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PubMed2004

Genetic effects of air pollution on forest tree species of the Carpathian Mountains.

The effects of air pollution on the genetic structure of Norway spruce, European silver fir and European beech were studied at four polluted sites in Slovakia, Romania and Czech Republic. In order to reduce potential effects of site heterogeneity on the health condition, pair-wise sampling of pollution-tolerant and sensitive trees was applied. Genotypes of sampled trees were determined at 21 isozyme gene loci of spruce, 18 loci of fir and 15 loci of beech. In comparison with Norway spruce, fewer genetic differences were revealed in beech and almost no differentiation between pollution-tolerant and sensitive trees was observed in fir. In adult stands of Norway spruce, sensitive trees exhibited higher genetic multiplicity and diversity. The decline of pollution-sensitive trees may result thus in a gradual genetic depletion of pollution-exposed populations of Norway spruce through the loss of less frequent alleles with potential adaptive significance to altered stressing regimes in the future. Comparison of the subsets of sensitive and tolerant Norway spruce individuals as determined by presence or absence of discolorations ("spruce yellowing") revealed different heterozygosity at 3 out of 11 polymorphic loci.

Abies↗
PubMed2004

Assessing plant response to ambient ozone: growth of young apple trees in open-top chambers and corresponding ambient air plots.

Open-top chambers (OTCs) and corresponding ambient air plots (AA) were used to assess the impact of ambient ozone on growth of newly planted apple trees at the Montague Field research center in Amherst, MA. Two-year-old apple trees (Malus domestica Borkh 'Rogers Red McIntosh') were planted in the ground in circular plots. Four of the plots were enclosed with OTCs where incoming air was charcoal-filtered (CF); four were enclosed with OTCs where incoming air was not charcoal-filtered (NF) and four were not enclosed, allowing access to ambient air conditions (AA). Conditions in both CF and NF OTCs resulted in increased tree growth and changed incidence of disease and arthropod pests, compared to trees in AA. As a result, we were not able to use the OTC method to assess the impact of ambient ozone on growth of young apple trees in Amherst, MA.

Air Pollutants↗
PubMed2006

Gravitational infusion of ethylenediurea (EDU) into trunks protected adult European ash trees (Fraxinus excelsior L.) from foliar ozone injury.

Adult ash trees (Fraxinus excelsior L.), known to be sensitive or insensitive to ozone, determined by presence or absence of foliar symptoms in previous years, were treated with ethylenediurea (EDU) at 450 ppm by gravitational trunk infusion on six occasions at 21-day intervals in summer 2005 at Turin, Italy. At the end of the season, foliar ozone injury on EDU-treated trees was not complete, but was greatly and significantly reduced when compared to results from trees infused with water. Significant symptom reduction occurred at any crown level in the treated trees suggesting that EDU protected whole crowns. Gravitational infusion of EDU resulted in protection from ozone injury for ozone-sensitive ash trees. The amount of EDU needed to provide protection is assumed to be in the range 13-26 mg m(-2) leaf.

Environmental Exposure↗
PubMed2005

SEP-class genes in Populus tremuloides and their likely role in reproductive survival of poplar trees.

One of the most important processes to the survival of a species is its ability to reproduce. In plants, SEPALLATA-class MADS-box genes have been found to control the development of the inner whorls of flowers. However, while much is known about floral development in herbaceous plants, similar systems in woody trees remain poorly understood. Populus tremuloides (trembling aspen) is a widespread North American tree having important economic value, and its floral development differs from that of well-studied species in that the flowers have only two whorls and are truly unisexual. Sequence based analyses indicate that PTM3 (Populus tremuloides MADS-box 3), and a duplicate gene PTM4, are related to the SEPALLATA1-and 2-class of MADS-box genes. Another gene, PTM6, is related to SEP3, and each of these genes has a counterpart in the poplar genomic database along with additional members of the A, B, C, D, and E-classes of MADS-box genes. PTM3/4 and 6 are expressed in all stages of male and female aspen floral development. However, PTM3/4 is also expressed in the terminal buds, young leaves, and young stems. In situ RNA localization identified PTM3/4 and 6 transcripts predominantly in the inner, sexual whorl, within developing ovules of female flowers and anther primordia of male flowers. Tree researchers often use heterologous systems to help study tree floral development due to the long juvenile periods found in most trees. We found that the participation of PTM3/4 in floral development is supported by transgenic experiments in both P. tremuloides and heterologous systems such as tobacco and Arabidopsis. However, phenotypic artifacts were observed in the heterologous systems. Together the results suggest a role for poplar SEP-class genes in reproductive viability.

