The EFSA quantitative approach to pest risk assessment – methodological aspects and case studies

A new method for pest risk assessment and the identification and evaluation of risk‐reducing options is currently under development by the European Food Safety Authority (EFSA) Plant Health Panel. The draft method has been tested on pests of concern to the European Union (EU). The method is adaptable and can focus either on all the steps and sub‐steps of the assessment process or on specific parts if necessary. It is based on assessing changes in pest population abundance as the major driver of the impact on cultivated plants and on the environment. Like other pest risk assessment systems the method asks questions about the likelihood and magnitude of factors that contribute to risk. Responses can be based on data or expert judgment. Crucially, the approach is quantitative, and it captures uncertainty through the provision by risk assessors of quantile estimates of the probability distributions for the assessed variables and parameters. The assessment is based on comparisons between different scenarios, and the method integrates risk‐reducing options where they apply to a scenario, for example current regulation against a scenario where risk‐reducing options are not applied. A strategy has been developed to communicate the results of the risk assessment in a clear, comparable and transparent way, with the aim of providing the requestor of the risk assessment with a useful answer to the question(s) posed to the EFSA Plant Health Panel. The method has been applied to four case studies, two fungi, Ceratocystis platani and Cryphonectria parasitica, the nematode Ditylenchus destructor and the Grapevine flavescence dorée phytoplasma. Selected results from these case studies illustrate the types of output that the method can deliver.     

The molecular basis of the sparse fur mouse mutation

The ornithine transcarbamylase-deficient sparse fur mouse is an excellent model to study the most common human urea cycle disorder. The mutation has been well characterized by both biochemical and enzymological methods, but its exact nature has not been revealed. A single base substitution in the complementary DNA for ornithine transcarbamylase from the sparse fur mouse has been identified by means of a combination of two recently described techniques for rapid mutational analysis. This strategy is simpler than conventional complementary DNA library construction, screening, and sequencing, which has often been used to find a new mutation. The ornithine transcarbamylase gene in the sparse fur mouse contains a C to A transversion that alters a histidine residue to an asparagine residue at amino acid 117.     

Expression of Mitochondria‐Associated Genes (PPARGC1A,NRF‐1, BCL‐2 and BAX) in Follicular Development and Atresia of Goat Ovaries

Most follicles undergo atresia during the developmental process. Follicular atresia is predominantly regulated by apoptosis of granulosa cells, but the mechanism underlying apoptosis via the mitochondria‐dependent apoptotic pathway is unclear. We aimed to investigate whether the mitochondria‐associated genes peroxisome proliferator‐activated receptor‐gamma, coactivator1‐alpha (PPARGC1A), nuclear respiratory factor‐1 (NRF‐1), B‐cell CLL/lymphoma 2 (BCL‐2) and BCL2‐associated X protein (BAX) played a role in follicular atresia through this pathway. The four mitochondria‐associated proteins (PGC‐1α, which are encoded by the PPARGC1A gene, NRF‐1, BCL‐2 and BAX) mainly expressed in granulosa cells. The mRNA and protein levels of PPARGC1A/PGC‐1α and NRF‐1 in granulosa cells increased with the follicular development. These results showed that these genes may play a role in the regulation of the follicular development. In addition, compared with healthy follicles, the granulosa cell in atretic follicles had a reduced expression of NRF‐1, increased BAX expression and increased ratio of BAX to BCL‐2 expression. These results suggested that changes of the mitochondria‐associated gene expression patterns in granulosa cells may lead to follicular atresia during goat follicle development.     

A recombinant vaccine expressing a mammalian Mycobacterium sp. antigen is immunostimulatory but not protective in striped bass

A recombinant vaccine was constructed for piscine mycobacteriosis utilizing a Brucella abortus strain RB51 vector expressing a mammalian Mycobacterium sp. 85A antigen. Juvenile striped bass were inoculated with the resulting construct at doses equivalent to 10(6), 10(7), 10(8), 10(9), and 10(10) colony-forming units/fish. Blood and tissue samples from these fish demonstrated significant specific humoral and cell-mediated immune responses towards the 85A antigen in a dose-dependent manner. However, survival studies determined that inoculated fish failed to demonstrate cross-protective responses after live Mycobacterium marinum challenge 70 days post-inoculation.     

In silico prediction of Gallibacterium anatis pan-immunogens

The Gram-negative bacterium Gallibacterium anatis is a major cause of salpingitis and peritonitis in commercial egg-layers, leading to reduced egg production and increased mortality. Unfortunately, widespread multidrug resistance and antigenic diversity makes it difficult to control infections and novel prevention strategies are urgently needed. In this study, a pan-genomic reverse vaccinology (RV) approach was used to identify potential vaccine candidates. Firstly, the genomes of 10 selected Gallibacterium strains were analyzed and proteins selected on the following criteria; predicted surface-exposure or secretion, none or one transmembrane helix (TMH), and presence in six or more of the 10 genomes. In total, 42 proteins were selected. The genes encoding 27 of these proteins were successfully cloned in Escherichia coli and the proteins expressed and purified. To reduce the number of vaccine candidates for in vivo testing, each of the purified recombinant proteins was screened by ELISA for their ability to elicit a significant serological response with serum from chickens that had been infected with G. anatis. Additionally, an in silico prediction of the protective potential was carried out based on a protein property prediction method. Of the 27 proteins, two novel putative immunogens were identified; Gab_1309 and Gab_2312. Moreover, three previously characterized virulence factors; GtxA, FlfA and Gab_2156, were identified. Thus, by combining the pan-genomic RV approach with subsequent in vitro and in silico screening, we have narrowed down the pan-proteome of G. anatis to five vaccine candidates. Importantly, preliminary immunization trials indicated an in vivo protective potential of GtxA-N, FlfA and Gab_1309.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-014-0080-0) contains supplementary material, which is available to authorized users.     

Clinical characteristics and mode of inheritance of familial focal seizures in Standard Poodles

OBJECTIVE: To determine clinical characteristics and mode of inheritance of seizures in a family of Standard Poodles. DESIGN: Case series. ANIMALS: 90 Standard Poodles descended from the same maternal bloodline (30 with probable idiopathic epilepsy [PIE] and 60 without any history of seizures). PROCEDURES: Researchers contacted owners to determine whether dogs had ever had any seizures and, if so, the nature of any such seizures and any potential underlying causes. Dogs were considered to have PIE if they were between 6 months and 7.5 years old at the time of seizure onset and had no evidence of any underlying cause. To determine the mode of inheritance, segregation analyses were designed to allow the family to be analyzed as a whole, as opposed to as nuclear families. Competing models of inheritance were compared statistically for their ability to explain the data. RESULTS: Of the dogs with PIE, 28 (93%) had focal onset seizures with or without secondary generalization. Median age of onset was 3.7 years; 6 dogs were > 5 years old at the onset of seizures. Segregation analyses strongly suggested that PIE was inherited as a simple recessive autosomal trait with complete or almost complete penetrance. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that in this family of Standard Poodles, PIE was inherited as a simple recessive autosomal trait with complete or almost complete penetrance. Seizures often had focal, as opposed to generalized, onsets, and it was not uncommon for seizures to begin after 5 years of age.