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PubMed2002

[Analysis of lecithin-cholesterol acyltransferase cDNA and protein sequence from tree shrew].

OBJECTIVE: To acquire cDNA sequence of lecithin-cholesterol acyltransferase (LCAT) from tree shrew and analyze the sequence structure. METHODS: The first strand cDNA was acquired by reverse transcription using mRNA from tree shrew liver as template. By the method of SMART RACE PCR, tree shrew LCAT cDNA was acquired and deduced its amino acids sequence. The sequence and structure of tree shrew LCAT cDNA and amino acid were analyzed and predicted by the molecular software. RESULTS: Tree shrew LCAT cDNA is composed of 1,340 bp, including 2 bp 5' untranslated region (5' UTR), 1,320 bp open reading frame (ORF) which encodes protein precursor of 440 amino acids (24 amino acids signal peptide and 416 amino acids mature peptide), and 18 bp 3' untranslated region (3'UTR). The stop codon is TAA and there is a poly (A) signal sequence AATAAA and a 25 bp poly (A) tail. Tree shrew LCAT cDNA sequence has been accepted by GenBank as a new gene, accession number AF272861 and its homology with human and baboon was 90% and 89%, respectively. CONCLUSION: The sequence of LCAT cDNA in tree shrew has high identity with that of human and other experimental animal species.

Amino Acid Sequence↗

PubMed2005

[A cDNA microarray study of the differential expression of genes in signal transduction pathway during hepatocarcinogenesis in tree shrews].

OBJECTIVES: To study the differential expression of genes in signal transduction pathway (STP) during the hepatocarcinogenesis in tree shrews induced by AFB1 and/or HBV and to elucidate the molecular mechanism of hepatocellular carcinoma (HCC) development. METHODS: Adult tree shrews were divided into three groups: Group A was fed AFB1 only, Group B was infected firstly with HBV then fed AFB1 as in Group A, Group C served as the normal control. Liver biopsies were obtained at the 30th, 60th and 90th week of the experiment or until HCC occurred and the animals were sacrificed. Tree shrew-specific cDNA microarray was applied for detecting the differential expression of corresponding genes in each group at different time points during the experiment, and real time RT PCR was applied to verify the results of the cDNA microarray. RESULTS: Genes of IGF-II, C-rel, and NF-kappaB2 were differentially expressed between para-cancerous tissues and HCC tissues in both group A and group B, and the differential expression of bcl-2, cyclin A and CNTF was only seen in group B. Between the experimental groups A and B and the control group C, there were differential expressions of CNTF and cyclin A in the early 30th week and middle 60th week stage of hepatocarcinogenesis in tree shrews. Real time RT PCR results showed that the expression level of IGF-II and C-Rel in group A and of IGF-II in group B in HCC tissues were significantly lower than that in the adjacent non-cancerous tissues and in the biopsies taken at the 30th and 60th week of the experiment. Nevertheless, there were no significant differences between the para-cancerous tissues and the cancer tissues at the 30th and 60th week. These results were consistent with the cDNA microarray assay. The expression levels of C-Rel and CNTF in group B were not obviously altered in the para-cancerous tissues, HCC and at the 60th week, but they were significantly lower in these tissues than that in the tissues at the 30th week. In group A, the expression levels of CNTF in adjacent liver and HCC tissues were higher than that in para-cancerous lesions, but the difference did not reach a statistically significant level. In group C, the expression level of IGF-II, C-Rel and CNTF at different stages showed no significant differences, which was consistent with the cDNA microarray results. CONCLUSIONS: To apply the tree shrew-specific cDNA microarray to detect the differential expression of genes related to signal transduction pathway during tree shrew hepatocarcinogenesis could be a valuable utility for further comprehending the mechanism of HCC. IGF-II, NF-kappaB2, C-rel, Bcl-2, and cyclin A. CNTF may be involved in the occurrence and progress of HCC in tree shrews.

