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PubMed1994

Hippocampal glucocorticoid receptor expression in the tree shrew: regulation by psychosocial conflict.

1. This study was conducted to determine whether chronic psychosocial conflict alters the expression of glucocorticoid receptor (GR) mRNA in the hippocampus of male tree shrews (Tupaia belangeri). 2. To generate probes for the in situ hybridization, the tree shrew GR gene was partly cloned. There was a 90% homology between the deduced amino acid sequence of the cloned tree shrew GR and that of the corresponding human GR sequence. 35S-Labeled riboprobes which had been transcribed from the tree shrew GR clone hybridized to pyramidal neurons in all subregions of the tree shrew hippocampal formation and to granule neurons in the dentate gyrus. 3. After in situ hybridization, the expression of GR mRNA was semiquantitatively determined by counting silver grains over single neurons of the hippocampal formation of psychosocially stressed tree shrews and control animals. After 12 days of social conflict, the number of silver grains in the CA1 and CA3 pyramidal neurons of stressed animals was significantly lower than in controls. No statistically significant differences in mRNA expression were observed in the pyramidal neurons of the subiculum and in the granule neurons of the dentate gyrus. 4. The present results suggest that psychosocial stress leads to a site-specific down-regulation of hippocampal GR via modification of mRNA expression.

Amino Acid Sequence↗

PubMed1988

An evolutionary tree for invertebrate globin sequences.

A phylogenetic tree was constructed from 245 globin amino acid sequences. Of the six plant globins, five represented the Leguminosae and one the Ulmaceae. Among the invertebrate sequences, 7 represented the phylum Annelida, 13 represented Insecta and Crustacea of the phylum Arthropoda, and 6 represented the phylum Mollusca. Of the vertebrate globins, 4 represented the Agnatha and 209 represented the Gnathostomata. A common alignment was achieved for the 245 sequences using the parsimony principle, and a matrix of minimum mutational distances was constructed. The most parsimonious phylogenetic tree, i.e., the one having the lowest number of nucleotide substitutions that cause amino acid replacements, was obtained employing clustering and branch-swapping algorithms. Based on the available fossil record, the earliest split in the ancestral metazoan lineage was placed at 680 million years before present (Myr BP), the origin of vertebrates was placed at 510 Myr BP, and the separation of the Chondrichthyes and the Osteichthyes was placed at 425 Myr BP. Local "molecular clock" calculations were used to date the branch points on the descending branches of the various lineages within the plant and invertebrate portions of the tree. The tree divided the 245 sequences into five distinct clades that corresponded exactly to the five groups plants, annelids, arthropods, molluscs, and vertebrates. Furthermore, the maximum parsimony tree, in contrast to the unweighted pair group and distance Wagner trees, was consistent with the available fossil record and supported the hypotheses that the primitive hemoglobin of metazoans was monomeric and that the multisubunit extracellular hemoglobins found among the Annelida and the Arthropoda represent independently derived states.

Amino Acid Sequence↗

PubMed1984

The alignment of sets of sequences and the construction of phyletic trees: an integrated method.

In this paper we argue that the alignment of sets of sequences and the construction of phyletic trees cannot be treated separately. The concept of 'good alignment' is meaningless without reference to a phyletic tree, and the construction of phyletic trees presupposes alignment of the sequences. We propose an integrated method that generates both an alignment of a set of sequences and a phyletic tree. In this method a putative tree is used to align the sequences and the alignment obtained is used to adjust the tree; this process is iterated. As a demonstration we apply the method to the analysis of the evolution of 5S rRNA sequences in prokaryotes.

Base Sequence↗

PubMed1996

Construction and application of hierarchical decision tree for classification of ultrasonographic prostate images.

A non-parametric algorithm is described for the construction of a binary decision tree classifier. This tree is used to correlate textural features, computed from ultrasonographic prostate images, with the histopathology of the imaged tissue. The algorithm consists of two parts; growing and pruning. In the growing phase an optimal tree is grown, based on the concept of mutual information. After growing, the tree is pruned by an alternating interaction of two data sets. Moreover, the structure and performance of the constructed tree are compared to the results using a slightly modified corresponding growing and pruning algorithm. The modified algorithm provides better retrospective and prospective classification results than the original algorithm. The use of the tree for automated cancer detection in ultrasonographic prostate images results in retrospective and prospective accuracy of 77.9% and 72.3%, respectively. Using this tissue characterisation, a supporting tool is provided for the interpretation of transrectal ultrasonographic images.

Algorithms↗

PubMed1987

Progressive sequence alignment as a prerequisite to correct phylogenetic trees.

