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PubMed2004

A phase transition for a random cluster model on phylogenetic trees.

We investigate a simple model that generates random partitions of the leaf set of a tree. Of particular interest is the reconstruction question: what number k of independent samples (partitions) are required to correctly reconstruct the underlying tree (with high probability)? We demonstrate a phase transition for k as a function of the mutation rate, from logarithmic to polynomial dependence on the size of the tree. We also describe a simple polynomial-time tree reconstruction algorithm that applies in the logarithmic region. This model and the associated reconstruction questions are motivated by a Markov model for genomic evolution in molecular biology.

Cluster Analysis↗
PubMed2005

The context-tree kernel for strings.

We propose a new kernel for strings which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for string classification, with notable applications in proteomics. By using a Bayesian averaging framework with conjugate priors on a class of Markovian models known as probabilistic suffix trees or context-trees, we compute the value of this kernel in linear time and space while only using the information contained in the spectrum of the considered strings. This is ensured through an adaptation of a compression method known as the context-tree weighting algorithm. Encouraging classification results are reported on a standard protein homology detection experiment, showing that the context-tree kernel performs well with respect to other state-of-the-art methods while using no biological prior knowledge.

Algorithms↗
PubMed2006

Growing hierarchical tree SOM: an unsupervised neural network with dynamic topology.

In this paper we introduce a tree structured self-organizing network, called the Growing Hierarchical Tree SOM (GHTSOM), that combines unsupervised learning with a dynamic topology for hierarchical classification of unlabelled data sets. The main feature of the proposed model is a SOM-like self-organizing process that allows the network to adapt the topology of each layer of the hierarchy to the characteristics of the training set. In particular the self-organization is obtained in two steps: the first one concerns the learning phase and is finalized with the creation of a tree of SOMs, while the second one is in regard to the clustering phase and provides the formation of classes for each level of the tree (hence self-organization not only for training but also for the creation of topological connections). As a result the network works without the need for user-defined parameters. Experimental results are proposed on both synthetic and real data sets.

Algorithms↗
PubMed2005

Mossy cells and different subpopulations of pyramidal neurons are immunoreactive for cocaine- and amphetamine-regulated transcript peptide in the hippocampal formation of non-human primates and tree shrew (Tupaia belangeri).

Cocaine- and amphetamine-regulated transcript peptide mRNA was discovered in the rat striatum following cocaine and amphetamine administration. Since both psychostimulants elicit memory-related effects, localization of cocaine- and amphetamine-regulated transcript peptide in the hippocampal formation may have functional importance. Previous studies demonstrated different cellular localizations of cocaine- and amphetamine-regulated transcript peptide in humans and in rodents. Mossy cells were cocaine- and amphetamine-regulated transcript-positive in the human dentate gyrus, whereas granule cells contained this peptide in the rat. In the present study, the localization of cocaine- and amphetamine-regulated transcript peptide was examined using immunohistochemistry in the hippocampal formation of the rhesus monkey (Macaca mulatta), the common marmoset monkey (Callithrix jacchus) and in the tree shrew (Tupaia belangeri). In these species principal neurons of the hippocampal formation were cocaine- and amphetamine-regulated transcript-immunoreactive. In both monkeys and tree shrews, mossy cells of the hilus were cocaine- and amphetamine-regulated transcript-positive whereas granule cells of the dentate gyrus were cocaine- and amphetamine-regulated transcript-negative. The dense cocaine- and amphetamine-regulated transcript-immunoreactive axonal plexus of the associational pathway outlined the inner one-third of the dentate molecular layer. In the hippocampus of the tree shrew and marmoset monkey, a subset of CA3 pyramidal cells were cocaine- and amphetamine-regulated transcript-immunoreactive. In the marmoset monkey, cocaine- and amphetamine-regulated transcript labeling was found only in layer V pyramidal cells of the entorhinal cortex, while in the rhesus monkey, pyramidal cells of layers II and III were cocaine- and amphetamine-regulated transcript-immunopositive. Our results show that cocaine- and amphetamine-regulated transcript positive neurons in the dentate gyrus of non-human primates are similar to that of the human. Furthermore, in the hippocampal formation of the tree shrew similar cocaine- and amphetamine-regulated transcript-immunoreactive cell-types were observed as in monkeys, supporting their evolutionary relationship with primates. Mossy cells and granule cells are members of a mutual excitatory intrahippocampal circuitry, therefore cocaine- and amphetamine-regulated transcript-immunoreactivity of these neurons in primates and rodents suggests that psychostimulants cocaine and amphetamine may induce memory-related effects at different points of the same excitatory circuitry in the hippocampal formation.