Animals↗

PubMed2004

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

MOTIVATION: Since the whole genome sequences for many species are currently available, computational predictions of RNA secondary structures and computational identifications of those non-coding RNA regions by comparative genomics become important, and require more advanced alignment methods. Recently, an approach of structural alignments for RNA sequences has been introduced to solve these problems. By structural alignments, we mean a pairwise alignment to align an unfolded RNA sequence into a folded RNA sequence of known secondary structure. Pair HMMs on tree structures (PHMMTSs) proposed by Sakakibara are efficient automata-theoretic models for structural alignments of RNA secondary structures, but are incapable of handling pseudoknots. On the other hand, tree adjoining grammars (TAGs) is a subclass of context-sensitive grammar, which is suitable for modeling pseudoknots. Our goal is to extend PHMMTSs by incorporating TAGs to be able to handle pseudoknots. RESULTS: We propose the pair stochastic tree adjoining grammars (PSTAGs) for modeling RNA secondary structures including pseudoknots and show the strong experimental evidences that modeling pseudoknot structures significantly improves the prediction accuracies of RNA secondary structures. First, we extend the notion of PHMMTSs defined on alignments of 'trees' to PSTAGs defined on alignments of "TAG (derivation) trees", which represent a top-down parsing process of TAGs and are functionally equivalent to derived trees of TAGs. Second, we modify PSTAGs so that it takes as input a pair of a linear sequence and a TAG tree representing a pseudoknot structure of RNA to produce a structural alignment. Then, we develop a polynomial-time algorithm for obtaining an optimal structural alignment by PSTAGs, based on dynamic programming parser. We have done several computational experiments for predicting pseudoknots by PSTAGs, and our computational experiments suggests that prediction of RNA pseudoknot structures by our method are more efficient and biologically plausible than by other conventional methods. The binary code for PSTAG method is freely available from our website at http://www.dna.bio.keio.ac.jp/pstag/.

Algorithms↗

PubMed2005

[Correlation between gap structure and tree diversity of mixed-broad-leaved Korean pine forests in northeast China].

This paper studied the regeneration of tree species in the gaps of broad-leaved Korean pine forest, with the tree diversity in gaps and under closed canopy compared, and the relationship between biodiversity and gap structure analyzed. The results indicated that there was a significant difference between tree species diversity in gaps and under canopy (P < 0.01). In regeneration layer, the biodiversity in terms of Shannon-Wiener, evenness, and abundance indices was higher in gap community than under forest canopy, while the dominance of certain species in terms of Simpson's dominance index was increased from gaps to closed canopy (P < 0.01) . The biodiversity of succession layer in gaps and under closed canopy had an opposite trend. Tree species diversity of different layers reacted differently to the change of gap size class, e.g., Shannon-Wiener and abundance indices were higher, but Simpson's dominance index was the lowest in the succession layer of medium-size gap(100-250 m2) in broadleaved Korean pine forest of Changbai Mountain. The Shannon-Wiener index and evenness index reached the highest in the size of > or =250 m2 and <100 m2, and reached the lowest in the size of 200-250 m2 in regeneration layer. Simpson's dominance index reached the highest in the size of 200-250 m2. On the whole, tree species of different layers reacted differently to the change of gap size class, and the gap size class with more seedlings was not corresponding to the size class containing more medium-size trees. With gaps aging, tree diversity indices in the two layers behaved reciprocally.

Biodiversity↗

PubMed1996

An empirical comparison of expert-derived and data-derived classification trees.

Classification trees provide an attractively transparent discrimination technique, and may be derived from both expert opinion and from data analysis. We consider a real and complex problem concerning the diagnosis of babies with suspected critical congenital heart disease into one of 27 classes. A full loss matrix for all possible misclassifications was obtained from clinical assessments. A tree derived from expert opinion was compared with those derived from analysis of 571 past cases, both for the full problem and for a subset of 6 diseases. Automatic methods for tree creation and pruning were found to have problems for rare diseases, and hand-pruning was carried out. Inclusion of costs led to much improved clinical performance, even for trees that had originally been constructed to minimize classification errors. The expert tree showed a specific building strategy that could not be reproduced automatically. The expert tree generally outperformed those derived from data, particularly in the ability to identify important composite features.

