SEARCH · PubMed Health

Results for “Spatial pattern formation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources

PubMed1991

Diffusion resistances between ADH-induced vacuoles and the extracellular space in rabbit collecting duct: evidence that most vacuoles are intracellular, endocytic compartments.

Large vacuoles form in the renal collecting duct following the onset of antidiuretic hormone (ADH)-stimulated water reabsorption. The aim of the present study was to test two alternative hypotheses regarding the origins of these structures: (1) the vacuoles constitute basilar, extracellular spaces that dilate as water flows through these spaces from cells into the peritubular compartment; or (2) the vacuoles represent intracellular, endocytic compartments that dilate during water reabsorption due to enhanced fluid phase endocytosis. Fluorescence-digital imaging microscopy was used to visualize the uptake into vacuoles of a hydrophilic fluorochrome (6 methoxy-N-[3 sulfopropyl] quinolinium) whose fluorescence is markedly quenched by halides. During their formation, most vacuoles (67%) accumulated the fluorochrome from the peritubular bath and trapped the dye well after (greater than 60 min) washing it from the bath. The spatial pattern of fluorescence within individual vacuoles indicated that the dye was trapped within these structures as a fluid-phase marker and was not bound to the vacuole margins. The fluorescence of dye trapped within vacuoles was virtually unaltered by changes in peritubular Cl- or Br- concentration that elicit dramatic quenching of dye-fluorescence in bulk solution, as expected if there exists a high diffusion resistance between the interiors of these structures and the peritubular space. These results indicate that most ADH-induced vacuoles represent endocytic compartments that are not directly connected to the extracellular space.

Animals↗

PubMedDate not supplied

Blinks as an index of cognitive activity during reading.

Horizontal and vertical EOG recordings of eye movements were analyzed to determine the spatial and temporal distribution of blinks and the patterns of eye movements (saccades and fixation pauses) exhibited by six subjects during the reading of stories presented in two formats (on paper and on a VDT). The frequency and placement of blinks was not affected by the presentation condition. Blinks were determined to be non-randomly distributed during reading. Significantly more blinks (36%) occurred in conjunction with saccades than the proportion of time consumed by saccades (12%) would predict. Significantly more blinks (36%) occurred in the vicinity of line change saccades, which accounts for 15% of reading time, and with fixation pauses associated with regressions (42%), which accounts for 26% of reading time, than with fixation pauses during normal reading (22%), which accounts for 60% of reading time. The results of the study suggest that blink behavior during reading is under perceptual and cognitive control.

Adult↗

PubMed2002

Two-dimensional analysis of the spacing of ocular dominance columns in normally raised and strabismic kittens.

In the primary visual cortex of cats, ferrets and macaque monkeys, the thalamocortical afferents conveying signals from the two eyes terminate in alternating regions of layer IV known as ocular dominance columns. Previous experiments have indicated that the periodicity of these columns can be influenced by visual experience: compared to normally raised animals both strabismic cats and cats raised with alternating monocular exposure displayed an increased spacing of adjacent ocular dominance columns in the primary visual cortex (area 17). However, recently it was shown that the formation of ocular dominance columns begins much earlier than previously supposed, indicating that early visual experience might only have a limited influence on the development of the spatial pattern of ocular dominance columns. We therefore visualized the complete pattern of ocular dominance columns in area 17 of normally raised and strabismic kittens during early postnatal development (age 3-6 weeks), particularly focussing on littermates. In addition, we used a previously developed spatial analysis (period statistics) to quantify columnar spacing two-dimensionally. We observed a pronounced interindividual variability in both normally raised and strabismic animals, with column spacings ranging from 783 to 1362 microm. In contrast to previous reports, there were no significant differences in columnar periodicity between normally raised and strabismic cats. These data indicate that rearing has less influence on column spacing while the interindividual variability is much greater than previously supposed, suggesting that genetic differences have an influence on column spacing.

Animals↗

PubMed2006

Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development.