Animals↗
PubMed2004

Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree.

The morphological classification of the protozoan phylum Parabasala is not in absolute agreement with the 16S rRNA phylogeny. However, there are strong indications that tree-construction artifacts play a considerable role in the shaping of the 16S rRNA tree. We have performed rigorous analyses designed to minimize such artifacts using the slow-fast and taxa-exclusion methods. The analyses, which included new sequences from the genera Monocercomonas and Hexamastix, in most respects confirmed the previously suggested tree topology and polyphyly of Hypermastigida and Monocercomonadidae but detected one artificial cluster of long branches (Trichonymphidae, Pseudotrichonymphidae, Hexamastix, and Tricercomitus). They also indicated that the rooting of the phylum on the trichonymphid branch is probably wrong and that reliable rooting on the basis of current data is likely impossible. We discuss the tree topology in the view of anagenesis of cytoskeletal and motility organelles and suggest that a robust taxonomic revision requires extensive analysis of other gene sequences.

Animals↗
PubMed2005

Sampling phylogenetic tree space with the generalized Gibbs sampler.

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

Algorithms↗
PubMed2003

Molecular cloning of an anuran V(2) type [Arg(8)] vasotocin receptor and mesotocin receptor: functional characterization and tissue expression in the Japanese tree frog (Hyla japonica).

In most amphibians, [Arg(8)] vasotocin (VT) has an antidiuretic effect that is coupled to the activation of adenylate cyclase. In contrast, mesotocin (MT) has a diuretic effect and acts via the inositol phosphate/calcium signaling pathway in amphibians. To further clarify the mechanisms of VT and MT activation, we report the molecular cloning of a VT receptor (VTR) and a MT receptor (MTR) from the Japanese tree frog, Hyla japonica. Tree frog VTR or MTR cDNA encoded 363 or 389 amino acids, and their amino acid sequences revealed close similarity to the mammalian vasopressin V(2) (51-52% identity) or toad MT (94% identity) receptors, respectively. Using CHO-K1 cells transfected with tree frog VTR, we observed elevated concentrations of intracellular cAMP following exposure of the cells to VT or other neurohypophysial hormones, whereas the cells transfected with MTR did not exhibit altered cAMP concentrations. The cells transfected with VTR exhibited the following efficiency for cAMP accumulation: VT = hydrin 1 > or = vasopressin > or = hydrin 2 > MT = oxytocin > isotocin. VTR or MTR mRNA exhibits a single 2.2- or 5.5-kb transcription band, respectively, and both are expressed in various tissues. VTR mRNA is clearly expressed in brain, heart, kidney, pelvic patch of skin, and urinary bladder, whereas brain, fat body, heart, kidney, and urinary bladder express MTR mRNA. Specifically, VTR mRNA in the pelvic patch or MTR mRNA in the dorsal skin is present at elevated levels in the skin. Characteristic distribution of VTR and MTR on osmoregulating organs indicates the ligands for these receptors would mediate a variety of functions. Further, the distribution of VTR in the skin would make the regional difference on cutaneous water absorption in response to VT in the Japanese tree frog.

Amino Acid Sequence↗
PubMed1999

Use of the aortic homograft in the reconstruction of complex tracheobronchial tree injuries.

