The establishment of heathland vegetation on ex-arable land: the response of Calluna vulgaris to soil acidification

The UK Biodiversity Action Plan has identified the creation of lowland heathland as an important objective. Heathland restoration studies have identified soil pH, elevated soil nutrients and large weed seed banks as major problems in the restoration of heathland vegetation on ex-arable land. Heathland vegetation is usually found on nutrient-poor acidic soils. Creating acidic soil conditions on ex-arable sites thus may produce a suitable environment for the establishment of heath vegetation. Soil acidification by the addition of sulphur has been shown to reduce the soil pH and the availability of nutrients in arable soils. A series of experiments was established to investigate the effects of soil acidification using sulphur on the establishment of Calluna vulgaris and the development of weed vegetation. The application of sulphur at 0.24 kg m(-2) to an arable soil was found to increase the survival rate of C. vulgaris cuttings planted in it. The mechanism of increased C. vulgaris survival appeared to be by sulphur application significantly reducing the cover of arable weeds arising from the soil seed bank. Higher rates of sulphur application (0.36 and 0.48 kg m(-2)) resulted in the death of many C. vidgaris plants. However C. vulgaris seedlings were able to establish successfully on these ex-arable soils within 1824 months following the addition of these levels of sulphur. The application of sulphur appears to offer a practical solution to heathland creation on ex-arable land. However, it may be necessary to provide an interval of between 18 and 24 months between the application of sulphur and the addition of C. vulgaris plants or seeds for the successful establishment of heathland vegetation. (C) 2003 Elsevier Ltd. All rights reserved.

Dynamics of QoI sensitivity in Mycosphaerella fijiensis in Costa Rica during 2000 to 2003

From 1997 onward, the strobilurin fungicide azoxystrobin was widely used in the main banana-production zone in Costa Rica against Mycosphaerella fijiensis var. difformis causing black Sigatoka of banana. By 2000, isolates of M. fijiensis with resistance to the quinolene oxidase inhibitor fungicides were common on some farms in the area. The cause was a single point mutation from glycine to alanine in the fungal target protein, cytochrome b gene. An amplification refractory mutation system Scorpion quantitative polymerase chain reaction assay was developed and used to determine the frequency of G 143A allele in samples of M. fijiensis. Two hierarchical surveys of spatial variability, in 2001 and 2002,found no significant variation in frequency on spatial scales <10 in. This allowed the frequency of G143A alleles on a farm to be estimated efficiently by averaging single samples taken at two fixed locations. The frequency of G 143A allele in bulk samples from I I farms throughout Costa Rica was determined at 2-month intervals. There was no direct relationship between the number of spray applications and the frequency of G143A on individual farms. Instead, the frequency converged toward regional averages, presumably due to the large-scale mixing of ascospores dispersed by wind. Using trap plants in an area remote from the main producing area, immigration of resistant ascospores was detected as far as 6 km away both with and against the prevailing wind.

The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

The photodimerisation of the alpha- and beta-forms of trans-cinnamic acid: a study of single crystals by vibrational microspectroscopy

Infrared and Raman microspectroscopy have been used to follow the photodimerisation reactions of single crystals, the alpha- and beta-forms of trans-cinnamic acid. This approach allows the starting materials and products -alpha-truxillic acid that has C-i symmetry and beta-truxinic acid, which has C-s symmetry-to be identified. It also allows the topotactic nature of the reaction to be confirmed. Attempts to produce the poorly-defined unreactive gamma-form of trans-cinnamic acid resulted only in a mixture of the alpha- and beta-forms. The findings suggest a wide role for these spectroscopic methods in monitoring solid-state organic reactions. (C) 2002 Elsevier Science B.V. All rights reserved.

