Sequential genome-wide association studies for monitoring adverse events in the clinical evaluation of new drugs

Pharmacovigilance, the monitoring of adverse events (AEs), is an integral part in the clinical evaluation of a new drug. Until recently, attempts to relate the incidence of AEs to putative causes have been restricted to the evaluation of simple demographic and environmental factors. The advent of large-scale genotyping, however, provides an opportunity to look for associations between AEs and genetic markers, such as single nucleotides polymorphisms (SNPs). It is envisaged that a very large number of SNPs, possibly over 500 000, will be used in pharmacovigilance in an attempt to identify any genetic difference between patients who have experienced an AE and those who have not. We propose a sequential genome-wide association test for analysing AEs as they arise, allowing evidence-based decision-making at the earliest opportunity. This gives us the capability of quickly establishing whether there is a group of patients at high-risk of an AE based upon their DNA. Our method provides a valid test which takes account of linkage disequilibrium and allows for the sequential nature of the procedure. The method is more powerful than using a correction, such as idák, that assumes that the tests are independent. Copyright © 2006 John Wiley & Sons, Ltd.

Identifying important endemic areas using ecoregions: birds and mammals in the Indo-Pacific

Concentrations of large numbers of endemic species have been singled out in prioritization exercises as significant areas for global biodiversity conservation. This paper describes bird and mammal endemicity in Indo-Pacific ecoregions. An ecoregion is a relatively large unit of land or water that contains a distinct assemblage of natural communities. We prioritize 133 ecoregions according to their levels of endemicity, and explain how variables such as biome type, whether the ecoregion is on an island or continental mass, montane or non-montane, correlate with the proportion of the total species assemblage that are endemic. Following an exploratory principal components analysis we classify all ecoregions according to the relationship between numbers of endemics and overall species richness. Endemicity is negatively correlated with species richness. We show that plotting the logit transformation of the endemicity of birds and mammals against log of species richness is a more effective and useful way of identifying important ecoregions than simply ordering ecoregions by the proportion of endemic species, or any other single measure. The plot, divided into 16 regions corresponding to the quartiles of the two variables, was used to identify ecoregions of high conservation value. These are the ecoregions with the highest endemicity and lowest species richness. Further analysis shows that island and montane ecoregions, regardless of their biome type, are by far the most important for endemic species.

Characterization and origin of infection of Rhizoctonia solani associated with Brassica oleracea crops in the UK

An extensive study was conducted to determine where in the production chain Rhizoctonia solani became associated with UK module-raised Brassica oleracea plants. In total, 2600 plants from 52 crops were sampled directly from propagators and repeat sampled from the field. Additional soil, compost and water samples were collected from propagation nurseries and screened using conventional agar isolation methods. No isolates of R. solani were recovered from any samples collected from propagation nurseries. Furthermore, nucleic acid preparations from samples of soil and compost from propagation nurseries gave negative results when tested for R. solani using real-time PCR. Conversely, R. solani was recovered from 116 of 1300 stem bases collected from field crops. All the data collected suggested R. solani became associated with B. oleracea in the field rather than during propagation. Parsimony and Bayesian phylogenetic studies of ribosomal DNA suggested the majority of further classified isolates belonged to anastomosis groups 2-1 (48/57) and AG-4HGII (8/57), groups known to be pathogenic on Brassica spp. in other countries. Many R. solani isolates were recovered from symptomless plant material and the possibilities for such an association are discussed.

Recent advances in the application of in vitro systems to plant improvement

The horticultural industry was instrumental in the early development and exploitation of genetic techniques over a century ago. This review will describe recent advances in a range of in vitro methods and their application to plant breeding, with especial emphasis on horticultural crops. These methods include improvements in the efficiency of haploid breeding techniques in many fruit and vegetable species using either microspore-derived or ovule-derived plants. Significant molecular information is now available to supplement these essentially empirical approaches and this may enable the more predictable application of these technologies in previously intransigent crops. Similarly there are now improved techniques for isolation of somatic hybrids, by application of either in vitro fertilisation or the culture of excised ovules from interspecific crosses. In addition to examples taken from the traditional scientific literature, emphasis will also be given to the use of patent databases as a valuable source of information on recent novel technologies developed in the commercial world.

