Analysis of cryptic, systemic Botrytis infections in symptomless hosts

Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. B. cinerea and B. pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.

Uncertainty assessment of a process-based integrated catchment model of phosphorus

Despite the many models developed for phosphorus concentration prediction at differing spatial and temporal scales, there has been little effort to quantify uncertainty in their predictions. Model prediction uncertainty quantification is desirable, for informed decision-making in river-systems management. An uncertainty analysis of the process-based model, integrated catchment model of phosphorus (INCA-P), within the generalised likelihood uncertainty estimation (GLUE) framework is presented. The framework is applied to the Lugg catchment (1,077 km2), a River Wye tributary, on the England–Wales border. Daily discharge and monthly phosphorus (total reactive and total), for a limited number of reaches, are used to initially assess uncertainty and sensitivity of 44 model parameters, identified as being most important for discharge and phosphorus predictions. This study demonstrates that parameter homogeneity assumptions (spatial heterogeneity is treated as land use type fractional areas) can achieve higher model fits, than a previous expertly calibrated parameter set. The model is capable of reproducing the hydrology, but a threshold Nash-Sutcliffe co-efficient of determination (E or R 2) of 0.3 is not achieved when simulating observed total phosphorus (TP) data in the upland reaches or total reactive phosphorus (TRP) in any reach. Despite this, the model reproduces the general dynamics of TP and TRP, in point source dominated lower reaches. This paper discusses why this application of INCA-P fails to find any parameter sets, which simultaneously describe all observed data acceptably. The discussion focuses on uncertainty of readily available input data, and whether such process-based models should be used when there isn’t sufficient data to support the many parameters.

Analysis of ochres from Clearwell Caves: the role of particle size in determining colour

Three ochre samples (A (orange-red in colour), B (red) and C (purple)) from Clearwell Caves, (Gloucestershire, UK) have been examined using an integrated analytical methodology based on the techniques of IR and diffuse reflectance UV-visible-NIR spectroscopy, X-ray diffraction, elemental analysis by ICP-AES and particle size analysis. It is shown that the chromophore in each case is haematite. The differences in colour may be accounted for by (i) different mineralogical and chemical composition in the case of the orange ochre, where hi,,her levels of dolomite and copper are seen and (ii) an unusual particle size distribution in the case of the purple ochre. When the purple ochre was ground to give the same particle size distribution as the red ochre then the colours of the two samples became indistinguishable. An analysis has now been completed of a range of ochre samples with colours from yellow to purple from the important site of Clearwell Caves. (C) 2004 Elsevier B.V. All rights reserved.

Sensitivity analysis of a catchment-scale nitrogen model

There are now considerable expectations that semi-distributed models are useful tools for supporting catchment water quality management. However, insufficient attention has been given to evaluating the uncertainties inherent to this type of model, especially those associated with the spatial disaggregation of the catchment. The Integrated Nitrogen in Catchments model (INCA) is subjected to an extensive regionalised sensitivity analysis in application to the River Kennet, part of the groundwater-dominated upper Thames catchment, UK The main results are: (1) model output was generally insensitive to land-phase parameters, very sensitive to groundwater parameters, including initial conditions, and significantly sensitive to in-river parameters; (2) INCA was able to produce good fits simultaneously to the available flow, nitrate and ammonium in-river data sets; (3) representing parameters as heterogeneous over the catchment (206 calibrated parameters) rather than homogeneous (24 calibrated parameters) produced a significant improvement in fit to nitrate but no significant improvement to flow and caused a deterioration in ammonium performance; (4) the analysis indicated that calibrating the flow-related parameters first, then calibrating the remaining parameters (as opposed to calibrating all parameters together) was not a sensible strategy in this case; (5) even the parameters to which the model output was most sensitive suffered from high uncertainty due to spatial inconsistencies in the estimated optimum values, parameter equifinality and the sampling error associated with the calibration method; (6) soil and groundwater nutrient and flow data are needed to reduce. uncertainty in initial conditions, residence times and nitrogen transformation parameters, and long-term historic data are needed so that key responses to changes in land-use management can be assimilated. The results indicate the general, difficulty of reconciling the questions which catchment nutrient models are expected to answer with typically limited data sets and limited knowledge about suitable model structures. The results demonstrate the importance of analysing semi-distributed model uncertainties prior to model application, and illustrate the value and limitations of using Monte Carlo-based methods for doing so. (c) 2005 Elsevier B.V. All rights reserved.

