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At least 1,045 records · Page 58Linked to original sources
PubMed1988

[Evolution of RNA-dependent RNA-polymerases from positive RNA viruses: comparison of phylogenetic trees constructed by different methods].

Presumptive phylogenetic trees of evolutionary conserved fragments of RNA-dependent RNA polymerases of 26 positive strand RNA viruses were generated using a simple clustering procedure or a novel approach based on the so-called maximal topologic similarity principle. The latter methodology involves a quantitative measure of the degree of correspondence between the topology of generated trees and structure of the initial distance matrix. The algorithm for tree construction based on the maximal topologic similarity principle does not include the assumption of evolutionary rate constancy, as opposed to the clustering procedure. Nevertheless, it is demonstrated that the trees generated by the two methods are topologically similar, indicating that no drastic change of evolutionary rate had occurred in evolution of the positive strand RNA virus RNA polymerases. This in turn suggests that RNA-dependent RNA polymerases (or at least their evolutionary conserved core domains used for construction of the phylogenetic trees) are principally functionally equivalent in all positive strand RNA viruses.

Algorithms↗
PubMed1984

Adenoviral infection in infant tree shrews.

An epizootic of fatal illness among infant common tree shrews (Tupaia glis) occurred in a research colony. Affected tree shrews were dehydrated, and ingested milk substitute remained in their stomachs for several hours without being digested. Twelve of 15 tree shrews born during a 3-month period died. The 4 tree shrews we were able to examine had intranuclear inclusions in the epithelium of the stomach and intestines, with mild to moderate multifocal necrosis. One tree shrew also had nasal epithelial inclusions and multiple foci of hepatocellular and biliary necrosis, with inclusions. The causative virus was identified as an adenovirus.

Adenoviridae↗
PubMed1994

Occurrence of the infective stage of Angiostrongylus cantonensis in the yellow tree monitor (Varanus bengalensis) in five Provinces of Thailand.

Twenty-two yellow tree monitors (Varanus bengalensis) were trapped and transported from 5 provinces, namely Lampang, Phitsanulok, Kamphaeng Phet, Tak and Prachin Buri to look for the infective larvae stage of Angiostrongylus cantonensis. In 4 provinces all of the yellow tree monitors were infected with the infective stage larvae of A. cantonensis altogether. Twenty-one of the 22 yellow tree monitors (95.5%) in the five provinces were infected. Our results of this study extend our knowledge of natural prevalence of A. cantonensis in yellow tree monitors. The snail eating habit of the yellow tree monitor might possibly be the source of the larvae.

Angiostrongylus cantonensis↗
PubMed1993

Morphologic characteristics and chemical composition of Christmas tree cataract.

PURPOSE: Christmas tree cataract consists of highly refractile multicolored "needles" crisscrossing the lens fibers of the deep cortex. The fact that the colors vary according to the angle of the incident light, and that in retroillumination only a dim outline of the cataract is seen, would suggest that Christmas tree cataract is a diffractive phenomenon. This study was performed to unravel the ultrastructure and chemical composition of the Christmas tree needles. METHODS: Eight lenses from donor eyes and four extracapsularly extracted lenses with Christmas tree cataract were investigated by scanning and transmission electron microscopy. The chemical composition was studied with energy-dispersive x-ray microanalysis and Raman microspectroscopy. RESULTS: Scanning electron microscope examination showed that the needles are smooth, rectangular, plate-like elements bordered by membranes and amorphous material and running crisscross through the lens. In the specimens for transmission electron microscopic examination, the needles proved to be largely dissolved, but the remains showed regular spacings of approximately 5 nm. Material identical in spacing and electron density was found in neighboring cells bound to a reticular membranous network originating from the fiber-limiting membranes. Energy-dispersive x-ray and Raman microanalysis showed that the needles have a high sulfur content and pronounced S-S, CS-SC, and C-S vibrations. The cytoplasm adjacent to the needles and reticular meshwork had an elevated Ca++ content. CONCLUSIONS: It is concluded that cystine is the most likely candidate for the Christmas tree needles and that the needles probably are formed as the result of an age-related aberrant breakdown of crystallins induced by elevated Ca++ levels.

