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Results for “Spatial pattern formation”

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PubMed2003

Gradients and thresholds: BMP response gradients unveiled in Drosophila embryos.

Bone morphogenetic proteins (BMP) direct dorsal-ventral patterning in both invertebrate and vertebrate embryos, with strong evolutionary conservation of molecular components of the pathway. Dorsal-ventral patterning of the early Drosophila embryo is a powerful experimental system to probe mechanisms of BMP gradient formation and interpretation. Recent studies have found that spatial patterns of activated BMP signal transducers in Drosophila go through an unexpected transition: a shallow gradient of weak responses at mid-cellularization changes to a step gradient of stronger responses in cellularized embryos. The transition between two gradients of different shape yields new insights into the progression of Drosophila dorsal-ventral patterning and raises new issues about the mechanisms of gradient formation.

Animals↗

PubMed2006

Regular patterns in dichotomically driven activator-inhibitor dynamics.

We investigate Turing pattern formation in the presence of additive dichotomous fluctuations in the context of an extended system with diffusive coupling and FitzHugh-Nagumo kinetics. The fluctuations vary in space and/or time. Depending on the realization of the dichotomous switching the system is, at a given time (for spatial disorder at a given position) in one of two possible excitable dynamical regimes. Each of the two excitable dynamics for itself does not support pattern formation. With proper dichotomous fluctuations, however, the homogeneous steady state is destabilized via a Turing instability. We investigate the influence of different switching rates (different correlation length of the spatial disorder) on pattern formation. We find three distinct mechanisms: For slow switching existing boundaries become unstable, for high rates the system exhibits "effective bistability" which allows for a Turing instability. For medium rates the fluctuations create spatial structures via a new mechanism where the influence of the fluctuations is twofold. First they produce local inhomogeneities, which then grow (again caused by fluctuations) until the whole space is covered. Utilizing a nonlinear map approach we show bistability of a period-one and a period-two orbit being associated with the steady homogeneous and the Turing pattern state, respectively. Finally, for purely static dichotomous disorder we find destabilization of homogeneous steady states for finite nonzero correlation length of the disorder resulting again in Turing patterns.

Journal Article↗

PubMed2004

Retinal pattern and the genetic basis of its formation in zebrafish.

The vertebrate nervous system contains an immense diversity of distinct cellular components that are organized into precise spatial patterns. The importance of accurate neuronal architecture is particularly obvious in the retina, where it is necessary for the formation of visual images. The retina is structured in a distinct layered pattern that is remarkably conserved in evolution, including phyla as diverse as primates and teleost fish. Genetic analysis in zebrafish reveals mechanisms that are essential for the formation of this architecture.

Animals↗

PubMed1997

Backfoot is a novel homeobox gene expressed in the mesenchyme of developing hind limb.

Homeobox genes play important roles in pattern formation during development. Here, we report the cloning and temporal and spatial expression patterns of a novel homeobox gene Backfoot (BFT for the human gene, and Bft for the mouse gene), whose expression reveals an early molecular distinction between forelimb and hind limb. BFT was identified as a sequence-specific DNA-binding protein. In addition to the homeodomain, it shares a carboxyl-terminal peptide motif with other paired-like homeodomain proteins. Northern hybridization analysis of RNAs from human tissues revealed that human BFT is highly expressed in adult skeletal muscle and bladder. During midgestation embryogenesis, mouse Bft is expressed in the developing hind limb buds, mandibular arches, and Rathke's pouch. The expression of Bft begins prior to the appearance of hind limb buds in mesenchyme but is never observed in forelimbs. At later stages of limb development, the expression is progressively restricted to perichondrial regions, most likely in tendons and ligaments. The timing and pattern of expression suggest that Bft plays multiple roles in hind limb patterning, branchial arch development, and pituitary development. Bft is likely identical to a mouse gene, Ptx1, that was recently isolated by Lamonerie et al. ([1996] Genes Dev. 10:1284-1295) and that has been suggested to play a role in pituitary development.

Adult↗

PubMed2000

The effect of nicotine on gene expression during spine fusion.

