A lightweight supercomputing web portal for inferring phylogenetic trees

In this paper we describe a lightweight Web portal developed for running computational jobs on a IBM JS21 Bladecenter cluster, ThamesBlue, for inferring and analyzing evolutionary histories. We first discuss the need for leveraging HPC as a enabler for molecular phylogenetics research. We go on to describe how the portal is designed to interface with existing open-source software that is typical of a HPC resource configuration, and how by design this portal is generic enough to be portable to other similarly configured compute clusters, and for other applications.

The effectiveness of somatic embryogenesis in eliminating the cocoa swollen shoot virus from infected cocoa trees

Investigations were undertaken on the use of somatic embryogenesis to generate cocoa swollen shoot virus (CSSV) disease free clonal propagules, from infected trees. Polymerase chain reaction (PCR) capillary electrophoresis revealed the presence of CSSV in all the callus tissues induced from the CSSV-infected Amelonado cocoa trees (T1, T2 and T4). The virus was transmitted to primary somatic embryos induced from the infected callus tissues at the rate of 10 (19%), 18 (14%) and 16 (15%) for T1, T2 and T4, respectively. Virus free primary somatic embryos from the infected callus tissues converted into plantlets tested CSSV negative by PCR/capillary electrophoresis 2 years after weaning. Secondary somatic embryos induced from the CSSV-infected primary somatic embryos revealed the presence of viral fragments at the rate of 4 (4%) and 9 (9%) for T2 and T4, respectively. Real-time PCR revealed 23 of the 24 secondary somatic embryos contained no detectable virus. Based on these findings, it is proposed that progressive elimination of the CSSV in infected cocoa trees occurred from primary embryogenesis to secondary embryogenesis. (C) 2008 Elsevier B.V. All rights reserved.

Shoot dieback in clipped young Golden Leyland (Cupressocyparis leylandii) trees - a physiological mechanism?

Shoot dieback is a problem in frequently trimmed Leyland hedges and is increasingly affecting gardeners’ choice of hedge trees, having a negative effect on a conifer nursery industry. Some damage can be attributed to the feeding by aphids, but it is unclear if there are also underlying physiological causes. In this study, we tested the hypothesis that shoot-clipping of conifer trees during adverse growing conditions (i.e. high air temperature and low soil moisture) could be leading to shoot ‘dieback’. Three-year-old Golden Leyland Cypress (x Cupressocyparis leylandii ‘Excalibur Gold’) plants were subjected to either a well-watered or droughted irrigation regime and placed in either a ‘hot’ (average day temperature = 40°C) or a ‘cool’ (average day temperature = 27°C) glasshouse compartment. Half of the plants from each glasshouse were clipped on Day 14 and again on Day 50. Measurements of soil moisture content (SMC), net CO2 assimilation rate (A), stomatal conductance (gs), branchlet xylem water potential (XWP), plant height and foliage colour were made. Within the clipped and unclipped treatments of both glasshouse compartments, plants from the droughted regime had significantly lower values for A, gs and XWP than those from the well-watered regime. However, there was no difference in these parameters between the hot and cool glasshouse compartments. The trends seen for A, gs and XWP of all treatments generally mirrored changes in SMC indicating a direct effect of water supply on these parameters. By the end of the experiment the overall foliage colour of plants from the hot glasshouse was darker than that of plants from the cool glasshouse and the overall foliage colour was also darker following shoot clipping. In general, shoot clipping led to increases in A, gs XWP and SMC. This may be due to the reduction in total leaf area leading to a greater supply of water for the remaining leaves. No shoot ‘dieback’ was observed in any treatment in response to drought stress or shoot-clipping.

Control of cocoa swollen shoot disease by eradicating infected trees in Ghana: A survey of treated and replanted areas

Cocoa farms that had been treated and replanted in Ghana during the most recent phase of the cocoa swollen shoot virus (CSSV) eradication campaign were surveyed. Farms that were replanted close to adjoining old cocoa farms or which contained old trees were common in most (38) of the 41 cocoa farms surveyed. CSSV infections were apparent in 20 (53%) out of these 38 farms and they pose a serious risk of causing early infections of the re-planted farms. Control strategies that isolate the newly planted farms by a boundary of immune crops as barriers to reduce CSSV re-infection are discussed. (c) 2005 Elsevier Ltd. All rights reserved.

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.

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.

Investigating scaling of an abstracted LCS utilising ternary and S-Expression alphabets

Utilising the expressive power of S-Expressions in Learning Classifier Systems often prohibitively increases the search space due to increased flexibility of the endcoding. This work shows that selection of appropriate S-Expression functions through domain knowledge improves scaling in problems, as expected. It is also known that simple alphabets perform well on relatively small sized problems in a domain, e.g. ternary alphabet in the 6, 11 and 20 bit MUX domain. Once fit ternary rules have been formed it was investigated whether higher order learning was possible and whether this staged learning facilitated selection of appropriate functions in complex alphabets, e.g. selection of S-Expression functions. This novel methodology is shown to provide compact results (135-MUX) and exhibits potential for scaling well (1034-MUX), but is only a small step towards introducing abstraction to LCS.

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.