A FAIR based approach to data sharing in Europe

The European fusion research activities have, over recent decades, generated a vast and varied set of data. The volume and diversity of the data that need to be catalogued and annotated make the task of organising and making the data available within a broader environment very challenging. Nevertheless, there are strong scientific drivers as well as incentives and mandates from national research agencies suggesting that a more coherent approach to data referencing, dissemination and sharing would provide strong benefits to the fusion research community and beyond. Here, we discuss the technical requirements and developments needed to transition the current, and future, range of fusion research data to an open and Findable, Accessible, Interoperable, and Reusable data sharing structure guided by the principle \u27as open as possible, as closed as necessary\u27. Here we propose a set of recommendations and technical implementations needed to form a European data sharing environment for the fusion research programmes. Consistency with the emerging IMAS (ITER Integrated Modelling and Analysis Suite) infrastructure is considered to facilitate future deployments

Linking Chronic Infection and Autoimmune Diseases: Mycobacterium avium Subspecies paratuberculosis, SLC11A1 Polymorphisms and Type-1 Diabetes Mellitus

(MAP) has been reported to be a possible trigger in the development of T1DM. gene (274C/T) associated to type 1 diabetic patients and not to controls. The presence of MAP DNA was also significantly associated with T1DM patients and not with controls. alter the processing or presentation of MAP antigens triggering thereby an autoimmune response in T1DM patients

Investigation of the association of the SLC11A1 gene with resistance/sensitivity of goats (Capra hircus) to paratuberculosis

SLC11A1 (solute carrier family 11 member A1) protein is located on the phagolysosome membrane of macrophages and participates in bacterial killing. Here we have extended our previous work on the investigation of the potential association of polymorphisms of the 3'untranslated region (UTR) of SLC11A1 gene with test-positivity of goats to Mycobacterium avium subsp. paratuberculosis (MAP). Blood, serum and faeces were collected from 223 adult goats, from nine goat farms from Greece with a long-term record of paratuberculosis but no vaccination or tuberculin testing. The samples were subjected to sequence and structure analysis of the SLC11A1 gene and were evaluated by ELISA, culture and real time polymerase chain reaction. The 3'UTR region of the targeted gene revealed 2 microsatellites consisting of a variable number of guanine-thymine repeats named regions A and B. Statistically significant association was recorded between genotypes of region B and ELISA results, whereas the presence of B7 allele was found to contribute to ELISA negativity. The comparison of the SLC11A1 mRNA level pre- and post-exposure to MAP shows elevated gene expression especially at the 3-h time point, in all macrophages tested regardless of their genotype. Unfortunately the latter could not be linked at a statistically significant level with any of the targeted genetic polymorphisms separately. In conclusion it can be stated that the evidence reported here provide the first indications on the association of B genotypes of the SLC11A1 gene and the detection of MAP-specific antibody by ELISA in goats. © 2010

Parturition affects test-positivity in sheep with subclinical paratuberculosis; investigation following a preliminary analysis

Within the context of an investigation focused at improving the effectiveness of test-and-removal for the control of ovine paratuberculosis, we recently conducted a preliminary study using ELISA and real time PCR to assess whether parturition affects test-positivity, in animals with subclinical paratuberculosis. Samples of faeces and blood were collected from 42 adult female animals, before (PP1) and after parturition (PP2), and before mating (PP3). In the preliminary stage of the analysis, only one of the animals tested reacted positively to ELISA (2.38%, 1 of 42), which corresponds to 2.8% of PCR-reactors (1 of 36). Therefore, the final stage the investigation was conducted using only real time PCR, which was applied to test samples of faeces collected from 85 animals, in 5 periods of sampling: 4–15/1–3 days (FP1/FP2) before and after parturition (FP3/FP4), and before mating (FP5). The result of the preliminary analysis indicated that PCR-positivity in terms of the number of shedders and the amount of MAP, is statistically significantly lower before parturition (PP1), whereas that of the final, higher in FP4 compared to FP5. Significantly higher levels of positivity in PP2 and FP4 were also recorded in connection with animals reacting positively to PCR more than once. In conclusion, in sheep with subclinical paratuberculosis, the period of 4–15 days postpartum is more suitable for the application of test-and-removal aiming to the control of the disease, using real time PCR. The use of ELISA for the same purpose is not recommended in the specific category of animals, due to low sensitivity. © 201

Diagnostic investigation for the detection of mycobacteria in samples of fish feeds and tissue from sea bream and sea bass with severe granulomatous lesions

We report on a case of a sea bass and sea bream aquaculture farm in Greece, with many incidents of severe dermal and visceral granulomatous lesions detected during routine inspection and post-mortem examination. The investigation was conducted on samples of fish feeds and fish feed ingredients available commercially, and tissue samples collected from the affected population, and consisted of molecular analysis and histopathology. The former was performed using five PCR assays targeting the main mycobacterial pathogens. Histopathology examination relied on staining of tissue sections of various visceral organs with hematoxylin-eosin and Ziehl-Neelsen. Presence of mycobacteria was demonstrated in the fish feeds (100% and 46.2% positive for Mycobacterium spp. and Mycobacterium avium, respectively), in the fish feed ingredients (73.3% and 33.3% positive for Mycobacterium spp. and Mycobacterium avium, respectively) and the tissue sections (76.5% and 3.9% positive for Mycobacterium marinum and Mycobacterium avium, respectively) that were examined. Sequence analysis of the PCR products was confirmatory of the specificity of the amplification process, at a 98% minimum level of identification. Histopathology revealed in all cases evidence consistent with mycobacterial infection. The result of the analysis indicates that fish are exposed to different mycobacterial species; this probably accumulates in large numbers over the years in the organic sediment collected on the seabed of the aquaculture, causing severe infections. © 2021 Elsevier B.V