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Results for “Spatial pattern formation”

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PubMed2000

Gene expression of TGF-beta, TGF-beta receptor, and extracellular matrix proteins during membranous bone healing in rats.

Poorly healing mandibular fractures and osteotomies can be troublesome complications of craniomaxillofacial trauma and reconstructive surgery. Gene therapy may offer ways of enhancing bone formation by altering the expression of desired growth factors and extracellular matrix molecules. The elucidation of suitable candidate genes for therapeutic intervention necessitates investigation of the endogenously expressed patterns of growth factors during normal (i.e., successful) fracture repair. Transforming growth factor beta1 (TGF-beta1), its receptor (Tbeta-RII), and the extracellular matrix proteins osteocalcin and type I collagen are thought to be important in long-bone (endochondral) formation, fracture healing, and osteoblast proliferation. However, the spatial and temporal expression patterns of these molecules during membranous bone repair remain unknown. In this study, 24 adult rats underwent mandibular osteotomy with rigid external fixation. In addition, four identically treated rats that underwent sham operation (i.e., no osteotomy) were used as controls. Four experimental animals were then killed at each time point (3, 5, 7, 9, 23, and 37 days after the procedure) to examine gene expression of TGF-beta1 and Tbeta-RII, osteocalcin, and type I collagen. Northern blot analysis was used to compare gene expression of these molecules in experimental animals with that in control animals (i.e., nonosteotomized; n = 4). In addition, TGF-beta1 and T-RII proteins were immunolocalized in an additional group of nine animals killed on postoperative days 3, 7, and 37. The results of Northern blot analysis demonstrated a moderate increase (1.7 times) in TGF-beta1 expression 7 days postoperatively; TGF-beta1 expression returned thereafter to near baseline levels. Tbeta-RII mRNA expression was downregulated shortly after osteotomy but then increased, reaching a peak of 1.8 times the baseline level on postoperative day 9. Osteocalcin mRNA expression was dramatically downregulated shortly after osteotomy and remained low during the early phases of fracture repair. Osteocalcin expression trended slowly upward as healing continued, reaching peak expression by day 37 (1.7 times the control level). In contrast, collagen type IalphaI mRNA expression was acutely downregulated shortly after osteotomy, peaked on postoperative days 5, and then decreased at later time points. Histologic samples from animals killed 3 days after osteotomy demonstrated TGF-beta1 protein localized to inflammatory cells and extracellular matrix within the fracture gap, periosteum, and peripheral soft tissues. On postoperative day 7, TGF-beta1 staining was predominantly localized to the osteotomized bone edges, periosteum, surrounding soft tissues, and residual inflammatory cells. By postoperative day 37, complete bony healing was observed, and TGF-beta1 staining was localized to the newly formed bone matrix and areas of remodeling. On postoperative day 3, Tbeta-RII immunostaining localized to inflammatory cells within the fracture gap, periosteal cells, and surrounding soft tissues. By day 7, Tbeta-RII staining localized to osteoblasts of the fracture gap but was most intense within osteoblasts and mesenchymal cells of the osteotomized bone edges. On postoperative day 37, Tbeta-RII protein was seen in osteocytes, osteoblasts, and the newly formed periosteum in the remodeling bone. These observations agree with those of previous in vivo studies of endochondral bone formation, growth, and healing. In addition, these results implicate TGF-beta1 biological activity in the regulation of osteoblast migration, differentiation, and proliferation during mandibular fracture repair. Furthermore, comparison of these data with gene expression during mandibular distraction osteogenesis may provide useful insights into the treatment of poorly healing fractures because distraction osteogenesis has been shown to be effective in the management of these difficult clinical cases.

Animals↗

PubMedDate not supplied

[Spatial aspects of the dynamics of blood coagulation. II. Phenomenological model].

Pattern formation dynamics of the blood clotting system was investigated using a reaction-diffusion model based on modern biochemical concepts. It is shown through analysis of the model that the pattern formation mechanism in the blood significantly differs from the well known fundamental Turing's mechanism. Within the mechanism discovered the human blood is treated as the specific new-type active medium, in which the pattern formation is determined by the interplay of two autowaves.