STUDY DESIGN: A rabbit model of posterolateral spine fusion was used to investigate the effect of nicotine on cytokine expression during spine fusion. OBJECTIVES: To determine the effects of nicotine on the known gene expression pattern of bone morphogens and related proteins expressed during spine fusion. SUMMARY OF BACKGROUND DATA: The mechanism by which nicotine increases the pseudarthrosis rate of spine fusion is unknown. Recently, a distinct temporal and spatial pattern of cytokine expression during bone formation has been described. The authors hypothesized that nicotine would alter this known pattern, thereby revealing the mechanism by which nicotine exerts its effect. METHODS: Twenty-eight New Zealand White rabbits underwent posterolateral spine fusion with autogenous bone graft. Fourteen rabbits received systemic nicotine by a miniosmotic pump. Fusions were harvested at 0, 2, 5, and 7 days and 2, 3, and 4 weeks after arthrodesis. Specimens were divided into the outer zones adjacent to the transverse processes and the central zones between the transverse processes. Gene expression of type I and II collagen, bone morphogenic protein-2, -4, and -6 and basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF) was then measured at each time point in each of the two zones. RESULTS: Nicotine inhibited expression of all cytokines measured, mainly in the central zone. However, the previously described temporal and spatial patterns of expression were preserved. CONCLUSIONS: Nicotine inhibits expression of a wide range of cytokines, including those associated with neovascularization and osteoblast differentiation. Therefore, the effects of nicotine appear to involve more than just local vasoconstriction.

Animals↗

PubMed2000

Lessons on pattern formation from planet WATOR.

It is well known that if reacting species experience unequal diffusion rates, then dynamics that lead to a constant steady state in a "well-mixed" environment can in a spatial setting lead to interesting patterns. In this paper, we focus on complementary pattern formation mechanisms that operate even when the diffusion rates are equal. In particular, we can say that when the mean-field ODE has an attracting periodic orbit then the stochastic spatial model will have large-scale spatial structures in equilibrium. We explore this mechanism in depth through the dynamics of the simulator WATOR.

Animals↗

PubMed2003

Spatial synchronization of regular optical patterns.

We investigate an extended, nonlinear optical experiment, exhibiting the spontaneous formation of hexagonal patterns out of a stationary bifurcation. The system is exposed to a two-dimensional spatially periodic forcing, namely, static hexagonal patterns, under variation of their spatial periodicity. Parameters are the strength of the forcing and the distance to pattern forming threshold. The system response is quantitatively characterized with different methods. We observe several locking regimes, where the system is entrained by the forcing. Most of the locking regimes can be related to resonances between the different critical wave numbers and the forcing wave number or its spatial harmonics. One particular locking appears to result from two of these simple resonances in a kind of generalized order m:n synchronization. The width of the locking regimes increases with forcing strength, apparently representing a spatial analog of Arnold tongues.

Journal Article↗

PubMed1997

Temporal and spatial control of murine GATA-3 transcription by promoter-proximal regulatory elements.

GATA-3 is expressed in a temporally dynamic manner and fulfills vital functions during vertebrate fetal development. Homozygous mGATA-3 mutant embryos die at midgestation, thus complicating the analysis of its contribution to the development of specific cell fates in the many tissues where it is expressed during embryogenesis. We show here that the elements controlling GATA-3 regulation can be precisely refined, using transgenic mice, to discrete cis-acting domains: within 6 kb surrounding the transcriptional initiation site, separate sequences were found to control the expression of mGATA-3 in early muscle masses, in a subset of PNS neurons, in the genital tubercle, and in the branchial arches. The branchial arch regulatory element is particularly robust and was refined to a discrete enhancer sequence lying between nt -2832 and -2462 from the transcription initiation site. The enhancer contains potential binding sites for many well-characterized transcription factors, suggesting that mGATA-3 transcriptional activity may be regulated by these proteins (or related family members) in the mesenchyme of the arches that contribute to formation of the jaw. These studies show that discrete regulatory elements required for the elaboration of complex developmental programs can be individually localized, suggesting that the developmentally transient expression of individual transcription factors collaboratively contributes to the temporal and spatial pattern of cellular differentiation leading to the formation of adult anatomy.

Animals↗

PubMed2004

CompuCell, a multi-model framework for simulation of morphogenesis.

MOTIVATION: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. RESULTS: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud. AVAILABILITY: Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/

Animals↗

PubMed1995

A network model of developmental gene hierarchy.

