Characterisation of genetic diversity in a large number of European pig populations has been undertaken with EC support. The populations sampled included local (rare) breeds, national varieties of the major international breeds, commercial lines and the Chinese Meishan breed. A second phase of the project will sample a further 50 Chinese breeds. Neutral genetic markers (AFLP and microsatellites), with individual or bulk typing, were used and compared.

DNA from 59 European pig populations was extracted on samples of about 50 individuals per population. Individuals were typed for 50 microsatellites and for 148 AFLP bands. A subset of 25 populations was typed for 20 microsatellites on pools of DNA. Allele frequencies were estimated by direct allele counting for the co-dominant markers. Frequencies of AFLP negative alleles (absent bands) were obtained by taking the square root of absent band frequencies. Within-breed variability was summarised using standard statistics: expected and observed heterozygosity, mean observed and effective numbers of alleles, and F statistics. Between-breed diversity analysis was based on a bootstrapped Neighbor-Joining (NJ) tree derived from Reynolds distances (DR). The standard distance of Nei (DS) was also calculated.

As part of further investigations into three linked haemorrhagic fever with renal syndrome (HFRS) cases in Wales and England, 21 rats from a breeding colony in Cherwell, and three rats from a household in Cheltenham were screened for hantavirus. Hantavirus RNA was detected in either the lungs and/or kidney of 17/21 (81%) of the Cherwell rats tested, higher than previously detected by blood testing alone (7/21, 33%), and in the kidneys of all three Cheltenham rats. The partial L gene sequences obtained from 10 of the Cherwell rats and the three Cheltenham rats were identical to each other and the previously reported UK Cherwell strain. Seoul hantavirus (SEOV) RNA was detected in the heart, kidney, lung, salivary gland and spleen (but not in the liver) of an individual rat from the Cherwell colony suspected of being the source of SEOV. Serum from 20/20 of the Cherwell rats and two associated HFRS cases had high levels of SEOV-specific antibodies (by virus neutralisation). The high prevalence of SEOV in both sites and the moderately severe disease in the pet rat owners suggest that SEOV in pet rats poses a greater public health risk than previously considered.

Neptunium-237 will be present in radioactive wastes over extended time periods due to its long half-life (2.13 × 106 years). Understanding its behaviour under conditions relevant to radioactive waste disposal is therefore of particular importance. Here, microcosm experiments were established using sediments from a legacy lime workings with high-pH conditions as an analogue of cementitious intermediate-level radioactive waste disposal. To probe the influence of Fe biogeochemistry on Np(V) in these systems, additional Fe(III) (as ferrihydrite) was added to select experiments. Biogeochemical changes were tracked in experiments with low levels of Np(V) (20 Bq ml–1; 3.3 μM), whilst parallel higher concentration systems (2.5 KBq ml–1; 414 μM) allowed X-ray absorption spectroscopy. As expected, microbial reduction processes developed in microbially-active systems with an initial pH of 10; however, during microbial incubations the pH dropped from 10 to ∼7, reflecting the high levels of microbial metabolism occurring in these systems. In microbially-active systems without added Fe(III), 90% sorption of Np(V) occurred within one hour with essentially complete removal by one day. In the ferrihydrite-amended systems, complete sorption of Np(V) to ferrihydrite occurred within one hour. For higher-activity sediments, X-ray absorption spectroscopy (XAS) at end points where Fe(II) ingrowth was observed confirmed that complete reductive precipitation of Np(V) to Np(IV) had occurred under similar conditions to low-level Np experiments. Finally, pre-reduced, Fe(III)-reducing sediments, with and without added Fe(III) and held at pH 10, were spiked with Np(V). These alkaline pre-reduced sediments showed significant removal of Np to sediments, and XAS confirmed partial reduction to Np(IV) with the no Fe system, and essentially complete reduction to Np(IV) in the Fe(III)-enriched systems. This suggested an indirect, Fe(II)-mediated pathway for Np(V) reduction under alkaline conditions. Microbial analyses using 16S rRNA gene pyrosequencing suggested a role for alkali-tolerant, Gram-positive Firmicutes in coupled Fe(III) reduction and Np immobilization in these experiments.

The utility of biological control for weed management in agroecosystems will increase with a greater understanding of the relationships between common weed and granivore species. Giant foxtail is an introduced, summer annual grass weed that is common throughout the United States and problematic in numerous crops. Harpalus pensylvanicus (DeGeer) (Coleoptera: Carabidae) is a common, native, omnivorous carabid beetle with a range that overlaps giant foxtail. In 2004 and 2005, H. pensylvanicus was captured from farm fields in Centre County, PA, and subjected to laboratory feeding trials to test the preference of giant foxtail and other species on predation by H. pensylvanicus. Weed species seed preference experiments that included “Choice” and “No Choice” treatments were conducted using giant foxtail, common lambsquarters, and velvetleaf. When given a choice amongst the three weed species, H. pensylvanicus preferred giant foxtail and common lambsquarters seeds equally compared to velvetleaf seeds. When given the choice, H. pensylvanicus preferred newly dispersed giant foxtail seeds over field-aged seeds. Phenology of giant foxtail seed shed relative to H. pensylvanicus activity density was also quantified in field experiments in 2005 and 2006. Giant foxtail seed rain was determined by collecting shed seeds from August through October using pan traps. Activity density of H. pensylvanicus was monitored for 72-h periods using pitfall traps from June to October. Peak activity density of H. pensylvanicus occurred at the onset of giant foxtail seed shed in both years; however, giant foxtail seed shed peaked approximately 30 to 50 d after H. pensylvanicus activity density. Future research should focus on management practices that enhance and support H. pensylvanicus populations later in the growing season to maximize suppression of giant foxtail and other weeds that shed palatable seeds later in the season.

