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PubMed2006

A compilation of two decades of mutagenicity test results with the Ames Salmonella typhimurium and L5178Y mouse lymphoma cell mutation assays.

As previously reported [Cameron, T. P., Rogers-Back, A. M., Lawlor, T. E., Harbell, J. W., Seifried, H. E., and Dunkel, V. C. (1991) Gentoxicity of multifunctional acrylates in the Salmonella/mammalian-microsome assay and mouse lymphoma TK+/- assay. Environ. Mol. Mutagen. 17, 264-271], the National Cancer Institute (NCI) shares the responsibility of selecting the most significant chemicals for carcinogenicity testing by the National Toxicology Program (NTP) and has used data from Salmonella and mouse lymphoma mutagenicity assays to aid in the selection and prioritization of chemicals to be further evaluated in chronic 2 year rodent studies. In addition, a number of antineoplastic and anti-AIDS drugs in preclinical evaluation were tested for the NCI's Division of Cancer Treatment Toxicology Branch. In the NCI/NTP chemical selection process, it is no longer necessary to test chemicals prior to sending them to the NTP so the NCI program has ceased performing mutagenicity tests. Some of the testing data has been made available in summary form in the Chemical Carcinogenisis Research Information System (CCRIS), which is searchable on the NLM TOXNET system. The limitations in using this source are that only summary results are available and many negative test results are not included. A summary table that presents the results for each compound is provided in the Appendix with raw data provided in the Supporting Information. The Appendix table contains the compound name, CAS number, and a summary of the data from the Ames test and the mouse lymphoma assay.

Animals↗
PubMed2004

Identification of genes involved in VEGF-mediated vascular morphogenesis using embryonic stem cell-derived cystic embryoid bodies.

The vasculature forms during development via two processes, vasculogenesis and angiogenesis, in which vessels form de novo from angioblast precursors or as sprouts from pre-existing vessels, respectively. A common and critical aspect of both processes is vascular morphogenesis, which includes branching of endothelial cell cords and lumen formation. Although ample evidence support the central role of vascular endothelial growth factor (VEGF) in both vasculogenesis and angiogenesis, the role of VEGF in vascular morphogenesis is unclear and little is known about the regulation of vascular morphogenesis, in general. We have used the in vitro vessel differentiation system of embryonic stem (ES) cell-derived cystic embryonic bodies (CEB) as a model for studying VEGF-mediated vessel formation. Whereas CEB formed from wild-type ES cells make well-formed vessel-like structures, CEB derived from VEGF-null ES cells contain PECAM-1-positive endothelial cells, but these cells do not participate in vascular morphogenesis. Using gene expression microarray analysis to compare gene expression in these two systems, we have been able to identify many genes and novel ESTs that are downstream of VEGF function, and which may be involved in VEGF-mediated vascular morphogenesis including caveolin-1 and HEY-1. These results support using the CEB model, in combination with gene knockout ES cells, for studying vascular morphogenesis.

Animals↗
PubMed2003

The developmental role of serotonin: news from mouse molecular genetics.

New genetic models that target the serotonin system show that transient alterations in serotonin homeostasis cause permanent changes to adult behaviour and modify the fine wiring of brain connections. These findings have revived a long-standing interest in the developmental role of serotonin. Molecular genetic approaches are now showing us that different serotonin receptors, acting at different developmental stages, modulate different developmental processes such as neurogenesis, apoptosis, axon branching and dendritogenesis. Our understanding of the specification of the serotonergic phenotype is improving. In addition, studies have revealed that serotonergic traits are dissociable, as there are populations of neurons that contain serotonin but do not synthesize it.

Aging↗
PubMed2001

Time-dependent master equation simulation of complex elementary reactions in combustion: application to the reaction of 1CH2 with C2H2 from 300-2000 K.

Computational simulations of the title reaction are presented, covering a temperature range from 300 to 2000 K. At lower temperatures we find that initial formation of the cyclopropene complex by addition of methylene to acetylene is irreversible, as is the stabilisation process via collisional energy transfer. Product branching between propargyl and the stable isomers is predicted at 300 K as a function of pressure for the first time. At intermediate temperatures (1200 K), complex temporal evolution involving multiple steady states begins to emerge. At high temperatures (2000 K) the timescale for subsequent unimolecular decay of thermalized intermediates begins to impinge on the timescale for reaction of methylene, such that the rate of formation of propargyl product does not admit a simple analysis in terms of a single time-independent rate constant until the methylene supply becomes depleted. Likewise, at the elevated temperatures the thermalized intermediates cannot be regarded as irreversible product channels. Our solution algorithm involves spectral propagation of a symmetrized version of the discretized master equation matrix, and is implemented in a high precision environment which makes hitherto unachievable low-temperature modelling a reality.

