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At least 1,225 records · Page 68Linked to original sources
PubMed1990

On the recovery of photosensitivity in two passerine species, American tree sparrows (Spizella arborea) and Harris' sparrows (Zonotrichia querula).

To test the hypothesis that a spontaneous increase in plasma luteinizing hormone (LH) signals recovery of photosensitivity in castrated passerine birds, LH concentrations were measured weekly in intact and in castrated photorefractory tree sparrows and Harris' sparrows transferred to short days. After 7 weeks on short days (Experiment 1) or after 1, 3, 5, 7, and 10 weeks (Experiment 2) were challenged with long days (1 week) to determine if photosensitivity had been restored. As evidenced by a significant LH response to photostimulation, tree sparrows had regained at least partial photosensitivity after 7 weeks on short days. However, during exposure to short days, plasma LH concentrations in castrated males did not differ from those in intact males, and plasma LH concentrations in intact or castrated males did not vary with time. The first indication that photosensitivity had been partially restored in Harris' sparrows came after 7 weeks on short days, when castrated males responded to photostimulation with a fourfold elevation in plasma LH concentration. However, before week 7 and through week 10, LH concentrations remained suppressed in both intact and castrated males retained on short days. These data show that recovery of photosensitivity in castrated tree sparrows and Harris' sparrows held on short days is not signaled by a spontaneous elevation in plasma LH concentration, and that plasma LH concentrations in acutely photosensitive intact male tree sparrows and Harris' sparrows held on short days are not suppressed because of gonadal negative feedback.

Animals↗
PubMed1996

Phylogenetic tree-building.

Cladistic analysis is an approach to phylogeny reconstruction that groups taxa in such a way that those with historically more-recent ancestors form groups nested within groups of taxa with more-distant ancestors. This nested set of taxa can be represented as a branching diagram or tree (a cladogram), which is an hypothesis of the evolutionary history of the taxa. The analysis is performed by searching for nested groups of shared derived character states. These shared derived character states define monophyletic groups of taxa (clades), which include all of the descendants of the most recent common ancestor. If all of the characters for a set of taxa are congruent, then reconstructing the phylogenetic tree is unproblematic. However, most real data sets contain incongruent characters, and consequently a wide range of tree-building methods has been developed. These methods differ in a variety of characteristics, and they may produce topologically distinct trees for a single data set. None of the currently-available methods are simultaneously efficient, powerful, consistent and robust, and thus there is no single ideal method. However, many of them appear to perform well under a wide range of conditions, with the exception of the UPGMA method and the Invariants method.

Algorithms↗
PubMed1984

A new approach to merging neuronal tree segments traced from serial sections.

The merging process which is one of the most significant problems in computer-aided reconstruction of neuronal trees has been investigated. This paper reports a new approach in merging tree segments traced from serial sections. The research was motivated by the fact that in most cases users can distinguish connectable cut ends of the different tree segments without any interaction, and with this knowledge merging can be easily solved by a computer program added to the neuron reconstruction program system at Semmelweis University Medical School, Budapest. Then, the merged neuron trees can be handled as if they had been digitized from one histological section.

Data Display↗
PubMed1992

Fractal dimension of dendritic tree of cerebellar Purkinje cell during onto- and phylogenetic development.

The cerebellar Purkinje cell has highly branched dendrites extending in a transverse plane to the cerebellar folium. Branching patterns of the dendrites were subjected to fractal analysis to obtain a quantitative measure of their intricacy. Using a square-covering method, we found that dendrites have a statistical self-similarity so that their fractal dimension can be evaluated. In postnatal mouse, dimensions of Golgi-stained Purkinje cells increased as dendrites developed. The time course of the dimension increase was correlated with development of the width and area of the dendritic fields. After the dimension reached the maximum value at postnatal day 20, the width and area further continued to grow until day 100. In human cerebellum, dimensions of Purkinje cell dendrites increased greatly during pregnancy and reached 97% of the adult value at birth. On the other hand, 41% of the adult dendritic field width and 11% of the adult area had been attained at birth. The physical size of dendrites increased in a more lagged phase than the dimensions, and growth proceeded mainly after birth. These observations indicate that after the maximum complexity and fundamental tree pattern have been attained, the overall tree size further increases. It is observed that phylogenetic development of dendritic trees of Purkinje cells in several species of vertebrates showed a correlation with the increase in dimensions. These studies demonstrated the potency of the fractal analysis in evaluating development of dendritic trees of neurons.

