Sub-project 10: Development of bioinformatic tools for the analysis of MACE data Host Organizations GenXPRO (Germany) Objectives : The ESR will be in charge of standardising pipelines that will be used for RNA-seq and MACE analyses by all the participants. He will be involved in performing next generation sequencing to characterise environmental adaptation. A single pipeline to analyse listerial transcriptomic and proteomic data will be developed and implemented by each partner for the sake of uniformity of all the data produced within List_MAPS. The ESR will be involved in the interpretation of transcriptomic and proteomic data for which pathway analyses and good data visualization will be required. A cytoscape app will be developed as visualization tool. Expected Results: MACE analysis pipeline. Database. Transcriptome comparisons in selected habitats. Data visualization tool. Duration (months) 24 Contact Dr. Bjorn ROTTER: rotter@genxpro.de
11. Development of innovative tools for rapid phenotypic characterisation of intraspecific diversity of Listeria monocytogenes (Joint supervision PhD) Host Organizations BioFilm Control (France) and GenXPRO (Germany) Objectives 1. The ESR will develop an assay to test biofilm phenotype in a large array of food processing-related environmental conditions (salt, acides, disinfectants, preservatives) in BFC facilities. He will be in charge of the development and validation of an in silico virulence assay. This assay will target specific mRNAs in order to estimate the virulence potential of strains of L. monocytogenes. Transcript targets will be selected and tested by qPCR in GXP premises. In the process of validation, virulence results of several strains collected in a humanised mouse model will be compared with the in silico analysis. Once these innovative tools will be validated, intraspecific phenotypic diversity (biofilm and virulence) will be assessed on a collection of environmental and clinical isolates of L. monocytogenes. Genotypic diversity will be assessed under the supervision of GPX. Expected Results : Adaptation of the BioFilm Ring test R to test food processing environmental conditions. Development of an innovative in silico virulence assay surrogate to animal models. Diversity results will inform stakeholders on the level of health hazard according to the strain. This in turn will help secure food safety all along the shelf life of foodstuff. Duration (months) 36 Contact : Dr. Thierry BERNARDI: thbe@biofilmcontrol.com Dr. Bjorn ROTTER: rotter@genxpro.de ELIGIBLE CRITERIA of Marie Sklokowska Curie actions: Researchers may be of any nationality Candidates shall at the time of recruitment by the host organization, be in the first four years (full-time equivalent research experience) of their research careers. Full-time equivalent research experience is measured from the date when a researcher obtained the degree which would formally entitle him or her to embark on a doctorate, either in the co