Aged↗
PubMed1996

An ultrastructural and lectin-histochemical study on the seminiferous epithelium of the common tree shrew (Tupaia glis).

The seminiferous epithelium of the common tree shrew (Tupaia glis) was investigated using transmission electron microscopy and lectin-histochemistry. It was compared with that of shrews examined in previous studies. Some peculiar structures were detected in the tree shrew spermatid at the electron microscopic level. The most characteristic feature was the disposition of mitochondria in early spermatids. In cap and early acrosome-phase spermatids, mitochondria accumulated in one area of the spermatid cytoplasm and then dispersed in the late acrosome phase. Subsequently they again clustered to form the middle piece of spermatozoa. While the lamellar structure was clearly seen in the caudal region of the spermatid nucleus, it gradually disappeared during the process of elongation. The dilated area in the postacrosomal space of early round spermatids was also characteristic. The dilation was not detected in elongated spermatids. These structures were not recognised in the seminiferous epithelium of shrews. With respect to lectin histochemistry, the binding patterns in the spermatid acrosome of the tree shrew were similar to those of the musk shrew. However, PNA and BPA, which reacted with the Sertoli cell cytoplasm of the musk shrew, showed no reaction in the tree shrew Sertoli cell. Thus, except for some lectin binding patterns in the spermatid acrosome, no close similarity was recognised in the morphology of the seminiferous epithelium between tree shrews and shrews.

Acrosome↗
PubMed1976

[Quantitative study of dendritic tree of large (regular) pyramidal cells of lamina V in rat anterior cingular cortex].

At three month old male rats the dendritic trees of 36 large pyramidal cells in the Vth layer of the anterior cingulate cortex were analyzed quantitatively by means of the Golgi-Kopsch method. 12 pyramidal cells were localized at the medial border of the regio praecentralis (neocortex), 12 cells were localized in the adjacent mesoarchicortex, 12 cells were localized in the mesoarchicortex, which are three subregions of the anterior cingulate cortex. By means of a varianz-analysis the values of the three subregions were compared, in order to verify a supposed gradient of differentiation. 1. In the three subregions basal the number and the branching behaviour of the dendrites are greater than apical. The pyramidal cells of the neocortex and of the mesoneocortex have significantly more basal dendrites of the 1st, 2nd, 3rd, and 4th order than those of the mesoarchocortex. There are significantly more apical dendrites of the 1st and 2nd order at pyramidal cells of the neocortex compared with the two other subregions. 2. The total lengths of the dendritic branches are in proportion to the dendritic numbers of the corresponding orders. There are following tendencies for the three subregions: the number and length of apical dendrites decrease with the increasing number of order, basally, however, the number and length first increase and than decrease. 3. The total length of all basal dendrites of a pyramidal cell is largest in the mesoneocortex, than follows the neocortex, least values they find in the mesoarchicortex. There are significant differences between every one of the three subregions. The values of the total dendritic tree of a pyramidal cell (total dendritic length, total number of dendrites, volume of the dendritic tree, number of branching sites and free endings, total apical dendritic length) show significant differences between neocortex and mesoarchicortex as well as between mesoneocortex and mesoarchicortex. There are no significant differences between noecortex and mesoneocortex. The values of the total dendritic tree demonstrate that neocortex and mesoneocortex have a similar organization, while the lamina V-pyramidal cells of the mesoarchicortex indicate a significantly smaller and less branched dendritic tree.

Animals↗
PubMed1998

Piecewise exponential survival trees with time-dependent covariates.

Survival trees methods are nonparametric alternatives to the semiparametric Cox regression in survival analysis. In this paper, a tree-based method for censored survival data with time-dependent covariates is proposed. The proposed method assumes a very general model for the hazard function and is fully nonparametric. The recursive partitioning algorithm uses the likelihood estimation procedure to grow trees under a piecewise exponential structure that handles time-dependent covariates in a parallel way to time-independent covariates. In general, the estimated hazard at a node gives the risk for a group of individuals during a specific time period. Both cross-validation and bootstrap resampling techniques are implemented in the tree selection procedure. The performance of the proposed survival trees method is shown to be good through simulation and application to real data.

Biometry↗
PubMed2003

Comparative functional analysis of skull morphology of tree-gouging primates.

