex to maintain its stability under continuous sensory bombardment. Modeling implies that the critical parameter of neocortex (analogous to angle of repose or temperature) is the mean firing rates of neurons that are homeostatically regulated by refractory periods everywhere at all times in cortex. The advantage of SOC in perception may be the ability it gives neocortex to generate instantaneous global state transitions (avalanches, bubbles) large enough to include the multiple sensory areas that are necessary to form gestalts (multisensory percepts).

Animals↗

PubMed2004

Cellular patterns in the inner retina of adult zebrafish: quantitative analyses and a computational model of their formation.

The mechanisms that control cellular pattern formation in the growing vertebrate central nervous system are poorly understood. In an effort to reveal mechanistic rules of cellular pattern formation in the central nervous system, quantitative spatial analysis and computational modeling techniques were applied to cellular patterns in the inner retina of the adult zebrafish. All the analyzed cell types were arrayed in nonrandom patterns tending toward regularity; specifically, they were locally anticlustered. Over relatively large spatial scales, only one cell type exhibited consistent evidence for pattern regularity, suggesting that cellular pattern formation in the inner retina is dominated by local anticlustering mechanisms. Cross-correlation analyses revealed independence between the patterns of different cell types, suggesting that cellular pattern formation may involve multiple, independent, homotypic anticlustering mechanisms. A computational model of cellular pattern formation in the growing zebrafish retina was developed, which featured an inhibitory, homotypic signaling mechanism, arising from differentiated cells, that controlled the spatial profile of cell fate decisions. By adjusting the spatial profile of this decaying-exponential signal, the model provided good estimates of all the cellular patterns that were observed in vivo, as objectively judged by quantitative spatial pattern analyses. The results support the hypothesis that cellular pattern formation in the inner retina of zebrafish is dominated by a set of anticlustering mechanisms that may control events at, or near, the spatiotemporal point of cell fate decision.

Animals↗

PubMed1988

Geometry and spatial patterns in Polysphondylium pallidum.

The formation of secondary sori in whorls of Polysphondylium pallidum provides an attractive model system for the study of symmetry breaking during morphogenesis. Tip-specific antibodies that permit detection of very early stages in this patterning process are available. We have found that the patterns of tip-specific antigen expression vary considerably depending on the size, shape, and developmental stage of the whorl. All of these patterns, however, are well explained by patterning models that rely on short-range autocatalysis and long-range inhibition, as exemplified by reaction-diffusion theories. In the context of reaction-diffusion, we discuss the possible effects of initial conditions, boundary conditions, and nonlinearities on the selection of patterns in P. pallidum whorls.

Models, Theoretical↗

PubMed2000

Ecological symmetry breaking can favour the evolution of altruism in an action-response game.

The evolution of altruistic behaviour is studied in a simple action-response game with a tunable degree of conflict of interest. It is shown that for the continuous, mixed-medium approach no stable polymorphism favours altruism. Ecological dynamics are explored with the addition of a spatial dimension and a local energy variable. A continuous spatial model with finite local range does not introduce any substantial difference in the results with respect to the level of altruism. However, the model illustrates how ecological coupling may lead to the formation of stable spatial patterns in the form of discrete and isolated clusters of players as a consequence of inverse density dependence. A discrete, individual-based model is built in which local interactions are also modelled as occurring within a finite neighbourhood of each individual and spatial positions are not restricted as in lattice models. This model shows substantially different results. A high level of altruism is observed for low (but positive) degrees of conflict and this level decreases linearly for higher degrees of conflict. The evolution of altruism is explained by studying the broken symmetries introduced by the spatial clusters themselves, mainly between their central and peripheral regions which, in combination with the discrete and the stochastic nature of the model, result in the stabilization of strategies in which players behave altruistically towards the same type. As a consequence of the activity of the players, energy resources at the centre of an altruistic cluster are very depleted; so much so that, for low conflict, fitter non-altruistic mutants may initially invade only to become locally extinct due to their less efficient use of energy as their numbers increase. In peripheral regions invader may subsist; however, for geometrical reasons long-lasting genealogies tend to originate only at the centre of a cluster.

Altruism↗

PubMed1995

Integro-differential equations and the stability of neural networks with dendritic structure.

We analyse the effects of dendritic structure on the stability of a recurrent neural network in terms of a set of coupled, non-linear Volterra integro-differential equations. These, which describe the dynamics of the somatic membrane potentials, are obtained by eliminating the dendritic potentials from the underlying compartmental model or cable equations. We then derive conditions for Turing-like instability as a precursor for pattern formation in a spatially organized network. These conditions depend on the spatial distribution of axo-dendritic connections across the network.

Animals↗

PubMed2003

Quantification of the spatial aspect of chaotic dynamics in biological and chemical systems.

The need to study spatio-temporal chaos in a spatially extended dynamical system which exhibits not only irregular, initial-value sensitive temporal behavior but also the formation of irregular spatial patterns, has increasingly been recognized in biological science. While the temporal aspect of chaotic dynamics is usually characterized by the dominant Lyapunov exponent, the spatial aspect can be quantified by the correlation length. In this paper, using the diffusion-reaction model of population dynamics and considering the conditions of the system stability with respect to small heterogeneous perturbations, we derive an analytical formula for an 'intrinsic length' which appears to be in a very good agreement with the value of the correlation length of the system. Using this formula and numerical simulations, we analyze the dependence of the correlation length on the system parameters. We show that our findings may lead to a new understanding of some well-known experimental and field data as well as affect the choice of an adequate model of chaotic dynamics in biological and chemical systems.