Blood Coagulation↗

PubMed1991

A comparative analysis of N-myc and c-myc expression and cellular proliferation in mouse organogenesis.

The distribution of c-myc and N-myc transcripts during mouse organogenesis was investigated by in situ hybridization and compared to proliferation in several tissues. Only c-myc expression was found during the formation of cartilage, brown adipose tissue, glandula submandibularis, thymus and liver. There was a temporally and spatially ordered expression of N-myc only during the organogenesis of brain, retina and eye lens. In some organs (e.g., in lung and tooth bud), c-myc and N-myc were expressed in a striking complementary pattern that reflected the ontogenic origins of different tissue components. Transcripts of both genes were found in the early gut epithelium, but as formation of villi began, the spatial expression pattern of N-myc and c-myc diverged. The results suggest a link between the proliferative state of cell types and the differential expression of N-myc vs. c-myc. Specifically, c-myc is only expressed in rapidly proliferating tissues, while N-myc expression often persists through cytodifferentiation, e.g., during development of eye lens, retina, telencephalon and gut epithelium. Thus, in spite of the structural similarities of N-myc and c-myc genes and proteins their developmental expression patterns suggest different functional roles.

Animals↗

PubMed1987

Three-dimensional representation of chemical gradients.

Perspective display techniques are applied to chemical and biochemical data sets. These represent spatially distributed gradients of reactive compounds that participate in pattern-formation processes due to reaction-diffusion or reaction-convection coupling. The patterns form in thin solution layers and are observed as chemical waves in the Belousov-Zhabotinskii reaction, as convection-induced stationary structures during oscillating glycolysis in yeast cytoplasm, and as the diffusive spreading of enzyme-catalyzed metabolic turnover in a substrate layer. The digital data are measured with a two-dimensional spectrophotometer based on a computerized video equipment with high spatial, temporal and intensity resolution. By application of three-dimensional procedures detailed structural properties of chemical and biochemical model systems will be presented yielding localization of reaction and transport events.

Journal Article↗

PubMed1986

Representation of DNA sequences by use of helical wheels to identify pattern formation with protein binding potential.

Similar to the protein segments with helical potential the three-dimensional structures of DNA sequences can be represented by a two-dimensional projection along the axis of the double helix. We will call this projection according to Schiffer and Edmundson "helical wheel". In the first place the wheels are employed here as graphical restatements of known sequences which represent binding sites of restriction-modification enzymes. Specific recognition of these sites has to be based on sequence related multi contact interactions of weak bonds. Because of the spatial and directional characteristics of H-bonds we will utilize the pattern formation of H-bond donor--and acceptor groups protruding into the major groove of the helix to identify the particular sequences. The characteristics of these patterns can be readily visualized and compared by examination of these wheels.

Amino Acid Sequence↗

PubMed1999

Gene expression in the epididymis.

The epididymis is a tubular organ exhibiting vectorial functions of sperm concentration, maturation, transport, and storage. The molecular basis for these functions is poorly understood. However, it has become increasingly clear that regional differences along the length of the duct play a role in epididymal physiology and that region-specific gene expression is involved in the formation of these differences. Although not an overtly segmented organ, the epididymis consists of a series of highly coiled "zones," separated by connective tissue septulae and distinct by cell morphology and their pattern of gene expression. Thus, it constitutes an interesting mammalian model to study how pattern formation is achieved by differential gene activity. A large number of epididymis-expressed genes have been cloned and analyzed at the molecular level, most of them have been characterized by a distinct temporal and spatial expression pattern within the organ. Only recently have theories been developed about how and when during ontogenesis this pattern formation takes place and what its significance might be. This review summarizes the current knowledge on regionalized gene expression in the epididymis and presents hypotheses concerning its ontogenetic origin and regulation in the adult.

Animals↗

PubMedDate not supplied

Using soil moisture and spatial yield patterns to identify subsurface flow pathways.