Aging↗
PubMed1989

Differences in ability of NO2 absorption in various broad-leaved tree species.

Absorption of nitrogen dioxide (NO(2)) by various broad-leaved tree species was determined by the (15)N dilution method. The tree seedlings were continuously exposed to 0.3 ppm (microl litre(-1)) NO(2) or the mixture of 0.3 ppm NO(2) and 0.1 ppm O(3) for 30 days. The total amount of NO(2)-nitrogen absorbed by a seedling during the 30-day exposure period primarily depended on the size of the seedling. Among the tested tree species, three cultivars of Populus showed the highest rate of NO(2) absorption per unit leaf area, reaching as much as 0.3 mg N per dm(2) per day. The absorption rates for Populus cultivars were more than four times greater than those for Viburnum or Cinnamomum which had the lowest rate. A highly significant correlation was recognised between the rate of NO(2) absorption and the stomatal conductance among the species. Three cultivars of Populus which had the highest rates of NO(2) absorption were most susceptible to the mixture of NO(2) and O(3). On the contrary, Cinnamomum, Viburnum and Quercus, which showed the lowest rate of NO(2) absorption, were very tolerant to the mixed gas. These results indicate that the species difference in susceptibility to the mixture of NO(2) and O(3) was mainly determined by the difference in rate of absorption of these gases. Exposure to NO(2) alone had no detrimental effect on the tested tree species.

Journal Article↗
PubMed1989

Simulation of effects of atmospheric ethylene on tree leaf shedding.

This study made a preliminary assessment of the possibility that ethylene contained in polluted atmospheres affects leaf shedding of trees. The effect of ethylene dosage (ppb x h) on leaf shedding at various temperatures was approximated by using a polynomial regression. The effect of ethylene dosage on shedding of tree leaves with various sensitivities to this hydrocarbon was simulated in connection with the relationship between ethylene concentrations (10-100 ppb), dosage periods (0-50 days) and temperature (10-30 degrees C). The simulated results indicated the possibility that, for the tree group having high sensitivity, the rate of leaf shedding due to a dosage of ethylene with a concentration as low as 20 ppb, which is commonly observed in urban atmospheres, increased with temperature. On the other hand, the same concentration scarcely influenced leaf shedding in the low sensitivity group even at a temperature as high as 30 degrees C. The results for the real atmosphere determined at the Tokyo metropolitan center indicated the possibility that, for trees having high sensitivity, the rate of leaf shedding increased with rises in both monthly ethylene concentrations and air temperatures and reached a maximum of 90% in July. But in December when the concentration again reached the same value as in July while the mean monthly air temperature was 9.3 degrees C, the rate was only 10%.

Journal Article↗
PubMed1995

Dispersal and mobility of heavy metals in relation to tree survival in an aerially contaminated woodland soil.

Nearly a century of metal deposition adjacent to a metal refinery in Prescot, north-west England has led to highly elevated metal levels in soils at a dominantly Acer pseudoplatanus woodland, but with incongruously and perplexingly few detrimental effects on trees. Dispersal and speciation of Cu, Cd, Zn, Pb and Ni in soil was found to be extremely variable, but spatial patterns of metals were inter-related and also related to soil pH and soil organic matter. These soil variables were all generally higher in soil directly beneath trees than in soil between trees, and were particularly high beneath the spreading canopy of Aesculus hippocastanum. It is argued that this heterogeneous dispersal and availability of metals in soils may explain the survival of mature trees and the successful establishment of seedlings within the woodland. Differing speciation and mobility has allowed high disappearance rates of metals since recent closure of the refinery, which may result in soil recovery at a faster rate than previously thought.

Journal Article↗
PubMed1983

A rare family tree of cultured rat cells showing a change in proliferative potential.

In most family trees examined by time-lapse cinemicrography of proliferative rat liver epithelial-like cells in primary culture, a clonal population first expanded, and then ceased to expand. We encountered one rare family tree in which a clonal population first expanded, stopped expanding for a while, and then began to expand again. In this family tree, we noted one particular intermitotic cell, all descendants of which divided during the period of observation when the rest of the cells had ceased division. We consider that this rare family tree showed for the first time part of the process of indefinite proliferation.

Animals↗
PubMedDate not supplied

A method for measurement of cross sectional area, segment length, and branching angle of airway tree structures in situ.