Journal Article↗
PubMed2005

Time-dependent quantum wave-packet description of the 1pi sigma* photochemistry of phenol.

The photoinduced hydrogen elimination reaction in phenol via the conical intersections of the dissociative 1pi sigma* state with the 1pi pi* state and the electronic ground state has been investigated by time-dependent quantum wave-packet calculations. A model including three intersecting electronic potential-energy surfaces (S0, 1pi sigma*, and 1pi pi*) and two nuclear degrees of freedom (OH stretching and OH torsion) has been constructed on the basis of accurate ab initio multireference electronic-structure data. The electronic population transfer processes at the conical intersections, the branching ratio between the two dissociation channels, and their dependence on the initial vibrational levels have been investigated by photoexciting phenol from different vibrational levels of its ground electronic state. The nonadiabatic transitions between the excited states and the ground state occur on a time scale of a few tens of femtoseconds if the 1pi pi*-1pi sigma* conical intersection is directly accessible, which requires the excitation of at least one quantum of the OH stretching mode in the 1pi pi* state. It is shown that the node structure, which is imposed on the nuclear wave packet by the initial preparation as well as by the transition through the first conical intersection (1pi pi*-1pi sigma*), has a profound effect on the nonadiabatic dynamics at the second conical intersection (1pi sigma*-S0). These findings suggest that laser control of the photodissociation of phenol via IR mode-specific excitation of vibrational levels in the electronic ground state should be possible.

Journal Article↗
PubMed1976

Kinetics of branch migration in double-stranded DNA.

The rate of branch migration in double stranded DNA has been measured by the use of a unique substrate formed by the action of the EcoRI restriction endonuclease on the dimeric figure-8 configuration of the replicative form DNA of phage G4. The figure-8 and the X-form derived from it contain a junction of the kind postulated to occur in the Holliday structure and to be an essential feature of a number of models of recombination. In the X-form this junction can branch migrate to an irreversible terminal configuration consisting of two linear monomers. The disappearance of X-forms was measured by electron microscopy. A treatment of branch migration as a random walk process was developed to permit the determination of the rate of the intrinsic process, a step movement of the junction by a distance of one base pair. A value of about 6 kilobase pairs per sec at 37 degrees was obtained.

Bacteriophages↗
PubMed1978

Regeneration of olfactory axons and synapse formation in the forebrain after bulbectomy in neonatal mice.

We removed the right olfactory bulb in neonatal mice, leaving the bulb on the left side intact as an internal control. At 5 days of survival time, we observed that the right cerebral hemisphere was displaced forward to occupy the region made vacant by removal of the bulb. The frontal cortex was, consequently, in close proximity to the lamina cribrosa. As a result of bulb ablation and severance of the fila olfactoria, the sensory perikarya underwent total retrograde degeneration, which peaked at 8 days. New neurons differentiated in the neuroepithelium from basal stem cells and, at 30 days of survival, mature sensory neurons were reconstituted. These new elements sent their axons through the lamina cribrosa to reach the protruding cerebral hemisphere, penetrating it and forming glomeruli-like structures directly in the host tissue. The "glomerulization" of the sensory fibers persisted and actually expanded between 60 and 120 days. The new glomeruli were organized intimately within the brain tissue, and large neurons of the cortex were observed to be in close proximity. Ultrastructural observations of the newly formed glomeruli demonstrated that typical sensory axon terminals profusely branched and synapsed with unidentified postsynaptic processes that penetrated the glomeruli from the surrounding cerebral tissue.

Animals↗
PubMed2000

Interpreting the universal phylogenetic tree.

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

Cell Size↗
PubMed2004

Quantum-mechanical research on nonlinear resonance and the problem of quantum chaos.

The quantum-mechanical investigation of nonlinear resonance in terms of approximation to moderate nonlinearity is reduced to the investigation of eigenfunctions and eigenvalues of the Mathieu-Schrodinger equation. The eigenstates of the Mathieu-Schrodinger equation are nondegenerate in a certain area of pumping amplitude values in the neighborhood of the classical separatrix. Outside this area, the system finds itself in a degenerate state for both small and large pumping amplitude values. Degenerate energy terms arise as a result of merging and branching of pairs of nondegenerate energy terms. Equations are obtained for finding the merging points of energy terms. These equations are solved by numerical methods. The main objective of this paper is to establish a quantum analog of the classical stochastic layer formed in the separatrix area. With this end in view, we consider a nonstationary quantum-mechanical problem of perturbation of the state of the Mathieu-Schrodinger equation. It is shown that in passing through the branching point the system may pass from the pure state to the mixed one. At multiple passages through branching points there develops the irreversible process of "creeping" of the system to quantum states. In that case, the observed population of a certain number of levels can be considered, in our opinion, to be a quantum analog of the stochastic layer. The number of populated levels is defined by a perturbation amplitude.

