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PubMed1996

Antifungal activity of the essential oil of Melaleuca alternifolia (tea tree oil) against pathogenic fungi in vitro.

The in vitro antifungal activity of tea oil, the essential oil of Melaleuca alternifolia, has been evaluated against 26 strains of various dermatophyte species, 54 yeasts, among them 32 strains of Candida albicans and other Candida sp. as well as 22 different Malassezia furfur strains. Minimum inhibitory concentrations (MIC) of tea tree oil were measured by agar dilution technique. Tea tree oil was found to be able to inhibit growth of all clinical fungal isolates. For the investigated dermatophytes MIC values from 1,112.5 to 4,450.0 micrograms/ml with a geometric mean of 1,431.5 micrograms/ml were demonstrated. Both C. albicans strains and the other strains belonging to the genus Candida and Trichosporon appeared to be slightly less susceptible to tea tree oil in vitro. However, their MIC values, which varied from 2,225.0 to 4,450.0 micrograms/ml (geometric mean 4,080 micrograms/ml), indicated moderate susceptibility to the essential oil of M. alternifolia. The lipophilic yeast M. furfur seemed to be most susceptible to tea tree oil. MIC values between 556.2 and 4,450.0 micrograms/ml (geometric mean 1,261.5 micrograms/ml) were found against the tested M. furfur strains. However, when calculated as percentage tea tree oil of the agar, the above-mentioned concentrations correspond to 0.5-0.44% tea tree oil content. These values are far below the usual relatively high therapeutic concentrations of the agent; approximately 5-10% solution or even the concentrated essential oil are used for external treatment. In comparison with tea tree oil, in vitro susceptibility against miconazole, an established topical antifungal, was tested. As expected, very low MIC values for miconazole were found for dermatophytes (geometric mean 0.2 microgram/ml), yeasts (geometric mean 1.0 microgram/ml), and M. furfur (geometric mean 2.34 micrograms/ml). It is suggested that the in vivo effect of tea tree oil ointment in the therapy of fungal infections of the skin and mucous membranes as well as in the treatment of dandruff, a mild form of seborrheic dermatitis, may be at least partly due to an antifungal activity of tea tree oil.

Antifungal Agents↗

PubMed2006

Taxonomic colouring of phylogenetic trees of protein sequences.

BACKGROUND: Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. RESULTS: We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. CONCLUSION: PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

Algorithms↗

PubMed2005

Do orthologous gene phylogenies really support tree-thinking?

BACKGROUND: Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. RESULTS: Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. CONCLUSION: Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

Algorithms↗

PubMed2006

Model selection for mixtures of mutagenetic trees.

The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have been applied to infer the order and rate of occurrence of these mutations. Understanding and predicting this evolutionary process is an important prerequisite for the rational design of antiretroviral therapies. In practice, mixtures models of K mutagenetic trees provide more flexibility and are often more appropriate for modelling observed mutational patterns. Here, we investigate the model selection problem for K-mutagenetic trees mixture models. We evaluate several classical model selection criteria including cross-validation, the Bayesian Information Criterion (BIC), and the Akaike Information Criterion. We also use the empirical Bayes method by constructing a prior probability distribution for the parameters of a mutagenetic trees mixture model and deriving the posterior probability of the model. In addition to the model dimension, we consider the redundancy of a mixture model, which is measured by comparing the topologies of trees within a mixture model. Based on the redundancy, we propose a new model selection criterion, which is a modification of the BIC. Experimental results on simulated and on real HIV data show that the classical criteria tend to select models with far too many tree components. Only cross-validation and the modified BIC recover the correct number of trees and the tree topologies most of the time. At the same optimal performance, the runtime of the new BIC modification is about one order of magnitude lower. Thus, this model selection criterion can also be used for large data sets for which cross-validation becomes computationally infeasible.

Bayes Theorem↗

PubMed2006

Association between split selection instability and predictive error in survival trees.