A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: "once a gap, always a gap." The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods.

Algorithms↗

PubMed2004

Uptake of tributyltin into willow trees.

BACKGROUND: Organotins have been used world-wide as antifoulants in ship paints. Repeatedly, severe effects on aquatic species have resulted. The use of organotins for this purpose was ruled out, and dumping of contaminated harbor sludge into the sea was prohibited. Land-based dumping is seen as an alternative. OBJECTIVE: This study investigates sorption, uptake and translocation of tributyltin (TBT) to willow trees in order to evaluate phytoremediation as treatment option. The study considers the influence of pH on the plant uptake of organotins. EXPERIMENTAL SET-UP: Chemicals investigated were the weak base tributyltin chloride (TBTCl) and the neutral tributyltin hydride (TBTH). Organotins were extracted from solution and plant material with toluene, and analyzed as tin by AAS with graphite oven. The pH in solution varied from pH 4 to pH 7. The sorption to living and dead roots, stems and leaves was measured in shaking experiments. The uptake into intact trees was measured at nominal levels of 1 and 10 mg TBT/l for TBTH and TBTCl at low and high pH. RESULTS: The sorption to roots and leaves dropped for dead tissue, but did not vary much with pH. The sorption to stems increased for dead stems and with pH. The solubility of TBTCl in water was below 10 mg/l and lowest at pH 4. Concentrations of TBTCl and TBTH in solutions with trees dropped rapidly to low values. Highest TBT contents in trees were found in roots and lower stems. The concentrations followed the concentrations in solution. The pH had only a small effect on the plant uptake of TBTCl, and no effect on the uptake of TBTH. No effective translocation to higher stems or leaves was found. DISCUSSION: An ion trap mechanism that accumulates the weak base TBTCl in the xylem sap of plants and leads to upward translocation could not be detected. Neither TBTCl at low or high pH, nor the neutral lipophilic chemical TBTH, were translocated effectively to leaves. The TBT+ cation sorbed strongly to plant tissue. The exact mechanism for the strong sorption of the cation is unknown, but similar effects have been observed for algae, liposomes and isolated biomembranes. CONCLUSIONS: Both the uptake of the neutral TBTH and the uptake of the neutral molecule form of TBTCl into willows was as is to be expected from theory. The cation TBT+ showed an unexpected behavior which has been observed before. No ion trap occurs, and the phytoextraction of TBT is not feasible. OUTLOOK: Planting trees, or other appropriate vegetation, could have a beneficial remediation effect by aeration of the TBT-contaminated soil or sludge. In a follow-up paper, the toxicity of TBT to willow trees will be described.

Biodegradation, Environmental↗

PubMed2006

Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.

Our ability to construct very large phylogenetic trees is becoming more important as vast amounts of sequence data are becoming readily available. Neighbor joining (NJ) is a widely used distance-based phylogenetic tree construction method that has historically been considered fast, but it is prohibitively slow for building trees from increasingly large datasets. We developed a fast variant of NJ called relaxed neighbor joining (RNJ) and performed experiments to measure the speed improvement over NJ. Since repeated runs of the RNJ algorithm generate a superset of the trees that repeated NJ runs generate, we also assessed tree quality. RNJ is dramatically faster than NJ, and the quality of resulting trees is very similar for the two algorithms. The results indicate that RNJ is a reasonable alternative to NJ and that it is especially well suited for uses that involve large numbers of taxa or highly repetitive procedures such as bootstrapping.

Algorithms↗

PubMed2005

Spatial assessment of the alder tree in Kushiro Mire, Japan using remotely sensed imagery--effects of the surrounding land use on Kushiro Mire.

The relationship between alder (Alnus japonica) distribution and surrounding land use in Kushiro Mire was spatially assessed using remotely sensed imagery. From the result, it was found out that the expanding area of alder trees in Kushiro Mire was affected by the agricultural land area in the upper course of the river basin and flooding in the lower course of the river. The soil sediments flowing into the Kushiro Mire from the agricultural land resulted in heavy sedimentation that favors the growth of alder trees. Consequently, the number and density of alder trees has increased. The future distribution of alder trees was predicted based on the mechanism of expansion of the alder-tree area in Kushiro Mire, and it was found that large vegetation areas in Kushiro Mire will be changed to areas with alder trees.

Agriculture↗

PubMed2005

Local diameter fully constrains dendritic size in basal but not apical trees of CA1 pyramidal neurons.