BACKGROUND/PURPOSE: The repair of complex tracheobronchial tree injuries often is associated with complications including stenosis and excessive granulation tissue formation. Patch reconstruction using pericardium or synthetic material decreases the incidence of stenosis. The authors report on the use of the ascending aorta cryopreserved homograft in reconstructing the tracheobronchial tree of three children. RESULTS: A 10 year old had a through-and-through gun shot wound to the left main stem bronchus with cartilaginous loss. A 12 year old double lung transplant recipient had a breakdown of one bronchial anastomosis after stent placement. A 1 year old had an acquired tracheoesophageal fistula secondary to a long standing foreign body. In all three patients, the aortic patches were secured with interrupted sutures. All three had uneventful recoveries, and postoperative bronchoscopy showed the patches to be completely covered with epithelium without stenosis or granulation tissue. CONCLUSIONS: This is the first report of the use of the cryopreserved ascending aorta homograft in the reconstruction of the tracheobronchial tree. The homograft is strong yet malleable. It gets completely covered with epithelium and results in no stenosis because of the lack of tension. These characteristics make it an attractive alternative for the patch reconstruction of complex tracheobronchial tree injuries.

Aorta↗
PubMed1998

Sex-specific regulation of marking behavior by sex hormones and conspecifics scent in tree shrews (Tupaia belangeri).

In tree shrews (Tupaia belangeri), both males and females mark their surroundings with urine and skin gland secretions. In this study we examined in standard tests the modulation of marking behavior of male and female tree shrews by hormones and chemical signals of conspecifics. Males mark more frequently than females in the absence of conspecific scent. Female scent elicits only low marking responses in both sexes. Male scent stimulates marking of both sexes, with a much higher response in females. Increasing amounts of male scent result in a corresponding increase in marking by females. In contrast, male marking is maximally stimulated by low scent concentrations of male conspecifics, whereas higher scent concentrations inhibit male marking. Gonadectomy diminishes male marking activities under all scent conditions, whereas in females only the response to male scent is reduced. In unscented cages, the low marking activities of castrated males and intact females are stimulated by treatment with testosterone or estradiol. In the presence of male scent, however, only testosterone, but not estradiol, stimulates marking of castrated males. Marking of intact males or females is not increased by either hormone. As this study shows, external (scent of conspecifics) and internal factors (sex hormone levels) interact to regulate tree shrews' marking behavior in a sex-specific manner. These results are discussed with respect to the sex-specific contexts and functions of tree shrews' marking behavior.

Animal Communication↗
PubMed2003

Metabolism of the soil and groundwater contaminants, ethylene dibromide and trichloroethylene, by the tropical leguminous tree, Leuceana leucocephala.

Ethylene dibromide (EDB; dibromoethane) and trichloroethylene (TCE) are hazardous environmental pollutants. The use of plants to treat polluted sites and groundwater, termed phytoremediation, requires plants that can both effectively remove the pollutant as well as grow in the climatic region of the site. In this paper, we report that the tropical leguminous tree, Leuceana leucocephala var. K636, is able to take up and metabolize EDB and TCE. The plants were grown in sterile hydroponic solution without its symbiont, Rhizobium. EDB and TCE were both metabolized by the plant, as indicated by the formation of bromide ion from EDB and trichloroethanol from TCE. Each plant organ was independently capable of debromination of EDB. L. leucocephala is being used to treat perched groundwater as part of a remedial alternative to address an accidental EDB spill in Hawaii. Bromide levels of plant tissues from the trees grown in the phytoremediation treatment cells at the Hawaii Site were elevated, indicating uptake and degradation of brominated compounds in the trees. This report is the first evidence of a tropical tree effectively metabolizing these common organic pollutants.

Biodegradation, Environmental↗
PubMed2002

Social stress in tree shrews: effects on physiology, brain function, and behavior of subordinate individuals.