OBJECTIVES: To evaluate split selection instability in six survival tree algorithms and its relationship with predictive error by means of a bootstrap study. METHODS: We study the following algorithms: logrank statistic with multivariate p-value adjustment without pruning (LR), Kaplan-Meier distance of survival curves (KM), martingale residuals (MR), Poisson regression for censored data (PR), within-node impurity (WI), and exponential log-likelihood loss (XL). With the exception of LR, initial trees are pruned by using split-complexity, and final trees are selected by means of cross-validation. We employ a real dataset from a clinical study of patients with gallbladder stones. The predictive error is evaluated using the integrated Brier score for censored data. The relationship between split selection instability and predictive error is evaluated by means of box-percentile plots, covariate and cutpoint selection entropy, and cutpoint selection coefficients of variation, respectively, in the root node. RESULTS: We found a positive association between covariate selection instability and predictive error in the root node. LR yields the lowest predictive error, while KM and MR yield the highest predictive error. CONCLUSIONS: The predictive error of survival trees is related to split selection instability. Based on the low predictive error of LR, we recommend the use of this algorithm for the construction of survival trees. Unpruned survival trees with multivariate p-value adjustment can perform equally well compared to pruned trees. The analysis of split selection instability can be used to communicate the results of tree-based analyses to clinicians and to support the application of survival trees.

Algorithms↗

PubMed2000

Pollen coupling of forest trees: forming synchronized and periodic reproduction out of chaos.

Many of the tree species in mature forests show masting; their reproductive activity has a large variance between years and is often synchronized between different individuals. In this paper, we analyse a globally coupled map model in which trees accumulate photosynthate every year, produce flowers when the energy reserve level exceeds a threshold, and set seeds and fruits at a rate limited by pollen availability. Without pollen limitation, the trees in the forest show independent chaotic fluctuation. Coupling of trees via pollen exchange results in reproduction being synchronized partially or completely over the forest. The whole forest shows diverse dynamical behaviors determined by the values of two essential parameters; the depletion coefficient k and the coupling strength beta. We find perfectly synchronized periodic reproduction, synchronized reproduction with a chaotic time series, clustering phenomena, and chaotic reproduction of trees without synchronization over individuals. There are many parameter windows in which synchronized reproduction of trees shows a stable periodic fluctuation. For perfectly synchronized forests, we can calculate all the Lyapunov exponents analytically. They show that synchronized reproduction of all the trees in the forest can only occur when trees flower at low (but positive) levels in a significant fraction of years, resulting in small fruit sets due to outcrossed pollen limitation. This is consistent with the observation that the distinction between mast years and non-mast years is often not clear cut.

Models, Biological↗

PubMed1997

Forest tree biotechnology.

The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium.

Biotechnology↗

PubMed2001

Managing urban trees and their soil envelopes in a contiguously developed city environment.

Urban Hong Kong is covered by high building, road, and population densities. Its urban morphology is inherently not conducive to extensive or high-grade greening. Recent renewal of old areas has squeezed out some limited interstitial plantable space, although in new development areas modest spaces have been earmarked for greenery. The study aims at evaluating the major constraints to urban trees and their companion urban soil envelopes and at providing specific recommendations to improve tree management in the city. The analysis covers the above-ground confinements that dampen tree performance, the less tangible but rather difficult institutional restrictions that impose a somewhat unnecessary lid on tree planting, the multiplicity of players and stakeholders involved in urban-tree management that militates against coordination and cooperation, the widespread occupation of underground space by utility lines often to the exclusion of trees, and the extremely poor quality of urban soils that are often used without amelioration to support tree growth. The management recommendations furnish practical suggestions and hints to improve the short- and long-term welfare of trees in terms of quality, quantity, and spatial distribution. The conclusion enumerates some concrete measures for consideration by decision-makers to upgrade the city's greenery to close the gap between science and policy.

Cities↗

PubMed2002

Axial and radial water transport and internal water storage in tropical forest canopy trees.

