This paper describes a new and rapid method for accurate quantification of the six ergot alkaloids, ergometrine, ergotamine, ergosine, ergocristine, ergocryptine, and ergocornine, by liquid chromatography-tandem mass spectrometry (LC-MS-MS). The six ergot alkaloids studied have been defined by the European Food Safety Authority (EFSA) as among the most common and physiologically active ones. In addition, the method enables the quantification of the corresponding six epimers (ergo-inines) of these ergot alkaloids. This is of considerable importance in terms of the differences in toxicity of the isomeric forms. The method involves extraction under alkaline conditions using a mixture of acetonitrile and ammonium carbonate buffer followed by a rapid clean-up using dispersive solid-phase extraction with PSA (primary secondary amine) and a short chromatographic LC-run (21 min) with subsequent MS-MS detection. The method was developed and validated using ten different cereal and food samples. The major strength of the new method compared with previously published techniques is the simplicity of the clean-up procedure and the short analysis time. The limits of quantification were 0.17 to 2.78 μg kg(-1) depending on the analyte and matrix. Recovery values for the 12 ergot alkaloids spiked into ten different matrices at levels of 5, 50, and 100 μg kg(-1) were between 69 and 105% for 85 of 90 recovery measurements made over six days. Measurement uncertainty values were highly satisfactory. At a concentration level of 5 μg kg(-1) the expanded measurement uncertainty ranged from ±0.56 to ±1.49 μg kg(-1), at a concentration level of 100 μg kg(-1) the expanded measurement uncertainty ranged from ±8.9 to ±20 μg kg(-1). Both LOQs and measurement uncertainties were dependent on the analyte but almost independent of the matrix. The method performance was satisfactory when tested in a mini-intercomparison study between three laboratories from three different countries.

In the United Kingdom, European badgers Meles meles are a protected species and an important wildlife reservoir of bovine tuberculosis. We conducted a survey of badger dens (main setts) in 1614 1 km squares across England and Wales, between November 2011 and March 2013. Using main setts as a proxy for badger social groups, the estimated mean density of badger social groups in England and Wales was 0.485 km 22 (95% confidence interval 0.449-0.521) and the estimated abundance of social groups was 71,600 (66,400-76,900). In the 25 years since the first survey in 1985-88, the annual rate of increase in the estimated number of badger social groups was 2.6% (2.2-2.9%), equating to an 88% (70-105%) increase across England and Wales. In England, we estimate there has been an increase of 103% (83-123%) in badger social groups, while in Wales there has been little change (225 to 149%).

Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is causing severe losses in cassava production in Kenya, Tanzania and Uganda. Two real-time RT-PCR assays based on TaqMan chemistry capable of detecting and distinguishing these two viruses are described. These assays were used to screen 493 cassava samples collected from western and coastal Kenya, the main cassava regions of Uganda and inland Tanzania. Both viruses were found in all three countries and across regions therein. Association of CBSD leaf symptom status with CBSV and UCBSV assay results was weak, confirming the need for a diagnostic assay. For leaf samples that were observed with CBSD-like leaf symptoms but shown as CBSV and UCBSV negative by the RT-PCR assay, deep sequencing using a Roche 454 GS-FLX was used to provide additional evidence for the absence of the viruses. The probability of the CBSD associated diagnostics detecting a single CBSV or UCBSV positive sample amongst other non-CBSD samples was modelled. The results of this study are discussed in the context of the application of diagnostics of CBSD-associated viruses under the Great Lakes Cassava Initiative and the need to minimize the risk of further spread of the viruses with cassava multiplication material. It is shown that high throughput testing undertaken at Fera of 300 cassava leaves taken from fields for seed multiplication, when analysed in pools of 10, has given a 95% probability of detecting 1% infected plants in the field.

