Applicability and sensitivity of PCR-SSCP method for milk species identification in cheese

Species identification in food has become a prominent issue in recent years as the importance of consumer protection has increased. DNA-based species identification methods were developed by researchers in the last two decades, as these are reliable, accurate, and low-cost techniques for species identification in raw and processed food products as well. In our study, universal primers were designed to conserved regions of mitochondrial 12S rRNA. Amplicons were heat-denatured and a PCR single strand conformation polymorphism (SSCP) method was developed to identify cattle, buffalo, sheep, and goat DNA. Sensitivity of this technique was tested on DNA mixtures of cattle-sheep, cattle-goat, and cattle-buffalo and the threshold limit of cattle DNA was 5%, 5%, and 3%, respectively. One hundred and five cheeses were purchased and collected from Bosnian and Hungarian farmers, retails, and supermarkets to reveal fraud, 32 percent of them (34 cheeses) were found to be mislabelled by species

Genomic and biological characterization of a velogenic Newcastle disease virus isolated from a healthy backyard poultry flock in 2010

<p>Abstract</p> <p>Background</p> <p>Newcastle disease virus (NDV) causes severe and economically important disease in poultry around the globe. None of NDV strains in Pakistan have been completely characterized and the role of rural poultry in harbouring NDV is unclear. Since they have a very important role for long-term circulation of the virus, samples were collected from apparently healthy backyard poultry (BYP) flocks. These samples were biologically analyzed using mean death time (MDT) and intracerebral pathogenicity index (ICPI), whereas genotypically characterized by the real-time PCRs coupled with sequencing of the complete genome.</p> <p>Findings</p> <p>Despite of being non-pathogenic for BYP, the isolate exhibited MDT of 49.6 h in embryonated chicken eggs and an ICPI value of 1.5. The F gene based real-time PCR was positive, whereas M-gene based was negative due to substantial changes in the probe-binding site. The entire genome of the isolate was found to be 15192 nucleotides long and encodes for six genes with an order of 3'-NP-P-M-F-HN-L-5'. The F protein cleavage site, an indicative of pathogenicity, was ¹¹²RRQKRF¹¹⁷. Complete genome comparison indicated that the RNA dependent RNA polymerase gene was the most and the phosphoprotein was least conserved gene, among all the genes. The isolate showed an Y526Q substitution in the HN protein, which determines neuraminidase receptor binding and fusion activity of NDV. Phylogenetic analysis, based on F and HN genes, classified this isolate into genotype VII, a predominant genotype responsible for ND outbreaks in Asian countries. However, it clustered well apart from other isolates in this genotype to be considered a new subgenotype (VII-f).</p> <p>Conclusions</p> <p>These results revealed that this isolate was similar to virulent strains of NDV and was avirulent in BYP either due to resistance of local breeds or due to other factors such as substantial mutations in the HN protein. Furthermore, we have characterized the first isolate of NDV, which could act as domestic reference strain and could help in development and selection of appropriate strain of NDV for vaccine in the country.</p

Methodological Framework for Data Collection and Analysis

This D1.3 Framework for data collection and analysis is rooted in Work Package (WP) 1, Task 1.5 Develop data collection framework for multiple case study, including the SPOTTERON ICT platform. It is an integrated framework for data collection and analysis in WP 2 (social inclusion study) and WP 3 (social innovation and gender studies). In particular it addresses the work of Task 2.4 - Develop and refine the design and methodology for each case study; T3.1 Cross-case analysis of social inclusion opportunities; T3.2 Cross-case gender analysis; T3.3 Cross-case analysis of innovation processes, social change and the role of citizen social science (CSS); and T3.4 Cross�case analysis for positive drivers. The primary focus is on the social inclusion sub study, but the framework also touches on the social innovation and gender studies. It provides details of the 10 local cases being developed in nine countries in a multiple case study of co-creative youth citizen social science (Y-CSS) in Europe. This Report comprises four parts: (1) anintroductory overview of YouCount’s six overlapping WPs and four sub studies; (2) the planned participatory and co-creative research design and approachfor the multiple case study and use of ICT tools for inclusive science practices; (3) details the data collection methods that are both common to, and unique to the local cases; and (4) sets out the data analysis strategy and preliminary plans for cross case analyses. The main target group for this Deliverable is the YouCount consortium partners themselves as this document collates the plans and descriptions of the common methodological approach in the local cases as well as highlighting variations across the cases. It serves as a reference document for all YouCount team members including individuals joining the project at a later stage. As flexibility is at the heart of the YouCount approach, this is a ‘living’ document, offering an initial starting point that will be further amended to reflect empirical findings and practical experience at the end of the stud