Subsurface soil water dynamics can influence crop growth and the fate of surface-applied fertilizers and pesticides. Recently, a method was proposed using only ground-penetrating radar (GPR) and digital elevation maps (DEMs) to identify locations where subsurface water converged into discrete pathways. For this study, the GPR protocol for identifying horizontal subsurface flow pathways was extended to a 3.2-ha field, uncertainty is discussed, and soil moisture and yield patterns are presented as confirming evidence of the extent of the subsurface flow pathways. Observed soil water contents supported the existence of discrete preferential funnel flow processes occurring near the GPR-identified preferential flow pathways. Soil moisture also played a critical role in the formation of corn (Zea mays L.) grain yield patterns with yield spatial patterns being similar for mild and severe drought conditions. A buffer zone protocol was introduced that allowed the impact of subsurface flow pathways on corn grain yield to be quantified. Results indicate that when a GPR-identified subsurface clay layer was within 2 m of the soil surface, there was a beneficial impact on yield during a drought year. Furthermore, the buffer zone analysis demonstrated that corn grain yields decreased as the horizontal distance from the GPR-identified subsurface flow pathways increased during a drought year. Averaged real-time soil moisture contents at 0.1 m also decreased with increasing distance from the GPR-identified flow pathways. This research suggests that subsurface flow pathways exist and influence soil moisture and corn grain yield patterns.

Agriculture↗

PubMed2004

Chemical waves and pattern formation in the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/water lamellar system.

The present work deals with the spatially extended oscillatory Belousov Zhabotinsky reaction-diffusion system carried out in an anisotropic environment of phosphatidylcholines/water binary system, which presents layered aqueous domains separated by lipid bilayers. We report the occurrence of stable Turing patterns, spiral waves, and other exotic structures in phospholipids bilayers that are generally used as a models for cell plasma membranes.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1996

Origin of primordial germ cells in the prestreak chick embryo.

The temporal and spatial pattern of segregation of the avian germline from the formation of the area pellucida to the beginning of primitive streak formation (stages VII-XIV, EG&K) was investigated using the culture of whole embryos and central and peripheral embryo fragments on vitelline membranes at stages VII-IX, immunohistological analysis of whole mount embryos and sections with monoclonal antibodies MC-480 against stage-specific embryonic antigen-1 (SSEA-1) and EMA-1, and with the culture of dispersed blastoderms at stages IX-XIV with and without on STO feeder layer. Whole embryos at intrauterine stages developed up to the formation of the primitive streak despite the absence of area pellucida expansion. Primordial germ cells (PGCs) appeared in the cultures of whole embryos and only in central fragments containing a partially formed area pellucida at stages VII-IX. When individual stage IX-XIV embryos were dispersed and cultured without a feeder layer, 25-45 PGCs/embryo were detected only with stage X-XIV, but not with stage IX blastoderms. However, the culture of dispersed cells from the area pellucida of stages IX-XIII on STO feeder layers yielded about 150 PGCs/embryo. The carbohydrate epitopes recognized by anti-SSEA-1 and EMA-1 first appeared at stage X on cells in association with polyingressing cells on the ventral surface of the epiblast and later on the dorsal surface of the hypoblast. The SSEA-1-positive hypoblast cells gave rise to chicken PGCs when cultured on a feeder layer of quail blastodermal cells. From these observations, we propose that the segregation and development of avian germline is a gradual, epigenetic process associated with the translocation of SSEA-1/EMA-1-positive cells from the ventral surface of the area pellucida at stage X to the dorsal side of the hypoblast at stages XI-XIV.

Animals↗

PubMed2003

Selectivity of verbal memory deficit in schizophrenic patients and their relatives.

