Teaching - Università degli Studi della Tuscia

Scienze omiche applicate (objectives)

TRAINING OBJECTIVES

1) Homics is a set of biomolecular disciplines that belongs to the life sciences and which is divided into different themes (genomics, transcriptomics, proteomics, metabolomics).
The main objective of the course is to enable the student to face the study of the main analytical techniques and instruments by deepening his knowledge of modern omic analyzes, essentially applied to a modern vision of early diagnosis. The student will be prepared to face the search for new diagnostic markers in clinical and non-clinical analyzes. At the end of the lectures, during the scheduled workshop (24h), students are given the opportunity to work individually on practical and practical topics. In this way, the student will acquire the ability to analyze the different protein expression starting from protein extracts and the possibility of applying modern analytical tools.

b) EXPECTED LEARNING RESULTS:

1) Knowledge and understanding:
Having acquired a good analytical ability in the field of omics and biotechnology

2) Knowledge and applied comprehension skills:
Knowing how to integrate the knowledge acquired in the individual disciplines into an interdisciplinary knowledge necessary to face any complex problem in the biotechnology sector, in particular being able to apply the knowledge of mass spectrometry to the various applications related to biotechnology.

3) Autonomy of judgment
Students will have to develop the ability to process complex and / or fragmentary information and to arrive at original and autonomous ideas and judgments capable of finding and critically selecting sources of bibliographic data, databases, and the
scientific literature. The autonomy of judgment is developed through the critical study of scientific articles.

4) Communication skills:
The student will be able to hold a critical public discussion on the topics covered in particular will be able to apply proteomics and metabolomics techniques for any scientific topic of interest .. Will be able to work in a team in the field of design and execution of experimental protocols as laboratory credits are foreseen.

5) Ability to learn:
The student will have the ability to identify, apply and develop innovative techniques in the relevant field of
work autonomously.

Code

18430

Language

ITA

Type of certificate

Profit certificate

Credits

Scientific Disciplinary Sector Code

BIO/11

Contact Hours

Exercise Hours

Type of Activity

Core compulsory activities

Teacher	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.
Dates of beginning and end of teaching activities	From 02/03/2020 to 12/06/2020
Delivery mode	Traditional
Attendance	not mandatory
Evaluation methods	Oral exam