Heat and stable isotope tracers were used to study axial and radial water transport in relation to sapwood anatomical characteristics and internal water storage in four canopy tree species of a seasonally dry tropical forest in Panama. Anatomical characteristics of the wood and radial profiles of sap flow were measured at the base, upper trunk, and crown of a single individual of Anacardium excelsum, Ficus insipida, Schefflera morototoni, and Cordia alliodora during two consecutive dry seasons. Vessel lumen diameter and vessel density did not exhibit a consistent trend axially from the base of the stem to the base of the crown. However, lumen diameter decreased sharply from the base of the crown to the terminal branches. The ratio of vessel lumen area to sapwood cross-sectional area was consistently higher at the base of the crown than at the base of the trunk in A. excelsum, F. insipida and C. alliodora, but no axial trend was apparent in S. morototoni. Radial profiles of the preceding wood anatomical characteristics varied according to species and the height at which the wood samples were obtained. Radial profiles of sap flux density measured with thermal dissipation sensors of variable length near the base of the crown were highly correlated with radial profiles of specific hydraulic conductivity (k(s)) calculated from xylem anatomical characteristics. The relationship between sap flux density and k(s) was species-independent. Deuterium oxide (D(2)O) injected into the base of the trunk of the four study trees was detected in the water transpired from the upper crown after only 1 day in the 26-m-tall C. alliodora tree, 2 days in the 28-m-tall F. insipida tree, 3 days in the 38-m-tall A. excelsum tree, and 5 days in the 22-m-tall S. morototoni tree. Radial transport of injected D(2)O was detected in A. excelsum, F. insipida and S. morototoni, but not C. alliodora. The rate of axial D(2)O transport, a surrogate for maximum sap velocity, was positively correlated with the predicted sapwood k(s) and with tree height normalized by the relative diurnal water storage capacity. Residence times for the disappearance of the D(2)O tracer in transpired water ranged from 2 days in C. alliodora to 22 days in A. excelsum and were positively correlated with a normalized index of diurnal water storage capacity. Capacitive exchange of water between stem storage compartments and the transpiration stream thus had a profound influence on apparent rates of axial water transport, the magnitude of radial water movement, and the retention time in the tree of water taken up by the roots. The inverse relationship between internal water exchange capacity and k(s) was consistent with a trade-off contributing to stability of leaf water status through highly efficient water transport at one extreme and release of stored water at the other extreme.

Biological Transport↗

PubMed2006

Fitness consequences of pheromone production and host selection strategies in a tree-killing bark beetle (Coleoptera: Curculionidae: Scolytinae).

Timing of arrival at a resource often determines an individual's reproductive success. Tree-killing bark beetles can reproduce in healthy trees by attacking in adequate numbers to overcome host defences that could otherwise be lethal. This process is mediated by aggregation and antiaggregation pheromones. Beetles that arrive early in such a "mass attack" must contend with undiminished tree defences, and produce enough pheromones to attract more beetles, but have a head start on gallery construction and egg-laying. Beetles that arrive late may be impeded by competition and diminishing availability of phloem, but should experience fewer costs associated with pheromone production and battling tree defences. We investigated relationships between timing of arrival, body size, pheromone production and fitness in the southern pine beetle, Dendroctonus frontalis. In field experiments, we captured beetles that arrived early (pioneers) and late on slash pine trees, Pinus elliottii, and measured pheromone amounts in their hindguts. We marked gallery entrances of beetles as they landed on a tree and measured their reproductive success after the attack terminated. We found no difference in body size or pheromone amounts between early and late arrivers. Most beetles arrived at the middle of the attack sequence, and excavated longer galleries per day than early arrivers. The number of offspring produced per day by beetles that established galleries midway through mass attack was higher than those that arrived early or very late in the sequence. Our results suggest that beetles do not exhibit adaptive phenotypic plasticity in pre-landing pheromone production, depending on the extent of previous colonisation of a host. Rather, it appears that stabilising selection favours beetles that attack in the middle of the sequence, and contributes to attack synchrony. Synchronous attack on trees is essential before population booms characteristic of tree-killing bark beetles can occur in nature.

Animals↗

PubMed1989

Tree graphs of RNA secondary structures and their comparisons.

To facilitate comparison of RNA secondary structures each structure is represented as an ordered labeled tree. Several alternate secondary structures yielding a set of trees can be computed for any given RNA molecule (sequence). Frequently recurring subtrees are searched in this set of trees. The consensus structure motifs are then selected and used to construct a secondary structure model of the RNA. Given the difficulties involved in RNA secondary structure calculations, this procedure may significantly improve our predictive capabilities. In addition, the change of secondary structures between two different RNA sequences is described as a transformation of ordered trees. The transferable ratio of tree A from tree B is defined as a proportion of the largest common subtrees in trees A and B occurring in tree A. The method is applied to the study of the mechanism of human alpha 1 globin pre-mRNA splicing. In the study, two tentative splicing mechanisms, A and B, with different orders of intron excision from alpha 1 globin pre-mRNA have been stimulated. A possible relationship between the structural features of the secondary structures and the order of intron excision in the pathway of precursor splicing of human alpha 1 globin is discussed.

Base Sequence↗

PubMed2006

A tree-based decision rule for identifying profile groups of cases without predefined classes: application in diffuse large B-cell lymphomas.

