LVB: parsimony and simulated annealing in the search for phylogenetic trees

Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.

Extraction and determination of ellagic acid content in chestnut bark and fruit

Chestnuts are an important economic resource in the chestnut growing regions, not only for the fruit, but also for the wood. The content of ellagic acid (EA), a naturally occurring inhibitor of carcinogenesis, was determined in chestnut fruits and bark. EA was extracted with methanol and free ellagic acid was determined by HPLC with UV detection, both in the crude extract and after hydrolysis. The concentration of EA was generally increased after hydrolysis due to the presence of ellagitannins in the crude extract. The concentration varied between 0.71 and 21.6 ing g(-1) (d.w.) in un-hydrolyzed samples, and between 2.83 and 18.4 mg g(-1) (d.w.) ill hydrolyzed samples. In chestnut fruits, traces of EA were present in the seed, with higher concentrations in the pellicle and pericarp. However, all fruit tissues had lower concentrations of EA than had the bark. The concentration of EA in the hydrolyzed samples showed a non-linear correlation with the concentration in the unhydrolyzed extracts. (C) 2008 Elsevier Ltd. All rights reserved.

Towards the automatic reconstruction of dendritic trees using particle filters

The 3D reconstruction of a Golgi-stained dendritic tree from a serial stack of images captured with a transmitted light bright-field microscope is investigated. Modifications to the bootstrap filter are discussed such that the tree structure may be estimated recursively as a series of connected segments. The tracking performance of the bootstrap particle filter is compared against Differential Evolution, an evolutionary global optimisation method, both in terms of robustness and accuracy. It is found that the particle filtering approach is significantly more robust and accurate for the data considered.

Trees outside forests and rural livelihoods: a study of Chitwan District, Nepal

Trees outside forests (TOF) in Nepal’s Terai have significantly increased over the past decade. The Chitwan District was one of the focus districts in the Terai Community Forestry Development Project that promoted a tree seedling distribution program. This paper examines the current position of tree integration on farmland and its contribution to livelihoods of rural households in this district. Interviews with local key informants, government and non-government agencies and woodbased industries, as well as an in-depth study of 32 households were used to describe the constraints faced by the households in management of trees on farmland. Most households cited disease, poor growth, lack of preferred tree species, lack of technical support, an uncertain tree market, and lack of financial support as constraints. Despite the important role of trees in subsistence and marketbased rural livelihood diversification, and the consequent reduction in pressure on national forests from on-farm trees, current government policies and practices fail to recognise the value of these trees. It is argued that there is substantial potential for improving on-farm trees to enhance rural livelihoods. A responsive service mechanism centred on tree growing households would help the management of tree resources on the farmland.

Societal choice for climate change futures: trees, biotechnology and clean development

The rate and magnitude of predicted climate change require that we urgently mitigate emissions or sequester carbon on a substantial scale in order to avoid runaway climate change. Geo- and bioengineering solutions are increasingly proposed as viable and practical strategies for tackling global warming. Biotechnology companies are already developing transgenic “super carbon-absorbing” trees, which are sold as a cost-effective and relatively low-risk means of sequestering carbon. The question posed in this article is, Do super carbon trees provide real benefits or are they merely a fanciful illusion? It remains unclear whether growing these trees makes sense in terms of the carbon cost of production and the actual storage of carbon. In particular, it is widely acknowledged that “carbon-eating” trees fail to sequester as much carbon as they oxidize and return to the atmosphere; moreover, there are concerns about the biodiversity impacts of large-scale monoculture plantations. The potential social and ecological risks and opportunities presented by such controversial solutions warrant a societal dialogue.

Biomass functions and expansion factors in young Norway spruce (Picea abies [L.] Karst) trees

Roots, stems, branches and needles of 160 Norway spruce trees younger than 10 years were sampled in seven forest stands in central Slovakia in order to establish their biomassfunctions (BFs) and biomassexpansionfactors (BEFs). We tested three models for each biomass pool based on the stem base diameter, tree height and the two parameters combined. BEF values decreased for all spruce components with increasing height and diameter, which was most evident in very young trees under 1 m in height. In older trees, the values of BEFs did tend to stabilise at the height of 3–4 m. We subsequently used the BEFs to calculate dry biomass of the stands based on average stem base diameter and tree height. Total stand biomass grew with increasing age of the stands from about 1.0 Mg ha−1 at 1.5 years to 44.3 Mg ha−1 at 9.5 years. The proportion of stem and branch biomass was found to increase with age, while that of needles was fairly constant and the proportion of root biomass did decrease as the stands grew older.

The trees and the bees: using enforcement and income projects to protect forests and rural livelihoods through spatial joint production

Forest managers in developing countries enforce extraction restrictions to limit forest degradation. In response, villagers may displace some of their extraction to other forests, which generates “leakage” of degradation. Managers also implement poverty alleviation projects to compensate for lost resource access or to induce conservation. We develop a model of spatial joint production of bees and fuelwood that is based on forest-compatible projects such as beekeeping in Thailand, Tanzania, and Mexico. We demonstrate that managers can better determine the amount and pattern of degradation by choosing the location of both enforcement and the forest-based activity.

Distributed hoeffding trees for pocket data mining

Collaborative mining of distributed data streams in a mobile computing environment is referred to as Pocket Data Mining PDM. Hoeffding trees techniques have been experimentally and analytically validated for data stream classification. In this paper, we have proposed, developed and evaluated the adoption of distributed Hoeffding trees for classifying streaming data in PDM applications. We have identified a realistic scenario in which different users equipped with smart mobile devices run a local Hoeffding tree classifier on a subset of the attributes. Thus, we have investigated the mining of vertically partitioned datasets with possible overlap of attributes, which is the more likely case. Our experimental results have validated the efficiency of our proposed model achieving promising accuracy for real deployment.

