Epidemiological risk assessment using linked network and grid based modelling: Phytophthora ramorum and Phytophthora kernoviae in the UK

We developed a stochastic simulation model incorporating most processes likely to be important in the spread of Phytophthora ramorum and similar diseases across the British landscape (covering Rhododendron ponticum in woodland and nurseries, and Vaccinium myrtillus in heathland). The simulation allows for movements of diseased plants within a realistically modelled trade network and long-distance natural dispersal. A series of simulation experiments were run with the model, representing an experiment varying the epidemic pressure and linkage between natural vegetation and horticultural trade, with or without disease spread in commercial trade, and with or without inspections-with-eradication, to give a 2 x 2 x 2 x 2 factorial started at 10 arbitrary locations spread across England. Fifty replicate simulations were made at each set of parameter values. Individual epidemics varied dramatically in size due to stochastic effects throughout the model. Across a range of epidemic pressures, the size of the epidemic was 5-13 times larger when commercial movement of plants was included. A key unknown factor in the system is the area of susceptible habitat outside the nursery system. Inspections, with a probability of detection and efficiency of infected-plant removal of 80% and made at 90-day intervals, reduced the size of epidemics by about 60% across the three sectors with a density of 1% susceptible plants in broadleaf woodland and heathland. Reducing this density to 0.1% largely isolated the trade network, so that inspections reduced the final epidemic size by over 90%, and most epidemics ended without escape into nature. Even in this case, however, major wild epidemics developed in a few percent of cases. Provided the number of new introductions remains low, the current inspection policy will control most epidemics. However, as the rate of introduction increases, it can overwhelm any reasonable inspection regime, largely due to spread prior to detection. (C) 2009 Elsevier B.V. All rights reserved.

HDC poinsettia tracker: flexible graphical tracking software

Growing pot poinsettia and similar crops involves careful crop monitoring and management to ensure that height specifications are met. Graphical tracking represents a target driven approach to decision support with simple interpretation. HDC (Horticultural Development Council) Poinsettia Tracker implements a graphical track based on the Generalised Logistic Curve, similar to that of other tracking packages. Any set of curve parameters can be used to track crop progress. However, graphical tracks must be expected to be site and cultivar specific. By providing a simple Curve fitting function, growers can easily develop their own site and variety specific ideal tracks based on past records with increasing quality as more seasons' data are added. (C) 2009 Elsevier B.V. All rights reserved.

Spatio-temporal analysis of an invasive plant pathogen (Phytophthora ramorum) in England and Wales

Phytophthora ramorum is a damaging invasive plant pathogen and was first discovered in the UK in 2002. Spatial point analyses were applied to the occurrence of this disease in England and Wales during the period of 2003-2006 in order to assess its spatio-temporal spread. Out of the 4301 garden centres and nurseries (GCN) surveyed, there were 164, 105, 123 and 41 sites with P. ramorum in 2003, 2004, 2005 and 2006, respectively. Spatial analysis of the observed point patterns of GCN outbreaks suggested that these sites were significantly clumped within a radius of ca 60 km in 2003, but not in later years. Further analyses were conducted to determine the relationship of GCN outbreak sites over two consecutive years and thus to infer possible disease spread over time. This analysis suggested that disease spread among GCN sites was most likely to have occurred within a distance of 60 km for 2003-2004, but not for the later years. There were 35, 63, 81 and 58 sites with P. ramorum in the semi-natural environment (SNE). Analyses were carried out to assess whether infected GCN sites could act as an inoculum source of infected SNE plants or vice versa. In all years, there was a significant spatial closeness among GCN and SNE outbreak sites within a distance of 1 km. But a significant relationship over a longer distance (within 60 km) was only observed between cases in 2003 and 2004. These analyses suggest that statutory actions taken so far appear to have reduced the extent of long-distance spread of P. ramorum among garden centres and nurseries, but not the disease spread at a shorter distance between GCN and SNE sites.