Arabidopsis↗
PubMed2005

A case study found that a regression tree outperformed multiple linear regression in predicting the relationship between impairments and Social and Productive Activities scores.

OBJECTIVE: Many important physiologic and clinical predictors are continuous. Clinical investigators and epidemiologists' interest in these predictors lies, in part, in the risk they pose for adverse outcomes, which may be continuous as well. The relationship between continuous predictors and a continuous outcome may be complex and difficult to interpret. Therefore, methods to detect levels of a predictor variable that predict the outcome and determine the threshold for clinical intervention would provide a beneficial tool for clinical investigators and epidemiologists. STUDY DESIGN AND SETTING: We present a case study using regression tree methodology to predict Social and Productive Activities score at 3 years using five modifiable impairments. The predictive ability of regression tree methodology was compared with multiple linear regression using two independent data sets, one for development and one for validation. RESULTS: The regression tree approach and the multiple linear regression model provided similar fit (model deviances) on the development cohort. In the validation cohort, the deviance of the multiple linear regression model was 31% greater than the regression tree approach. CONCLUSION: Regression tree analysis developed a better model of impairments predicting Social and Productive Activities score that may be more easily applied in research settings than multiple linear regression alone.

Aged↗
PubMed2004

Analysis of phenetic trees based on metabolic capabilites across the three domains of life.

Here, we used data of complete genomes to study comparatively the metabolism of different species. We built phenetic trees based on the enzymatic functions present in different parts of metabolism. Seven broad metabolic classes, comprising a total of 69 metabolic pathways, were comparatively analyzed for 27 fully sequenced organisms of the domains Eukarya, Bacteria and Archaea. Phylogenetic profiles based on the presence/absence of enzymatic functions for each metabolic class were determined and distance matrices for all the organisms were then derived from the profiles. Unrooted phenetic trees based upon the matrices revealed the distribution of the organisms according to their metabolic capabilities, reflecting the ecological pressures and adaptations that those species underwent during their evolution. We found that organisms that are closely related in phylogenetic terms could be distantly related metabolically and that the opposite is also true. For example, obligate bacterial pathogens were usually grouped together in our metabolic trees, demonstrating that obligate pathogens share common metabolic features regardless of their diverse phylogenetic origins. The branching order of proteobacteria often did not match their classical phylogenetic classification and Gram-positive bacteria showed diverse metabolic affinities. Archaea were found to be metabolically as distant from free-living bacteria as from eukaryotes, and sometimes were placed close to the metabolically highly specialized group of obligate bacterial pathogens. Metabolic trees represent an integrative approach for the comparison of the evolution of the metabolism and its correlation with the evolution of the genome, helping to find new relationships in the tree of life.

Animals↗
PubMed2006

IgE cross-reactivity between the major peanut allergen Ara h 2 and tree nut allergens.