Iron oxides resulting from the corrosion of large quantities of steel that are planned to be installed throughout a deep geological disposal facility (GDF) are expected to be one of the key surfaces of interest for controlling radionuclide behaviour under disposal conditions. Over the lengthy timescales associated with a GDF, the system is expected to become anoxic so that reduced Fe(II) phases will dominate. Batch experiments have therefore been completed in order to investigate how a model reduced Fe-oxide surface (wüstite, Fe1–xO) alters as a function of exposure to aqueous solutions with compositions representative of conditions expected within a GDF. Additional experiments were performed to constrain the effect that highly alkaline solutions (up to pH 13) have on the adsorption behaviour of the uranyl (UO2 2+) ion onto the surfaces of both wüstite and portlandite [Ca(OH)2; representative of the expected cementitious phases]. Surface co-ordination chemistry and speciation were determined by ex situ X-ray absorption spectroscopy measurements (both X-ray absorption near-edge structure analysis (XANES) and extended X-ray absorption fine structure analysis (EXAFS)). Diffraction, elemental analysis and XANES showed that the bulk solid composition and Fe oxidation state remained relatively unaltered over the time frame of these experiments (120 h), although under alkaline conditions possible surface hydroxylation is observed, due presumably to the formation of surface hydroxyl complexes. The surface morphology, however, is altered significantly with a large degree of roughening and an observed decrease in the average particle size. Reduction of U(VI) to U(IV) occurs during adsorption in almost all cases and this is interpreted to indicate that wüstite may be an effective reductant of U during surface adsorption. This work also shows that increasing the carbonate concentration in reactant solutions dramatically decreases the adsorption coefficients for U on both wüstite and portlandite, consistent with U speciation and surface reactivity determined in other studies. Finally, the EXAFS results include new details about exactly how U bonds to this metal oxide surface.

The objective of this study was to estimate the sensitivity and specificity of a culture method and a polymerase chain reaction (PCR) method for detection of two Campylobacter species: C. jejuni and C. coli. Data were collected during a 3-year survey of UK broiler flocks, and consisted of parallel sampling of caeca from 436 batches of birds by both PCR and culture. Batches were stratified by season (summer/non-summer) and whether they were the first depopulation of the flock, resulting in four sub-populations. A Bayesian approach in the absence of a gold standard was adopted, and the sensitivity and specificity of the PCR and culture for each Campylobacter subtype was estimated, along with the true C. jejuni and C. coli prevalence in each sub-population. Results indicated that the sensitivity of the culture method was higher than that of PCR in detecting both species when the samples were derived from populations infected with at most one species of Campylobacter. However, from a mixed population, the sensitivity of culture for detecting both C. jejuni or C. coli is reduced while PCR is potentially able to detect both species, although the total probability of correctly identifying at least one species by PCR is similar to that of the culture method.

The Australian Square Kilometre Array Pathfinder (ASKAP) will give us an unprecedented opportunity to investigate the transient sky at radio wavelengths. In this paper we present VAST, an ASKAP survey for Variables and Slow Transients. VAST will exploit the wide-field survey capabilities of ASKAP to enable the discovery and investigation of variable and transient phenomena from the local to the cosmological, including flare stars, intermittent pulsars, X-ray binaries, magnetars, extreme scattering events, interstellar scintillation, radio supernovae, and orphan afterglows of gamma-ray bursts. In addition, it will allow us to probe unexplored regions of parameter space where new classes of transient sources may be detected. In this paper we review the known radio transient and variable populations and the current results from blind radio surveys. We outline a comprehensive program based on a multi-tiered survey strategy to characterise the radio transient sky through detection and monitoring of transient and variable sources on the ASKAP imaging timescales of 5 s and greater. We also present an analysis of the expected source populations that we will be able to detect with VAST.

Around the world large quantities of sludge wastes derived from nuclear energy production are currently kept in storage facilities. In the UK, the British government has marked sludge removal as a top priority as these facilities are nearing the end of their operational lifetimes. Therefore chemical understanding of uranium uptake in Mg-rich sludge is critical for successful remediation strategies. Previous studies have explored uranium uptake by the calcium carbonate minerals, calcite and aragonite, under conditions applicable to both natural and anthropogenically perturbed systems. However, studies of the uptake by Mg-rich minerals such as brucite [Mg(OH)2], nesquehonite [MgCO3·3H2O] and hydromagnesite [Mg5(CO3)4 (OH)2·4H2O], have not been previously conducted. Such experiments will improve our understanding of the mobility of uranium and other actinides in natural lithologies as well as provide key information applicable to nuclear waste repository strategies involving Mg-rich phases. Experiments with mineral powders were used to determine the partition coefficients (Kd) and coordination of UO22+ during adsorption and co-precipitation with brucite, nesquehonite and hydromagnesite. The Kd values for the selected Mg-rich minerals were comparable or greater than those published for calcium carbonates. Extended X-ray absorption fine structure analysis results showed that the structure of the uranyl-triscarbonato [UO2(CO3)3] species was maintained after surface attachment and that uptake of uranyl ions took place mainly via mineral surface reactions.