Teacher
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TIMPERIO Anna Maria
(syllabus)
COURSE CONTENT - Definition of "omics" sciences Description of the program and of the modalities of the examination Safety rules to be adopted in scientific laboratories - Proteomics definition: expression and functional proteomics, proteomic analysis strategies. Native electrophoresis (BLUE-NATIVE gel), single and bi-dimensional (1D-GEL, 2D-GEL) Iso-electro-focusing (IEF) Reverse phase chromatography RP-HPLC - Applications of proteomics for the study of tumor cells and for early diagnosis for the presence of biomarkers (examples) - Laboratory 1 Protein extraction from material to be defined Determination of protein concentration (Brendford method) Use of the spectrophotometer - Laboratory 2 Mono-dimensional electrophoresis (1D-SDS-PAGE) Cutting bands from the gel and digestion in trypsin (Label Free) - Laboratory 3 Reverse phase HPLC: construction of a gradient Determination of slope and study of the chromatogram - Metabolomics definition: Sample preparation techniques for metabolome analysis. Chromatographic and mass spectrometric methods used to characterize metabolites that function as biomarkers Examples of metabolomics studies in clinical research: Application of metabolomics in the study of autism - Lipidomics defining major lipids and determining determination in mass spectrometry determination of the red cell membranes - Foodomic definition. determination of flavonoids, vitamins in foods - Laboratory 3 Extraction of metabolites according to the method of (Bligh & Dyer) - Mass Spectrometry: General Main sources, analyzers and detectors Analysis of proteins, peptides, metabolites, lipids in intact mass Tandem mass: meaning and purposes - Laboratory 4 Determination of the intact mass of a protein Determination of amino-acid sequence with mass spectrometry Determination of the main lipid classes Determination of flavonoids Statistics: Normalization and equalization, missing values. o Probability and null hypothesis o Descriptive statistics Programs and websites for the identification of proteins, metabolites and lipids. o Sequence database (MAVEN, SEQUEST, MASCOT, LIPID SEARCH, LIPID GATWAY, N and METABOANALYST) o Algorithms for the "de novo sequencing" software PEAKS. Complexity reduction: • Subcellular fractionation o Lysis of cells and homogenization of tissues o Separation of subcellular fractions o Proteomics, metabolomics and lipidomics of the membrane o Proteomics, metabolomics, lipidomics of organelles and intracellular compartments Immunoprecipitation • Immunoprecipitation to reduce the complexity of a mass spectrometric sample • Functional Proteomics and Immunoprecipitation Systems biology • Protein networks and meta-analysis o Elements of graph topology o Construction of a protein network (non-directional graph). o Statistical validation of a protein network o Over-representation analysis o Hierarchical analysis of proteomic data (directional graphs). or Meta-analysis • Ontological classification and pathway o Gene ontology (GO) o Structure of GO o Types of annotations in GO o Browsing in ontologies: Quick GO and other GO browsers o Ontological classification and pathway: specific applications
(reference books)
Power point slides shown in class by the teacher will be provided in PDF format. The books or articles in magazines from which some specific topics are taken will be indicated by the teacher during the lesson.
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