Allergy to peanut and tree nuts is characterised by a high frequency of life-threatening anaphylactic reactions and typically lifelong persistence. Although peanut is the most common cause of nut allergy, peanut allergic patients are frequently also sensitive to tree nuts. It is not known if this is due to cross-reactivity between peanut and tree nut allergens. In this study, the major peanut allergen Ara h 2 was cloned from peanut cDNA, expressed in E. coli cells as a His-tag fusion protein and purified using a Ni-NTA column. Immunoblotting, ELISA and basophil activation indicated by CD63 expression all confirmed the IgE reactivity and biological activity of rAra h 2. To determine whether or not this allergen plays a role in IgE cross-reactivity between peanut and tree nuts, inhibition ELISA was performed. Pre-incubation of serum from peanut allergic patients with increasing concentrations of almond or Brazil nut extract inhibited IgE binding to rAra h 2. Purified rAra h 2-specific serum IgE antibodies also bound to proteins present in almond and Brazil nut extracts by immunoblotting. This indicates that the major peanut allergen, Ara h 2, shares common IgE-binding epitopes with almond and Brazil nut allergens, which may contribute to the high incidence of tree nut sensitisation in peanut allergic individuals.

2S Albumins, Plant↗
PubMed2005

The tree of eukaryotes.

Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical 'supergroups', each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.

Journal Article↗
PubMed2004

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes.

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.

Animals↗
PubMed2002

Multi-generational analysis and visualization of the vascular tree in 3D micro-CT images.

Micro-CT scanners can generate large high-resolution three-dimensional (3D) digital images of small-animal organs, such as rat hearts. Such images enable studies of basic physiologic questions on coronary branching geometry and fluid transport. Performing such an analysis requires three steps: (1) extract the arterial tree from the image; (2) compute quantitative geometric data from the extracted tree; and (3) perform a numerical analysis of the computed data. Because a typical coronary arterial tree consists of hundreds of branches and many generations, it is impractical to perform such an integrated study manually. An automatic method exists for performing step (1), extracting the tree, but little effort has been made on the other two steps. We propose an environment for performing a complete study. Quantitative measures for arterial-lumen cross-sectional area, inter-branch segment length, branch surface area and others at the generation, inter-branch, and intra-branch levels are computed. A human user can then work with the quantitative data in an interactive visualization system. The system provides various forms of viewing and permits interactive tree editing for "on the fly" correction of the quantitative data. We illustrate the methodology for 3D micro-CT rat heart images.

Animals↗
PubMed1999

A three-dimensional model for arterial tree representation, generated by constrained constructive optimization.

The computational method of constrained constructive optimization (CCO) has been generalized in two important respects: (1) arterial model trees are now grown within a convex, three-dimensional piece of tissue and (2) terminal flow variability has been incorporated into the model to account for the heterogeneity of blood flow observed in real vascular beds. Although no direct information from topographic anatomy enters the model, computer-generated CCO trees closely resemble corrosion casts of real arterial trees, both on a visual basis and with regard to morphometric parameters. Terminal flow variability was found to induce transitions in the connective structure early in the trees' development. The present generalization of CCO offers--for the first time--the possibility to generate optimized arterial model trees in three dimensions, representing a realistic geometrical substrate for hemodynamic simulation studies. With the implementation of terminal flow variability the model is ready to simulate processes such as the adaptation of arterial diameters to changes in blood flow rate or the formation of different patterns of angiogenesis induced by changing needs of blood supply.

Algorithms↗
PubMed1997

Age-related changes of the noradrenergic innervation of rat tracheo-bronchial tree and pulmonary vasculature.

Age-related changes of the noradrenergic innervation of the tracheo-bronchial tree and of pulmonary vasculature were investigated in male Wistar rats of 3 months (young), 12 months (adult) and 24 months (old/aged), using catecholamine histofluorescence techniques associated with image analysis and by high pressure liquid chromagraphy with electrochemical detection. In young rats, blue-green fluorescent nerve fibres supply tracheo-bronchial smooth muscle and tracheal and bronchial glands, which are innervated by a delicate network of nerve fibres rich in varicosities. Pulmonary artery and vein are sparsely innervated. They are supplied with nerve fibres distributed in the vasa vasorum or the adventitia and the outer tunica media. The higher noradrenaline concentrations were found in the trachea and extraparenchymal bronchi, followed by pulmonary vein and pulmonary artery. The density and pattern of noradrenergic innervation of the tracheo-bronchial tree, or of the pulmonary vasculature, were similar in young and adult rats. In aged rats, a loss of noradrenergic innervation involving primarily the supply to the smooth muscle of the tracheo-bronchial tree was observed. Histofluorescence techniques demonstrated a higher sensitivity than noradrenaline assay in detecting changes of the sympathetic innervation of the tracheo-bronchial tree and of the pulmonary vasculature. The possible significance of reduced noradrenergic innervation of the tracheo-bronchial tree in aged rats is discussed.