Accurate quantitative measurements of airway and vascular dimensions are essential for evaluating function in both the normal and in the diseased lung. This report describes a new integrated method for three-dimensional (3D) extraction and analysis of pulmonary tree structures using data from High Resolution Computed Tomography (HRCT). Serially scanned two-dimensional (2D) slices of the lower left lobe of isolated dog lungs were stacked to create a volume of data. Airway and vascular trees were extracted using a 3D seeded region-growing algorithm based on differences in CT number between wall and lumen. In the region-growing step, voxels in the lumen are tagged with a distance descriptor to identify points along the tree structure equidistant from the seed point. To obtain quantitative data, we reduced each tree to its central axis. From the central axis, branch length was measured as the distance between two successive branch points, branch angle was measured as the angle produced by two daughter branches, and cross-sectional area was measured from a plane perpendicular to the central axis point. Data derived from these methods can be used to localize and quantify structural differences both during different physiologic conditions and in pathologic lungs.

Algorithms↗
PubMed1994

Molecular phylogeny of Eubacteria: a new multiple tree analysis method applied to 15 sequence data sets questions the monophyly of gram-positive bacteria.

Phylogenetic relationships between the major eubacterial phyla were studied using the sequences of 15 homologous bacterial genes. Neither the classical concatenation strategy nor a new multiple tree analysis method involving statistical tests of the inferred phylogenetic relationships provided any (solid) conclusions about eubacterial phylogeny; no pairs of eubacterial phyla proved to be closer to each other in the 15 reconstructed trees than would be expected for trees with random topologies. The phylogeny of Eubacteria therefore appears to be tightly bush-like. Moreover, results from both concatenation and multiple tree analysis raise doubts concerning the monophyly of the so-called Gram-positive bacteria phylum, since the monophyly hypothesis is no more strongly supported by data than its alternatives. It is noteworthy that the structural bases for the Gram-positive phenotype are not incompatible with the hypothesis of independent emergence of this character at two different times.

Bacteria↗
PubMed2006

Using classification trees to profile adolescent smoking behaviors.

The purpose of this study was to explore the interactive nature of various predictor variables in profiling adolescent smoking behaviors characterized by intention to smoke, current, situational, and established smoking using classification trees. The data (n = 3610) were obtained from cross-sectional telephone surveys of the Florida Anti-Tobacco Media Evaluation Program. Three classification trees were constructed, namely, intention versus no intention to smoke among non-smokers, current smokers versus non-smokers, and established versus situational smokers. The tree model for the intention model revealed that social and health risks are important in the context of peer smoking. Certain variables such as peer smoking and alcohol consumption retained their relative importance across the tree classifiers demonstrating that smoking intention may be predictable using some of the same variables as in current or more dependent smoking.

Adolescent↗
PubMed2006

Construction of evolutionary tree models for nasopharyngeal carcinoma using comparative genomic hybridization data.

Nasopharyngeal carcinoma (NPC) is a malignancy associated with remarkable racial and geographic factors. The development and progression of NPC may involve the accumulation of multiple genetic alterations over a long time. For understanding the putative order of genetic alteration in NPC tumorigenesis, we used evolutionary tree models (branching and distance-based tree models) to analyze comparative genomic hybridization (CGH) data of previously published NPC cases (n = 103). Consistent loss of 3p for both tree models was an important early event in NPC progression. Chromosome 12 gain was another important early event, and may represent a subclass different from 3p- derived subclasses of NPC. The tree models also suggested that at least two subclasses of 3p- derived NPC, one marked by 1q+, 9p-, and 13q- and the other marked by 14q-, 16q-, 9q-, and 1p-.

DNA, Neoplasm↗
PubMed2005

Integer linear programming as a tool for constructing trees from quartet data.

The task of the quartet puzzling problem is to find a best-fitting binary X-tree for a finite n-set from confidence values for the 3n4 binary trees with exactly four leaves from X, its fitness being measured by the sum of the confidence values of all "induced" four-leaves subtrees. We describe a method for finding an exact solution of this problem by integer linear programming. Similar procedures can also be used for finding, e.g. best-fitting "circular" networks. A crucial problem in this context is, of course, how to obtain the input confidence values for the quartet trees. We propose to use inner products of rate-matrix diagonals calculated for pairs of taxa and present the trees resulting from applying our approach to two data sets of up to 36 mitochondrial sequences of mammals including an outgroup.

Journal Article↗
PubMed2006

PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance.

Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method.

Algorithms↗
PubMed2006

Application of plant DNA markers in forensic botany: genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites.