Social stress is known to be involved in the etiology of central nervous disorders such as depression. In recent years, animal models have been developed that use chronic stress to induce neuroendocrine and central nervous changes that might be similar to those occurring in the course of the development of depressive disorders. The present review gives a summary of observations made in the tree shrew chronic social stress model. During periods of daily social stress, male tree shrews develop symptoms that are known from many depressed patients such as persistent hyperactivities of both the hypothalamic-pituitary-adrenal (HPA) axis and sympathetic nervous system, disturbances in sleeping patterns, and reduced motor activity. Moreover, various physiological parameters indicate an acceleration of the over all metabolic rate in socially stressed tree shrews. Some of these parameters can be renormalized by antidepressants thus supporting the view of the tree shrew social stress paradigm as model for major depression. In the brains of socially stressed animals, monoamine receptors show dynamic changes that reflect adaptation to the persistent monoaminergic hyperactivity during periods of chronic stress. In addition to the changes in neurotransmitter systems, there are structural changes in neurons, e.g., retraction of the dendrites of hippocampal pyramidal neurons. Together, these processes are suggested as a cause of behavioral alterations that can be counteracted by antidepressants in this naturalistic social stress model.

Animals↗
PubMed1997

A novel procedure for mediastinal vagotomy inhibits neurogenic inflammation in rat bronchial tree.

Tachykinin-containing sensory axons originating from the cervical vagal nerves and the first several pairs of thoracic spinal nerves are involved in neurogenic inflammation evoked by capsaicin in the bronchial tree. Unilateral degeneration of the cervical vagal trunk by surgical lesion inhibits neurogenic inflammation in the ipsilateral bronchial airways. The vagal trunk has two main branches, the thoracic vagus nerve and recurrent laryngeal nerve in the thorax. The main purpose of this study was to determine whether the thoracic vagus nerve or recurrent laryngeal nerve was significantly involved in the neural control of bronchial inflammation in the rat. A novel and safe surgical procedure was used for selectively cutting the right thoracic vagal trunk, thoracic vagus nerve, or recurrent laryngeal nerve by introducing the surgical instrument through an aperture between the first and second ribs in the ventral wall of the rostral mediastinum. This surgical operation could be completed without causing a pneumothorax. After 2 postoperative weeks, the effects of denervation on capsaicin-induced plasma extravasation in the respiratory tract were tested. Either right thoracic vagal trunk transection or thoracic vagus section significantly decreased plasma extravasation in the right bronchial tree. Thoracic vagus section was obviously more effective. Evans blue extravasation in the right lobar bronchi was reduced by 44-78% after thoracic vagal trunk transection, while that in the right mainstem and lobar bronchi was reduced by 58-81% after thoracic vagus section. Area densities of India ink-labeled leaky blood vessels in the right lobar bronchi were reduced by 40-65% after thoracic vagal trunk transection, and those in the right mainstem and lobar bronchi were reduced by 83-88% after thoracic vagus neurectomy. Recurrent laryngeal neurectomy did not change the plasma extravasation induced by capsaicin in the trachea and bronchi. These results suggest that capsaicin-sensitive fibers running in the vagal trunk, which largely mediated neurogenic inflammation in the bronchial tree, were projected into the thoracic vagus nerve which, in turn, sent these nerve fibers to the ipsilateral bronchial tree. For the trachea, the remaining sensory fibers surviving denervation might provide sufficient tachykinins to trigger neurogenic inflammation.

Animals↗
PubMed2000

Niche versus chance and tree diversity in forest gaps.

Studies that are unprecedented in scale, detail or approach show that niche partitioning contributes less, and chance events more, than expected to maintaining tree species richness via gap dynamics in tropical and temperate forests. Some tree species are differentially adapted for regeneration in different gap microenvironments. However, the stochastic availability of gaps, and limited recruitment of juveniles, mean that gaps are filled mostly by chance occupants rather than by best adapted species. This chance survival can slow competitive exclusion and maintain tree diversity. Gap dynamics do not explain the latitudinal gradient in tree richness.