Adrenergic alpha-Agonists↗
PubMed2001

Use of tree rings to investigate the onset of contamination of a shallow aquifer by chlorinated hydrocarbons.

Oaks (Quercus velutina Lam.) growing over a shallow aquifer contaminated by chlorinated hydrocarbons were studied to determine if it was possible to estimate the approximate year that contamination began. The annual rings of some trees downgradient from the contaminant release site contained elevated concentrations of chloride possibly derived from dechlorination of contaminants. Additionally, a radial-growth decline began in these trees at approximately the same time that chloride became elevated. Growth did not decline in trees that contained smaller concentrations of chloride. The source of elevated chloride and the corresponding reductions in tree growth could not be explained by factors other than contamination. On the basis of tree-ring evidence alone, the release occurred in the late 1960s or early 1970s. Contaminant release at a second location apparently occurred in the mid- to late 1970s, suggesting that the area was used for disposal for at least 5 years and possibly longer.

Environmental Monitoring↗
PubMed2000

Seasonal ozone response of mature beech trees (Fagus sylvatica) at high altitude in the Bavarian forest (Germany) in comparison with young beech grown in the field and in phytotrons.

Mature beech trees (Fagus sylvatica) grown at two different altitudes in the Bavarian forest were compared with young beech trees grown at nearby field sites or in phytotrons for their macroscopic and physiological responses to different ozone (O(3)) exposures. Cumulative O(3) exposure expressed as the sum of hourly mean concentrations above the canopy ranged between 100 and 150 microl l(-1) h, with the vertical O(3) profiles at the higher altitude site being enhanced by 30%. O(3) profiles at all sites were reduced by up to 20% with increasing depth within and beneath the canopy. The leaf discoloration that developed in the absence of premature leaf loss was similar in the sun foliage of mature and young trees (including plant grown in the phytotron). Injury became apparent at low O(3) exposures, expressed as accumulated hourly means over a threshold of 40 nl l(-1) (AOT40 <3.5 microl l(-1) h) at the lower site in both the mature trees and the young beech at the field site, but only occurred when AOT40 values reached 7 microl l(-1) h at the upper site, and 6 microl l(-1) h in the phytotrons. However, the association between injury and O(3) exposure was improved when cumulative ozone uptake to sun leaves was the ozone index, used with values of about 3 mmol m(-2) resulting in visible injury in both mature and young beech growing in phytotrons. Under high ozone exposure levels of inositol were lowered, whilst concentrations of lignin-like materials were enhanced in mature beech. Similar responses were observed in young beech grown in phytotrons. As the sun foliage was affected by only a small and variable extent each year, the seasonal O(3) impact at high altitude did not appear to pose an acute risk to mature beech trees.

Journal Article↗
PubMed2003

Modelling the impacts of strategic tree plantings on salt loads and flows in the Macquarie river catchment, NSW, Australia.

In Australia, problems of dryland and stream salinity have recently become the focus of a National Action Plan. In many river catchments, preliminary stream salt load and salinity targets have been set to define maximum permissible export levels in 2015. Afforestation has been proposed as a strategy for meeting these targets, although several studies suggest that widespread commercial tree plantations are likely to deliver net dis-benefits. However, the impacts on stream salt loads of more localised tree plantings in high salt yielding areas have not been quantified. In this paper we use a simple empirical model to predict the effects of various strategic and non-strategic tree planting scenarios on flows and salt loads in the mid-Macquarie catchment, New South Wales. A simple salt routing model is then used to estimate the effect of these changes on salt loads at the end-of-valley monitoring site for the Macquarie catchment. Results suggest that widespread land management interventions will be required to meet the preliminary salt load targets for this catchment. On their own, small-scale, strategic tree planting in high salt export areas of the mid-Macquarie area will not have a significant impact on salt loads at the end-of-valley monitoring site. While widespread tree plantings may reduce salt loads in the longer term, they are likely to cause streamflow losses in the shorter term. Thus, stream salinities are expected to rise initially, due to the different response times of groundwater and surface water systems to land use change.