Computational modeling of dendritic morphology is a powerful tool for quantitatively describing complex geometrical relationships, uncovering principles of dendritic development, and synthesizing virtual neurons to systematically investigate cellular biophysics and network dynamics. A feature common to many morphological models is a dependence of the branching probability on local diameter. Previous models of this type have been able to recreate a wide variety of dendritic morphologies. However, these diameter-dependent models have so far failed to properly constrain branching when applied to hippocampal CA1 pyramidal cells, leading to explosive growth. Here we present a simple modification of this basic approach, in which all parameter sampling, not just bifurcation probability, depends on branch diameter. This added constraint prevents explosive growth in both apical and basal trees of simulated CA1 neurons, yielding arborizations with average numbers and patterns of bifurcations extremely close to those observed in real cells. However, simulated apical trees are much more varied in size than the corresponding real dendrites. We show that, in this model, the excessive variability of simulated trees is a direct consequence of the natural variability of diameter changes at and between bifurcations observed in apical, but not basal, dendrites. Conversely, some aspects of branch distribution were better matched by virtual apical trees than by virtual basal trees. Dendritic morphometrics related to spatial position, such as path distance from the soma or branch order, may be necessary to fully constrain CA1 apical tree size and basal branching pattern.

Animals↗

PubMed2005

Changes in heartwood chemistry of dead yellow-cedar trees that remain standing for 80 years or more in southeast Alaska.

We measured the concentrations of extractable bioactive compounds in heartwood of live yellow-cedar (Chamaecyparis nootkatensis) trees and five classes of standing snags (1-5, averaging 4, 14, 26, 51, and 81 years-since-death, respectively) to determine how the concentrations changed in the slowly deteriorating snags. Three individuals from each of these six condition classes were sampled at four sites spanning a 260-km distance across southeast Alaska, and the influence of geographic location on heartwood chemistry was evaluated. Cores of heartwood were collected at breast height and cut into consecutive 5-cm segments starting at the pith. Each segment was extracted with ethyl acetate and analyzed by gas chromatography. Concentrations of carvacrol, nootkatene, nootkatol, nootkatone, nootkatin, and total extractives (a sum of 16 compounds) for the inner (0-5 cm from pith), middle (5-10 cm from pith), and surface (outer 1.1-6.0 cm of heartwood) segments from each core were compared within each tree condition class and within segments across condition classes. Heartwood of class 1 and 2 snags had the same chemical composition as live trees. The first concentration changes begin to appear in class 3 snags, which coincides with greater heartwood exposure to the external environment as decaying sapwood sloughs away, after losing the protective outer bark. Within core segments, the concentrations of all compounds, except nootkatene, decrease between snag classes 2 and 5, resulting in the heartwood of class 5 snags having the lowest quantities of bioactive compounds, although not different from the amounts in class 4 snags. This decline in chemical defense is consistent with heartwood of class 5 snags being less decay-resistant than heartwood of live trees, as observed by others. The unique heartwood chemistry of yellow cedar and the slow way it is altered after death allow dead trees to remain standing for up to a century with a profound impact on the ecology of forests in southeast Alaska where these trees are in decline.

Acetates↗

PubMed1976

The growth of the dendritic trees of Purkinje cells in irradiated agranular cerebellar cortex.

The heads of noenatal Wistar rats were irradiated with 200 rads daily from birth to the 10th day post-partum. Ten litters each containing 5 animals were killed at 30 days post-partum and their brains treated by the Golgi-Cox technique. The dendritic trees of 24 Purkinje cells were analysed using the quantitative technique of network analysis, and comparisons made between parameters obtained from 20 normal Purkinje cells. All dendritic trees in agranular irradiated cortex were markedly reduced in size (as indicated by total dendritic length and total number of segments) although mean path lengths were normal. Segment lengths were normal over proximal branches, but uniformly increased over distal branches. Abnormal appendages, called 'giant spines' were observed on many dendrites. They were often some 10 mum in length and their presence effectively reduced segment lengths, increased the frequency of trichotomy and deviated growth from the normal random terminal pattern so that long collateral branching topologies were formed. Nevertheless, trichotomy was uniformly reduced in those trees without 'giant spines' and the distribution of branching patterns suggested that growth had proceeded by random terminal dichotomy. These results demonstrate that the development of dendritic trees is retarded in the agranular irradiated cerebellum, where synaptogenesis is very greatly reduced below normal. The quantitative changes in segment lengths, size of trees, and trichotomy accord with those predicted by the filopodial synaptogenic hypothesis of dendritic growth formulated by Vaughn et al. 99, whilst the results of the topological analysis suggest that branching is established by a degree of non-random interaction between growing dendrites and their substrate. 'Claw-like' dendritic complexes within some Purkinje cell trees may have been induced by aberrent fibre bundles of few surviving granule cells.