Journal Article↗
PubMed1996

Susceptibility of transient and commensal skin flora to the essential oil of Melaleuca alternifolia (tea tree oil).

OBJECTIVES: The purpose of this study was to determine the susceptibility of a range of transient and commensal skin flora to the essential oil of Melaleuca alternifolia, or tea tree. METHODS: A modified broth microdilution method was used. Polyoxyethylene sorbitan mono-oleate detergent was added to the test medium to enhance solubility of the tea tree oil. RESULTS: Serratia marcescens had the lowest minimum inhibitory concentration (MIC90) of 0.25%. The highest MIC90 was 3% for Pseudomonas aeruginosa. The lowest minimum bactericidal concentration (MBC90) was 0.25% for S. marcescens and Klebsiella pneumoniae, whereas the highest was 8% for Staphylococcus capitis. CONCLUSIONS: S. aureus and most of the gram-negative bacteria tested were more susceptible to tea tree oil than the coagulase-negative staphylococci and micrococci. These results suggest that tea tree oil may be useful in removing transient skin flora while suppressing but maintaining resident flora.

Gram-Negative Bacteria↗
PubMed2000

Environmental control of stomatal conductance in forest trees of the Great Smoky Mountains National Park.

To determine if stomatal conductance (g(s)) of forest trees could be predicted from measures of leaf microclimate, diurnal variability in in situ g(s) was measured in black cherry (Prunus serotina), red maple (Acer rubrum), and northern red oak (Quercus rubra). Relative to overstory trees, understory saplings exhibited little diurnal variability in g(s) and ozone uptake. Depending on species and site, up to 30% of diurnal and seasonal variation in g(s )of overstory trees was explained by photosynthetically active radiation and vapor pressure deficit. Daily maximum g(s) was significantly related to soil moisture in overstory northern red oak and black cherry (R(2) ranged from 33 to 65%). Although g(s) was not fully predicted using instantaneous measures of leaf microclimate, ozone uptake of large forest trees was reduced by low soil moisture.

Journal Article↗
PubMed2003

'Event tree' analysis of out-of-hospital cardiac arrest data: confirming the importance of bystander CPR.

OBJECTIVE: The British National Service Framework (NSF) for heart disease commended the 'Utstein style' for auditing out-of-hospital cardiac arrests. The NSF also set standards for pre-hospital treatment and response times. To increase the flexibility of Utstein, an 'event tree' technique is proposed as an audit tool. Event trees consist of nodes and branches on which numbers, percentages or probability values are entered. METHODS: Using the London Ambulance Service's (LAS) 1997 database on 3,759 out-of-hospital cardiac arrests, 2,772 arrests witnessed by lay bystanders or unwitnessed were analysed focusing on bystander cardiopulmonary resuscitation (BCPR) and response times. RESULTS: The Utstein template showed that witnessed arrests in ventricular fibrillation (VF) or ventricular tachycardia (VT) who had received BCPR achieved a return of spontaneous circulation (ROSC) in the field significantly more often than non-BCPR recipients-26 versus 16% (P=0.006). But the likelihood of being admitted to a hospital bed, and discharged alive, was only marginally better for BCPR recipients. To examine the influence of BCPR on the presenting rhythm an event tree showed that in 48% of witnessed BCPR cases the presenting rhythm was VF/VT, whereas, for witnessed non-BCPR cases, 27% were in VF/VT (P<0.0001). With unwitnessed arrests, 31% of BCPR cases were in VF/VT compared with 18% for non-BCPR cases (P<0.0001). Call to scene time was less than 8 min for 66% of all VF/VT arrests. CONCLUSION: The event trees, when combined with the Utstein template, demonstrated the importance of examining comprehensively datasets for both witnessed and unwitnessed cardiac arrests when monitoring performance standards. The analyses also emphasised the relevance of community programmes in Greater London for teaching basic life saving skills.