In this paper, we examined the utility of a forward growing classification tree as a supplement to cluster analysis for deriving a decision rule for the identification of profile groups when the cases do not belong to predefined classes. The technique was applied for the identification of low and high proliferation profile groups of diffuse large B-cell lymphomas according to the immunohistochemical expression levels of proliferation proteins. In a forward growing classification tree method, the size of the tree is controlled by the improvement (threshold value) in the apparent misclassification rate after each split. The classes used in the tree were defined using k-means clustering. The decision rule consisted of the splitting points of the split variables used. The methodology was applied to the histology data from 79 cases of diffuse large B-cell lymphomas. Ten classes of individual cases were derived from k-means clustering. Then, a classification tree with a threshold of 2% was used to derive the decision rule. Branches at the left side of the tree consisted of individuals with a low proliferation profile and branches at the right side of the tree consisted of cases with a high proliferation profile. The classification tree, as a supplement method, not only identified but also provided decision rules for identifying profile groups. Finally, it also allowed for exploration of the data structure.

Algorithms↗

PubMed2006

Assessing the potential of native tree species for carbon sequestration forestry in Northeast China.

Although the native forests of China are exceptionally diverse, only a small number of tree species have been widely utilized in forest plantations and reforestation efforts. We used dendrochronological sampling methods to assess the potential growth and carbon sequestration of native tree species in Jilin Province, Northeast China. Trees were sampled in and near the Changbaishan Biosphere Reserve, with samples encompassing old-growth, disturbed forest, and plantations. To approximate conditions for planted trees, sampling focused on trees with exposed crowns (dominant and co-dominant individuals). A log-linear relationship was found between diameter increment and tree diameter, with a linear decrease in increment with increasing local basal area; no significant differences in these patterns between plantations and natural stands were detected for two commonly planted species (Pinus koraiensis and Larix olgensis). A growth model that incorporates observed feedbacks with individual tree size and local basal area (in conjunction with allometric models for tree biomass), was used to project stand-level biomass increment. Predicted growth trajectories were then linked to the carbon process model InTEC to provide estimates of carbon sequestration potential. Results indicate substantial differences among species, and suggest that certain native hardwoods (in particular Fraxinus mandshurica and Phellodendron amurense), have high potential for use in carbon forestry applications. Increased use of native hardwoods in carbon forestry in China is likely to have additional benefits in terms of economic diversification and enhanced provision of "ecosystem services", including biodiversity protection.

Biodiversity↗

PubMed1997

Predominant tree aeroallergens of the Washington, DC area: a six year survey (1989-1994).

OBJECTIVE: A 6-year (1989 to 1994) aerobiologic survey of the Washington DC area was performed to identify predominant area tree pollens, atmospheric concentrations, and peak flowering periods. METHODS: Aeroallergen sampling was conducted using a volumetric rotating-arm impaction Rotorod sampler (Sampling Technologies, Inc, Los Altos Hills, California). RESULTS: The Washington DC pollen calendar may begin as early as January when pollen of the Cupresseacea, Aceracea, Pinaceae, and Betulaceae are observed in small amounts. February through June encompasses the major part of our tree season with considerable overlapping of pollination periods for various trees. The Ulmaceae have two distinct pollinating times with later flowering species of elm pollinating August through October coinciding with ragweed season. April is usually the month with the highest weekly average concentrations. Each year oaks contribute more than 50% of the total tree pollen count followed by pollen of the Pinacea, Cupresseacea, Moracea, and Betuleacea. Times for onset of pollination as well as peak atmospheric concentrations varied from year to year. High production years for some tree aeroallergens are low years for others. CONCLUSION: The Washington DC area is exposed to significant atmospheric concentrations of tree pollen from February through June. Establishing what area tree aeroallergens predominate with respect to their atmospheric concentrations and peak pollinating times is essential for the effective diagnosis and treatment of the tree-allergic patient.

Air Pollutants↗

PubMed2003

Identification, measurement and interpretation of tree rings in woody species from mediterranean climates.