Journal Article↗
PubMed2006

Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

The impetus for the recent development and emergence of automated function prediction methods is an exponentially growing flood of new experimental data, the interpretation of which is hindered by a shortage of reliable annotations for proteins that lack experimental characterization or significant homologs in current databases. Here we introduce PFP, an automated function prediction server that provides the most probable annotations for a query sequence in each of the three branches of the Gene Ontology: biological process, molecular function, and cellular component. Rather than utilizing precise pattern matching to identify functional motifs in the sequences and structures of these proteins, we designed PFP to increase the coverage of function annotation by lowering resolution of predictions when a detailed function is not predictable. To do this we extend a traditional PSI-BLAST search by extracting and scoring annotations (GO terms) individually, including annotations from distantly related sequences, and applying a novel data mining tool, the Function Association Matrix, to score strongly associated pairs of annotations. We show that PFP can correctly assign function using only weakly similar sequences with a significantly better accuracy and coverage than a standard PSI-BLAST search, improving it more than fivefold. The most descriptive annotations predicted by PFP (GO depth > or = 8) can identify a significant subgraph in the GO with > 60% accuracy and approximately 100% coverage for our benchmark set. We also provide examples of the superb performance of PFP in an assessment of automated function prediction servers at the Automated Function Prediction Special Interest Group meeting at ISMB 2005 (AFP-SIG '05).

Algorithms↗
PubMed2004

Differential correlates of diet and phylogeny on the shape of the premaxilla and anterior tooth in sparid fishes (Perciformes: Sparidae).

We explore the correlational patterns of diet and phylogeny on the shape of the premaxilla and anterior tooth in sparid fishes (Perciformes: Sparidae) from the western Mediterranean Sea. The premaxilla is less variable, and in spite of the presence of species-specific features, a common structural pattern is easily recognizable in all species (i.e. the ascending and the articular processes are fused in a single branch, as in many percoid fishes). In contrast, tooth shape is more variable, and different structural types can be recognized (e.g. canine-like or incisive). Coupling geometric morphometric and comparative methods we found that the relationship between shape, diet and phylogeny also differs between premaxilla and tooth. Thus, the shape of the premaxilla is significantly correlated with food type, whereas the shape of the teeth is not correlated with diet, and probably reflects the species phylogenetic relationships. Two biological roles, resistance against compressive forces generated in the buccal cavity and the size of the oral gape, would explain the ecomorphological patterns of the premaxilla. The premaxilla and anterior tooth appear to evolve at different rates (mosaic evolution) and represent an example of morphological traits belonging to the same functional unit but following uncoupled evolutionary pathways.

Adaptation, Biological↗
PubMed1992

A redescription of schizogony of Cytauxzoon felis in the domestic cat.

Cytauxzoon felis is a protozoan parasite that is transmitted by Dermacentor variabilis ticks and causes a uniformly fatal disease in domestic cats. In order to study schizogony and merozoite formation, D. variabilis nymphs were allowed to feed on domestic cats experimentally infected with C. felis, after which the molted adult ticks were fed on susceptible cats. Lung and liver tissues were collected from the cats during clinical cytauxzoonosis and were fixed for light and transmission electron microscopy. Some stages of parasite development were evident with light microscopy, but specific events associated with merogony could be documented only with electron microscopy. Schizogony was observed in endothelial macrophages of all tissues examined. The parasite appeared first as a multinucleated syncytium in which nuclear proliferation was evident. As the parasite syncytium developed, it became an increasingly elaborate labyrinth with extensive branches that were interconnected by thin processes of parasite cytoplasm. Organelles, including mitochondria and rhoptries, became apparent. Merozoite formation seemed to occur by rapid sequential fission along the margins of the multinucleated sporont in the cytoplasm of the host cell. As the sporont became smaller, merozoites were produced in a rosette-like configuration from the remaining parasite mass. Merozoites entered erythrocytes directly by endocytosis, without apparent injury to these cells. The sequence of events associated with merozoite formation in Cytauxzoon felis described herein differs from the previous description for this species and appears to be analogous to that described for the genus Theileria.

