Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “branching process”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,171 records · Page 65Linked to original sources
PubMed1989

Chondroitin sulfate proteoglycan synthesis and reutilization of beta-D-xyloside-initiated chondroitin/dermatan sulfate glycosaminoglycans in fetal kidney branching morphogenesis.

Branching morphogenesis and chondroitin sulfate proteoglycan synthesis by explanted fetal mouse kidneys were previously shown to be inhibited by p-nitrophenyl beta-D-xylopyranoside (beta-D-xyloside) while glomerular development and heparan sulfate proteoglycan synthesis were unaffected. The metabolic fate of fetal kidney explant proteoglycans was investigated to determine whether or not recovery of proteoglycan synthesis and morphogenesis occur after exposure to beta-D-xyloside. Chondroitin sulfate proteoglycan synthesis resumed within 4 hr of removal of beta-D-xyloside and was enhanced once beta-D-xyloside-initiated chondroitin/dermatan-35SO4 glycosaminoglycans (GAGs) were released from the tissue. Radioactivity incorporated into beta-D-xyloside-initiated chondroitin/dermatan-35SO4 GAGs during labeling in the presence of beta-D-xyloside was reutilized in the synthesis of chondroitin-35SO4 proteoglycan during a 24-hr chase in nonradioactive medium without beta-D-xyloside. Further, highly purified beta-D-xyloside-initiated chondroitin/dermatan-35SO4 GAGs were taken up by kidneys more avidly than was free [35S]sulfate. These 35S-GAGs were degraded and reutilized in the synthesis of chondroitin-35SO4 proteoglycan. Ureteric bud branching resumed 48 hr after beta-D-xyloside was removed from the incubation medium. These findings support the idea that both chondroitin sulfate proteoglycan synthesis and proteoglycan processing may be involved in branching morphogenesis.

Animals↗
PubMed2004

Delayed absorption of macular edema accompanying serous retinal detachment after grid laser treatment in patients with branch retinal vein occlusion.

PURPOSE: To study the detailed process of macular edema (ME) absorption after grid laser photocoagulation in patients with branch retinal vein occlusion (BRVO). The influence of pretreatment serous retinal detachment (SRD) at the fovea on patient outcome was also evaluated. DESIGN: Retrospective, interventional, comparative case series. PARTICIPANTS: Thirty-seven BRVO patients presenting with severe ME. METHODS: Patients were treated with grid laser photocoagulation with 6 months of follow-up examinations. Baseline and post-treatment examinations included measurements of visual acuity (VA), fluorescein angiography, and detailed imaging of ME by optical coherence tomography (OCT). Macular thickness was defined as the distance from the inner retinal surface to the outer border of the sensory retina (foveal retinal thickness) and also to the inner border of the retinal pigment epithelium including the SRD (total foveal elevation). MAIN OUTCOME MEASURES: Post-treatment macular thickness with OCT, VA converted to the logarithm of the minimum angle of resolution, and absorption of SRD, and correlations of macular thickness and VA both before and after treatment. RESULTS: Total foveal elevation and VA were significantly improved at 1, 3, and 6 months after treatment. There was also a significant correlation between reduction of total foveal elevation and increase in VA. Fourteen eyes (37.8%) displayed SRD, as evidenced by OCT at the baseline. In eyes without SRD, foveal retinal thickness and VA had significantly improved in a time-dependent manner. However, although SRD itself was almost absorbed 6 months after treatment, the improvement of both VA and total foveal elevation in eyes with pretreatment SRD was not significant compared with baseline conditions. Both post-treatment total foveal elevation and VA of eyes with SRD tended to be worse than eyes without SRD. CONCLUSION: The presence of subfoveal SRD retards the absorption of ME and recovery of VA after grid laser photocoagulation in patients with BRVO.

Absorption↗
PubMed1994

Differential processing of human and rat E1 alpha precursors of the branched-chain alpha-keto acid dehydrogenase complex caused by an N-terminal proline in the rat sequence.