Algorithms↗

PubMed1993

A comparison of logistic regression to decision-tree induction in a medical domain.

This paper compares the performance of logistic regression to decision-tree induction in classifying patients as having acute cardiac ischemia. This comparison was performed using the database of 5773 patients originally used to develop the logistic-regression tool and test it prospectively. Both the ability to classify cases and the ability to estimate the probability of ischemia were compared on the default tree generated by the C4 version of ID3. They were also compared on a tree optimized on the learning set by increased pruning of overspecified branches, and on a tree incorporating clinical considerations. Both the LR tool and the improved trees performed at a level fairly close to that of the physicians, although the LR tool definitely performed better than the decision tree. There were a number of differences in the performance of the two methods, shedding light on their strengths and weaknesses.

Algorithms↗

PubMed2001

A conflict between two evolutionary levels in trees.

Due to the lack of germ line segregation in plants, it is possible to consider plant evolution (but not the evolution of most animals) as being composed of two evolutionary levels: 1. Intra-organism, in which the replicating unit is a part of the tree (e.g. a branch), reproduction is asexual, mutations are somatic, and selection operates only upon traits relevant to vegetative growth. 2. Inter-organism, in which the replicating unit is the whole tree, reproduction is sexual, and selection operates upon all the traits. In this work, a case of a conflict between these two levels is studied. The dynamics of a mutation, which is advantageous on the branch level but harmful for the whole tree, are discussed for a one-locus two-allele model. Several cases are considered: dominant, partially dominant, and haploid. Necessary and sufficient conditions for fixation of such a mutation are found. The model predicts that as the longevity of a tree species increases, the trees are expected to be more strongly shifted from their optimal growth-to-reproduction ratio towards growth, and resource allocation between branches and other tree parts is expected to be shifted in favor of the branches. Traditional approach, considering the second level only, is justified as a limit case for short longevity.

Biological Evolution↗

PubMed1996

Effects of pruning of a decision-tree for the ear, nose, and throat realm in primary health care based on case-notes.

In the primary health care center of Mjölby a sample of case notes in the ear-nose- and-throat realm (N = 425) was computer processed using an inductive rule-based decision-tree generating program. As a result of incomplete information in the case-files, the decision trees were "noisy," e.g., had branches and leaves without meaning. This led to a need for "pruning." Various methods were tried. The effects of different methods of decision-tree generating and pruning are discussed. The choice of root argument and branching of the decision-trees suggested by the software was the most clinically applicable. The "statistic" approach to pruning gave the most compact and still most clinically relevant decision-tree. The pruned and edited decision trees are compared with a previously published preliminary essential data set for the ear-nose- and-throat realm in primary health care and then discussed as a possible decision support system for various primary health care groups in a practice setting.

Algorithms↗

PubMed2004

Retrospective selection of elite parent trees using paternity testing with microsatellite markers: an alternative short term breeding tactic for Eucalyptus.

The conventional way to drive modifications in old forest tree seed orchards is to establish progeny trials involving each parent tree and then evaluate its contribution to the performance of the progeny by estimating its general and specific combining ability (GCA and SCA). In this work, we successfully applied an alternative parent selection tactic based on paternity testing of superior offspring derived from a hybrid seed orchard established with a single Eucalyptus grandis seed parents and six E. urophylla pollen parents. A battery of 14 microsatellite markers was used to carry out parentage tests of 256 progeny individuals including two independent samples of selected trees and one control unselected sample, all derived from 6-year-old forest stands in eastern Brazil. Paternity determination was carried out for all progeny individuals by a sequential paternity exclusion procedure. Exclusion was declared only when the obligatory paternal allele in the progeny tree was not present in the alleged parent tree for at least four independent markers to avoid false exclusions due to mutation or null alleles. After maternity checks to identify seed mixtures and selfed individuals, the paternity tests revealed that approximately 29% of the offspring was sired by pollen parents outside the orchard. No selfed progeny were found in the selected samples. Three pollen parents were found to have sired essentially all of the offspring in the samples of selected and non-selected progeny individuals. One of these three parents sired significantly more selected progeny than unselected ones ( P< or =0.0002 in a Fisher exact test). Based on these results, low-reproductive-successful parents were culled from the orchard, and management procedures were adopted to minimize external pollen contamination. A significant difference ( P<0.01) in mean annual increment was observed between forest stands produced with seed from the orchard before and after selection of parents and revitalization of the orchard. An average realized gain of 24.3% in volume growth was obtained from the selection of parents as measured in forest stands at age 2-4 years. The marker-assisted tree-breeding tactic presented herein efficiently identified top parents in a seed orchard and resulted in an improved seed variety. It should be applicable for rapidly improving the output quality of seed orchards, especially when an emergency demand for improved seed is faced by the breeder.