The Hedgehog (Hh) and Notch signal transduction pathways control a variety of developmental processes including cell fate choice, differentiation, proliferation, patterning and boundary formation. Because many components of these pathways are conserved, it was predicted and confirmed that pathway components are largely intact in the sea urchin genome. Spatial and temporal location of these pathways in the embryo, and their function in development offer added insight into their mechanistic contributions. Accordingly, all major components of both pathways were identified and annotated in the sea urchin Strongylocentrotus purpuratus genome and the embryonic expression of key components was explored. Relationships of the pathway components, and modifiers predicted from the annotation of S. purpuratus, were compared against cnidarians, arthropods, urochordates, and vertebrates. These analyses support the prediction that the pathways are highly conserved through metazoan evolution. Further, the location of these two pathways appears to be conserved among deuterostomes, and in the case of Notch at least, display similar capacities in endomesoderm gene regulatory networks. RNA expression profiles by quantitative PCR and RNA in situ hybridization reveal that Hedgehog is produced by the endoderm beginning just prior to invagination, and signals to the secondary mesenchyme-derived tissues at least until the pluteus larva stage. RNA in situ hybridization of Notch pathway members confirms that Notch functions sequentially in the vegetal-most secondary mesenchyme cells and later in the endoderm. Functional analyses in future studies will embed these pathways into the growing knowledge of gene regulatory networks that govern early specification and morphogenesis.

Amino Acid Sequence↗

PubMed1998

Expression of the SOX10 gene during human development.

SOX10, a new member of the SOX gene family, is a transcription factor defective in the Dom (Dominant megacolon) mouse and in the human Shah-Waardenburg syndrome. To help unravel its physiological role during human development, we studied SOX10 gene expression in embryonic, fetal, and adult human tissues by Northern blot and in situ hybridization. As in mice, the human SOX10 gene was essentially expressed in the neural crest derivatives that contribute to the formation of the peripheral nervous system, and in the adult central nervous system. Nevertheless, it was more widely expressed in humans than in rodents. The spatial and temporal pattern of SOX10 expression supports an important function in neural crest development.

Blotting, Northern↗

PubMed2005

Growth factors in lung development.

Organized and coordinated lung development follows transcriptional regulation of a complex set of cell-cell and cell-matrix interactions resulting in a blood-gas interface ready for physiologic gas exchange at birth. Transcription factors, growth factors, and various other signaling molecules regulate epithelial-mesenchymal interactions by paracrine and autocrine mechanisms. Transcriptional control at the earliest stages of lung development results in cell differentiation and cell commitment in the primitive lung bud, in essence setting up a framework for pattern formation and branching morphogenesis. Branching morphogenesis results in the formation of the conductive airway system, which is critical for alveolization. Lung development is influenced at all stages by spatial and temporal distribution of various signaling molecules and their receptors and also by the positive and negative control of signaling by paracrine, autocrine, and endocrine mechanisms. Lung bud formation, cell differentiation, and its interaction with the splanchnic mesoderm are regulated by HNF-3beta, Shh, Nkx2.1, HNF-3/Forkhead homolog-8 (HFH-8), Gli, and GATA transcription factors. HNF-3beta regulates Nkx2.1, a transcription factor critical to the formation of distal pulmonary structures. Nkx2.1 regulates surfactant protein genes that are important for the development of alveolar stability at birth. Shh, produced by the foregut endoderm, regulates lung morphogenesis signaling through Gli genes expressed in the mesenchyme. FGF10, produced by the mesoderm, regulates branching morphogenesis via its receptors on the lung epithelium. Alveolization and formation of the capillary network are influenced by various factors that include PDGF, vascular endothelial growth factor (VEGF), and retinoic acid. Epithelial-endothelial interactions during lung development are important in establishing a functional blood-gas interface. The effects of various growth factors on lung development have been demonstrated by gain- or loss-of-function studies in null mutant and transgenic mice models. Understanding the role of growth factors and various other signaling molecules and their cellular interactions in lung development will provide us with new insights into the pathogenesis of bronchopulmonary dysplasia and disorders of lung morphogenesis.

Gene Expression Regulation, Developmental↗

PubMed1990

Positional cues and differential gene expression in somatic embryos of higher plants.

