Standard and Light-Cycler PCR methods for animal DNA species detection in animal feedstuffs

In this work four species-specific primers and probes were designed and evaluated for the detection and quantification of bovine, ovine, swine and chicken mitochondrial DNA in feeds. PCR primers were optimized using conventional and Real Time PCR, to detect short species-specific sequences amplifiable from heat treated material. Both methods confirmed the high specificity of the primers designed. Real time quantitative PCR assay allowed the detection of as few as 0.01 ng and 0.05 ng of ovine and bovine genomic DNA, respectively. The detection limit for swine and chicken genomic DNA was 0.5 ng. Sensitivity levels observed in DNA extracted from meat samples processed according to EU legislation were different compared to those in genomic DNAs previously described. They resulted in swine 5 fg of MBM DNA, in chicken 25 ng, in ovine and bovine 50 ng. We confirmed the efficiency and specificity of primers in RT-PCR to detect 0.5% of bovine, ovine, swine and chicken MBM in contaminated feedstuffs. (C) 2007 Elsevier Ltd. All rights reserved

Making Bipedal Robot Experiments Reproducible and Comparable: The Eurobench Software Approach

This study describes the software methodology designed for systematic benchmarking of bipedal systems through the computation of performance indicators from data collected during an experimentation stage. Under the umbrella of the European project Eurobench, we collected approximately 30 protocols with related testbeds and scoring algorithms, aiming at characterizing the performances of humanoids, exoskeletons, and/or prosthesis under different conditions. The main challenge addressed in this study concerns the standardization of the scoring process to permit a systematic benchmark of the experiments. The complexity of this process is mainly due to the lack of consistency in how to store and organize experimental data, how to define the input and output of benchmarking algorithms, and how to implement these algorithms. We propose a simple but efficient methodology for preparing scoring algorithms, to ensure reproducibility and replicability of results. This methodology mainly constrains the interface of the software and enables the engineer to develop his/her metric in his/her favorite language. Continuous integration and deployment tools are then used to verify the replicability of the software and to generate an executable instance independent of the language through dockerization. This article presents this methodology and points at all the metrics and documentation repositories designed with this policy in Eurobench. Applying this approach to other protocols and metrics would ease the reproduction, replication, and comparison of experiments.This study is supported by the European Union’s Horizon 2020 research and innovation program under Grant Agreement no 779963, project Eurobench

[Enteric viruses and bacteriological parameters in molluscs]

Eighty-seven samples of shellfish were collected considering: type of mollusc, origin, growing area, monitoring or for human purpose. The bacteriological parameters were: Fecal Coliforms, Escherichia coli, and Salmonella; whereas the virological parameters included: Hepatitis A and E virus, Rotavirus, Astrovirus and Enterovirus. In total, 63.2% of samples had normal bacteria values, only one sample was Salmonella positive. The percentage of positive samples for Hepatitis A virus was 5.7%, Rotavirus 29.9%, Astrovirus 27.6%, Enterovirus 10.3%. The recovery of hepatitis E virus was always negative, whereas 13 samples (14.9%) were positive for two viruses

[Enteric viruses and bacteriological parameters in molluscs]

Eighty-seven samples of shellfish were collected considering: type of mollusc, origin, growing area, monitoring or for human purpose. The bacteriological parameters were: Fecal Coliforms, Escherichia coli, and Salmonella; whereas the virological parameters included: Hepatitis A and E virus, Rotavirus, Astrovirus and Enterovirus. In total, 63.2% of samples had normal bacteria values, only one sample was Salmonella positive. The percentage of positive samples for Hepatitis A virus was 5.7%, Rotavirus 29.9%, Astrovirus 27.6%, Enterovirus 10.3%. The recovery of hepatitis E virus was always negative, whereas 13 samples (14.9%) were positive for two viruses

Identification and sequence analysis of hepatitis A virus detected in market and environmental bivalve molluscs

In Italy in 1998, hepatitis A virus (HAV) was responsible for an infectious disease transmitted by contaminated bivalve molluscs. To determine the presence of HAV in the bivalves collected during a 1-year follow-up study, hepatitis A RNA was extracted and amplified by a nested reverse transcriptase-PCR method overlapping the VP1/2A region. The HAV genome was detected in 24 (14.1%) of 170 samples: 19 clams (Tapes decussates and Tapes semidecussatus), 1 oyster (Crossostea gigas), and 4 mussels (Mytillus galloprovincialis). Eleven positive samples were collected from marketing areas, and 13 positive samples were collected from growing areas. Seventeen of the 24 positive samples had been taken from domestic products, and 7 had been imported. Sequence analysis showed the presence of genotypes IA and IB. Our results suggest significant presence of HAV in bivalves from both marketing (public consumption) and environmental (growing) areas

Identification and sequence analysis of hepatitis A virus detected in market and environmental bivalve molluscs

In Italy in 1998, hepatitis A virus (HAV) was responsible for an infectious disease transmitted by contaminated bivalve molluscs. To determine the presence of HAV in the bivalves collected during a 1-year follow-up study, hepatitis A RNA was extracted and amplified by a nested reverse transcriptase-PCR method overlapping the VP1/2A region. The HAV genome was detected in 24 (14.1%) of 170 samples: 19 clams (Tapes decussates and Tapes semidecussatus), 1 oyster (Crossostea gigas), and 4 mussels (Mytillus galloprovincialis). Eleven positive samples were collected from marketing areas, and 13 positive samples were collected from growing areas. Seventeen of the 24 positive samples had been taken from domestic products, and 7 had been imported. Sequence analysis showed the presence of genotypes IA and IB. Our results suggest significant presence of HAV in bivalves from both marketing (public consumption) and environmental (growing) areas