Brazil↗

PubMed2005

Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.

Bacteria↗

PubMed2007

Rhizosphere-bacterial community in Eperua falcata (Caesalpiniaceae) a putative nitrogen-fixing tree from French Guiana rainforest.

The rainforest of French Guiana is still largely unaffected by human activity. Various pristine sites like the Paracou Research Station are devoted to study this tropical ecosystem. We used culture-independent techniques, like polymerase chain reaction-temperature gradient gel electrophoresis, and construction of clone libraries of partial 16S rRNA and nifH genes, to analyze the composition of the bacterial community in the rhizosphere of mature trees of Eperua falcata and Dicorynia guianensis, both species within the Caesalpiniaceae family. E. falcata is one of the more abundant pioneer tree species in this ecosystem and so far, no root nodules have ever been found. However, its nitrogen-fixing status is regarded as "uncertain", whereas D. guianensis is clearly considered a non-nitrogen-fixing plant. The rhizospheres of these mature trees contain specific bacterial communities, including several currently found uncultured microorganisms. In these communities, there are putative nitrogen-fixing bacteria specifically associated to each tree: D. guianensis harbors several Rhizobium spp. and E. falcata members of the genera Burkholderia and Bradyrhizobium. In addition, nifH sequences in the rhizosphere of the latter tree were very diverse. Retrieved sequences were related to bacteria belonging to the alpha-, beta-, and gamma-Proteobacteria in the E. falcata rhizoplane, whereas only two sequences related to gamma-Proteobacteria were found in D. guianensis. Differences in the bacterial communities and the abundance and diversity of nifH sequences in E. falcata rhizosphere suggest that this tree could obtain nitrogen through a nonnodulating bacterial interaction.

Bacteria↗

PubMed2001

Identification of processes governing long-term accumulation of 137Cs by forest trees following the Chernobyl accident.

The regularities of 137Cs distribution in trees (Pinus sylvestris and Betula pendula) growing in different types of forest ecosystems were investigated. High levels of heterogeneity of 137Cs activity concentrations in different parts of the trees, resulting from their varied metabolism have been shown. The data obtained demonstrate a non-uniform character of 137Cs distribution along the trunks, which can be explained by radionuclide fixation by the xylem vessel walls and by geometry changes along the tree trunk. It has been found that the radial distribution of 137Cs in the tree trunk is dependent on the availability of 137Cs in soil, which governs the transfer of this radionuclide via xylem sap and on the properties of the xylem. The accumulation of 137Cs by trees was influenced by the vertical distribution and availability of 137Cs in the soil as well as by the root biomass distribution in different soil horizons. A bioavailability factor, which takes into account the vertical distribution of radiocesium in soil, bioavailability of this radionuclide and distribution of root biomass in different soil horizons is proposed for comparative analyses of 137Cs transfer from soil to trees in different types of forest ecosystems.

Cesium Radioisotopes↗

PubMed2006

Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three?