Animals↗

PubMed1997

Blood-filled spaces with and without filler materials in guided bone regeneration. A comparative experimental study in the rabbit using bioresorbable membranes.

The aim of the present study was to evaluate the effect of natural deproteinized bone mineral on the temporal and spatial pattern of bone formation in a guided bone regeneration model system while using a bioresorbable membrane device. A periosteal skin flap was raised uncovering the calvaria of 20 rabbits. A stiff hemispherical dome made of polylactic acid was placed onto the roughened calvaria and anchored by screws. Prior to placement, the dome was either filled with peripheral blood (control group, 8 rabbits) or with blood and OsteoGraf/N-300 (test group, 12 rabbits). At 1 month, histologic sections revealed bone regeneration in both test and control domes to various degrees. In the test domes, bone height reached 78% (67-83) and bone volume was 11% (6-17), while in the control domes, bone height was 45% (14-67) and bone volume 6% (1-11). At 2 months, bone height was unchanged in the test group at 70% (67-83) and bone volume had only slightly increased to 16% (11-21). In the controls, height increased to 86% (60-100) and volume to 20% (9-27). Thus, in this model system, natural bone mineral fill contributed to accelerate initial bone neogenesis, while it did not contribute to increasing bone volume or bone height at later observation stages.

Animals↗

PubMed2003

Chemotherapy and antiangiogenesis--drug-specific, dose-related effects.

Dose-response effects of fluorouracil, paclitaxel, doxorubicin, cisplatin, methotrexate, cyclophosphamide and etoposide on VEGF165/164-mediated angiogenesis using the rat mesenteric-window angiogenesis assay are reported. VEGF is a pivotal pro-angiogenic factor in most tumors. Microvessel spatial extension, density, pattern formation and segment length were assessed quantitatively and objectively. A single i.v. injection of each drug was given at a low, intermediate or high dose, 7 days before sacrifice. All the drugs elicited significant responses in terms of one or more measured variables. Only paclitaxel, doxorubicin and cyclophosphamide significantly suppressed the overall angiogenic response (p < or = 0.0001, p < or = 0.0002 and p < or = 0.05, respectively), however. Taking toxicity into account, paclitaxel was more potent in inhibition of angiogenesis than the other agents. No clear correlation was found between drug half-life, the degree of toxic effects (in terms ofbody weight changes) and the antiangiogenic effect. The antiangiogenic effects were distinctly drug specific.

Animals↗

PubMed1998

Spatiotemporal dynamics of clotting and pattern formation in human blood.

We examined the spatial dynamics of in vitro clot growth in human blood and plasma and found that initially, a clot grows at a constant speed, then abruptly stops and becomes surrounded by an 'inhibition zone' in which coagulation is strongly suppressed. We also observed the formation of 'stratified structures' (target patterns) in which solid layers alternated with liquid plasma. These and other spatial regimes of clotting are explained in terms of two interacting concentration waves propagating without attenuation. The experimental results are consistent with a hypothesis that blood is a bi-excitable medium, a new type of excitable medium.

Blood Coagulation↗

PubMed2000

A cell type-specific effect of calcium on pattern formation and differentiation in dictyostelium discoideum.

Spatial gradients of sequestered and free cellular calcium (Ca2+) exist in the slug of Dictyostelium discoideum (Maeda and Maeda, 1973; Tirlapur et al., 1991; Azhar et al., 1995; Cubitt et al., 1995). When we vary intracellular Ca2+ with the help of calcium buffers and the ionophore Br-A23187, there are striking effects on slug morphology, patterning and cell differentiation. In the presence of a calcium ionophore, high external Ca2+ levels lead to an increase of intracellular sequestered and free Ca2+, the formation of long slugs, a decrease in the fraction of genetically defined prespore cells and 'stalky' fruiting bodies. Conversely, a lowering of external Ca2+ levels results in a decrease of intracellular Ca2+, the formation of short slugs, an increase in the prespore fraction and 'spory' fruiting bodies. We infer that Ca2+ plays a significant morphogenetic role in D. discoideum development, by selectively promoting the prestalk pathway relative to the prespore pathway.

Animals↗

PubMed1993

Wave mechanisms of pattern formation in microbial populations.

The occurrence of spatially ordered structures plays an important role in biology (examples: morphogenesis, ecosystems, dynamics of populations, etc.). Turing proposed a reaction-diffusion process that is the basis for most theoretical studies of stationary biological pattern formation. Now, when Turing structures are obtained in experiments (40 years after Turing's publication), it is interesting to discover whether Turing structures are the only mechanism used by nature in biological pattern formation. In microbial growth, we have found experimental evidence of an alternative to the Turing model that is based on waves displayed in excitable media. In studies of Escherichia coli populations, we observed that interacting taxis waves create motionless patterns. Taxis waves consuming two different substrates (serine and aspartic acid) were involved. Taxis waves consuming serine stop when they collide. However, those supported by consumption of aspartic were initiated at the collision line. Colliding and annihilating in turn, the waves give rise to stationary pattern formation, and wave theory provides an alternative to the classical Turing mechanism.

Animals↗