Biogenic nitric oxide emissions from soils: impact on NOx and ozone over West Africa during AMMA (African Monsoon Multidisciplinary Analysis) - observational study

Chemical and meteorological parameters measured on board the Facility for Airborne Atmospheric Measurements (FAAM) BAe 146 Atmospheric Research Aircraft during the African Monsoon Multidisciplinary Analysis (AMMA) campaign are presented to show the impact of NOx emissions from recently wetted soils in West Africa. NO emissions from soils have been previously observed in many geographical areas with different types of soil/vegetation cover during small scale studies and have been inferred at large scales from satellite measurements of NOx. This study is the first dedicated to showing the emissions of NOx at an intermediate scale between local surface sites and continental satellite measurements. The measurements reveal pronounced mesoscale variations in NOx concentrations closely linked to spatial patterns of antecedent rainfall. Fluxes required to maintain the NOx concentrations observed by the BAe-146 in a number of cases studies and for a range of assumed OH concentrations (1×106 to 1×107 molecules cm−3) are calculated to be in the range 8.4 to 36.1 ng N m−2 s−1. These values are comparable to the range of fluxes from 0.5 to 28 ng N m−2 s−1 reported from small scale field studies in a variety of non-nutrient rich tropical and sub-tropical locations reported in the review of Davidson and Kingerlee (1997). The fluxes calculated in the present study have been scaled up to cover the area of the Sahel bounded by 10 to 20 N and 10 E to 20 W giving an estimated emission of 0.03 to 0.30 Tg N from this area for July and August 2006. The observed chemical data also suggest that the NOx emitted from soils is taking part in ozone formation as ozone concentrations exhibit similar fine scale structure to the NOx, with enhancements over the wet soils. Such variability can not be explained on the basis of transport from other areas. Delon et al. (2008) is a companion paper to this one which models the impact of soil NOx emissions on the NOx and ozone concentration over West Africa during AMMA. It employs an artificial neural network to define the emissions of NOx from soils, integrated into a coupled chemistry-dynamics model. The results are compared to the observed data presented in this paper. Here we compare fluxes deduced from the observed data with the model-derived values from Delon et al. (2008).

Family-based association analysis with ordered categorical phenotypes, covariates and interactions

Genetic association analyses of family-based studies with ordered categorical phenotypes are often conducted using methods either for quantitative or for binary traits, which can lead to suboptimal analyses. Here we present an alternative likelihood-based method of analysis for single nucleotide polymorphism (SNP) genotypes and ordered categorical phenotypes in nuclear families of any size. Our approach, which extends our previous work for binary phenotypes, permits straightforward inclusion of covariate, gene-gene and gene-covariate interaction terms in the likelihood, incorporates a simple model for ascertainment and allows for family-specific effects in the hypothesis test. Additionally, our method produces interpretable parameter estimates and valid confidence intervals. We assess the proposed method using simulated data, and apply it to a polymorphism in the c-reactive protein (CRP) gene typed in families collected to investigate human systemic lupus erythematosus. By including sex interactions in the analysis, we show that the polymorphism is associated with anti-nuclear autoantibody (ANA) production in females, while there appears to be no effect in males.

A comparison of energy use in conventional and integrated arable farming systems in the UK

The LINK Integrated Farming Systems (LINK-IFS) Project (1992-1997) was setup to compare conventional and integrated arable farming systems (IAFS), concentrating on practical feasibility and economic viability, but also taking into account the level of inputs used and environmental impact. As part of this, an examination into energy use within the two systems was also undertaken. This paper presents the results from that analysis. The data used is from the six sites within the LINK-IFS Project, spread through the arable production areas of England and from the one site in Scotland, covering the 5 years of the project. The comparison of the energy used is based on the equipment and inputs used to produce I kg of each crop within the conventional and integrated rotations, and thereby the overall energy used for each system. The results suggest that, in terms of total energy used, the integrated system appears to be the most efficient. However, in terms of energy efficiency, energy use per kilogram of output, the results are less conclusive. (C) 2003 Elsevier Science B.V. All rights reserved.