The N-terminal sequences of the E1 alpha, E1 beta and E2 subunits of the human branched-chain alpha-keto acid dehydrogenase complex have been determined by microsequencing. The N-terminal of human E1 beta and E2 subunits (Val and Gly, respectively) are identical to those of the corresponding rat and bovine subunits. However, the N-terminus of the human E1 alpha subunit (Ser) is identical to bovine, but differs from the rat E1 alpha (Phe) subunit. Comparison of the N-terminal sequences of human and rat E1 alpha subunits shows that the serine residue at the +1 position in the human sequence is replaced by a proline residue in the rat sequence. The presence of the proline residue apparently causes a 5'-shift by one residue in the cleavage site by the mitochondrial processing peptidase in the rat sequence, when compared to the human sequence. The results provide evidence that the mitochondrial processing peptidase cannot cleave an X-Pro bond, similar to trypsin, chymotrypsin and microsomal signal peptidases.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
PubMed1994

Postmitotic oligodendrocytes generated during postnatal cerebral development are derived from proliferation of immature oligodendrocytes.

The phenotype of proliferating glia is examined during postnatal rodent development by combining immunocytochemistry (ICC) with 3H-thymidine autoradiography (ARG) to identify cells in the S phase of the cell cycle. Antibodies (ABs) which are specific for cells in the oligodendrocyte (OL) lineage were utilized, with emphasis placed upon the proliferation of OLs as it remains unclear whether this cell type divides in situ. The results show that proliferating cells stain with ABs which are specific for OLs and myelin glycolipids. The proliferating OLs (oligodendroblasts), although they do not appear to have formed myelin sheaths, have quite elaborate and distinctive morphologies. These oligodendroblasts give rise to very long, thin processes which in turn have additional branches. Their cytoarchitecture corresponds closely to cells described as oligodendroblasts with electron microscopy and whose processes often appear to be in the initial phase of myelination (Skoff et al: J. Comp. Neurol. 169:291-312, 1976a). These proliferating OLs are still quite immature because the expression of myelin specific proteins is only occasionally observed in 3H-thymidine labeled cells. The phenotype of the oligodendroblasts is quite different from that of proliferating astrocytes (astroblasts). As shown in previous studies (Skoff; Dev. Biol. 139:149-163, 1990), the astroblasts, which are identified by the presence of glial fibrillary acidic protein (GFAP), usually have thick, stubby processes, and both their nucleus and cytoplasm are larger and of lighter density than those found in oligodendroblasts. In early myelinating regions of the cerebrum, glycolipid positive cells account for the majority of the 3H-thymidine labeled cells. This data, when combined with the quantification of proliferating astrocytes (ASs) from previous immunocytochemical and electron microscopic studies, indicate that oligodendroblasts and astroblasts constitute the vast majority of the proliferating glia in the brain and in optic nerve at times when ASs and OLs are being generated. In normal postnatal cerebral development, the immature ASs and OLs which proliferate are the direct, immediate precursors for most postmitotic ASs and OLs.

Animals↗
PubMed1990

Growth, structure and dynamics of real neurons: model studies and experimental results.

One of the most striking features of vertebrate neurons is the immense diversity of their dendritic branching patterns, bearing witness to the range of operations subserved by dendritic membranes. The paper deals with three questions which naturally arise in this context: 1) What kind of growth process leads to a particular branching pattern? 2) How can we quantify such patterns? 3) Is it possible to derive a functional characterization related to the dendritic pattern so quantified? Probabilistic growth models were tested against morphological data derived from experiments with mammalian sensory-motor neurons, and their fractal dimensions were determined. The functionality of the dendritic neuron types was evaluated by electrotonic modelling of the synaptic transfer properties. The results support the hypothesis that a close relationship between dendritic pattern and neuron function might exist. The nonlinear properties of neuronal membranes represent the other determinant of neuron function. Using the Hodgkin-Huxley model for description, the functional role of the repolarizing ionic currents in the periodic activity of nerve membranes was analyzed. New models have been developed which allow the analytical treatment of both passive membrane voltage changes in neurons with branching dendrites and nerve impulse propagation in non-uniform axons.