Some of the relatives of people with schizophrenia show impairments of memory and executive function. It is not known, however, whether within these domains there is a class of processes that is especially impaired. Seventy schizophrenic or schizoaffective patients, 115 of their relatives and 66 normal controls underwent a series of assessments evaluating modality specific recall/learning, and aspects of executive functioning, including, planning ability, spatial working memory, strategy formation and rapid mental flexibility. The pattern of performance across cognitive processes was assessed using z-scores that allow direct comparison between tests with different raw score metrics. Selectivity of deficit was evaluated by subtracting the z-score of each cognitive process from the mean of the z-scores of those remaining. Patients performed out worse than controls on most measures, with verbal immediate recall and visual memory/learning the most impaired. Their relatives showed lower scores than controls on verbal and visual memory/learning and strategy formation; verbal memory and strategy formation remained impaired after eliminating those relatives with a psychiatric diagnosis. Consistent with the findings in their schizophrenic kin, healthy relatives also showed disproportionate impairments in verbal immediate recall. Our finding of a selective deficit in verbal memory among relatives suggests that such impairment constitutes a familial, probably genetic, risk factor for schizophrenia.

Adolescent↗

PubMed1997

Msx2 is a transcriptional regulator in the BMP4-mediated programmed cell death pathway.

Homeobox-containing genes play an important role in patterning processes that occur during embryogenesis. Programmed cell death is a key process during pattern formation. The mechanisms by which programmed cell death is spatially regulated are not well characterized. Msx1 and Msx2 are two closely related homeobox-containing genes that are expressed at sites where cellular proliferation and programmed cell death occur, including the developing limb and the cephalic neural crest. Tissue interactions are necessary for the maintenance of Msx1 and Msx2 expression and programmed cell death. It has been demonstrated that BMP4 can regulate cell death at these same sites as well as induce Msx expression. These observations lead to the hypothesis that Msx2 is a key regulator of cell death in the BMP-mediated pathway. Embryonic stem cell lines will undergo processes typical of early embryogenesis upon aggregation and have recently been shown to provide a model system for programmed cell death. In contrast to ES cells, we see that P19 cells do not undergo pronounced cell death upon aggregation; however, constitutive ectopic Msx2 expression in P19 cells results in a marked increase in apoptosis induced upon aggregation but has no effect when cells are grown as a monolayer. If aggregates are allowed to interact with a substrate, the process of programmed cell death is completely inhibited. Addition of BMP4 to aggregated P19 cells also results in cell death; however, BMP4 does not increase levels of cell death in Msx2-expressing cells. Addition of BMP4 to P19 cells results in an induction of Msx2 transcription consistent with its proposed role in cell death in the embryo. Our data support a model by which BMP4 induces programmed cell death via an Msx2-mediated pathway and provide direct functional evidence that Msx2 expression is a regulator of this process.

Apoptosis↗

PubMed1996

Coordination dynamics of trajectory formation.

The present study aims to understand the neurally based coordination dynamics (multistability, loss of stability, transitions, etc.) of trajectory formation in a simple task. Six subjects produced two spatial patterns of coordination in the xy plane by alternating the abduction-adduction and flexion-extension motions of their right index finger. Each pattern was characterized by a unique temporal ratio between the x and y directions of motion: (1) a figure zero, a 1:1 temporal pattern; and (2) a figure eight, a 2:1 temporal pattern. The patterns were produced rhythmically and movement frequency was scaled across ten frequency plateaus, with ten cycles of motion per step. As movement frequency increased, switching from a figure eight to a figure zero was observed at critical cycling frequencies. The switch from pattern (2) to pattern (1) was identified in the spatial trajectory and power spectra of x(t) and y(t). En route to the transition, enhancement of fluctuations was observed in the Fourier amplitudes of x(t) and y(t), specifically at f0 (the metronome frequency) and 2f0 (the first harmonic of f0). Interestingly, there was no difference in the spatial variability of the two patterns. Overall, the data demonstrate that spatial patterns of coordination can be characterized in terms of the temporal relationship between the spatial components of the trajectory itself. We discuss the experimental findings in relation to other end-point planning and multijoint control strategies, as well as the much more general problem of temporal synchronization in many interlimb and intralimb coordination tasks.

Adult↗

PubMed2006

Ethylene in induced conifer defense: cDNA cloning, protein expression, and cellular and subcellular localization of 1-aminocyclopropane-1-carboxylate oxidase in resin duct and phenolic parenchyma cells.