Australia↗
PubMed2000

Reduction of aflatoxin B(1) adduct biomarkers by oltipraz in the tree shrew (Tupaia belangeri chinensis).

The risk of liver cancer is greatest in people both infected with hepatitis B virus (HBV) and highly exposed to aflatoxin B(1) (AFB(1)). The tree shrew (Tupaia belangeri chinensis) is a unique species that can be infected with human HBV, is susceptible to AFB(1)-induced liver cancer, and shows a synergistic interaction between HBV and AFB(1) for liver cancer. In this regard, the tree shrew may be useful for evaluating experimental chemoprevention strategies relevant to high-risk human populations as it mirrors the human epidemiology of liver cancer. To begin developing the model for chemoprevention study, two groups of tree shrews were fed 400 microg AFB(1)/kg b.wt. in milk daily for 4 weeks. One week prior to AFB(1) administration, one group also received oltipraz (0.5 mmol/kg, p.o.) daily for 5 weeks. At weekly intervals, 1 ml of blood and a 24-h urine sample were obtained from each animal. Aflatoxin-albumin adducts in serum were determined by a radioimmunological assay and aflatoxin-N(7)-guanine adducts in urine were measured by HPLC. Aflatoxin-albumin adducts increased rapidly in 2 weeks to plateau at 20 pmol/mg protein, and they diminished after cessation of AFB(1) exposure. Oltipraz significantly attenuated the overall burden of aflatoxin-albumin adducts throughout the exposure period with a median reduction of 80%. In a single cross-sectional analysis at the end of AFB(1) dosing, oltipraz treatment decreased urinary aflatoxin-N(7)-guanine by 93%. Collectively, these results indicate that oltipraz reduces AFB(1) risk biomarkers in the tree shrew in a manner similar to that observed in rodents and humans, and establishes a rationale to evaluate cancer chemoprevention by oltipraz in human HBV-infected, AFB(1) exposed tree shrews.

Aflatoxin B1↗
PubMed1997

Cardiac mechanical energy and effects on the arterial tree.

Blood flow pulsatility is the result of the heart's activity as a pump unable to develop steady flow, and its interaction with the arterial tree. Thus, the heart is a cyclic energy generator whose adequate function requires the two phases of this cycle to be normal. Diastolic properties determine the degree of filling of the ventricles and the strength of the following systole. Systole, in turn, must generate enough energy to overcome forces opposing ejection. These can be divided into internal (the mechanical characteristics of the ventricle itself) and external loads (the characteristics of the arterial tree). As a result, hydraulic energy is imparted to blood (external ventricular work) that manifests itself as blood pressure and flow. Given the cyclic nature of cardiac activity, the external ventricular work has steady and pulsatile components. The steady component is energy lost during steady flow because of vascular resistance, and the pulsatile work is that lost in arterial pulsations and mainly depends on the aortic impedance. Thus, the characteristics of the arterial tree will determine the relative contribution of these two components to blood flow and the efficency of the heart. In addition, the arterial tree modifies the different waves (pressure and flow) traveling in the circulation. These modifications have important consequences for cardiac function. The ventricle and the arterial tree constitute a coupled biological system, and its overall performance is a function of the behavior of each unit at any given moment.

Aorta↗
PubMed2005

PoInTree: a polar and interactive phylogenetic tree.

PoInTree (Polar and Interactive Tree) is an application that allows to build, visualize and customize phylogenetic trees in a polar interactive and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component (Steema software).

Algorithms↗