Development of a method for Bayesian nonparametric ROC analysis with application to an ELISA for Johne's disease in dairy cattle

Six hundred and sixty-eight dairy cattle were tested for Johne's disease using a direct-fecal real-time polymerase chain reaction (rt-PCR), fecal culture, and serum enzyme-linked immunosorbent assay (ELISA). Likelihood ratios (LRs) were estimated for five categories of sample-to-positive (S/P) values for the ELISA: <0.1, 0.1-0.249, 0.25-0.399, 0.4-0.999, > or =1.0. The statistical method assumed a single multinomial model for cross-classified rt-PCR, fecal culture results, and ELISA category strata. Conditional dependence between tests was investigated by the inclusion of all possible pairwise dependence terms. Sensitivity covariance between ELISA and fecal culture was estimated as 0.017. Estimates for the accuracy of the ELISA at the usual cutoff of 0.25S/P was 67.2% and 95.2% for sensitivity and specificity, respectively for a model that adjusted for the dependence between ELISA and fecal culture. The area under the receiver-operating characteristic (ROC) curve (95% probability interval) for the ELISA was 0.867 (0.796, 0.928). Point estimates for likelihood ratios (95% probability intervals) were 0.24 (0.11, 0.38), 1.52 (0.48, 3.27), 2.49 (0.31, 13.4), 6.33 (2.54, 16.5), and 103 (25.0, 2412) for the categories <0.1, 0.1-0.249, 0.25-0.399, 0.4-0.999, >/=1.0, respectively. Assumptions concerning the underlying distribution of test results for infected and uninfected animals were not necessary and this model can be employed for the general estimation of LRs and ROC curves in absence of knowledge concerning true disease status.     

Seroprevalence of and agroecological risk factors for Mycobacterium avium subspecies paratuberculosis and neospora caninum infection among adult beef cattle in cow-calf herds in Alberta, Canada

A province-wide cross-sectional seroprevalence and agroecological risk factor study of Mycobacterium avium subspecies paratuberculosis (MAP) and Neospora caninum (NC) infection among cattle in 100 cow-calf herds in Alberta was conducted. The seroprevalence of MAP in adult cattle was 1.5% across all herds. Using a widely accepted herd test cutpoint of 2 or more seropositive cows out of 30 animals tested, 7.9% of herds were estimated to be infected (95% confidence interval (CI): 2.3-23.4%). Seroprevalence of MAP differed by agroecological region; specifically, cattle and herds in areas with high soil pH (> 7.0), southern latitudes, and arid climates had a moderately reduced risk of infection (P < 0.10). Seroprevalence of NC infection was 9.7% among adult beef cattle province-wide--these levels also varied by agroecological region--with 91.0% of herds infected overall.     

A decision-support system for Salmonella in broiler-chicken flocks

We built a decision-support system to assess the risk of contamination of chicken-broiler flocks by Salmonella at the end of the rearing period. This system was developed from the survey data from 85 chicken-broiler flocks located in western France. First, we estimated the probability of contamination of the house by Salmonella before placement of day-old chicks via a cleansing inspection using a visual-inspection grid, a decontamination evaluation using count-plates, and risk factors for Salmonella persistence in the barn after cleansing and disinfection. Second, we estimated (using a logistic model) the probability of prevalent contamination of the flock by Salmonella at the end of the rearing period. Validation was carried out on 60 flocks selected from seven production companies in western France. The risk estimated by the model was compared to the Salmonella status of the flock (gold standard) assessed by samples taken from the environment of the broilers and analysed with classical bacteriological methods. The sensitivity was 97.8% and the specificity 64.3%.     

Equine sarcoids: Bovine Papillomavirus type 1 transformed fibroblasts are sensitive to cisplatin and UVB induced apoptosis and show aberrant expression of p53

Bovine papillomavirus type 1 infects not only cattle but also equids and is a causative factor in the pathogenesis of commonly occurring equine sarcoid tumours. Whilst treatment of sarcoids is notoriously difficult, cisplatin has been shown to be one of the most effective treatment strategies for sarcoids. In this study we show that in equine fibroblasts, BPV-1 sensitises cells to cisplatin-induced and UVB-induced apoptosis, a known cofactor for papillomavirus associated disease, however BPV-1 transformed fibroblasts show increased clonogenic survival, which may potentially limit the therapeutic effects of repeated cisplatin treatment. Furthermore we show that BPV-1 increases p53 expression in sarcoid cell lines and p53 expression can be either nuclear or cytoplasmic. The mechanism and clinical significance of increase/abnormal p53 expression remains to be established.     

First evidence of spawning migration by goldfish (Carassius auratus); implications for control of a globally invasive species

Goldfish (Carassius auratus) was one of the first fishes to be domesticated and has been widely introduced across the globe, but is now considered one of the world's worst invasive aquatic species. Surprisingly, there is a dearth of information on its spatial and temporal movement patterns, which hampers the development of effective control programmes. We examined the movement patterns of an introduced population of C. auratus in a south‐western Australian river using passive acoustic telemetry. The study population had a high residency index within the array (i.e. proportion of all days at liberty that, on average, each fish was detected by a receiver) with fish being detected on 64% of days. The individuals were also reasonably mobile, travelling a mean of 0.30 km (linear river kilometres).day^‐1 within the array, and one fish moved 231.3 km over the 365‐day study period (including 5.4 km in a 24 hr period). Importantly, C. auratus displayed significant seasonal movement patterns including a clear shift in habitats during its breeding period with most mature individuals being detected in an off‐channel wetland during that time. The results of this study strongly suggest that C. auratus undertook a spawning migration into a lentic habitat. These results have important implications for developing control programmes for the species, such as targeting connections to off‐channel lentic systems during its breeding period.     