Assembling spatially explicit landscape models of pollen and spore dispersal by wind for risk assessment

Models of windblown pollen or spore movement are required to predict gene flow from genetically modified (GM) crops and the spread of fungal diseases. We suggest a simple form for a function describing the distance moved by a pollen grain or fungal spore, for use in generic models of dispersal. The function has power-law behaviour over sub-continental distances. We show that air-borne dispersal of rapeseed pollen in two experiments was inconsistent with an exponential model, but was fitted by power-law models, implying a large contribution from distant fields to the catches observed. After allowance for this 'background' by applying Fourier transforms to deconvolve the mixture of distant and local sources, the data were best fit by power-laws with exponents between 1.5 and 2. We also demonstrate that for a simple model of area sources, the median dispersal distance is a function of field radius and that measurement from the source edge can be misleading. Using an inverse-square dispersal distribution deduced from the experimental data and the distribution of rapeseed fields deduced by remote sensing, we successfully predict observed rapeseed pollen density in the city centres of Derby and Leicester (UK).

Predicting the functional response of a farmland bird

1. Mechanistic models may be able to predict how changes in agricultural practice influence farmland bird populations. A key component of these models is the link between food and competitor densities and the rate at which birds consume food, i.e. the functional response. 2. This paper tests whether the functional response of a farmland bird, the rook Corvus frugilegus, can be predicted from three parameters: searching speed, food detection distance and handling time. It is often difficult to measure the functional response of farmland birds directly, but it may be possible to measure behavioural parameters more quickly. 3. We performed experiments in which rooks fed on a range of artificial food densities in two grass sward heights. Food detection distance was greater in the shorter sward, but sward height did not influence searching speed or handling time. The functional response could be accurately predicted in both sward heights. 4. We show that the functional response of a farmland bird can be predicted from parameters that can be measured more quickly than the alternative of measuring the functional response directly. This implies that the functional responses of other farmland birds may be predicted using a minimum of information.

Graphical tracking systems revisited: a practical approach to computer scheduling in horticulture

Graphical tracking is a technique for crop scheduling where the actual plant state is plotted against an ideal target curve which encapsulates all crop and environmental characteristics. Management decisions are made on the basis of the position of the actual crop against the ideal position. Due to the simplicity of the approach it is possible for graphical tracks to be developed on site without the requirement for controlled experimentation. Growth models and graphical tracks are discussed, and an implementation of the Richards curve for graphical tracking described. In many cases, the more intuitively desirable growth models perform sub-optimally due to problems with the specification of starting conditions, environmental factors outside the scope of the original model and the introduction of new cultivars. Accurate specification for a biological model requires detailed and usually costly study, and as such is not adaptable to a changing cultivar range and changing cultivation techniques. Fitting of a new graphical track for a new cultivar can be conducted on site and improved over subsequent seasons. Graphical tracking emphasises the current position relative to the objective, and as such does not require the time consuming or system specific input of an environmental history, although it does require detailed crop measurement. The approach is flexible and could be applied to a variety of specification metrics, with digital imaging providing a route for added value. For decision making regarding crop manipulation from the observed current state, there is a role for simple predictive modelling over the short term to indicate the short term consequences of crop manipulation.

Developing protocols for nursery based scheduling trials

Most existing crop scheduling models are cultivar specific and are developed using academic resources. As such they rarely meet the particular needs of a grower. A series of protocols have been created to generate effective schedules for a changing product range using data generated on site at a commercial nursery. A screening programme has been developed to help determine a cultivar's photoperiod sensitivity and vernalisation requirement. Experimental conditions were obtained using a cold store facility set to 5degreesC and photoperiod cloches. Eight and 16 hour photoperiod treatments were achieved at low cost by growing plants in cloches of opaque plastic with a motorised rolling screen. Natural light conditions were extended where necessary using a high pressure sodium lamp. Batches of plants were grown according to different schedules based on these treatments. The screening programme found Coreopsis grandiflora 'Flying Saucers' to be a long day plant. Data to form the basis of graphical tracks was taken using variations on commercial schedules. The work provides a nursery based approach to the continuous improvement of crop scheduling practises.