Many primates habitually feed on tree exudates such as gums and saps. Among these exudate feeders, Cebuella pygmaea, Callithrix spp., Phaner furcifer, and most likely Euoticus elegantulus elicit exudate flow by biting into trees with their anterior dentition. We define this behavior as gouging. Beyond the recent publication by Dumont ([1997] Am J Phys Anthropol 102:187-202), there have been few attempts to address whether any aspect of skull form in gouging primates relates to this specialized feeding behavior. However, many researchers have proposed that tree gouging results in larger bite force, larger internal skull loads, and larger jaw gapes in comparison to other chewing and biting behaviors. If true, then we might expect primate gougers to exhibit skull modifications that provide increased abilities to produce bite forces at the incisors, withstand loads in the skull, and/or generate large gapes for gouging. We develop 13 morphological predictions based on the expectation that gouging involves relatively large jaw forces and/or jaw gapes. We compare skull shapes for P. furcifer to five cheirogaleid taxa, E. elegantulus to six galagid species, and C. jacchus to two tamarin species, so as to assess whether gouging primates exhibit these predicted morphological shapes. Our results show little morphological evidence for increased force-production or load-resistance abilities in the skulls of these gouging primates. Conversely, these gougers tend to have skull shapes that are advantageous for creating large gapes. For example, all three gouging species have significantly lower condylar heights relative to the toothrow at a given mandibular length in comparison with closely related, nongouging taxa. Lowering the height of the condyle relative to the mandibular toothrow should reduce the stretching of the masseters and medial pterygoids during jaw opening, as well as position the mandibular incisors more anteriorly at wide jaw gapes. In other words, the lower incisors will follow a more vertical trajectory during both jaw opening and closing. We predict, based on these findings, that tree-gouging primates do not generate unusually large forces, but that they do use relatively large gapes during gouging. Of course, in vivo data on jaw forces and jaw gapes are required to reliably assess skull functions during gouging.

Anatomy, Comparative↗
PubMed1998

Self-organizing tree-growing network for the classification of protein sequences.

The self-organizing tree algorithm (SOTA) was recently introduced to construct phylogenetic trees from biological sequences, based on the principles of Kohonen's self-organizing maps and on Fritzke's growing cell structures. SOTA is designed in such a way that the generation of new nodes can be stopped when the sequences assigned to a node are already above a certain similarity threshold. In this way a phylogenetic tree resolved at a high taxonomic level can be obtained. This capability is especially useful to classify sets of diversified sequences. SOTA was originally designed to analyze pre-aligned sequences. It is now adapted to be able to analyze patterns associated to the frequency of residues along a sequence, such as protein dipeptide composition and other n-gram compositions. In this work we show that the algorithm applied to these data is able to not only successfully construct phylogenetic trees of protein families, such as cytochrome c, triosephophate isomerase, and hemoglobin alpha chains, but also classify very diversified sequence data sets, such as a mixture of interleukins and their receptors.

Algorithms↗
PubMed2003

Maintaining hydraulic control using deep rooted tree systems.

Groundwater phytotechnology systems are currently being used to control the migration of contaminant plumes and remove groundwater that flows into containment areas. Trees in such systems function by reducing recharge and using groundwater via transpiration. A stand of deep-rooted trees can act as a biological "pump", removing a substantial amount of water from the saturated zone. Depth to groundwater compared to rooting depth is an important consideration. Many useful tree species are not naturally deep-rooted, but various cultural practices can produce trees with roots that are deep enough to tap into the water table. Hydraulic control can be calculated or modeled using equations that compare transpired water to groundwater flow and take into account site-specific geologic and climatic variables. However, field measurements should be carried out whenever possible to obtain more precise estimates of groundwater capture and control.

Biodegradation, Environmental↗
PubMed1990

Systemically wound-responsive genes in poplar trees encode proteins similar to sweet potato sporamins and legume Kunitz trypsin inhibitors.

