Project description:Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. However, reliable systems affording parallel testing of thousands of patients for pathogen infection have not yet been routinely employed. Here we describe “Systematic Parallel Analysis of RNA coupled to Sequencing for Covid-19 screening” (C19-SPAR-Seq), a multiplexed, readily automated platform for SARS-CoV-2 detection capable of analyzing tens of thousands of patient samples in a single instrument run. To address strict requirements for control of assay parameters and output demanded by clinical diagnostics, we employed a control-based Precision-Recall and Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of several hundred patients performed with a specificity of 100% and sensitivity of 91% on samples with low viral loads. Our study thus establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.
Project description:For the toxicological risk assessment of genetically modified (GM) food components, the European Food Safety Agency advises to use an adapted version of the 90-day oral toxicity study in rodents, originally designed for the toxicity testing of chemicals. Since in GM crop testing scenarios the crop under evaluation is specifically intended as a food / feed component, some testing aspects are conceptually different from testing chemical compounds and thus need careful consideration. One key consideration relates to the appropriate dose level to evaluate the GM crop as a component of the experimental diet. The aim of this study was to develop and optimize methods that are required for advancing the use of zebrafish feeding trials for the toxicological safety evaluation of GM crops. Using maize as a case study, we investigated the effects of an increasing maize substitution dose level in the diets of zebrafish, using non-GM maize. In addition, we investigated the effect of the presence of maize in the diets (0% or 25% of maize substitution levels) on mRNA transcriptional profiles in the zebrafish liver.