Much of the organization of higher vascular plants is determined during the formation of the embryo. In addition to the zygotic embryo which results from sexual fertilization in the ovule, many plants are capable of producing embryos from somatic cells. Of particular interest to plant developmental biologists is the phenomenon of somatic embryogenesis in cultures of the domesticated carrot which, because of its tractable nature in experimental manipulations, is presently regarded as a suitable model for studying pattern formation in plants. This short review considers the state of our knowledge concerning the origin and perception of positional information in plant embryos, and the temporal and spatial expression of genes. The available data provide a number of promising leads for cell-cell interactions in embryos, and there are some clear indications that the spatial distribution of certain gene products is correlated with changes in morphology. However, there is, as yet, insufficient evidence with which to forge a link between positional cues and the expression of genes which influence developmental transitions in embryos.

Cell Differentiation↗

PubMed2001

Neurotrimin expression during cerebellar development suggests roles in axon fasciculation and synaptogenesis.

We investigated the temporal expression of the neural cell adhesion molecule, neurotrimin, in the rat cerebellum and the brainstem from birth to adulthood using immunoreactive labeling. A wave of expression accompanied the development of projection pathways extending from brainstem nuclei (pons/inferior olive) through the cerebellar peduncles into the arbor vitae and disappeared with myelination by P14. Immuno-EM revealed expression of neurotrimin on the surface of unmyelinated axons but not on astrocytes or oligodendroglia. With the development of the molecular and internal granular layers, intense labeling occurred on the surface of parallel fiber bundles, granule cells and mossy fibers. With synaptogenesis, each excitatory junction was labeled by the immunoreaction. By P21, neurotrimin reactivity decreased on the surfaces of neuronal somata, dendrites and axons but remained at excitatory synaptic contact sites in both the molecular and granular layers. The spatial-temporal expression pattern of neurotrimin suggests that this adhesion molecule plays a role in axonal fasciculation of specific cerebellar systems and may also be involved in the formation of excitatory synapses and their stabilization into adulthood.

Afferent Pathways↗

PubMed2003

From the Cover: Segmented spiral waves in a reaction-diffusion system.

Pattern formation in reaction-diffusion systems is often invoked as a mechanism for biological morphogenesis. Patterns in chemical systems typically occur either as propagating waves or as stationary, spatially periodic, Turing structures. The spiral and concentric (target) waves found to date in spatially extended chemical or physical systems are smooth and continuous; only living systems, such as seashells, lichens, pine cones, or flowers, have been shown to demonstrate segmentation of these patterns. Here, we report observations of segmented spiral and target waves in the Belousov-Zhabotinsky reaction dispersed in water nanodroplets of a water-in-oil microemulsion. These highly ordered chemical patterns, consisting of short wave segments regularly separated by gaps, form a link between Turing and trigger wave patterns and narrow the disparity between chemistry and biology. They exhibit aspects of such fundamental biological behavior as self-replication of structural elements and preservation of morphology during evolutionary development from a simpler precursor to a more complex structure.

Biophysical Phenomena↗

PubMedDate not supplied

Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice.

We have carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. By using Affymetrix GeneChip microarrays, we found a distinct pattern of age-related change, consisting mostly of gene overexpression in the middle-aged mice, suggesting that the induction of negative regulators in the middle-aged hippocampus could be involved in impairment of learning. Interestingly, we report changes in transcript levels for genes that could affect synaptic plasticity. Those changes could be involved in the memory deficits we observed in the 15-month-old mice. In agreement with previous reports, we also found altered expression in genes related to inflammation, protein processing, and oxidative stress.

Aging↗

PubMed2007

Insights into the gyrification of developing ferret brain by magnetic resonance imaging.

The developmental mechanisms underlying the formation of human cortical convolutions (gyri and sulci) remain largely unknown. Genetic causes of lissencephaly (literally 'smooth brain') would imply that disorders in neuronal migration cause the loss of cortical convolutions. However, prior studies have suggested that loss of sulci and gyri can also arise from impaired proliferation, disrupted lamination and loss of intracortical connections. To gain further insight into the mechanisms underlying the formation of cortical convolutions, we examined the progressive brain development of the gyrencephalic ferret. In this study, we used magnetic resonance imaging to follow the temporal and spatial pattern of neuronal migration, proliferation and differentiation in relation to the onset and development of cortical convolutions. In this manner, we demonstrate that the onset of gyrification begins largely after completion of neuronal proliferation and migration. Gyrification occurs in a lateral to medial gradient, during the period of most rapid cerebral cortical growth. Cortical folding is also largely complete prior to myelination of the underlying cortical axons. These observations are consistent with gyrification arising secondary to cortical processes involving neuronal differentiation.