Animals↗

PubMed1988

Link-Vertex Analysis of Purkinje cell dendritic trees from the murine cerebellum.

A method of analysis of dendritic trees is described, called Link-Vertex Analysis, which defines the branching patterns (topology) by means of a discontinuous function, the terminal/link (T/L) vertex ratio, computed at all successive vertex orders within a network, and represented as a graphical plot for a given tree. The T/L vertex ratio is defined as the number (n) of terminal (pendant) vertices (Vp) divided by the total number (n) of all link vertices (both dichotomous, Vd, and trichotomous, Vt) multiplied by the number of segments arising from each vertex--i.e., nVp/(2nVd + 3nVt) per vertex order. Hypotheses of growth are simulated by computer modelling and the distributions of computer generated T/L vertex ratios per order compared with those of actual dendritic trees. The differential distribution of T/L vertex ratios per order in trees grown by either random terminal or random segmental branching discriminates between these two forms of growth. Significant advances of this method include the detection of regional variations in growth and remodelling in a tree and the incorporation of Vt with little perturbation of the Vd data. The analytical powers of this method have been tested using the dendritic fields of 20-day-old mouse cerebellar Purkinje cells defining possible temporal sequences and relative contributions of random and non-random terminal growth, and also the frequency of branching over a growth front relative to that of the rest of the tree.

Animals↗

PubMed1977

Morphology of branching trees related to entropy.

Analyses of river systems by geomorphologists have suggested that for minimal entropy production in the movement of water down the river the fall in altitude should be equal in each order of branching of the tributaries. In this paper the same concepts have been applied to the bronchial tree and pulmonary arterial tree, assuming that the energy associated with pressure difference is analogous to that associated with altitude difference in rivers. The morphology of the bronchial tree is such that, given laminar flow or air, the calculated pressure difference across each order is equal. This may indicate that the bronchial tree is designed for minimal entropy production. In the arterial tree, however, this result is not obtained, probably because we do not know how to calculate the pressure drop in blood flowing through a branching system. It is therefore not currently possible, on the basis of this approach, to say whether the pulmonary arterial tree is designed for minimal entropy production or not.

Airway Resistance↗

PubMed1994

Growth and physiology of Northern Red Oak: preliminary comparisons of mature tree and seedling responses to ozone.

Considerable progress has been made during the past decade in the development of mechanistic models that allow complex chemical, physical, and biological processes to be evaluated in the global change context. However, quantitative predictions of the response of individual trees, stands, and forest ecosystems to pollutants and climatic variables require extrapolation of existing data sets, derived largely from seedling studies, to increasing levels of complexity with little or no understanding of the uncertainties associated with these extrapolations. Consequently, a project designed to address concerns associated with scaling from seedling to mature tree responses was initiated. During the 1990 and 1991 growing seasons, mature northern red oak (Quercus rubra L.) trees and seedlings were exposed to subambient, ambient, and twice ambient ozone (O(3)) concentrations. The initial focus of the study was to identify possible trends and obvious differences between mature trees and seedlings, both in terms of growth and physiology and in response to O(3). Generally, mature trees exhibited a greater decrease in photosynthesis rates over the growing season than did the seedlings. Ozone treatments had no consistent effect on gas exchange rates of seedlings, but the twice ambient O(3) treatment resulted in reduced photosynthesis rates in the mature tree. Despite no effect of O(3) on seedling gas exchange rates, total seedling biomass was significantly less at the end of the 1991 growing season for those seedlings exposed to twice ambient O(3) levels. Disproportionate reductions in root biomass also resulted in reduced root to shoot ratios at elevated O(3) concentrations.

Journal Article↗

PubMed1996

Growth and nutrition of Quercus rubra L. seedlings and mature trees after three seasons of ozone exposure.

Seedling growth and nutritional status have been shown to be sensitive to ozone, but the influence of multi-season ozone exposure on mature tree growth and nutrition has not been examined. To determine if seedlings and mature trees were similarly affected by ozone exposure, growth and nutrient concentrations in northern red oak (Quercus rubra L.) 4-year-old seedlings and 32-year-old mature trees were examined after treatment with subambient, ambient and twice ambient concentrations of ozone for three growing seasons. SUM00 values summed over the three growing seasons were 147, 255 and 507 ppm-h, respectively, for the subambient, ambient and twice ambient exposures. For mature trees, no influence of ozone treatment on lower stem diameter growth, stem growth within the mid-canopy and foliar biomass was observed. Seedling height was increased by ozone, but biomass and diameter were unaffected. A reduction in the specific leaf weight of leaves in response to ozone coincident with the loss of recurrent flushing was observed in seedlings. Ozone exposure reduced foliar nitrogen concentrations and increased woody tissue nutrient concentrations in seedlings and mature trees at the end of the third growing season. These results suggest an influence of ozone on retranslocation processes in seedlings and mature trees.