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.

Introduction: perspectives for economically important wild species and neglected crops in the Mediterranean

The Mediterranean region is one of the major centres of origin and diversification of cultivated plants and many crop wild relatives are found there. In addition, many native species are still widely harvested from the wild for food, medicine and other uses and some of these have potential for development as alternative crop especially in marginal zones. While there have been several recent initiatives that address the cataloguing and conservation of these species, such as the Network on Identification, Conservation and Use of Wild Plants in the Mediterranean Region (MEDUSA and the Bioversity International (IPGRI) studies on Underutilized Mediterranean Species (VMS), no comprehensive assessment has yet been made and little work undertaken on their agricultural potential. It has been confidently predicted that consequences of global change in the Mediterranean region - population movements and migrations, changes in disturbance regimes, and climate change - will be serious. One the one hand, this will affect the survival prospects of many of these underutilized species and on the other hand it will enhance their importance as the source of potential new crop germplasm. The conservation and availability of genetic diversity of both crops and underutilized species is essential if we are to be able to meet the increasing demand for food and other crops that will be adapted to the new ecoclimatic envelopes that will develop in the region as a consequence of global change. The rapid rate of climatic and other change that is expected adds urgency to the task of assessing, conserving and sustainably using this rich diversity of wild species of economic value in the region but new strategies will be need to be developed to achieve this. The Mediterranean region has the potential of becoming a major source of new crop development in the coming decades.

Behavioral changes associated with a population density decline in the facultatively social red fox

Understanding the causal mechanisms promoting group formation in carnivores has been widely investigated, particularly how fitness components affect group formation. Population density may affect the relative benefits of natal philopatry versus dispersal. Density effects on individual behavioral strategies have previously been studied through comparisons of different populations, where differences could be confounded by between-site effects. We used a single population of red foxes (Vulpes vulpes) in the city of Bristol, UK, that underwent a natural perturbation in density to compare key changes in 1) group structure, 2) within-group relatedness, 3) mating system, 4) dispersal, and 5) dominance attainment. At high densities (19.6-27.6 adults km(-2)), group sex ratios were equal and included related and unrelated individuals. At low densities (4.0-5.5 adults km(-2)), groups became female biased and were structured around philopatric females. However, levels of within-group relatedness were unchanged. The genetic mating patterns changed with no instances of multiple-paternity litters and a decline in the frequency of extrapair litters of cubs from <= 77% to <= 38%. However, the number of genetically monogynous groups did not differ between periods. Dispersal was male biased at both high and low densities. At high density, most dominant males in the study groups appeared to have gained dominance after dispersing, but natal philopatry was an equally successful strategy at low density; conversely, most dominant females were philopatric individuals at both high and low densities. These results illustrate how density may alter behavioral strategies such as mating patterns and how this, in turn, alters group structure in a single population.

Variation in the ovarian reserve Is linked to alterations in intrafollicular estradiol production and ovarian biomarkers of follicular differentiation and oocyte quality in cattle

The mechanisms whereby the high variation in numbers of morphologically healthy oocytes and follicles in ovaries (ovarian reserve) may have an impact onovarian function, oocyte quality, and fertility are poorly understood. The objective was to determine whether previously validated biomarkers for follicular differentiation and function, as well as oocyte quality differed between cattle with low versus a high antral follicle count (AFC). Ovaries were removed (n = 5 per group) near the beginning of the nonovulatory follicular wave, before follicles could be identified via ultrasonography as being dominant, from heifers with high versus a low AFC. The F1, F2, and F3 follicles were dissected and diameters determined. Follicular fluid and thecal, granulosal, and cumulus cells and the oocyte were isolated and subjected to biomarker analyses. Although the size and numerous biomarkers of differentiation, such as mRNAs for the gonadotropin receptors, were similar, intrafollicular concentrations of estradiol and the abundance of mRNAs for CYP19A1 in granulosal cells and ESR1, ESR2, and CTSB in cumulus cells were greater, whereas mRNAs for AMH in granulosal cells and TBC1D1 in thecal cells were lower for animals with low versus a high AFC during follicle waves. Hence, variation in the ovarian reserve may have an impact on follicular function and oocyte quality via alterations in intrafollicular estradiol production and expression of key genes involved in follicle-stimulating hormone action (AMH) and estradiol (CYP19A1) production by granulosal cells, function and survival of thecal cells (TBC1D1), responsiveness of cumulus cells to estradiol (ESR1, ESR2), and cumulus cell determinants of oocyte quality (CTSB).