When the lower leaves of hybrid poplar trees are mechanically wounded, several novel mRNAs accumulate in the unwounded upper leaves (Parsons TJ, Bradshaw HD, Gordon MP: Systemic accumulation of specific mRNAs in response to wounding in poplar trees, Proc Natl Acad Sci USA, in press). A partial cDNA clone corresponding to a transcript from the wound-responsive gene designated win 3 (wound-inducible) has been cloned by differential hybridization to 32P-labelled cDNA from the leaves of wounded trees. Northern blots show a large accumulation of win 3 transcripts in the unwounded leaves of wounded trees. Southern blot analysis of poplar DNA suggests that win 3 is a member of a multigene family. The nucleotide sequences of several win 3 cDNA clones have been determined, indicating that at least three win 3 gene family members are transcribed. A genomic clone of a win 3 gene family member has been isolated and a 1.5 kb Hind III fragment containing the predicted protein-coding and 5' upstream regions has been sequenced. The putative win 3 gene product is similar to the major soluble proteins of sweet potato tubers, sporamin A and sporamin B. Both Win3 and the sporamins share significant amino acid sequence identity with Kunitz-type trypsin inhibitors from legume seeds. The Kunitz family of proteinase inhibitors thus joints three other proteinase inhibitor families which are systemically responsive to wounding.

Amino Acid Sequence↗
PubMed1998

Phylogenetic analysis of reptilian hemoglobins: trees, rates, and divergences.

Phylogenetic relationships among reptiles were examined using previously published and newly determined hemoglobin sequences. Trees reconstructed from these sequences using maximum-parsimony, neighbor-joining, and maximum-likelihood algorithms were compared with a phylogenetic tree of Amniota, which was assembled on the basis of published morphological data. All analyses differentiated alpha chains into alphaA and alphaD types, which are present in all reptiles except crocodiles, where only alphaA chains are expressed. The occurrence of the alphaD chain in squamates (lizards and snakes only in this study) appears to be a general characteristic of these species. Lizards and snakes also express two types of beta chains (betaI and betaII), while only one type of beta chain is present in birds and crocodiles. Reconstructed hemoglobin trees for both alpha and beta sequences did not yield the monophyletic Archosauria (i.e., crocodilians + birds) and Lepidosauria (i.e., Sphenodon + squamates) groups defined by the morphology tree. This discrepancy, as well as some other poorly resolved nodes, might be due to substantial heterogeneity in evolutionary rates among single hemoglobin lineages. Estimation of branch lengths based on uncorrected amino acid substitutions and on distances corrected for multiple substitutions (PAM distances) revealed that relative rates for squamate alphaA and alphaD chains and crocodilian beta chains are at least twice as high as those of the rest of the chains considered. In contrast to these rate inequalities between reptilian orders, little variation was found within squamates, which allowed determination of absolute evolutionary rates for this subset of hemoglobins. Rate estimates for hemoglobins of lizards and snakes yielded 1.7 (alphaA) and 3.3 (beta) million years/PAM when calibrated with published divergence time vs. PAM distance correlates for several speciation events within snakes and for the squamate left and right arrow sphenodontid split. This suggests that hemoglobin chains of squamate reptiles evolved approximately 3.5 (alphaA) or approximately 1.7 times (beta) faster than their mammalian equivalents. These data also were used to obtain a first estimate of some intrasquamate divergence times.

Alligators and Crocodiles↗
PubMed2001

The water-soluble components of the essential oil of Melaleuca alternifolia (tea tree oil) suppress the production of superoxide by human monocytes, but not neutrophils, activated in vitro.

OBJECTIVE: To evaluate the regulatory properties of the essential oil of Melaleuca alternifolia (tea tree oil) on the production of oxygen derived reactive species by human peripheral blood leukocytes activated in vitro. MATERIALS AND METHODS: The ability of tea tree oil to reduce superoxide production by neutrophils and monocytes stimulated with N-formyl-methionyl-leucyl-phenylalanine (fMLP), lipopolysaccharide (LPS) or phorbol 12-myristate 13-acetate (PMA) was examined. RESULTS: The water-soluble fraction of tea tree oil had no significant effect on agonist-stimulated superoxide production by neutrophils, but significantly and dose-dependently suppressed agonist-stimulated superoxide production by monocytes. This suppression was not due to cell death. Chemical analysis identified the water-soluble components to be terpinen-4-ol, alpha-terpineol and 1,8-cineole. When examined individually, terpinen-4-ol significantly suppressed fMLP- and LPS- but not PMA-stimulated superoxide production; alpha-terpineol significantly suppressed fMLP-, LPS- and PMA-stimulated superoxide production; 1,8-cineole was without effect. CONCLUSION: Tea tree oil components suppress the production of superoxide by monocytes, but not neutrophils, suggesting the potential for selective regulation of cell types by these components during inflammation.