Development of Stem-base Pathogens on Different Cultivars of Winter Wheat Determined by Quantitative PCR

The progress of development of stem-base pathogens in crops of second winter wheat was plotted in nine experiments in three years. The amount of each pathogen present was determined by quantitative PCR. Where Tapesia yallundae was present in quantifiable amounts, it usually developed earlier than the other eyespot pathogen, T. acuformis. Both species were usually present in greater amounts on cultivars which are more susceptible to eyespot. The sharp eyespot pathogen, Rhizoctonia cerealis, developed more erratically than either of the Tapesia spp. and there were no consistent effects on different cultivars. Fusarium spp., the cause of brown foot rot, were rarely present in quantifiable amounts, but Microdochium nivale was usually present as one or both of the varieties nivale and majus. Late-season (after anthesis) decreases in M. nivale suggest that any brown foot rot symptoms attributable to this fungus would have fully developed earlier. Cultivar differences in amounts of M. nivale were most clear in stems during internode extension and when relatively large amounts of DNA were present. Such differences approximately reflected eyespot susceptibility, cv. Soissons containing most and cv. Lynx containing least DNA. The results emphasise the difficulty in relating diagnoses, by quantitative PCR or other means, at early growth stages when decisions to apply fungicides against stem-base disease are made, to later disease severity.     

Resistance to pyraclostrobin, boscalid and multiple resistance to Pristine® (pyraclostrobin + boscalid) fungicide in Alternaria alternata causing alternaria late blight of pistachios in California

Pristine® (pyraclostrobin + boscalid) is a fungicide registered for the control of alternaria late blight in pistachio. A total of 95 isolates of Alternaria alternata collected from orchards with and without a prior history of Pristine® sprays were tested for their sensitivity towards pyraclostrobin, boscalid and Pristine® in conidial germination assays. The EC₅₀ values for 35 isolates from orchards without Pristine® sprays ranged from 0·09 to 3·14 µg mL^?1 and < 0·01 to 2·04 µg mL^?1 for boscalid and Pristine®, respectively. For pyraclostrobin, 27 isolates had EC₅₀ < 0·01 µg mL^?1 and six had low resistance (mean EC₅₀ value = 4·71 µg mL^?1). Only one isolate was resistant to all three fungicides tested, with EC₅₀ > 100 µg mL^?1. Among 59 isolates from the orchard with a history of Pristine® sprays, 56 were resistant to pyraclostrobin; only two were sensitive (EC₅₀ < 0·01 µg mL^?1) and one was weakly resistant (EC₅₀ = 10 µg mL^?1). For the majority of these isolates EC₅₀ values ranged from 0·06 to 4·22 µg mL^?1 for boscalid and from 0·22 to 7·74 µg mL^?1 for Pristine®. However, seven isolates resistant to pyraclostrobin were also highly resistant to boscalid and Pristine® and remained pathogenic on pistachio treated with Pristine®. Whereas strobilurin resistance is a common occurrence in Alternaria of pistachio, this is the first report of resistance to boscalid in field isolates of phytopathogenic fungi. No cross resistance between pyraclostrobin and boscalid was detected, suggesting that Pristine® resistance appears as a case of multiple resistance.     

Glazed lunar rocks: origin by impact

The glassy coating of lunar rock 12017 is enriched in 15 trace elements relative to the crystalline interior. It apparently consists chiefly of shock-melted rock, somewhat richer in rare earth elements and alkali metals than rock 12017 itself. The glass has been contaminated by about 0.5 percent carbonaceous-chondrite-like material or, alternatively, by a mixture of 0.06 to 0.3 percent fractionated meteoritic material and approximately 10 to 15 percent local soil. The glazing seems to represent molten material splashed from a nearby meteorite impact and not in situ melting by a sudden increase in solar luminosity.     

Genetic analysis of histone H4: essential role of lysines subject to reversible acetylation

The nucleosome is the fundamental unit of assembly of the chromosome and reversible modifications of the histones have been suggested to be important in many aspects of nucleosome function. The structure-function relations of the amino-terminal domain of yeast histone H4 were examined by the creation of directed point mutations. The four lysines subject to reversible acetylation were essential for histone function as the substitution of arginine or asparagine at these four positions was lethal. No single lysine residue was completely essential since arginine substitutions at each position were viable, although several of these mutants were slower in completing DNA replication. The simultaneous substitution of glutamine for the four lysine residues was viable but conferred several phenotypes including mating sterility, slow progression through the G2/M period of the division cycle, and temperature-sensitive growth, as well as a prolonged period of DNA replication. These results provide genetic proof for the roles of the H4 amino-terminal domain lysines in gene expression, replication, and nuclear division.