Gas-solid reactions of single crystals: a study of the reaction of bromine with single crystals of trans-cinnamic acid and a range of its derivatives by infrared and Raman microspectroscopy

Single crystals of trans-cinnamic acid and of a range of derivatives of this compound containing halogen substituents on the aromatic ring have been reacted with 165 Torr pressure of bromine vapour in a sealed desiccator at 20 degrees C for 1 week. Infrared and Raman microspectroscopic examination of the crystals shows that bromination of the aliphatic double bond, but not of the aromatic ring, has occurred. It is demonstrated also that the reaction is truly gas-solid in nature. A time-dependent study of these reactions shows that they do not follow a smooth diffusion-controlled pathway. Rather the reactions appear to be inhomogeneous and to occur at defects within the crystal. The reaction products are seen to flake from the surface of the crystal. It is shown, therefore, that these are not single crystal to single crystal transitions, as have been observed previously for the photodimerisation of trans-cinnamic acid and several of its derivatives. It is shown that there are no by-products of the reaction and that finely ground samples react to form the same products as single crystals.

Modeling the variability of single-cell lag times for Listeria innocua populations after sublethal and lethal heat treatments

Optical density measurements were used to estimate the effect of heat treatments on the single-cell lag times of Listeria innocua fitted to a shifted gamma distribution. The single-cell lag time was subdivided into repair time ( the shift of the distribution assumed to be uniform for all cells) and adjustment time (varying randomly from cell to cell). After heat treatments in which all of the cells recovered (sublethal), the repair time and the mean and the variance of the single-cell adjustment time increased with the severity of the treatment. When the heat treatments resulted in a loss of viability (lethal), the repair time of the survivors increased with the decimal reduction of the cell numbers independently of the temperature, while the mean and variance of the single-cell adjustment times remained the same irrespective of the heat treatment. Based on these observations and modeling of the effect of time and temperature of the heat treatment, we propose that the severity of a heat treatment can be characterized by the repair time of the cells whether the heat treatment is lethal or not, an extension of the F value concept for sublethal heat treatments. In addition, the repair time could be interpreted as the extent or degree of injury with a multiple-hit lethality model. Another implication of these results is that the distribution of the time for cells to reach unacceptable numbers in food is not affected by the time-temperature combination resulting in a given decimal reduction.

An EPN-based method for web service composition

Web service composition can be facilitated by an automatic process which consists of rules, conditions and actions. This research has adapted ElementaryPetri Net (EPN) to analyze and model the web services and their composition. This paper describes a set of techniques for representing transition rules, algorithm and workflow that web service composition can be automatically carried out.

Search adaptations and the challenges of the web

Search has become a hot topic in Internet computing, with rival search engines battling to become the de facto Web portal, harnessing search algorithms to wade through information on a scale undreamed of by early information retrieval (IR) pioneers. This article examines how search has matured from its roots in specialized IR systems to become a key foundation of the Web. The authors describe new challenges posed by the Web's scale, and show how search is changing the nature of the Web as much as the Web has changed the nature of search

Modeling entangled dynamics: comparison between stochastic single-chain and multichain models

To test the effectiveness of stochastic single-chain models in describing the dynamics of entangled polymers, we systematically compare one such model; the slip-spring model; to a multichain model solved using stochastic molecular dynamics(MD) simulations (the Kremer-Grest model). The comparison involves investigating if the single-chain model can adequately describe both a microscopic dynamical and a macroscopic rheological quantity for a range of chain lengths. Choosing a particular chain length in the slip-spring model, the parameter values that best reproduce the mean-square displacement of a group of monomers is determined by fitting toMDdata. Using the same set of parameters we then test if the predictions of the mean-square displacements for other chain lengths agree with the MD calculations. We followed this by a comparison of the time dependent stress relaxation moduli obtained from the two models for a range of chain lengths. After identifying a limitation of the original slip-spring model in describing the static structure of the polymer chain as seen in MD, we remedy this by introducing a pairwise repulsive potential between the monomers in the chains. Poor agreement of the mean-square monomer displacements at short times can be rectified by the use of generalized Langevin equations for the dynamics and resulted in significantly improved agreement.