Animals↗
PubMed2026

A Wagner-Meerwein-Like Rearrangement Generates a Vinyl Group in the Biosynthesis of the Polychlorinated Lipopeptides Fischerazoles.

The discovery of structurally unusual natural products is a major inspiration in the search for novel enzymatic transformations. In this study, we employ stable isotope-labeled precursor feeding and metabolomics to reveal highly unusual cyanobacterial lipopeptides-fischerazoles A-C. These metabolites contain a polychlorinated fatty acyl-derived moiety with a vinyl branch and an N-methylated carboxamide-thiazole terminus. Most strikingly, stable-isotope-labeled precursor supplementation showed that during fischerazole biosynthesis, a linear, hexadecanoic acid-derived intermediate is processed to yield the ultimately branched alkyl moiety. The branched carbon becomes part of the vinyl group together with an S-adenosyl methionine (SAM)-derived carbon. A candidate polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) fischerazoles biosynthetic gene cluster-fsh-was identified in the genome of the producing strain, Fischerella sp. PCC 9431. In vitro assays experimentally connected fsh genes to fischerazole biosynthesis and revealed that the SAM-dependent methyltransferase FshF catalyzes a Wagner-Meerwein-like rearrangement to generate the vinyl group from an ACP-tethered unsaturated fatty acid. The discovery of FshF, which is related to the well-characterized cyclopropane fatty acid synthases (CFASs), brings to light a new biocatalytic strategy for alkyl chain functionalization.

Lipopeptides↗
PubMed1994

Electrophysiological and morphological classification of myenteric neurons in the proximal colon of the guinea-pig.

Intracellular recordings were made from myenteric neurons in the proximal colon of the guinea-pig. The electrical behaviour of the neurons in response to intracellular depolarizing current pulses, and to internodal strand stimulation, was recorded. The intracellular electrode contained the intracellular marker biocytin which was injected into impaled neurons for subsequent histochemistry. Proximal colon myenteric neurons displayed electrophysiological properties similar to myenteric neurons in the small intestine, and were classified as either AH- or S-neurons. AH-neurons were characterized by the presence of a slow afterhyperpolarization following an action potential. Internodal strand stimulation evoked slow excitatory synaptic potentials in five out of six AH-neurons tested, but did not evoke fast excitatory synaptic potentials in 26 AH-neurons tested. S-neurons lacked a slow afterhyperpolarization, but internodal strand stimulation evoked fast excitatory synaptic potentials in all 113 neurons and slow excitatory synaptic potentials in seven out of 17 tested. A subpopulation of AH-neurons displayed a rhythmic oscillation in membrane potential which could be triggered by an action potential. S-neurons could be subdivided into those that fired tonically and those that fired phasically in response to long depolarizing current pulses. About 80% of the AH-neurons were immunoreactive for calbindin, as were 10% of S-neurons. A further 17% of S-neurons, but no AH neurons, were calretinin immunoreactive. Morphological analysis of filled neurons revealed eight distinct classes. Neurons electrophysiologically classified as AH typically had a large, oval soma and several long tapering processes. Processes of AH-neurons branched into many adjacent ganglia. Almost all S-neurons were uniaxonal and many axons ended in an expansion bulb in the myenteric plexus. S-neurons typically had broad, lamellar processes, or short, spiny processes. Roughly equal proportions of S-neurons had oral or anal projection. However, almost all S-neurons that were immunoreactive for calbindin or calretinin projected orally. The results indicate that myenteric neurons in the proximal colon of the guinea-pig are electrophysiologically similar to myenteric neurons in the small intestine, but there are a greater number of morphological and chemical categories.

Action Potentials↗
PubMed1990

Heterogeneity in the distribution and morphology of microglia in the normal adult mouse brain.