Anti-Infective Agents, Local↗
PubMed2006

Primary colonization and breakdown of igneous rocks by endemic, succulent elephant trees (Pachycormus discolor) of the deserts in Baja California, Mexico.

Trees growing in rocks without soil are uncommon. In two arid regions in Baja California, Mexico, field surveys found large numbers of rock-colonizing elephant trees (Pachycormus discolor (Benth.) Coville ex Standl. (Mexican name: copalquin) growing in igneous rocks (granite and basalt) as primary colonizers without the benefit of soil or with a very small amount of soil generated by their own growth. Many adult trees broke large granite boulders and were capable of wedging, growing in, and colonizing rocks and cliffs made of ancient lava flows. This is the first record of a tree species, apart from the previously recorded cacti, capable of primary colonization of rocks and rock rubble in hot deserts.

Acclimatization↗
PubMed2002

Climatic and stream-flow controls on tree growth in a Western montane riparian forest.

Humans have severely impacted riparian ecosystems through water diversions, impoundments, and consumptive uses. Effective management of these important areas is becoming an increasingly high priority of land managers, particularly as municipal, industrial, and recreational demands for water increase. We examined radial tree growth of four riparian tree species ( Pinus jeffreyi, Populus trichocarpa, Betula occidentalis, and Pinus monophylla) along Bishop Creek, California, and developed models relating basal area increment (BAI) and relative basal area increment (RBAI) to climatic and stream flow variables. Between years 1995-1999, univariate regression analysis with stream flow explained 29 to 61% of the variation in BAI and RBAI among all species except P. trichocarpa; growth by P. trichocarpa was not significantly related to stream flows over this period. Stepwise linear regression indicated that species responded differently to climatic variables, and models based on these variables explained between 33 to 86% of variation in BAI and RBAI during the decade of the 1990s. We examined branch growth of P. trichocarpa for sensitivity to differences in stream flow regimes and found that annual branch growth did not vary between a high- and low-flow site, but that annual branch growth was significantly higher in wet years with greater stream flows. Our results support the establishment of site-specific management goals by land managers that take into account all of the important tree species present in riparian ecosystems and their differential responses to altered hydrologic condition. Instream flow requirements for maintaining tree growth and vigor are only one of the species-specific responses that need to be evaluated, and these assessments should attempt to separate experimentally stream-flow (managed) controls from climatic (unmanaged) controls on growth.

Betula↗
PubMed2005

Potential tree species for use in the restoration of unsanitary landfills.

Given that they represent the most economical option for disposing of refuse, waste landfills are widespread in urban areas. However, landfills generate air and water pollution and require restoration for landscape development. A number of unsanitary waste landfills have caused severe environmental problems in developing countries. This study aimed to investigate the colonization status of different tree species on waste landfills to assess their potential for restoring unsanitary landfills in South Korea. Plot surveys were conducted using 10 x 10-m quadrats at seven waste landfill sites: Bunsuri, Dugiri, Hasanundong, Gomaeri, Kyongseodong, Mojeonri, and Shindaedong. We determined the height, diameter at breast height (DBH), and number of tree species in the plots, and enumerated all saplings < or =1 m high. Because black locust, Robinia pseudoacacia, was the dominant tree species in the waste landfills, we measured the distance from the presumed mother plant (i.e., the tallest black locust in a patch), height, and DBH of all individuals in black locust patches to determine patch structure. Robinia pseudoacacia, Salix koreensis, and Populus sieboldii formed canopy layers in the waste landfills. The basal area of black locust was 1.51 m(2)/ha, and this species had the highest number of saplings among all tree species. The diameter of the black locust patches ranged from 3.71 to 11.29 m. As the patch diameter increased, the number of regenerated saplings also tended to increase, albeit not significantly. Black locust invaded via bud banks and spread clonally in a concentric pattern across the landfills. This species grew well in the dry habitat of the landfills, and its growth rate was very high. Furthermore, black locust has the ability to fix nitrogen symbiotically; it is therefore considered a well-adapted species for waste landfills. Eleven woody species were selected for screening: Acer palmatum, Albizzia julibrissin, Buxus microphylla var. koreana, Ginkgo biloba, Hibiscus syriacus, Koelreuteria paniculata, Ligustrum obtusifolium, Liriodendron tulipifera, Pinus koraiensis, Pinus thunbergii, and Sophora japonica. As a result of a comparison of the total ratio (sum of shoot extension and diameter growth at the landfill relative to a reference site) and mortality, six species (Liriodendron tulipifera, Albizzia julibrissin, Ligustrum obtusifolium, Buxus microphylla var. koreana, Hibiscus syriacus, and Sophora japonica), which had a total ratio >1 and experienced low mortality, are recommended as potentially suitable species for waste landfill remediation. We suggest that mixed plantations of ubiquitous adaptable species and naturally occurring black locust will enhance the landscape through synergistic effects.