NMR studies of the conformational effect of single and double 3'-S-phosphorothiolate substitutions within deoxythymidine trinucleotides

NMR spectroscopy has been used to investigate the conformational effects of single and two consecutive 3′-S-phosphorothiolate modifications within a deoxythymidine trinucleotide. The presence of a single 3′-phosphorothioate modification shifts the conformation of the sugar ring it is attached to, from a mainly south to north pucker; this effect is also transmitted to the 3′-neighbour deoxyribose. This transmission is thought to be caused by favourable stacking of the heterocyclic bases. Similar observations have been made previously by this group. When two adjacent modifications are present, the conformations of the attached deoxyribose rings are again shifted almost completely to the north, however, there is no transmission to the 3′ deoxyribose ring. Base proton chemical shift analysis and molecular modelling have been used to aid elucidation of the origin of this feature. The observation for the dimodified sequence is consistent with our previously reported results for a related system in which spaced modifications are more thermodynamically stable than consecutive ones.

Fit for planning? An evaluation of the application of development viability appraisal models in the UK planning system

The aim of this paper is to critically examine the application of development appraisal to viability assessment in the planning system. This evaluation is of development appraisal models in general and also their use in particular applications associated with estimating planning obligation capacity. The paper is organised into four themes: · The context and conceptual basis for development viability appraisal · A review of development viability appraisal methods · A discussion of selected key inputs into a development viability appraisal · A discussion of the applications of development viability appraisals in the planning system It is assumed that readers are familiar with the basic models and information needs of development viability appraisal rather than at the cutting edge of practice and/or academe

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.

Effective LAI and CHP of a single tree from small-footprint full-waveform LiDAR

This letter has tested the canopy height profile (CHP) methodology as a way of effective leaf area index (LAIe) and vertical vegetation profile retrieval at a single-tree level. Waveform and discrete airborne LiDAR data from six swaths, as well as from the combined data of six swaths, were used to extract the LAIe of a single live Callitris glaucophylla tree. LAIe was extracted from raw waveform as an intermediate step in the CHP methodology, with two different vegetation-ground reflectance ratios. Discrete point LAIe estimates were derived from the gap probability using the following: 1) single ground returns and 2) all ground returns. LiDAR LAIe retrievals were subsequently compared to hemispherical photography estimates, yielding mean values within ±7% of the latter, depending on the method used. The CHP of a single dead Callitris glaucophylla tree, representing the distribution of vegetation material, was verified with a field profile manually reconstructed from convergent photographs taken with a fixed-focal-length camera. A binwise comparison of the two profiles showed very high correlation between the data reaching R2 of 0.86 for the CHP from combined swaths. Using a study-area-adjusted reflectance ratio improved the correlation between the profiles, but only marginally in comparison to using an arbitrary ratio of 0.5 for the laser wavelength of 1550 nm.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Can a computerised training paradigm assist people with intellectual disabilities to learn cognitive mediation skills? A randomised experiment

Aims: The aim was to examine whether specific skills required for cognitive behavioural therapy (CBT) could be taught using a computerised training paradigm with people who have intellectual disabilities (IDs). Training aimed to improve: a) ability to link pairs of situations and mediating beliefs to emotions, and b) ability to link pairs of situations and emotions to mediating beliefs. Method: Using a single-blind mixed experimental design, sixty-five participants with IDs were randomised to receive either computerised training or an attention-control condition. Cognitive mediation skills were assessed before and after training. Results: Participants who received training were significantly better at selecting appropriate emotions within situation beliefs pairs, controlling for baseline scores and IQ. Despite significant improvements in the ability of those who received training to correctly select intermediating beliefs for situation-feelings pairings, no between-group differences were observed at post-test. Conclusions: The findings indicated that computerised training led to a significant improvement in some aspects of cognitive mediation for people with IDs, but whether this has a positive effect upon outcome from therapy is yet to be established. (C) 2015 Elsevier Ltd. All rights reserved.