We have examined the distribution of microglia in the normal adult mouse brain using immunocytochemical detection of the macrophage specific plasma membrane glycoprotein F4/80. We were interested to learn whether the distribution of microglia in the adult brain is related to regional variation in the magnitude of cell death during development and resulting monocyte recruitment, or whether the adult distribution is influenced by other local microenvironmental cues. We further investigated the possibility that microglia are sensitive to their microenvironment by studying their morphology in different brain regions. Microglia are present in large numbers in all major divisions of the brain but are not uniformly distributed. There is a more than five-fold variation in the density of immunostained microglial processes between different regions. More microglia are found in gray matter than white. Particularly, densely populated areas include the hippocampus, olfactory telencephalon, basal ganglia and substantia nigra. In comparison, the less densely populated areas include fibre tracts, cerebellum and much of the brainstem. The cerebral cortex, thalamus and hypothalamus have average cell densities. There was no simple relationship between the amount of developmental cell death and the adult distribution of microglia. An estimate of the total number of microglia in the adult mouse brain, 3.5 x 10(6), is comparable to that found in the liver on a weight for weight basis. However, microglia possess up to twice the surface area of membrane of Kupffer cells, the large resident macrophages of the liver. The proportion of cells that were microglia varied from 5% in the cortex and corpus callosum, to 12% in the substantia nigra. Microglia vary in morphology depending on their location. They were broadly classified into three categories. Compact cells are rounded cells, sometimes with one or two short thick limbs, bearing short processes ("bristles"). They resemble Kupffer cells of the liver and are found exclusively in sites lacking a blood-brain barrier. Longitudinally branched cells are found in fibre tracts and possess several long processes which are usually aligned parallel to, or more occasionally perpendicular to, the longitudinal axis of the nerve fibres. Radially branched cells are found throughout the neuropil. They can be extremely elaborate and there is wide variation in the length and complexity of branching of the processes. There was no evidence of monocyte-like cells in the adult CNS. The systematic variation in microglial morphology provides further evidence that these cells are sensitive to their microenvironment.

Animals↗
PubMed1997

Functional characterization of equine neutrophils in response to calcium ionophore A23187 and phorbol myristate acetate ex vivo.

Equine neutrophils (PMN) play a critical role in inflammatory processes in horses. The objective of this study was to characterize equine PMN function ex vivo following stimulation with calcium ionophore A23187 (A23187) and phorbol myristate acetate (PMA). These stimulants trigger different branches of the PMN activation process that occurs in vivo. Equine PMN were isolated from the whole blood of six clinically normal geldings using a one-step discontinuous Percoll gradient technique. Neutrophil aggregation, degranulation, and superoxide anion production were evaluated in assay systems which had previously been established to quantitate PMN function. Dose-response curves for A23187 and PMA were derived for the three functions. Results indicate that equine PMN aggregation and superoxide anion production are more responsive to activation by PMA as the maximum change in percent transmittance and maximum nanomoles of superoxide anion produced following PMA stimulation (60.8% and 10.4 nmol per 10(6) cells, respectively) were greater than those values stimulated by A23187 (41.5% and 5.2 nmol per 10(6) cells, respectively). However, degranulation was found to be more responsive to A23187 stimulation (maximum percent degranulation: 56.1%) than to PMA stimulation (maximum percent degranulation: 30.7%). Dose-response curves following A23187 and PMA stimulation revealed that superoxide anion production had the lowest threshold concentration among the three functions. Degranulation had the highest threshold concentration among the three functions for both stimulants. Results indicate that equine PMN functions differ in their dependence on second messengers in the activation pathway. These functions also occur in a dose-dependent manner and differ in the threshold concentrations required for their stimulation.

Animals↗
PubMed2004

In vivo imaging of synapse formation on a growing dendritic arbor.

The form of a neuron's dendritic arbor determines the set of axons with which it may form synaptic contacts, thus establishing connectivity within neural circuits. However, the dynamic relationship between dendrite growth and synaptogenesis is not well understood. To observe both processes simultaneously, we performed long-term imaging of non-spiny dendritic arbors expressing a fluorescent postsynaptic marker protein as they arborized within the optic tectum of live zebrafish larvae. Our results indicate that almost all synapses form initially on newly extended dendritic filopodia. A fraction of these nascent synapses are maintained, which in turn stabilizes the subset of filopodia on which they form. Stabilized filopodia mature into dendritic branches, and successive iterations of this process result in growth and branching of the arbor. These findings support a 'synaptotropic model' in which synapse formation can direct dendrite arborization.