Cost-benefit analysis model of badger (Meles meles) culling to reduce cattle herd tuberculosis breakdowns in Britain, with particular reference to badger perturbation

Bovine tuberculosis (TB)is an important economic disease. Badgers (Meles meles) are the wildlife source implicated in many cattle outbreaks of TB in Britain, and extensive badger control is a controversial option to reduce the disease. A badger and cattle population model was developed, simulating TB epidemiology; badger ecology, including postcull social perturbation; and TB-related farm management. An economic cost-benefit module was integrated into the model to assess whether badger control offers economic benefits. Model results strongly indicate that although, if perturbation were restricted, extensive badger culling could reduce rates in cattle, overall an economic loss would be more likely than a benefit. Perturbation of the badger population was a key factor determining success or failure of control. The model highlighted some important knowledge gaps regarding both the spatial and temporal characteristics of perturbation that warrant further research.

Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo

We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The method fits a continuous-time Markov model to a pair of traits, seeking the best fitting models that describe their joint evolution on a phylogeny. We employ the methodology of reversible-jump ( RJ) Markov chain Monte Carlo to search among the large number of possible models, some of which conform to independent evolution of the two traits, others to correlated evolution. The RJ Markov chain visits these models in proportion to their posterior probabilities, thereby directly estimating the support for the hypothesis of correlated evolution. In addition, the RJ Markov chain simultaneously estimates the posterior distributions of the rate parameters of the model of trait evolution. These posterior distributions can be used to test among alternative evolutionary scenarios to explain the observed data. All results are integrated over a sample of phylogenetic trees to account for phylogenetic uncertainty. We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye and analysed by two-dimensional difference gel electrophoresis. Gel images analysed off-line, using the DeCyder image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Analysis of ochres from Clearwell Caves: the role of particle size in determining colour

Three ochre samples (A (orange-red in colour), B (red) and C (purple)) from Clearwell Caves, (Gloucestershire, UK) have been examined using an integrated analytical methodology based on the techniques of IR and diffuse reflectance UV-visible-NIR spectroscopy, X-ray diffraction, elemental analysis by ICP-AES and particle size analysis. It is shown that the chromophore in each case is haematite. The differences in colour may be accounted for by (i) different mineralogical and chemical composition in the case of the orange ochre, where hi,,her levels of dolomite and copper are seen and (ii) an unusual particle size distribution in the case of the purple ochre. When the purple ochre was ground to give the same particle size distribution as the red ochre then the colours of the two samples became indistinguishable. An analysis has now been completed of a range of ochre samples with colours from yellow to purple from the important site of Clearwell Caves. (C) 2004 Elsevier B.V. All rights reserved.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Quantitative thermal imaging analysis of aircraft materials: through skin sensing (Invited Paper)

Thermal non-destructive testing (NDT) is commonly used for assessing aircraft structures. This research work evaluates the potential of pulsed -- transient thermography for locating fixtures beneath aircraft skins in order to facilitate accurate automated assembly operations. Representative aluminium and carbon fibre aircraft skin-fixture assemblies were modelled using thermal modelling software. The assemblies were also experimentally investigated with an integrated pulsed thermographic evaluation system, as well as using a custom built system incorporating a miniature un-cooled camera. Modelling showed that the presence of an air gap between skin and fixture significantly reduced the thermal contrast developed, especially in aluminium. Experimental results show that fixtures can be located to accuracies of 0.5 mm.

An entropy-based financial decision support system (e-FDSS) for project analysis in construction SMEs

Uncertainty contributes a major part in the accuracy of a decision-making process while its inconsistency is always difficult to be solved by existing decision-making tools. Entropy has been proved to be useful to evaluate the inconsistency of uncertainty among different respondents. The study demonstrates an entropy-based financial decision support system called e-FDSS. This integrated system provides decision support to evaluate attributes (funding options and multiple risks) available in projects. Fuzzy logic theory is included in the system to deal with the qualitative aspect of these options and risks. An adaptive genetic algorithm (AGA) is also employed to solve the decision algorithm in the system in order to provide optimal and consistent rates to these attributes. Seven simplified and parallel projects from a Hong Kong construction small and medium enterprise (SME) were assessed to evaluate the system. The result shows that the system calculates risk adjusted discount rates (RADR) of projects in an objective way. These rates discount project cash flow impartially. Inconsistency of uncertainty is also successfully evaluated by the use of the entropy method. Finally, the system identifies the favourable funding options that are managed by a scheme called SME Loan Guarantee Scheme (SGS). Based on these results, resource allocation could then be optimized and the best time to start a new project could also be identified throughout the overall project life cycle.