Members of the Pinaceae family have complex chemical defense strategies. Conifer defenses associated with specialized cell types of the bark involve constitutive and inducible accumulation of phenolic compounds in polyphenolic phloem parenchyma cells and oleoresin terpenoids in resin ducts. These defenses can protect trees against insect herbivory and fungal colonization. The phytohormone ethylene has been shown to induce the same anatomical and cellular defense responses that occur following insect feeding, mechanical wounding, or fungal inoculation in Douglas fir (Pseudotsuga menziesii) stems (Hudgins and Franceschi in Plant Physiol 135:2134-2149, 2004). However, very little is known about the genes involved in ethylene formation in conifer defense or about the temporal and spatial patterns of their protein expression. The enzyme 1-aminocyclopropane-1-carboxylate oxidase (ACO) catalyzes the final step in ethylene biosynthesis. We cloned full-length and near full-length ACO cDNAs from three conifer species, Sitka spruce (Picea sitchensis), white spruce (P. glauca), and Douglas fir, each with high similarity to Arabidopsis thaliana ACO proteins. Using an Arabidopsis anti-ACO antibody we determined that ACO is constitutively expressed in Douglas fir stem tissues and is up-regulated by mechanical wounding, consistent with the wound-induced increase of ethylene levels. Immunolocalization showed cytosolic ACO is predominantly present in specialized cell types of the wound-induced bark, specifically in epithelial cells of terpenoid-producing cortical resin ducts, in polyphenolic phloem parenchyma cells, and in ray parenchyma cells.

Amino Acid Oxidoreductases↗

PubMed1998

An epidermis/papilla-specific oxalate oxidase-like protein in the defence response of barley attacked by the powdery mildew fungus.

A cDNA clone of a defence response transcript was isolated from a library prepared from barley leaves expressing papilla resistance towards the powdery mildew fungus, Blumeria (syn. Erysiphe) graminis f.sp. hordei (Bgh). The 904 bp sequence encodes a 229 amino acid polypeptide with a putative signal peptide of 23 amino acids. After cleavage, the protein has a mass of 22.3 kDa and exhibits up to 60% amino acid identity to certain dicot proteins, and 46% amino acid identity to barley oxalate oxidase; therefore we designated it HvOxOLP (for Hordeum vulgare oxalate oxidase-like protein). Single-base substitutions among several cDNA and RACE clones demonstrate a gene of many copies. Both the transcript and protein accumulate from 3 h after inoculation with Bgh. The transcript level peaks at 18-24 h and subsequently decreases, whereas the protein level is stable from 24 h after inoculation. The accumulation patterns are independent of the outcome of the barley/powdery mildew interaction, unlike that of PR proteins, for example. The transcript accumulates specifically in the inoculated epidermal tissue. This temporal and spatial expression pattern suggests a very close relationship to papilla formation. Immunoblot analyses have facilitated a demonstration that HvOxOLP, like oxalate oxidase, is a water-soluble 100 kDa oligomeric protein. The oligomer is heat-stable and SDS-tolerant, and it can be denatured into a 25 kDa monomer. Attempts to demonstrate oxalate oxidase activity for this protein have failed. However, the relationships to oxalate oxidase suggests that HvOxOLP may be involved in H2O2 generation necessary for, for example, cross-linking of cell wall components during formation of papillae.

Amino Acid Sequence↗

PubMed1994

Translational regulation of nanos by RNA localization.