Animals↗
PubMed1998

Sequence dependence of branch migratory minima.

The Holliday junction is a central intermediate in the process of genetic recombination. The position of its branch-point can relocate through an isomerization known as branch migration. This migration occurs because the branch-point is flanked by homologous symmetry. All attempts at modeling the kinetics of branch migration have relied on the assumption that branch migration minima are sequence-independent. We have tested that assumption here, using a competition assay based on symmetric immobile branched junctions; these are junctions that cannot undergo branch migration, despite the fact that they are flanked by homology. The assay used is predicated on the non-association of strands displaced in the assay; we have tested this assumption, and have performed our experiments under conditions where we know that it is true. We have measured the free energy of relocating a branched junction from a fixed non-homologous sequence to all possible dimeric symmetric sequences. We find that the assumption of sequence-independence is often valid, but that it is not universally true. We find that the flanking sequences can have a marked effect on the free energy measured, both for extensions of symmetry and for reversals of flanking nucleotides. We have varied the temperature in our experiments, and have derived both enthalpies and entropies for the different sequences. The entropies are largely unfavorable, whereas the enthalpies are largely favorable; regardless of the signs of these quantities, we see that this is another system where enthalpy-entropy compensation is operative.

Base Sequence↗
PubMed1990

In vitro splicing of fibronectin pre-mRNAs.

We have investigated the alternative splicing of the EIIIB exon of the rat fibronectin gene. Mini-gene constructs containing this exon and portions of adjacent introns and exons, when transfected into HeLa cells, are transcribed and spliced, but omit the EIIIB exon. In vitro, HeLa nuclear extracts similarly splice out (skip) the EIIIB exon from similarly structured transcripts. Therefore, the HeLa splicing apparatus recognizes as atypical the EIIIB exon and its flanking intron sequences, both in vivo and in vitro. We also report that alterations in the ionic conditions of the in vitro splicing reaction can promote the initiation of EIIIB exon inclusion, as reflected by the formation of intermediate and product RNAs related to the removal of the intron upstream of EIIIB. Processing of this intron correlates with the formation of complexes resembling intermediates in spliceosome assembly. The branch sites involved in this alternative processing pathway are rather distant from the EIIIB 3' splice site, and lie within a region which is well conserved in the fibronectin genes of other species. Thus, the intron upstream of EIIIB shows singular structure and behavior which probably have a bearing on the regulated alternative splicing of this exon.

Animals↗
PubMed2004

The influence of cluster formation on the photodissociation of sulfur dioxide: excitation to the E state.

A femtosecond pump-probe technique was employed to study the dissociation dynamics of sulfur dioxide and sulfur dioxide clusters in real time. Dissociation is initiated by a multiphoton scheme that populates the E state. The SO(2) (+) transient is fit to a biexponential decay comprising a fast and a slow component of 230 fs and 8 ps, respectively. The SO(+) transient consists of a growth component of 225 fs as well as a subsequent decay of 373 fs. The pump-probe response obtained from the monomer clearly shows the predissociative cleavage of a S-O bond. Upon cluster formation, a sequential increase in the fast decay component is observed for increasing cluster size, extending to 435 fs for (SO(2))(4) (+). The transient response of cluster dissociation products SO(SO(2))(n) (+), where n=1-3, reflects no growth component indicating that formation proceeds through the ion state. Therefore, cluster formation results in a caging effect, which impedes the dissociation process. Further direct evidence for our proposed mechanism is obtained by a technique that employs a comparison of the amplitude coefficients of each respective component of the fit. This method makes possible the determination of branching ratios of competing relaxation processes and thereby the influence of cluster formation on each can be resolved. The caging effect is attributed to a steric hindrance placed on the SO(2) chromophore, preventing it from attaining a linear geometry necessary for dissociation.