Animals↗
PubMed1994

Sensitization of insensitive branches of C nociceptors in human skin.

1. Eighteen cutaneous mechanosensitive C nociceptors were recorded from the peroneal nerves of healthy human subjects. Their identity was continuously monitored by intracutaneous electrical stimulation, and their activation by mechanical or transcutaneous electrical stimulation was detected by slowing of conduction velocity during the relative refractory period. 2. Mechanoreceptive fields (mRFs) mapped with suprathreshold von Frey hair stimuli covered an area of 99 +/- 21 mm2 (mean +/- S.E.M.). Two of the units had separate mRFs, with borders about 0.5-1.5 cm apart from each other and the largest of these units had a maximal diameter of 4.5 cm. 3. Successive topical application of mustard oil and capsaicin induced expansions of mRFs by 57 +/- 14 mm2 in eight of fifteen units. 4. In twelve units transcutaneous electrical stimulation delivered through a pointed electrode was used for mapping the electroreceptive fields (eRFs). The borders of the eRFs and the mRFs were identical for two of twelve units only. In the other ten units additional mechano-insensitive areas (55 +/- 22 mm2) were detected from which transcutaneous electrical stimuli could activate the respective unit. 5. Application of mustard oil and capsaicin to these mechano-insensitive areas sensitized five of eight units to mechanical stimuli. In these cases the mRF after sensitization exactly corresponded to the eRF. 6. It is concluded that there are insensitive branches in human mechanosensitive cutaneous C nociceptors that can be detected by transcutaneous electrical stimulation and sensitized by topical application of chemical irritants. Activation of those branches in the course of inflammatory processes may contribute to spatial summation at central synapses and hence to hyperalgesia.

Adult↗
PubMed1992

In vitro resolution of poxvirus replicative intermediates into linear minichromosomes with hairpin termini by a virally induced Holliday junction endonuclease.

Available evidence suggests that one or more late viral gene products are involved in processing poxvirus replicative intermediates into mature progeny hairpin-terminated genomes. Cloned versions of the Shope fibroma virus (SFV) replicated telomere in the inverted repeat configuration were used as substrates to assay lysates from poxvirus-infected cells for protein fractions that participate in the resolution of the circular substrate plasmid into a linear minichromosome with viral hairpin termini. An activity in a crude protein fraction obtained from vaccinia virus-infected cells at late times during the replicative cycle was capable of accurately resolving all poxviral inverted repeat replicative intermediates tested. The resolved linear products are identical to the products of in vivo resolution and possessed symmetrical nicks which mapped at the borders of the inverted repeat sequence. Strand-specific nicks were also identified, which mapped within the telomere resolution target sequence known to be required for telomere resolution in vivo. The resolving activity that we have identified is specific to virus-infected cells at late times during replication and cleaves cloned poxviral telomeric substrates in a fashion expected of a classic Holliday junction-resolving enzyme in addition to possessing a telomere resolution target-specific nicking activity. Although a Holliday junction-resolving activity would also be expected to play a role in the recombination induced by poxvirus infection, the appearance of the activity described here only after the commencement of viral late protein synthesis suggests that it functions strictly at late times. Other non-viral Holliday junction analogs can also be cleaved by this extract, suggesting that this component of the resolution activity may also play a role in other viral processes that require cleavage of a branched DNA structure. Thus, we have identified a poxviral activity that may be a part of a protein complex which resolves concatemeric replicative intermediates of viral DNA as well as participate in general recombination late during infection.

Animals↗
PubMed2002

Molecular control of cortical dendrite development.

Dendritic morphology has a profound impact on neuronal information processing. The overall extent and orientation of dendrites determines the kinds of input a neuron receives. Fine dendritic appendages called spines act as subcellular compartments devoted to processing synaptic information, and the dendritic branching pattern determines the efficacy with which synaptic information is transmitted to the soma. The acquisition of a mature dendritic morphology depends on the coordinated action of a number of different extracellular factors. Here we discuss this evidence in the context of dendritic development in the cerebral cortex. Soon after migrating to the cortical plate, neurons extend an apical dendrite directed toward the pial surface. The oriented growth of the apical dendrite is regulated by Sema3A, which acts as a dendritic chemoattractant. Subsequent dendritic development involves signaling by neurotrophic factors and Notch, which regulate dendritic growth and branching. During postnatal development the formation and stabilization of dendritic spines are regulated in part by patterns of synaptic activity. These observations suggest that extracellular signals play an important role in regulating every aspect of dendritic development and thereby exert a critical influence on cortical connectivity.