We review the literature dealing with mediterranean climate, vegetation, phenology and ecophysiology relevant to the understanding of tree-ring formation in mediterranean regions. Tree rings have been used extensively in temperate regions to reconstruct responses of forests to past environmental changes. In mediterranean regions, studies of tree rings are scarce, despite their potential for understanding and predicting the effects of global change on important ecological processes such as desertification. In mediterranean regions, due to the great spatio-temporal variability of mediterranean environmental conditions, tree rings are sometimes not formed. Often, clear seasonality is lacking, and vegetation activity is not always associated with regular dormancy periods. We present examples of tree-ring morphology of five species (Arbutus unedo, Fraxinus ornus, Quercus cerris, Q. ilex, Q. pubescens) sampled in Tuscany, Italy, focusing on the difficulties we encountered during the dating. We present an interpretation of anomalies found in the wood structure and, more generally, of cambial activity in such environments. Furthermore, we propose a classification of tree-ring formation in mediterranean environments. Mediterranean tree rings can be dated and used for dendrochronological purposes, but great care should be taken in selecting sampling sites, species and sample trees.

Climate↗

PubMed2004

The limits to tree height.

Trees grow tall where resources are abundant, stresses are minor, and competition for light places a premium on height growth. The height to which trees can grow and the biophysical determinants of maximum height are poorly understood. Some models predict heights of up to 120 m in the absence of mechanical damage, but there are historical accounts of taller trees. Current hypotheses of height limitation focus on increasing water transport constraints in taller trees and the resulting reductions in leaf photosynthesis. We studied redwoods (Sequoia sempervirens), including the tallest known tree on Earth (112.7 m), in wet temperate forests of northern California. Our regression analyses of height gradients in leaf functional characteristics estimate a maximum tree height of 122-130 m barring mechanical damage, similar to the tallest recorded trees of the past. As trees grow taller, increasing leaf water stress due to gravity and path length resistance may ultimately limit leaf expansion and photosynthesis for further height growth, even with ample soil moisture.

Biological Transport↗

PubMed2002

Tea tree oil reduces histamine-induced skin inflammation.

BACKGROUND: Tea tree oil is the essential oil steam-distilled from Melaleuca alternifolia, an Australian native plant. In recent years it has become increasingly popular as an antimicrobial for the treatment of conditions such as tinea pedis and acne. OBJECTIVES: To investigate the anti-inflammatory properties of tea tree oil on histamine-induced weal and flare. METHODS: Twenty-seven volunteers were injected intradermally in each forearm (study and control assigned on an alternating basis) with histamine diphosphate (5 microg in 50 microL). Flare and weal diameters and double skin thickness were measured every 10 min for 1 h to calculate flare area and weal volume. At 20 min, 25 microL of 100% tea tree oil was applied topically to the study forearm of 21 volunteers. For six volunteers, 25 microL paraffin oil was applied instead of tea tree oil. RESULTS: Application of liquid paraffin had no significant effect on histamine-induced weal and flare. There was also no difference in mean flare area between control arms and those on which tea tree oil was applied. However, mean weal volume significantly decreased after tea tree oil application (10 min after tea tree oil application, P = 0.0004, Mann-Whitney U-test). CONCLUSIONS: This is the first study to show experimentally that tea tree oil can reduce histamine-induced skin inflammation.

Adult↗

PubMed1999

Influence of organic matter, cations and surfactants on the antimicrobial activity of Melaleuca alternifolia (tea tree) oil in vitro.

The effect of some potentially interfering substances and conditions on the antimicrobial activity of Melaleuca alternifolia (tea tree) oil was investigated. Agar and broth dilution methods were used to determine minimum inhibitory and cidal concentrations of tea tree oil in the presence and absence of each potentially interfering substance. Activity was determined against Gram-positive and -negative bacteria, and Candida albicans. Minimum inhibitory or cidal concentrations differed from controls by two or more dilutions, for one or more organisms, where Tween-20, Tween-80, skim-milk powder and bovine serum albumin were assessed. These differences were not seen when assays were performed in anaerobic conditions, or in the presence of calcium and magnesium ions. The effect of organic matter on the antimicrobial activity of tea tree oil was also investigated by an organic soil neutralization test. Organisms were exposed to lethal concentrations of tea tree oil ranging from 1-10% (v/v), in the presence of 1-30% (w/v) dry bakers' yeast. After 10 min contact time, viability was determined. At > or = 1%, organic matter compromised the activity of each concentration of tea tree oil against Staphylococcus aureus and C. albicans. At 10% or more, organic matter compromised the activity of each tea tree oil concentration against Pseudomonas aeruginosa. Organic matter affected 1 and 2% tea tree oil, but not 4 and 8%, against Escherichia coli. In conclusion, organic matter and surfactants compromise the antimicrobial activity of tea tree oil, although these effects vary between organisms.

Agar↗