Localization of the maternally synthesized nanos (nos) RNA to the posterior pole of the Drosophila embryo provides the source for a posterior-to-anterior gradient of Nos protein. Correct spatial regulation of nos activity is essential for normal pattern formation. High local concentrations of Nos protein in the posterior of the embryo are necessary to inhibit translation of the transcription factor Hunchback in this region, and thus permit expression of genes required for abdomen formation (see ref. 5 for review). By contrast, misexpression of Nos protein at the anterior of the embryo prevents translation of the anterior morphogen Bicoid, suppressing head and thorax development. Posterior localization of nos RNA is mediated by sequences within the nos 3' untranslated region (3'UTR) and requires the function of eight genes of the 'posterior group'. Although the unlocalized nos RNA is stable in embryos from females mutant for any of the posterior group genes, these embryos appear to lack nos activity because they develop the abdominal defects characteristic of embryos produced by nos mutant females. We report here that unlocalized nos RNA is translationally repressed. Translational repression is mediated by the nos 3'UTR and can be alleviated either by replacement of the 3'UTR with heterologous 3'UTR sequences or by posterior localization. Thus, RNA localization provides a novel mechanism for translational regulation.

Animals↗

PubMed1999

Retinoic acid given at late embryonic stage depresses sonic hedgehog and Hoxd-4 expression in the pharyngeal area and induces skeletal malformation in flounder (Paralichthys olivaceus) embryos.

During the development of pharyngeal cartilages, signal molecules, including sonic hedgehog (shh) and various growth factors, as well as Hox genes are expressed in the pharyngeal area. To elucidate whether shh and Hoxd-4 function in pharyngeal cartilage formation in teleost jaw and gill primordia, spatial and temporal patterns of shh expression in flounder (Paralichthys olivaceus) embryonic pharynx were examined. The effects of retinoic acid (RA) on shh and Hoxd-4 expression and the patterning of pharyngeal cartilages were analyzed. At the prim-5 stage, when cartilage precursor cells aggregate in the pharyngeal primordia, pharyngeal endoderm expressed shh in two domains, in portions of the mandibular and hyoid primordia and in the gill primordia. After a further 40 h, shh domains expanded at the posterior edge of the endoderm of each mandibular, hyoid and gill primordium, concurrent with the growth of the primordia. A new shh expression domain appeared at the endodermal border of the mouth. Retinoic acid treatment depressed shh and Hoxd-4 expression, and also reduced the amount of expansion of the shh expression domains. Pharyngeal cartilages that formed in these embryos were malformed; their growth direction was shifted posteriorly and size was reduced. This provides the possibility that shh and Hoxd-4 regulate the growth and direction of pharyngeal cartilage precursor cells and that RA disturbs their expression, causing skeletal malformation.

Amino Acid Sequence↗

PubMed2006

Resonant and nonresonant patterns in forced oscillators.

Uniform oscillations in spatially extended systems resonate with temporal periodic forcing within the Arnold tongues of single forced oscillators. The Arnold tongues are wedge-like domains in the parameter space spanned by the forcing amplitude and frequency, within which the oscillator's frequency is locked to a fraction of the forcing frequency. Spatial patterning can modify these domains. We describe here two pattern formation mechanisms affecting frequency locking at half the forcing frequency. The mechanisms are associated with phase-front instabilities and a Turing-like instability of the rest state. Our studies combine experiments on the ruthenium catalyzed light-sensitive Belousov-Zhabotinsky reaction forced by periodic illumination, and numerical and analytical studies of two model systems, the FitzHugh-Nagumo model and the complex Ginzburg-Landau equation, with additional terms describing periodic forcing.

Biomechanical Phenomena↗

PubMed1992

StuA is required for cell pattern formation in Aspergillus.

The stunted (stuA) gene product is required for the orderly differentiation and spatial organization of cell types of the Aspergillus nidulans conidiophore. Expression of the stuA gene is complex. Two transcripts, stuA alpha and stuA beta, are initiated from separate promoters. Transcription of both RNAs increases approximately 50-fold during the establishment of developmental competence. Induction-dependent transcriptional and post-transcriptional regulatory mechanisms further enhance expression 15-fold. Consistent with the latter observation, both transcripts have structural features characteristic of RNAs subject to translational control. Conidiophore morphogenesis requires regulatory interactions between the products of the stuA, bristle (brlA), and abacus (abaA) genes. Enhanced stunted expression is cell type specific and dependent on a functional BrlA protein. StuA affects the spatial localization of AbaA by acting directly, or indirectly, to repress abaA expression.

Amino Acid Sequence↗