Evidence for an inhibitory role of bone morphogenetic protein(s) in the follicular-luteal transition in cattle

Bone morphogenetic proteins (BMPs) and their receptors are expressed in ovarian theca cells (TC) and granulosa cells (GC) and BMPs have been implicated in the regulation of several aspects of follicle development including thecal androgen production and granulosal oestrogen production. Their potential involvement in luteal function has received less attention. in this study, we first compared relative abundance of mRNA transcripts for BMPs, activin-beta A and BMP/activin receptors in bovine corpus luteum (CL) and follicular theca and granulosa layers before undertaking functional in vitro experiments to test the effect of selected ligands (BMP6 and activin A) on luteinizing bovine TC and GC. Relative to P-actin transcript abundance, CL tissue contained more BMP4 and -6 mRNA than granulosa, more BMP2 mRNA than theca but much less activin-beta A mRNA than both granulosa and theca. Transcripts for all seven BMP/activin receptors were readily detected in each tissue and two transcripts (BMPRII, ActRIIA) were more abundant in CL than either theca or granulosa, consistent with tissue responsiveness. In vitro luteinization of TC and GC from antral follicles (4-6 mm) was achieved by culturing with 5% serum for 6 days. Treatment with BMP6 (0, 2, 10, and 50 ng/ml) and activin A (0, 2, 10 and 50 ng/ml) under these conditions dose-dependently suppressed forskolin-induced progesterone (P-4) secretion from both cell types without affecting cell number. BMP6 reduced forskolin-stimulated upregulation of STAR mRNA and raised 'basal' CYP17A1 mRNA level in theca-lutein cells without affecting expression of CYP11A1 or hydroxy-Delta-5-steroid dehydrogenase, 3 beta- and steroid Delta-isomerase 1 (HSD3B1). In granulosa-lutein cells, STAR transcript abundance was not affected by BMP6, whereas forskolin-induced expression of CYP11A1, HSD3B1, CYP19A1 and oxytocin transcripts was reduced. In both cell types, follistatin attenuated the suppressive effect of activin A and BMP6 on forskolin-induced P4 secretion but had no effect alone. Granulosa-lutein cells secreted low levels of endogenous activin A (similar to 1 ng/ml); BMP6 reduced this, while raising follistatin secretion thus decreasing activin A:follistatin ratio. Collectively, these findings support inhibitory roles for BMP/activin signalling in luteinization and steroidogenesis in both TC and GC.

Anthraquinone catalysis in the glucose-driven reduction of indigo to leuco-indigo

Anthraquinone immobilised onto the surface of indigo microcrystals enhances the reductive dissolution of indigo to leuco-indigo. Indigo reduction is driven by glucose in aqueous NaOH and a vibrating gold disc electrode is employed to monitor the increasing leuco-indigo concentration with time. Anthraquinone introduces a strong catalytic effect which is explained by invoking a molecular "wedge effect'' during co-intercalation of Na+ and anthraquinone into the layered indigo crystal structure. The glucose-driven indigo reduction, which is in effective in 0.1 M NaOH at 65 degrees C, becomes facile and goes to completion in the presence of anthraquinone catalyst. Electron microscopy of indigo crystals before and after reductive dissolution confirms a delamination mechanism initiated at the edges of the plate-like indigo crystals. Catalysis occurs when the anthraquinone-indigo mixture reaches a molar ratio of 1:400 (at 65 degrees C; corresponding to 3 mu M anthraquinone) with excess of anthraquinone having virtually no effect. A strong temperature effect ( with a composite E-A approximate to 120 kJ mol(-1)) is observed for the reductive dissolution in the presence of anthraquinone. The molar ratio and temperature effects are both consistent with the heterogeneous nature of the anthraquinone catalysis in the aqueous reaction mixture.