As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

DNA, Plant↗
PubMed2005

Mycological survey of ripped service tree fruits (Sorbus domestica L.) with an emphasis on toxinogenic fungi.

To investigate a possible incidence of microscopic fungi in ripped service tree (Sorbus domestica L.) fruits, a mycological survey was carried out during October-November 2003 in Slovakia. This rare kind of fruit is renowned for its significant curative actions in various human and animal diseases. The study revealed that all 24 surface sterilized fruits analysed were contaminated with fungi. The most dominant endogenous contaminant encountered was Cladosporium cladosporioides (Fres.) de Vries followed by Alternaria alternata (Fr.) Keissler and Penicillium expansum Link with 88%, 63% and 54% frequency, respectively. Furthermore, 24 other fungal species were associated with the fruits as well. P. expansum (40), P. carneum (Frisvad) Frisvad/Penicillium paneum Frisvad (35) and P. griseofulvum Dierckx (6) isolates recovered from the fruits were screened by an agar plug method for production of mycotoxin patulin, all with positive results. In addition, citrinin, griseofulvin and zearalenon production by appropriate species isolates were detected. Despite of a limited number of samples of the service tree fruits examined during this study, it was concluded that the ripening of service tree fruits is accompanied with the presence of typical rotting-fungi as well as of some others, which have not previously been reported in connection with fruit. Furthermore, it was suggested that the ripped service tree fruits should be considered as a potential source of significant fungal secondary metabolites including mycotoxins. Secondary metabolite profiles of the species identified during the study were included here.

Colony Count, Microbial↗
PubMed2006

Analysis of IgE binding proteins of mesquite (Prosopis juliflora) pollen and cross-reactivity with predominant tree pollens.

Pollen from the mesquite tree, Prosopis juliflora, is an important source of respiratory allergy in tropical countries. Our aim was to partially characterize the IgE binding proteins of P. juliflora pollen extract and study cross-reactivity with prevalent tree pollen allergens. Intradermal tests with P. juliflora and five other tree pollen extracts were performed on respiratory allergy patients from Bikaner (arid) and Delhi (semi arid). Prosopis extract elicited positive skin reactions in 71/220 of the patients. Sera were collected from 38 of these 71 patients and all demonstrated elevated specific IgE to P. juliflora. Immunoblotting with pooled patients' sera demonstrated 16 IgE binding components, with components of 24, 26, 29, 31, 35, 52, 58, 66 and 95 kDa recognized by more than 80% of individual patients' sera. P. juliflora extract is allergenically potent requiring 73 ng of self-protein for 50% inhibition of IgE binding in ELISA inhibition. Cross-inhibition assays showed close relationship among P. juliflora, Ailanthus excelsa, Cassia siamea and Salvadora persica. IgE binding components of 14, 41, 52 and 66 kDa were shared allergens whereas 26 and 29 kDa were specific to P. juliflora. The findings suggest that purification of cross-reactive allergens will be helpful for diagnosis and immunotherapy of tree pollen allergic patients.

Adolescent↗
PubMed2005

Biochemical responses in leaves of two apple tree cultivars subjected to progressing drought.

The influence of water deprivation on potted apple trees (Malus domestica Borkh.) was investigated. Biochemical responses including ascorbic acid, glutathione (GSH), tocopherols, chlorophylls, carotenoids, free amino acids, and soluble carbohydrates were measured in leaves of diploid 'Elstar' and triploid 'Jonagold Wilmuta' subjected to progressive drought. Leaf water potential was chosen to be the primary indicator of water stress in tested plants. Time courses of measured biochemical parameters showed that mild drought did not significantly affect the chosen stress indicators. Moderate drought increased the concentrations of ascorbic acid, total GSH, beta-carotene, zeaxanthin and alpha-tocopherol, indicating the adaptation to oxidative stress in apple trees. Moderate drought also increased concentration of soluble carbohydrates, mostly due to increased sorbitol concentration. Severe drought negatively affected vitality of apple trees, and caused a decrease in sorbitol concentration. Severe drought also caused decreases in ascorbic acid, total GSH, beta-carotene, alpha-tocopherol and chlorophyll concentrations, which, together with the increase in oxidised GSH concentration, indicated severe damage due to oxidative stress. Severe drought increased free amino acid concentration, which was probably the result of increased proteolysis. Zeaxanthin concentration remained high even in leaves of apple trees subjected to severe drought stress. The results were similar for both tested apple cultivars.

Adaptation, Physiological↗