Allied Health Personnel↗
PubMed2000

Role of the axodendritic tree in the functioning of helix bursting neurons: generation of pacemaker activity and propagation of action potentials along the axon.

The purpose of this study was to determine the role of the axodendritic tree in the generation of bursting pacemaker activity in the identified Helix RPa1 neuron, which is homologous to the Aplysia R15 cell, and propagation of action potentials along the axons. In doing so, I used recording of RPa1 neuron electrical activity after cutting off the right or left parietovisceral connections, the two-electrode voltage-clamp technique, registration of electrical activity of visceral nerve containing RPa1 axon branches, isolation of the RPa1 neuron and puff application of oxytocin on it. Cutting of the right (but not left) parietovisceral connection in all cases (more than 15 preparations) evoked complete disappearance of bursting pacemaker activity in the RPa1 neuron and hyperpolarization of its membrane potential up to -65 to -67 mV. Such silent state of the RPa1 neuron was maintained after its complete isolation from the ganglion. The described cutting did not result in a change of bursting activity of the pacemaker neuron V7 located in the visceral ganglion, although isolation of the V7 neuron also eliminated its own activity. Puff application of oxytocin (10 microM in a micropipette) on to the RPa1 neuron both after cutting the right parietovisceral connection or isolation of the neuron from the ganglion resulted in all cases (more than 10 cells) in transient depolarization with development of beating, oscillatory or bursting activity. Voltage clamping of RPa1 soma in the intact ganglion at a level close to zero membrane current sometimes, and, as a rule, at a more depolarized level, revealed bursting-like oscillations of membrane current, reflecting electrical bursting activity in the unclamped remote region of a neuron, most likely in the dendritic tree. Voltage clamping of RPa1 soma possessing bursting activity reveals bursting-like oscillation of membrane current and prevents propagation of corresponding axon action potentials in the visceral nerve. Controversially, clamping of RPa1 soma possessing beating activity exhibits a beating-like oscillation of membrane current and does not prevent propagation of corresponding action potentials in the nerve. Within the framework of the developed hypothesis that persistent bursting pacemaker activity of the RPa1 neuron is due to a constant activation of its peptidergic synaptic inputs [Kononenko N. I. (1993) Comp. Biochem. Physiol. 106A, 135-147], the experimental results were interpreted in the manner that these synapses and, correspondingly, the locus of electrical bursting activity generation, are localized on the dendritic tree of the RPa1 neuron mainly or possibly exclusively in the visceral ganglion. It is hypothesized that bursting and beating neuronal activities are due to functioning of different loci of the dendritic tree, regarding their electrical relations with axon branches.

Action Potentials↗
PubMed1999

Mapping of cytoskeletal components in the hippocampal formation of the tree shrew (Tupaia belangeri).

The distribution of the major cytoskeletal components in frontal cryosections of the hippocampal formation of adult male tree shrews (Tupaia belangeri) was immunohistochemically investigated by using commercially available antibodies. Actin-immunolabeling was evident in all layers of the dentate gyrus as well as in the regio superior (CA1) and the regio inferior (CA3). Neurofilament 160 was detected only in the molecular layer of the dentate gyrus and in the axons of the granule cells (mossy fibers). For beta-tubulin, the microtubule associated proteins (MAPs) MAP2AB, MAP2ABC and Tau, immunoreactivity was evident within the granule cells and within the somatodendritic compartment of pyramidal neurons. Granule cells and the somata of the pyramidal neurons were intensely labeled for kinesin. Our findings show the elaborate expression of cytoskeletal proteins in the hippocampal formation of the tree shrew, relatively similar to what is seen in other species but with also some important differences, such as the immunonegativity of the axonal compartment for Tau in the tree shrew, which is contrary to what we see in the mouse (unpublished data). These findings provide useful insights regarding the organization of the hippocampal formation of the tree shrew and are fundamental for further research in this field.

Actins↗