A network model of development governing the whole temporal and spatial hierarchy of early embryogenesis and pattern formation in Drosophila is introduced. The network is related to a neural network model, with its units being developmental genes mostly connected by the genes' DNA-binding products. The developmental network's agreement with predictions regarding architecture and function of the neural network provides adequate grounds for an analogy between the two. The model is tested through computer simulations--predictions compare favorably with experimental observations. The model not only incorporates a program of control at gene level, but also makes a direct connection with current molecular studies throughout the whole hierarchy of the early embryogenesis of Drosophila.

Animals↗

PubMed2005

Nutrients and toxin producing phytoplankton control algal blooms - a spatio-temporal study in a noisy environment.

A phytoplankton-zooplankton prey-predator model has been investigated for temporal, spatial and spatio-temporal dissipative pattern formation in a deterministic and noisy environment, respectively. The overall carrying capacity for the phytoplankton population depends on the nutrient level. The role of nutrient concentrations and toxin producing phytoplankton for controlling the algal blooms has been discussed. The local analysis yields a number of stationary and/or oscillatory regimes and their combinations. Correspondingly interesting is the spatio-temporal behaviour, modelled by stochastic reaction-diffusion equations. The present study also reveals the fact that the rate of toxin production by toxin producing phytoplankton (TPP) plays an important role for controlling oscillations in the plankton system. We also observe that different mortality functions of zooplankton due to TPP have significant influence in controlling oscillations, coexistence, survival or extinction of the zoo-plankton population. External noise can enhance the survival and spread of zooplankton that would go extinct in the deterministic system due to a high rate of toxin production.

Animals↗

PubMed1994

Promoter analysis meets pattern formation: transcriptional regulatory genes in sea urchin embryogenesis.

Analyses of spatial and temporal gene control mechanisms in the sea urchin embryo have identified several important trans-regulatory factors, including some that are related to known developmental control genes of the fly and mouse. Recent advances in gene perturbation technologies, including the use of antisense oligonucleotides to target mRNAs in early-stage embryos, as well as the injection of mRNAs into zygotes to express genes ectopically, have made it possible to test the functions of such factors directly.

Animals↗

PubMed1991

Multiple intercellular signalling systems control the development of the Caenorhabditis elegans vulva.

Developmental, genetic and molecular studies indicate that multiple intercellular signalling systems interact to specify the types and spatial patterns of cells generated during the formation of the vulva of the nematode Caenorhabditis elegans. Two classes of evolutionarily conserved transmembrane receptors and a Ras protein function in these signalling systems. The biology of vulval development provides a framework for understanding how cell interactions control the development of animals as diverse as nematodes, insects and mammals.

Animals↗

PubMed1994

A novel POU domain gene, zebrafish pou2: expression and roles of two alternatively spliced twin products in early development.

POU domain proteins are a large family of transcriptional regulatory proteins, many of which are implicated in the control of gene expression during early development. We describe here the cloning and expression of zebrafish pou2, a novel POU domain gene related to the mouse germ-line-specific transcription factor oct-3. Zebrafish pou2 is maternally expressed, and the transcripts are present from the one-cell stage to the gastrula stage. In situ hybridization analyses revealed that the transcripts were present in all blastomeres until the midblastula stage and that the expression was restricted to the epiblast during gastrulation. We found that alternatively spliced transcripts, t-pou2 RNAs, were also expressed in the embryos. In contrast to the Pou2 product, the t-Pou2 product lacks DNA-binding activity because of its incomplete POU domain structure. To examine the roles of the Pou2 and t-Pou2 products, we increased their expression in the embryo by microinjection of synthetic pou2 and t-pou2 RNAs into the fertilized eggs at the one-cell stage. Most embryos that developed from the eggs injected with pou2 RNA did not show any obvious developmental defects. In contrast, overexpression of the t-Pou2 product greatly affected the embryonic development: There was strong developmental retardation or arrest due to the incomplete gastrulation. In the affected embryos, expression of zebrafish T gene was reduced and the hypoblast formation was disturbed. Temporal and spatial expression patterns and the effects of overexpression of these products on development are consistent with the idea that the Pou2 and t-Pou2 proteins are involved in early development of zebrafish embryos. They may be involved in the proliferation of blastomeres in undetermined state at the blastula stage and/or the early cell commitment events at the gastrula stage. Also, our results indicate that different products generated as a result of alternative splicing from the same gene possess distinct functional capacities.