Animals↗

PubMed2003

Influence of spatiotemporally correlated noise on structure formation in excitable media.

We discuss the influence of additive, spatiotemporally correlated (i.e., colored) noise on pattern formation in a two-dimensional network of excitable systems. The signature of spatiotemporal stochastic resonance (STSR) is analyzed using cross-correlation and information theoretic measures. It is found that the STSR behavior is affected by both the spatial and temporal correlations of the noise due to an interplay with the length scales of the deterministic network. Increasing the spatiotemporal noise correlation shifts the occurrence of STSR to smaller values of the noise variance. Additionally, if the spatial correlation of the noise exceeds that of the network, the excitation patterns disappear in favor of cloudy structures, directly rendering the underlying spatial noise field.

Journal Article↗

PubMed1993

Differential expression of multiple fork head related genes during gastrulation and axial pattern formation in the mouse embryo.

Four genes encoding fork-head-domain-containing proteins (FD genes) have been isolated from a mouse 8.5 days post coitum (p.c.) embryo cDNA library. Two are mouse homologues of rat HNF-3 beta and HNF-3 alpha. The other two are novel and have been named MF-1 and MF-2 (for mesoderm/mesenchyme fork head). Wholemount in situ hybridization of embryos between 6.5 and 9.5 days p. c. shows that each gene has a unique expression pattern. HNF-3 beta is expressed in the node, notochord, floor plate and gut, while HNF-3 alpha is mainly in the definitive endoderm and gut, but also in the floor plate of the midbrain. These results suggest that HNF-3 beta and HNF-3 alpha, in addition to their known functions as transcriptional activators in adult liver, play a role in body axis formation, neural tube patterning and definitive endoderm formation during gastrulation. MF-1 RNA is present in non-notochordal mesoderm, and in neural-crest-derived head mesenchyme, while MF-2 transcripts are found in the sclerotomes of the somites and in head mesenchyme, including that from neural crest. Studies on gastrulation stage embryos suggest that the early temporal and spatial patterns of HNF-3 beta, MF-1 and HNF-3 alpha correlate with populations of cells undergoing commitment to different developmental fates. A model is proposed linking FD gene expression with gastrulation events in the mouse.

Amino Acid Sequence↗

PubMed1996

TBP binds the transcriptionally inactive TA5 sequence but the resulting complex is not efficiently recognised by TFIIB and TFIIA.

The binding of TBP (TFIID) to the TATA box has been considered to direct promoter recognition and pre-initiation complex formation because it is the first event leading to basal transcription by RNA polymerase II. Here, we analyse the binding of yeast TBP to a consensus TATAAA box and two point mutations, TAAAAA (inactive) and TATATA (active). Despite the fact that the TAAAAA sequence does not support transcription in vitro, yeast TBP binds the three sequences showing, in this sense, only a limited sequence specificity. However, the TBP-TAAAAA complex cannot be recognised by other basal transcription factors, in particular by TFIIB. DNase I footprinting patterns of the TBP-TAAAAA complex are different from those observed in functional TBP-TATA box complexes, indicating that, most likely, it is a different spatial arrangement of the TBP-DNA complex that prevents formation of the TFIIB-TBP-TAAAAA complex, also seriously impairing entry of TFIIA to the complex. DNA deformability of the A/T-rich sequences appears to be an important determinant in the formation of a productive TBP-TATA complex. These results indicate that the transcriptional competence of A/T-rich sequences is determined not only by TBP binding, but also by the ability of other basal transcription factors to recognise the preformed TBP-DNA complexes.

Base Sequence↗

PubMed2001

Reproductive pair correlations and the clustering of organisms.

Clustering of organisms can be a consequence of social behaviour, or of the response of individuals to chemical and physical cues. Environmental variability can also cause clustering: for example, marine turbulence transports plankton and produces chlorophyll concentration patterns in the upper ocean. Even in a homogeneous environment, nonlinear interactions between species can result in spontaneous pattern formation. Here we show that a population of independent, random-walking organisms ('brownian bugs'), reproducing by binary division and dying at constant rates, spontaneously aggregates. Using an individual-based model, we show that clusters form out of spatially homogeneous initial conditions without environmental variability, predator-prey interactions, kinesis or taxis. The clustering mechanism is reproductively driven-birth must always be adjacent to a living organism. This clustering can overwhelm diffusion and create non-poissonian correlations between pairs (parent and offspring) or organisms, leading to the emergence of patterns.