Thorn-dwelling ants provide antiherbivore defence for camelthorn trees, Vachellia erioloba, in Namibia

Ants are widely employed by plants as an antiherbivore defence. A single host plant can associate with multiple, symbiotic ant species, although usually only a single ant species at a time. Different plant-ant species may vary in the degree to which they defend their host plant. In Kenya, ant–acacia interactions are well studied, but less is known about systems elsewhere in Africa. A southern African species, Vachellia erioloba, is occupied by thorn-dwelling ants from three different genera. Unusually, multiple colonies of all these ants simultaneously and stably inhabit trees. We investigated if the ants on V. erioloba (i) deter insect herbivores; (ii) differ in their effectiveness depending on the identity of the herbivore; and (iii) protect the tree against an important herbivore, the larvae of the lepidopteran Gonometa postica. We show that experimental exclusion of ants leads to greater levels of herbivory on trees. The ants inhabiting V. erioloba are an effective deterrent against hemipteran and coleopteran, but not lepidopteran herbivores. Defensive services do not vary among ant species, but only Crematogaster ants exhibit aggression towards G. postica. This highlights the potential of the V. erioloba–ant mutualism for studying ant–plant interactions that involve multiple, simultaneously resident thorn-dwelling ant species.

Soil injections of carbohydrates improve fine root growth of established urban trees

Four established mature tree species (Aesculus hippocastanum L., Betula pendula Roth., Primus avium L. and Quercus rohur L.) commonly planted in UK urban landscapes were subjected to soil injections of the carbohydrate sucrose at 25, 50 and 70g per litre of water. Fine root dry weight was recorded at month 5 following soil injections. Soil injections of sucrose significantly increased fine root dry weight compared to controls, however; growth responses were influenced by species and the concentration of sucrose applied. Results indicate soil injections of sucrose ≥ 50g litre of water may be able to improve root growth of established mature trees. Such a response is desirable as root damage following construction is a frequent problem encountered by established trees growing in UK towns and cities.

Inhibition of proinflammatory biomarkers in THP1 macrophages by polyphenols derived from chamomile, meadowsweet and willow bark.

Antiinflammatory compounds in the diet can alleviate excessive inflammation, a factor in the pathogenesis of common diseases such as rheumatoid arthritis, atherosclerosis and diabetes. This study examined three European herbs, chamomile (Matricaria chamomilla), meadowsweet (Filipendula ulmaria L.) and willow bark (Salix alba L.), which have been traditionally used to treat inflammation and their potential for use as antiinflammatory agents. Aqueous herbal extracts and isolated polyphenolic compounds (apigenin, quercetin and salicylic acid, 0–100 μM) were incubated with THP1 macrophages, and interleukin (IL)-1β, IL-6 and tumour necrosis factor-alpha (TNF-) were measured. At concentrations of 10 μM, both apigenin and quercetin reduced IL-6 significantly ( p < 0.05). Apigenin at 10 μM and quercetin at 25 μM reduced TNF- significantly ( p < 0.05). Amongst the herbal extracts, willow bark had the greatest antiinflammatory activity at reducing IL-6 and TNF- production. This was followed by meadowsweet and then chamomile. The lowest effective antiinflammatory concentrations were noncytotoxic (MTT mitochondrial activity assay). The Comet assay, which was used to study the protective effect of the isolated phenols against oxidative damage, showed positive results for all three polyphenols. These are the first findings that demonstrate the antiinflammatory capacity of these herbal extracts.

Land use intensity and trees on farms in Malawi

Rapidly increasing population densities in Malawi have put a huge strain on the existing agricultural land and the surrounding woodland. Smallholder agriculture is the dominant economic activity of Malawi’s rural population and many farmers have been forced to cultivate marginal lands with less fertile soils, making conditions much more difficult to grow crops. Natural woodland is under increasing pressure from the opening of new lands for cultivation and the increased demand for firewood, timber and other woody resources, with rural households historically obtaining most of their complementary inputs and saleable commodities from nearby areas of forest (Arnold, 1997a). Despite this increasing pressure, woodlands are not being cleared indiscriminately; selected indigenous species are left standing in fields and around households. These are joined by exotic species that are planted and maintained. These trees provide products and services that are vital, yielding food, firewood, building materials and medicine, replenishing soil fertility and protecting against soil erosion. Following a Boserupian approach, this study attempts to establish the reality of a trajectory of enhanced on-farm tree planting and management as population pressure mounts and as part of a more general process of agricultural intensification. The study examines the combination of factors (social, economic, political and environmental) that either stimulate or discourage on-farm tree planting on smallholdings in Malawi, highlighting how woodland resource use changes over a gradient of land use intensity. This study gives a detailed insight into the way that tree planting and management in the smallholder farming system in Malawi works and identifies a trend of increased tree planting/management alongside an increase in agricultural intensification. However, there is no single ‘path’ of intensification; the link between agricultural change and tree planting is complex and there are many trajectories of intensification that a farmer may follow, dependent on his/her social or economic circumstances. The study recommends that agroforestry interventions give rigorous consideration to the needs of the local community, and the suitability of trees to address those needs, before embarking on programmes that advocate tree planting and management as a panacea.