Adaptation, Physiological↗
PubMed2004

Differential expression patterns of two cellulose synthase genes are associated with primary and secondary cell wall development in aspen trees.

The quality and quantity of cellulose deposited in the primary and secondary cell walls of plants vary in accordance with their biological function. However, the molecular basis of such cellulose heterogeneity has so far remained unclear. Since enrichment of better-quality cellulose, in terms of increased degree of polymerization and crystallinity, is one of the goals of forest biotechnology, our main objective is to decipher the roles of distinct cellulose synthase (CesA) genes in tree development, with special reference to wood production. Here, we report two full-length CesA cDNAs, PtrCesA3 and PtrCesA4, from an economically important tree aspen (Populus tremuloides). PtrCesA3 is orthologous to the Arabidopsis AtCesA4 gene involved in secondary wall formation, whereas PtrCesA4 is orthologous to the Arabidopsis AtCesA1 gene involved in primary cell wall formation. To define the specific cell types expressing these CesA genes, we explored the natural distribution patterns of PtrCesA3 and PtrCesA4 transcripts in a variety of aspen organs, such as leaves, petiole, stem, and roots, using in situ hybridization with hypervariable region-specific antisense riboprobes. Such a side-by-side comparison suggested that PtrCesA3 is exclusively expressed in secondary-wall-forming cells of xylem and phloem fibers, whereas PtrCesA4 is predominantly expressed in primary-wall-forming expanding cells in all aspen organs examined. These findings suggest a functionally distinct role for each of these two types of PtrCesAs during primary and secondary wall biogenesis in aspen trees, and that such functional distinction appears to be conserved between annual herbaceous plants and perennial trees.

Cell Wall↗
PubMed2006

Xylem-specific and tension stress-responsive coexpression of KORRIGAN endoglucanase and three secondary wall-associated cellulose synthase genes in aspen trees.

In nature, angiosperm trees develop tension wood on the upper side of their leaning trunks and drooping branches. Development of tension wood is one of the straightening mechanisms by which trees counteract leaning or bending of stem and resume upward growth. Tension wood is characterized by the development of a highly crystalline cellulose-enriched gelatinous layer next to the lumen of the tension wood fibers. Thus experimental induction of tension wood provides a system to understand the process of cellulose biosynthesis in trees. Since KORRIGAN endoglucanases (KOR) appear to play an important role in cellulose biosynthesis in Arabidopsis, we cloned PtrKOR, a full-length KOR cDNA from aspen xylem. Using RT-PCR, in situ hybridization, and tissue-print assays, we show that PtrKOR gene expression is significantly elevated on the upper side of the bent aspen stem in response to tension stress while KOR expression is significantly suppressed on the opposite side experiencing compression stress. Moreover, three previously reported aspen cellulose synthase genes, namely, PtrCesA1, PtrCesA2, and PtrCesA3 that are closely associated with secondary cell wall development in the xylem cells exhibited similar tension stress-responsive behavior. Our results suggest that coexpression of these four proteins is important for the biosynthesis of highly crystalline cellulose typically present in tension wood fibers. Their simultaneous genetic manipulation may lead to industrially relevant improvement of cellulose in transgenic crops and trees.

Arabidopsis Proteins↗