Omics sciences (2020/2021)

Course code
Alessandra Maria Bossi
Teaching is organised as follows:
Unit Credits Academic sector Period Academic staff
MODULO II 6 CHIM/01-ANALYTICAL CHEMISTRY See the unit page See the unit page
MODULO I 6 AGR/07-AGRICULTURAL GENETICS See the unit page See the unit page

Learning outcomes

Transcriptomic (theory part) The theory part of this course aims to explain what a transcriptomic analyses is and for which purpose it can be applied. Furthermore it aims to provide knowledge about the different approaches and technique which can be applied for a transcriptomic analysis. By the end of the course students will be able to approach planning of transcriptomic analysis and to understand transcriptomic data and their interpretation presented in scientific paper. Transcriptomic (laboratory part) The laboratory part of this Course has as main aim to provide to students the knowledge for the correct design, application and interpretation of a transcriptomic analysis. Students will have the opportunity to approach and discuss the experimental design for a transcriptomic experiment, to deal with preparation of samples for RNASeq analysis and will apply bioinformatics tools to interpret transcriptomic data. Metabolomics (theory part) - define the “targeted” and “untargeted” metabolomics approaches; -discriminate the critical points of an experimental design; -organize a plan for the extraction and analysis of metabolites suitable for the metabolites/class of metabolites of interest; -describe the key elements for the raw data process till the production of the FQM (Feature Quantification Matrix); -use statistical approaches suitable to the experimental problem; -apply the metabolomics analysis to the investigation of the biological complexity of cells/ tissues/ organs/organisms, from the point of view of the small molecules, as intermediates or end products of the metabolism; -use an appropriate scientific language. Metabolomics (laboratory part) -plan an experimental design; -interpret some mass spectra; -identify some simple metabolites through the fragmentation trees; -process a complex metabolomics experiment through specific software; -analyse a complex metabolomics experiment using the suitable statistic approaches; -acquire an appropriate language. Proteomics (theory part) The aim of the module is to provide the theoretical basis for addressing a proteomic analysis. The module begins by providing knowledge about the physico-chemical characteristics of the protein sample and about the related methods to handle and fractionate such sample. Subsequently the proteomics methods are explained, providing knowledge on the separative methods used in proteomics (in gel, gel free), in mass spectrometric analysis of peptides and finally on the identification of proteins. The module aims to provide theoretical-strategic proteomics skills: the knowledge of the protein material and of the sample in analysis, mastering the methods to extract proteins from the sample, decision-making skills in the choice of the separative method; basic analysis skills in mass spectrometry and spectra reading; research skills on in silico databases for protein identification, result validation skills; ability to define a quantitative strategy of proteomic analysis. The educational path aims to provide all the necessary knowledge to mature the ability to apply the proteomics investigation to agro-industrial problems, including the adulteration of foods, the origin and traceability of raw materials. Proteomics (laboratory part) The practicals are intended to furnish wet-lab proteomic-abilities to the student. It aims at bringing the student closer to the methods and protocols typical of the proteomic research, helping to translate the theory into experimental phases. The bases of the wet-lab proteomic analysis are provided, addressing the issue of the experimental design, the sample processing, the gel separation methods and the silico analysis. The laboratory is aimed at developing experimental proteomics skills. The type of samples selected for the laboratory will be the traceability of the food product.