Internal necrosis of carrot has been observed in UK carrots for at least 10 years, and has been anecdotally linked to virus infection. In the 2009 growing season some growers had up to 10% of yield with these symptoms. Traditional diagnostic methods are targeted towards specific pathogens. By using a metagenomic approach with high throughput sequencing technology, other, as yet unidentified causes of root necrosis were investigated. Additionally a statistical analysis has shown which viruses are most closely associated with disease symptoms. Carrot samples were collected from a crop exhibiting root necrosis (102 Affected: 99 Unaffected) and tested for the presence of the established carrot viruses: Carrot red leaf virus (CtRLV), Carrot mottle virus (CMoV), Carrot red leaf associated viral RNA (CtRLVaRNA) and Parsnip yellow fleck virus (PYFV). The presence of these viruses was not associated with symptomatic carrot roots either as single viruses or in combinations. A sub-sample of carrots of mixed symptom status was subjected to MiSeq sequencing. The results from these tests suggested Carrot yellow leaf virus (CYLV) was associated with symptomatic roots. Additionally a novel Torradovirus, a novel Closterovirus and two novel Betaflexiviradae related plant viruses were detected. A specific diagnostic test was designed for CYLV. Of the 102 affected carrots, 98% were positive for CYLV compared to 22% of the unaffected carrots. From these data we conclude that although we have yet to practically demonstrate a causal link, CYLV appears to be strongly associated with the presence of necrosis of carrots.

The homogeneity of analytical samples and the stability of pesticides during the sample processing of oranges and tomatoes were evaluated. The mean concentrations of 14C-labeled chlorpyrifos in analytical portions (subsamples) after processing show that homogeneity is dependent on sample type as well as the processing procedure. The homogeneity of analytical samples of tomatoes processed cryogenically was much better than those processed at ambient temperature. For tomatoes, the minimum analytical portion masses required for between-analytical portion variation of < 0.3 Ho were 110 and 5 g for processing at ambient and cryogenic temperatures, respectively. Results for orange showed that analytical portion sizes of 5 g provided sufficient homogeneity from both sample processing procedures. Assessments of pesticide stability demonstrated that most were relatively stable during processing at either ambient or cryogenic temperatures. However, some pesticides, including dichlofluanid, chlorothalonil, tolylfluanid, and dicloran, appeared to suffer much greater losses (>20%) during processing at ambient temperature. For these analytes, loss is interpreted as chemical degradation.

This paper presents a draft protocol for analyzing the results of validation studies for qualitative methods of detection which is designed to meet three competing goals: (1) to give correct answers, (2) have a broad scope of application, and (3) be accessible to a wide range of users. The draft protocol can be applied to the validation of methods by collaborative trial or to single-laboratory studies. The protocol produces an estimate of the probability of a positive response with a prediction interval within which 95% of laboratories (or analytical runs) are expected to fall when the method is applied in practice. The interval is calculated from the observed reproducibility (or within-laboratory reproducibility) standard deviation. Then a simple plot of prediction intervals for the probability of detection against the concentration of analyte, where the concentration is known, is used to provide an estimate of the range of limits of detection and false positive probability that we can expect to see when the validated method is applied in practice. The use of the draft protocol is demonstrated using results produced by three collaborative trials. A simulation study showed that a conclusion that a method is fit for purpose that is generated by the draft protocol is likely to be safe.

There is currently no published consensus approach to validation of small-molecule biomarker methods. This paper presents a generic approach to endogenous method validation for consideration as bioanalytical best practice for this type of assay.

Pest and pathogens pose a major threat to food security and the natural environment, and these threats are moving around the globe. Trade, travel and transport have major roles to play in this and thus to improve plant biosecurity, we need enhanced phytosanitary inspection systems. In order to achieve this, there is a role for the more effective use of diagnostic technology, such as field-based testing or the use of next generation sequencing technology. In this review we examine the opportunities and challenges posed by using new technology within a plant biosecurity context, but in contrast to previous reviews, here we focus on practical challenges associated with deployment and routine use, rather than specific technical issues. These key challenges include the need to accelerate the development and deployment of new technologies into the field, the accelerated discovery of new pathogens and the need for new risk assessment approaches, and improvements to our understanding of how best to deploy and use new diagnostic tools for maximum impact. Throughout we focus on how interdisciplinary approaches are important to help us improve our understanding and achieve our goals.