In Fennoscandian boreal forests, soil pH and N supply generally increase downhill as a result of water transport of base cations and N, respectively. Simultaneously, forest productivity increases, the understory changes from ericaceous dwarf shrubs to tall herbs; in the soil, fungi decrease whereas bacteria increase. The composition of the soil microbial community is mainly thought to be controlled by the pH and C-to-N ratio of the substrate. However, the latter also determines the N supply to plants, the plant community composition, and should also affect plant allocation of C below ground to roots and a major functional group of microbes, mycorrhizal fungi. We used phospholipid fatty acids (PLFAs) to analyze the potential importance of mycorrhizal fungi by comparing the microbial community composition in a tree-girdling experiment, where tree belowground C allocation was terminated, and in a long-term (34 years) N loading experiment, with the shifts across a natural pH and N supply gradient. Both tree girdling and N loading caused a decline of ca. 45% of the fungal biomarker PLFA 18:2omega6,9, suggesting a common mechanism, i.e., that N loading caused a decrease in the C supply to ectomycorrhizal fungi just as tree girdling did. The total abundance of bacterial PLFAs did not respond to tree girdling or to N loading, in which cases the pH (of the mor layer) did not change appreciably, but bacterial PLFAs increased considerably when pH increased across the natural gradient. Fungal biomass was high only in acid soil (pH < 4.1) with a high C-to-N ratio (>38). According to a principal component analysis, the soil C-to-N ratio was as good as predictor of microbial community structure as pH. Our study thus indicated the soil C-to-N ratio, and the response of trees to this ratio, as important factors that together with soil pH influence soil microbial community composition.

Bacteria↗

PubMed2005

Phenology of temperate trees in tropical climates.

Several North American broad-leaved tree species range from the northern United States at approximately 47 degrees N to moist tropical montane forests in Mexico and Central America at 15-20 degrees N. Along this gradient the average minimum temperatures of the coldest month (T (Jan)), which characterize annual variation in temperature, increase from -10 to 12 degrees C and tree phenology changes from deciduous to leaf-exchanging or evergreen in the southern range with a year-long growing season. Between 30 and 45 degrees N, the time of bud break is highly correlated with T (Jan) and bud break can be reliably predicted for the week in which mean minimum temperature rises to 7 degrees C. Temperature-dependent deciduous phenology-and hence the validity of temperature-driven phenology models-terminates in southern North America near 30 degrees N, where T (Jan)>7 degrees C enables growth of tropical trees and cultivation of frost-sensitive citrus fruits. In tropical climates most temperate broad-leaved species exchange old for new leaves within a few weeks in January-February, i.e., their phenology becomes similar to that of tropical leaf-exchanging species. Leaf buds of the southern ecotypes of these temperate species are therefore not winter-dormant and have no chilling requirement. As in many tropical trees, bud break of Celtis, Quercus and Fagus growing in warm climates is induced in early spring by increasing daylength. In tropical climates vegetative phenology is determined mainly by leaf longevity, seasonal variation in water stress and day length. As water stress during the dry season varies widely with soil water storage, climate-driven models cannot predict tree phenology in the tropics and tropical tree phenology does not constitute a useful indicator of global warming.

Greenhouse Effect↗

PubMed2006

Mesostigmatid mites (Acari: Mesostigmata) on rainforest tree trunks: arboreal specialists, but substrate generalists?

Predatory mites (Acari: Mesostigmata) on tree trunks without significant epiphytic growth in a subtropical rainforest in Eastern Australia were assessed for habitat specificity (i.e. whether they are tree trunk specialists or occupying other habitats) and the influence of host tree and bark structure on their abundance, species richness and species composition. The trunks of nine tree species from eight plant families representing smooth, intermediate and rough bark textures were sampled using a knockdown insecticide spray. In total, 12 species or morphospecies of Mesostigmata (excluding Uropodina sensu stricto) were collected, most of which are undescribed. Comparison with collections from other habitats indicates that epicorticolous Mesostigmata are mainly represented by suspended soil dwellers (six species), secondarily by generalists (four species) and a bark specialist (one species). A typical ground-dwelling species was also found but was represented only by a single individual. In terms of abundance, 50.5% of individuals were suspended soil dwellers, 40.7% bark specialists, and 8.3% generalists. Host species and bark roughness had no significant effect on abundance or species richness. Furthermore, there was no clear effect on species composition. The distribution of the most frequently encountered species suggests that most mesostigmatid mites living on bark use many or most rainforest tree species, independent of bark roughness. These findings support the hypothesis that some epicorticolous Mesostigmata use tree trunks as 'highways' for dispersing between habitat patches, while others use it as a permanent habitat.