Using historical lesion volume data in the design of a new phase II clinical trial in acute stroke

Background and Purpose-Clinical research into the treatment of acute stroke is complicated, is costly, and has often been unsuccessful. Developments in imaging technology based on computed tomography and magnetic resonance imaging scans offer opportunities for screening experimental therapies during phase II testing so as to deliver only the most promising interventions to phase III. We discuss the design and the appropriate sample size for phase II studies in stroke based on lesion volume. Methods-Determination of the relation between analyses of lesion volumes and of neurologic outcomes is illustrated using data from placebo trial patients from the Virtual International Stroke Trials Archive. The size of an effect on lesion volume that would lead to a clinically relevant treatment effect in terms of a measure, such as modified Rankin score (mRS), is found. The sample size to detect that magnitude of effect on lesion volume is then calculated. Simulation is used to evaluate different criteria for proceeding from phase II to phase III. Results-The odds ratios for mRS correspond roughly to the square root of odds ratios for lesion volume, implying that for equivalent power specifications, sample sizes based on lesion volumes should be about one fourth of those based on mRS. Relaxation of power requirements, appropriate for phase II, lead to further sample size reductions. For example, a phase III trial comparing a novel treatment with placebo with a total sample size of 1518 patients might be motivated from a phase II trial of 126 patients comparing the same 2 treatment arms. Discussion-Definitive phase III trials in stroke should aim to demonstrate significant effects of treatment on clinical outcomes. However, more direct outcomes such as lesion volume can be useful in phase II for determining whether such phase III trials should be undertaken in the first place. (Stroke. 2009;40:1347-1352.)

The effects of environmental perturbation and measurement error on estimates of the shape parameter in the theta-logistic model of population regulation

The theta-logistic is a widely used generalisation of the logistic model of regulated biological processes which is used in particular to model population regulation. Then the parameter theta gives the shape of the relationship between per-capita population growth rate and population size. Estimation of theta from population counts is however subject to bias, particularly when there are measurement errors. Here we identify factors disposing towards accurate estimation of theta by simulation of populations regulated according to the theta-logistic model. Factors investigated were measurement error, environmental perturbation and length of time series. Large measurement errors bias estimates of theta towards zero. Where estimated theta is close to zero, the estimated annual return rate may help resolve whether this is due to bias. Environmental perturbations help yield unbiased estimates of theta. Where environmental perturbations are large, estimates of theta are likely to be reliable even when measurement errors are also large. By contrast where the environment is relatively constant, unbiased estimates of theta can only be obtained if populations are counted precisely Our results have practical conclusions for the design of long-term population surveys. Estimation of the precision of population counts would be valuable, and could be achieved in practice by repeating counts in at least some years. Increasing the length of time series beyond ten or 20 years yields only small benefits. if populations are measured with appropriate accuracy, given the level of environmental perturbation, unbiased estimates can be obtained from relatively short censuses. These conclusions are optimistic for estimation of theta. (C) 2008 Elsevier B.V All rights reserved.

In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere

IVET was used to identify genes that are specifically expressed in the rhizosphere of the pea-nodulating bacterium Rhizobium leguminosarum A34. A library of R. leguminosarum A34 cloned in the integration vector pIE1, with inserts upstream of a promoter-less purN:gfp:gusA, was conjugated into purN host RU2249 and recombined into the genome. After removal of colonies that expressed the reporter genes of the vector under laboratory conditions, the library was inoculated into a nonsterile pea rhizosphere. The key result is that 29 rhizosphere-induced loci were identified. Sequence analysis of these clones showed that a wide variety of R. leguminosarum A34 genes are expressed specifically in the rhizosphere including those encoding proteins involved in environmental sensing, control of gene expression, metabolic reactions and membrane transport. These genes are likely to be important for survival and colonization of the pea rhizosphere.