Journal Article↗
PubMed2000

Gray-scale skeletonization of small vessels in magnetic resonance angiography.

Interpretation of magnetic resonance angiography (MRA) is problematic due to complexities of vascular shape and to artifacts such as the partial volume effect. We present new methods to assist in the interpretation of MRA. These include methods for detection of vessel paths and for determination of branching patterns of vascular trees. They are based on the ordered region growing (ORG) algorithm that represents the image as an acyclic graph, which can be reduced to a skeleton by specifying vessel endpoints or by a pruning process. Ambiguities in the vessel branching due to vessel overlap are effectively resolved by heuristic methods that incorporate a priori knowledge of bifurcation spacing. Vessel paths are detected at interactive speeds on a 500-MHz processor using vessel endpoints. These methods apply best to smaller vessels where the image intensity peaks at the center of the lumen which, for the abdominal MRA, includes vessels whose diameter is less than 1 cm.

Algorithms↗
PubMed2002

Diversity and distribution of a deeply branched novel proteobacterial group found in anaerobic-aerobic activated sludge processes.

A novel coccobacilli group found previously in enhanced biological phosphorus removal (EBPR) systems was further revealed to have a high degree of diversity and distribution in various activated sludge systems. Phylogenetic analysis based on 14 existing and 18 newly retrieved 16S rRNA sequences revealed that these sequences formed a novel cohesive cluster with seven subgroups in the gamma-Proteobacteria. Fluorescence in situ hybridization with a set of probes designed specifically targeting the novel group at different hierarchical levels showed that the novel group with a coccoid (2-4 micro m) to occasionally long-rod (up to 20 micro m) shape widely distributed and in some cases predominated in sludge samples taken from nine lab- and full-scale EBPR systems (10-50% of total cells) and four conventional activated sludge systems (1-10%). Variation of predominance was also observed among those subgroups in systems showing deteriorated or effective EBPR activity.

Aerobiosis↗
PubMed2005

Signals which build a tubule.

The phenomenon of branching morphogenesis is a fundamental process critical for development of several tubular organs including lung, mammary gland, and kidney. In the case of kidney, the ureteric bud (UB) that extends out from a pre-existing epithelial tube, the Wolffian duct, gives rise to the branched collecting duct system while the surrounding metanephric mesenchyme undergoes mesenchymal-epithelial transition to form the proximal parts of the nephron. These events are mediated by several soluble factors that act in a cooperative fashion either as pro or anti tubulogenic factors. Among the growing list of such molecules are the members of the FGF, TGF-beta, and Wnt families as well as GDNF, HGF, and EGF. Cells respond to these soluble factors by initiating signaling pathways that regulate cell proliferation, cell migration and cell morphogenesis. These signaling pathways are also regulated in parallel by cell-cell and cell-matrix interactions, leading to the complex events necessary for tubule formation. Recent in-vitro and in-vivo studies have begun to shed light on the overall regulation of this phenomenon while the specific subcellular mechanisms are only beginning to be understood. This review focuses on our understanding of the morphogenic responses that regulate in-vitro tubulogenesis and how they may help us to ultimately understand this process in vivo in the kidney.

Cell Communication↗
PubMed2002

New inferences from tree shape: numbers of missing taxa and population growth rates.

The relative positions of branching events in a phylogeny contain information about evolutionary and population dynamic processes. We provide new summary statistics of branching event times and describe how these statistics can be used to infer rates of species diversification from interspecies trees or rates of population growth from intraspecies trees. We also introduce a phylogenetic method for estimating the level of taxon sampling in a clade. Different evolutionary models and different sampling regimes can produce similar patterns of branching events, so it is important to consider explicitly the model assumptions involved when making evolutionary inferences. Results of an analysis of the phylogeny of the mosquito-borne flaviviruses suggest that there could be several thousand currently unidentified viruses in this clade.

Animals↗