Animals↗

PubMed1981

Polymerized tree pollen antigens.

Aqueous extracts of tree pollen were partially purified and polymerized with methods previously established for preparation of ragweed and grass polymers. The polymerized tree preparations were antigenic as demonstrated by ability to elicit immediate-type skin reactivity in humans and to induce an immune response in rabbits. The polymerized tree antigen was 100- to 10,000-fold less skin reactive than monomer tree antigen in tree pollen-sensitive patients but both preparations had similar antigenicity in rabbits. These results demonstrate that polymerized tree antigens can be prepared and should have the therapeutic potential already demonstrated for polymerized ragweed preparations.

Animals↗

PubMed1995

The relationship between an endangered North American tree and an endophytic fungus.

BACKGROUND: The Florida torreya (Torreya taxifolia) began a catastrophic decline in the late 1950s and is now the rarest tree in North America for which a full species designation has been established. The trees have common plant disease symptoms, but the reason for the decline has never been identified. T. taxifolia's imminent extinction gains special poignancy through its close relationship to the Pacific yew (Taxus brevifolia), which produces the potent anticancer agent, taxol. RESULTS: An examination of the endophytic fungal communities of wild torreyas consistently found a filamentous fungus, Pestalotiopsis microspora, associated with diseased trees and also with most symptomless trees. P. microspora can be cultured in the laboratory, and when it is introduced into greenhouse-grown torreyas, it causes disease symptoms similar to those seen in the field. The fungus can then be reisolated from these deliberately infected trees. The phytotoxins pestalopyrone, hydroxypestalopyrone and pestaloside have been isolated and characterized from axenic fungal cultures, and both pestalopyrone and hydroxypestalopyrone can be isolated from artificially infected torreyas. In addition, pestaloside has antifungal activity against other fungal endophytes of T. taxifolia. CONCLUSIONS: The filamentous fungus, P. microspora, has an endophytic-pathologic relationship with T. taxifolia. The fungus resides in the inner bark of symptomless trees, and physiological or environmental factors could trigger its pathological activity. P. microspora produces the phytotoxins pestalopyrone, hydroxypestalopyrone, and pestaloside which give rise to the disease. Pestaloside, which also has antifungal activity, could reduce competition from other fungal endophytes within the host.

Acetylation↗

PubMed2004

Using tree analysis pattern and SELDI-TOF-MS to discriminate transitional cell carcinoma of the bladder cancer from noncancer patients.

OBJECTIVE: To determine whether SELDI protein profiling of urine coupled with a tree analysis pattern could differentiate TCC from noncancer patients. METHODS: The ProteinChip Arrays were performed on a ProteinChip PBS II reader of the ProteinChip Biomarker System. The study was divided into two phases: a preliminary phase with construction of tree analysis pattern, and a testing phase with test urine samples. Generation of the tree analysis pattern was performed by a training data set consisting of 104 samples. The validity of the tree analysis pattern was then challenged with a test set of 68 samples. RESULTS: Average of 187 mass peaks was detected in the urine samples, and five of these peaks were used to construct the tree analysis pattern. The classification pattern correctly predicted 91.67-94.64% of the samples for both of the two groups in the training set, for an overall correct classification of about 93%. The pattern correctly predicted 72.0% (49 of 68) of the test samples, with 71.4% (25 of 35) of the TCC samples, 72.7% (24 of 33) of the noncancer samples. CONCLUSIONS: The high sensitivity and specificity obtained by the urine protein profiling approach demonstrate that SELDI-TOF-MS combined with a tree analysis pattern can both facilitate discriminate TCC bladder cancer with noncancer and provide an innovative clinical diagnostic platform improve the detection of TCC bladder cancer patients.

Adult↗