Journal Article↗

PubMed1990

The integration of the cerebral and coronary circulations with the dynamic system structure of brain and myocardium and the form of the cerebral and coronary artery trees.

Cerebral and coronary arterial trees lack functional anastomoses and are 'non-redundant' in the number of arteries. These two morphological characteristics expose brain and myocardium to vascular pathologies. An elementary model common to the cerebral and myocardial blood supply permits an explanation of the two characteristics. On the ground of this model the brain and the myocardium are represented as dynamic systems--organ-systems--made up of units, these corresponding to neurons and to cardiac cells. A flow of information between the units determines variations of state of the units. The whole of the variations of state of the units gives the organ-system function. The artery tree is considered as an information channel--tree-channel--that conveys information to the units. This artery-transmitted information determines the way the units function. The tree-channel always emits the same message. Therefore the artery-transmitted information does not cause local or temporal variations in the functioning of the units. On the contrary, if the tree-channel is noised the ending branches will emit randomly varied messages. Such random emission--disorder--will cause random loco-temporal variations in the functioning of the units. Consequently the functioning of the organ-system will be disturbed. It is shown that a low number of branches lowers the quantity of disorder that a noised tree-channel can emit. The absence of anastomoses avoids combinatory phenomena between the diverse messages that would increase the disorder. Biological and pathological evidence supports the model and the explanation.

Animals↗

PubMed2005

Image quality of volume rendering of the bronchial tree: Kymogram-gated versus retrospectively ECG-gated and non-gated multi-row detector CT.

RATIONALE AND OBJECTIVE: To compare the image quality of three different heart-cycle-synchronized computed tomography (CT) reconstruction algorithms for volume-rendered (VR) 3D visualization of the bronchial tree. MATERIALS AND METHODS: Kymogram-gated, retrospectively ECG-gated, and non-ECG-gated reconstructions of the bronchial tree were performed from 4-detector-row CT data in 10 subjects. The raw data were reconstructed in 10 phases of the cardiac cycle using ECG-gated and kymogram-gated technique, respectively. For both reconstructions, the optimal artifact-free diastolic phase was determined. VR reconstructions of the bronchial tree were generated from these two data sets and from the non-gated data. Stairstep artifacts of the main bronchi, artifacts in the lung parenchyma, and the extent of bronchial tree visualization were rated by two blinded, independent readers. RESULTS: Kymogram-gated reconstruction showed stairstep artifacts in the main bronchi to the same extent as non-gated reconstruction, but less compared to ECG-gated reconstruction (P < .001). Artifacts in the lung parenchyma were similar with kymogram-gated and non-gated reconstruction, but less compared to ECG-gated reconstruction (P < 0.01). Kymogram-gated reconstruction showed no differences in visualization of segmental and subsegmental bronchi compared to ECG-gated reconstruction, but was inferior to the non-gated reconstruction (P < 0.05). CONCLUSION: Kymogram-gated reconstruction of CT data results in fewer artifacts when compared to the ECG-gated algorithm. Best visualization of the bronchial tree at a low artifact level is obtained with non-gated CT data. It remains therefore the method of choice for VR 3D data post-processing of the bronchial tree.

Adult↗

PubMed2005

Immunoglobulin variable-region gene mutational lineage tree analysis: application to autoimmune diseases.

Lineage trees have frequently been drawn to illustrate diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. In order to extract more information from IGV sequences, we developed a novel mathematical method for analyzing the graphical properties of IgV gene lineage trees, allowing quantification of the differences between the dynamics of SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we investigated trees generated from published IGV sequence data from B cell clones participating in autoimmune responses in patients with Myasthenia Gravis (MG), Rheumatoid Arthritis (RA), and Sjögren's Syndrome (SS). At present, as no standards exist for cell sampling and sequence extraction methods, data obtained by different research groups from two studies of the same disease often vary considerably. Nevertheless, based on comparisons of data groups within individual studies, we show here that lineage trees from different individual patients are often similar and can be grouped together, as can trees from two different tissues in the same patient, and even from IgG- and IgA-expressing B cell clones. Additionally, lineage trees from most studies reflect the chronic character of autoimmune diseases.

Arthritis, Rheumatoid↗