Alternative Splicing↗

PubMed2005

Density dependence, spatial scale and patterning in sessile biota.

Sessile biota can compete with or facilitate each other, and the interaction of facilitation and competition at different spatial scales is key to developing spatial patchiness and patterning. We examined density and scale dependence in a patterned, soft sediment mussel bed. We followed mussel growth and density at two spatial scales separated by four orders of magnitude. In summer, competition was important at both scales. In winter, there was net facilitation at the small scale with no evidence of density dependence at the large scale. The mechanism for facilitation is probably density dependent protection from wave dislodgement. Intraspecific interactions in soft sediment mussel beds thus vary both temporally and spatially. Our data support the idea that pattern formation in ecological systems arises from competition at large scales and facilitation at smaller scales, so far only shown in vegetation systems. The data, and a simple, heuristic model, also suggest that facilitative interactions in sessile biota are mediated by physical stress, and that interactions change in strength and sign along a spatial or temporal gradient of physical stress.

Analysis of Variance↗

PubMedDate not supplied

[The electrophysiological correlates of the involvement in a pathological process of the thalamo-hypothalamic structures of the human brain].

Comparative EEG studies (with the normative data control) were carried out in patients with different anatomic-topographical variants of craniopharyngioma, effecting the hypothalamus (12 patients) and involving thalamo-subcortical structures in the pathological process (17 patients). Characteristics of EEG reorganization were found to be determined in the first instance by the stage of development of the focal process. Analysis of the regional characteristics and intercentral relations of the brain biopotentials revealed besides the common features, the differences in the effects of certain diencephalic structures on the spatial-temporal EEG organization. Hypothalamic areas exert mainly global influence on the EEG pattern formation. Thalamic structures influence genesis of the rhythmic activity forms and their intercentral relations more differentially and make more important contribution to the formation of the balanced (in norm) pattern of the brain electrical processes spatial-temporal organization.

Cerebral Ventricle Neoplasms↗

PubMed2003

The segmentation clock: converting embryonic time into spatial pattern.

In most animal species, the anteroposterior body axis is generated by the formation of repeated structures called segments. In vertebrate segmentation, a specialized mesodermal structure called the somite gives rise to skeletal muscles, vertebrae, and some dermis. Formation of the somites is a rhythmic process that involves an oscillator--the segmentation clock--driven by Wnt and Notch signaling. The clock ticks in somite precursors and halts when they reach a specific maturation stage defined as the wavefront, established by fibroblast growth factor and Wnt signaling. This process converts the temporal oscillations into the periodic spatial pattern of somite boundaries. The study of somite development provides insights into the spatiotemporal integration of signaling systems in the vertebrate embryo.

Animals↗

PubMed1982

Changes in the distribution of fibronectin during limb regeneration in newts using immunocytochemistry.

The distribution of fibronectin in regenerating newt limbs was studied using immunocytochemistry. At appropriate intervals after the initial amputation at the elbow (10-30 days), animals were reamputated at the shoulder and processed for light microscopy. The peroxidase-antiperoxidase technique was used to localize affinity-purified antibodies to fibronectin in limb tissues. At the amputation site, fibronectin was associated with basal laminae and connective tissues adjacent to dedifferentiating limb tissues destined to form the regeneration blastema. Accumulation and growth of the blastema was accompanied by the apparent de novo synthesis of fibronectin, where it appeared randomly in the interstitium between blastemal cells. The onset of chondrogenesis was characterized by a central condensation of prechondroblasts that formed the cartilage anlagen. Fibronectin formed an amorphous network between presumptive chondroblasts. As the mature cartilage phenotype was expressed and chondrocytes became isolated in lacunae, fibronectin was greatly reduced and then disappeared. The extracellular matrix surrounding undifferentiated blastemal cells still contained fibronectin. Fibronectin was also found in high concentrations between differentiating myoblasts. A condensation of fibronectin was also observed beneath the epidermis at the distal limb tip at the onset of digit formation. These observations are consistent with the hypothesis that fibronectin may play a key role in the morphogenetic events that result in the spatial organization and subsequent differentiation of cells during pattern formation in the regenerating limb.

Amputation, Surgical↗