Models, Biological↗

PubMed1984

The early development of mystacial vibrissae in the mouse.

The initial generation of the pattern of mystacial vibrissae (whiskers) in the mouse is described. The maxillary process is present in 10-day embryos but has a relatively flat surface. Beginning at approximately 11.5 days, the first sign of vibrissal development is the formation of ridges and grooves on the maxillary and lateral nasal processes. The first vibrissal rudiment to form subsequently appears posterior to the most ventral groove on the maxillary process. It is the most ventral whisker of the posterior, vertical row. The next few rudiments appear: dorsal to the first, also in the vertical row; and anterior to the first, on the ventral-most ridge and in the groove beneath it. Formation of vibrissal rudiments continues in a dorsal and anterior progression usually by an apparent partitioning of the ridges into vibrissal units. The hypothesis that this patterning of mystacial vibrissae might be determined by the pattern of innervation in the early mouse snout was investigated. Nerve trunks and branches are present in the maxillary process well before any sign of vibrissal formation. Because innervation is so widespread there appears to be no immediate temporal correlation between the outgrowth of a nerve branch to a site and the generation of a vibrissa there. Furthermore, at the time just prior to the formation of the first follicle rudiment, there is little or no nerve branching to the presumptive site of that first follicle while branches are found more dorsally where vibrissae will not form until later. Thus, a one-to-one spatial correlation between nerve and follicle sites also appears to be lacking. The developmental changes in ultrastructure within the neurites of the trunks and branches as well as the apparent rearrangements of the nerve trunks suggest that early innervation of the snout is a labile phenomenon and that the vibrissal pattern begins to be established before the neural pattern is completely developed. The results indicate that vibrissal pattern formation is likely to be a complex process relying on the interplay of the cells and tissues involved, rather than on unidirectional instructions from neurons to other cell types.

Animals↗

PubMed2001

Activation and repression by the C-terminal domain of Dorsal.

In the Drosophila embryo, Dorsal, a maternally expressed Rel family transcription factor, regulates dorsoventral pattern formation by activating and repressing zygotically active fate-determining genes. Dorsal is distributed in a ventral-to-dorsal nuclear concentration gradient in the embryo, the formation of which depends upon the spatially regulated inhibition of Dorsal nuclear uptake by Cactus. Using maternally expressed Gal4/Dorsal fusion proteins, we have explored the mechanism of activation and repression by Dorsal. We find that a fusion protein containing the Gal4 DNA-binding domain fused to full-length Dorsal is distributed in a nuclear concentration gradient that is similar to that of endogenous Dorsal, despite the presence of a constitutively active nuclear localization signal in the Gal4 domain. Whether this fusion protein activates or represses reporter genes depends upon the context of the Gal4-binding sites in the reporter. A Gal4/Dorsal fusion protein lacking the conserved Rel homology domain of Dorsal, but containing the non-conserved C-terminal domain also mediates both activation and repression, depending upon Gal4-binding site context. A region close to the C-terminal end of the C-terminal domain has homology to a repression motif in Engrailed - the eh1 motif. Deletion analysis indicates that this region mediates transcriptional repression and binding to Groucho, a co-repressor known to be required for Dorsal-mediated repression. As has previously been shown for repression by Dorsal, we find that activation by Dorsal, in particular by the C-terminal domain, is modulated by the maternal terminal pattern-forming system.

Amino Acid Motifs↗

PubMed1996

Cellular correlates to spatial learning in the rat hippocampus.

Learning through exploration gives increased synaptic field potentials in the perforant path/dentate synapses, largely due to an activity-dependent brain temperature increase. After temperature compensation, spatial learning was associated with small, but significant, STP-like changes of the field potential lasting 20-30 min. A group of spatially trained adult rats showed faster spatial learning and about 10% higher basal dendritic spine density (LY-filled) compared to two control groups. With unchanged dendritic length and branching pattern, the results suggest the formation of new synapses.

Animals↗