1,3-Dipolar cycloadditions to unsymmetrical ketone-derived chiral stabilized azomethine ylides: strategies for the synthesis of highly substituted amino acids

We report herein, the first generation of unsymmetrical ketone-derived chiral stabilized azomethine ylides. Intrairiolecular and intermolecular cycloaddition strategies have been utilized to synthesize both an enantiornerically pure bicyclic proline derivative and an enantionierically pure beta-hydroxy-alpha-amino acid.

Difluorinated analogues of shikimic acid

Investigations into the quinate to shikimate transformation have been carried out, the results of which have been exploited in the synthesis of a novel difluoromethylene homologue of shikimic acid from (-)-quinic acid. Martin's sulfurane {Ph2S[OC(CF3)(2)Ph](2)} was the reagent of choice for the key dehydration step of this synthesis. The results of investigations into the synthesis of the important natural product analogue, 6,6-difluoroshikimic acid are also reported. (C) 2003 Elsevier Science Ltd. All rights reserved.

Azide 1,3-dipolar cycloadditions to N-propynoyl and N-propenoyl (5R)-5-phenylmorpholin-2-one: diastereocontrolled aziridine formation

N-Propynoyl (5R)-5-phenylmorpholin-2-one undergoes nonregioselective cycloaddition with aromatic azides to furnish mixtures of the corresponding triazoles, whereas N-propenoyl (5R)-5-phenylmorpholin-2-one reacts to furnish the corresponding diastereoisomerically pure aziridines in moderate to good yields, presumably via the intermediate triazolines.

The component polypeptide chains of bovine insulin nucleate or inhibit aggregation of the parent protein in a conformation-dependent manner

Amyloid fibrils are typically rigid, unbrariched structures with diameters of similar to 10 nm and lengths up to several micrometres, and are associated with more than 20 diseases including Alzheimer's disease and type II diabetes. Insulin is a small, predominantly alpha-helical protein consisting of 51 residues in two disulfide-linked polypeptide chains that readily assembles into amyloid fibrils under conditions of low PH and elevated temperature. We demonstrate here that both the A-chain and the B-chain of insulin are capable of forming amyloid fibrils in isolation under similar conditions, with fibrillar morphologies that differ from those composed of intact insulin. Both the A-chain and B-chain fibrils were found to be able to cross-seed the fibrillization of the parent protein, although these reactions were substantially less efficient than self-seeding with fibrils composed of full-length insulin. In both cases, the cross-seeded fibrils were morphologically distinct from the seeding, material, but shared common characteristics with typical insulin fibrils, including a very similar helical repeat. The broader distribution of heights of the cross-seeded fibrils compared to typical insulin fibrils, however, indicates that their underling protofilament hierarchy may be subtly different. In addition, and remarkably in view of this seeding behavior, the soluble forms of the A-chain and B-chain peptides were found to be capable of inhibiting insulin fibril formation. Studies using mass spectrometry suggest that this behavior might be attributable to complex formation between insulin and the A-chain and B-chain peptides. The finding that the same chemical form of a polypeptide chain in different physical states can either stimulate or inhibit the conversion of a protein into amyloid fibrils sheds new light on the mechanisms underlying fibril formation, fibril strain propagation and amyloid disease initiation and progression. (c) 2006 Elsevier Ltd. All rights reserved.

Synthesis of enantiopure prolines via exo-stereoselective 1,3-dipolar cycloadditions to acetone-derived chiral stabilised azomethine ylides

The chiral stabilised azomethine ylide formed from condensation of the dimethyl acetal of acetone with (5S)-5-phenylmorpholinone undergoes stereoselective exo-cycloaddition reactions with a range of doubly and singly activated dipolarophiles when generated in the presence of excess (MgBr2OEt2)-O-.. The cycloadducts can be degraded to yield enantiomerically pure proline derivatives.