Animals↗
PubMed1984

Relation between discharge regularity and responses to externally applied galvanic currents in vestibular nerve afferents of the squirrel monkey.

Most vestibular nerve afferents can be classified as regularly or irregularly discharging. Two factors are theoretically identified as being potentially responsible for differences in discharge regularity. The first, ascribable to synaptic noise, is the variance (sigma v2) characterizing the transmembrane voltage fluctuations of the axon's spike trigger site, i.e., the place where impulses normally arise. The second factor is the slope (dmuv/dt) of the trigger site's postspike recovery function. Were (dmuv/dt) a major determinant of discharge regularity, the theory predicts that the more irregular the discharge of a unit, the greater should be its sensitivity to externally applied galvanic currents and the faster should be the postspike recovery of its electrical excitability. The predictions would not hold if differences in the discharge regularity between units largely reflected variations in sigma v. To test these predictions, the responses of vestibular nerve afferents to externally applied galvanic currents were studied in the barbiturate-anesthetized squirrel monkey. Current steps of 5-s duration and short (50 microsecond) shocks were delivered by way of the perilymphatic space of the vestibule. Results were similar regardless of which end organ an afferent innervated. The regularity of discharge of each unit was expressed by a normalized coefficient of variation (CV*). The galvanic sensitivity (beta p) of a unit, measured from its response to current steps, was linearly related to discharge regularity (CV*), there being approximately 20-fold variations in both variables across the afferent population. Various geometric factors--including fiber diameter, position of individual axons within the various nerve branches, and the configuration of unmyelinated processes within the sensory epithelium--are unlikely to have made a major contribution to the positive relation between beta P and CV*. The postspike recovery of electrical excitability was measured as response thresholds to shocks, synchronized to follow naturally occurring impulses at several different delays. Recovery in irregular units was more rapid than in regular units. Evidence is presented that externally applied currents acted at the spike trigger site rather than elsewhere in the sensory transduction process. We argue that the irregular discharge of some vestibular afferents offers no functional advantage in the encoding and transmission of sensory information. Rather, the irregularity of discharge is better viewed as a consequence of the enhanced sensitivity of these units to depolarizing influences, including afferent and efferent synaptic inputs.

Animals↗
PubMedDate not supplied

Capillary flow impairment and functional capillary density.

Functional capillary density is variable in both normal and diseased tissue. When this parameter is defined as the number of capillaries that possess red blood cell transit, changes in functional capillary density reflect mechanisms that modulate the entrance of red blood cells into the capillaries. These mechanisms have anatomical origin, whereby the capillary diameter changes, and may also be hydrodynamic, when flow conditions prevent red blood cells from entering a capillary branch. An intrinsic feature of both processes is that capillaries undergo lumenal changes. Capillary lumen is determined by a composite of mechanical and cellular factors, where intravascular pressure is one of the principal determinants affecting diameter as a consequence of the elastic properties of the capillary/tissue system. The hydration of the surrounding tissue and the cellular volume regulation of the endothelium are additional factors. There is increasing evidence that capillaries possess contractility and that this phenomenon has spontaneous components. Consequently, functional capillary density is the resultant of both passive and active processes present at the level of individual vessels.

Animals↗
PubMed2006

Egfr is essential for maintaining epithelial integrity during tracheal remodelling in Drosophila.

A fundamental requirement during organogenesis is to preserve tissue integrity to render a mature and functional structure. Many epithelial organs, such as the branched tubular structures, undergo a tremendous process of tissue remodelling to attain their final pattern. The cohesive properties of these tissues need to be finely regulated to promote adhesion yet allow flexibility during extensive tissue remodelling. Here, we report a new role for the Egfr pathway in maintaining epithelial integrity during tracheal development in Drosophila. We show that the integrity-promoting Egfr function is transduced by the ERK-type MAPK pathway, but does not require the downstream transcription factor Pointed. Compromising Egfr signalling, by downregulating different elements of the pathway or by overexpressing the Mkp3 negative regulator, leads to loss of tube integrity, whereas upregulation of the pathway results in increased tissue stiffness. We find that regulation of MAPK pathway activity by Breathless signalling does not impinge on tissue integrity. Egfr effects on tissue integrity correlate with differences in the accumulation of markers for cadherin-based cell-cell adhesion. Accordingly, downregulation of cadherin-based cell-cell adhesion gives rise to tracheal integrity defects. Our results suggest that the Egfr pathway regulates maintenance of tissue integrity, at least in part, through the modulation of cell adhesion. This finding establishes a link between a developmental pathway governing tracheal formation and cell adhesiveness.

Animals↗