PROTEOMICS, INTERACTOMICS AND METABOLOMICS

Fabrizio DAL PIAZ PROTEOMICS, INTERACTOMICS AND METABOLOMICS

0522100046
DEPARTMENT OF CHEMISTRY AND BIOLOGY "ADOLFO ZAMBELLI"
EQF7
BIOLOGY
2024/2025

OBBLIGATORIO
YEAR OF COURSE 2
YEAR OF DIDACTIC SYSTEM 2022
AUTUMN SEMESTER
CFUHOURSACTIVITY
1PROTEOMICA, INTERATTOMICA E METABOLOMICA (MODULO BIO/10)
216LESSONS
112LAB
2PROTEOMICA, INTERATTOMICA E METABOLOMICA (MODULO BIO/12)
216LESSONS
112LAB
Objectives
THE COURSE IS AIMED AT PROVIDING THE THEORETICAL BASIS OF PROTEOMICS, INTERACTOMICS AND METABOLOMICS, THROUGH THE STUDY OF THE STRUCTURAL PROPERTIES OF THE MOLECULES OF INTEREST.
AT THE END OF THE COURSE, THE STUDENT:
-WILL KNOW THE EXPERIMENTAL PROTOCOLS USED TO STUDY THE PROTEIN AND METABOLIC HERITAGE OF DIFFERENT LIVING SYSTEMS
-WILL HAVE LEARNED THE MOST EFFECTIVE TECHNIQUES IN THE STUDY OF PROTEIN INTERACTIONS
- WILL UNDERSTAND THE CHEMICAL-PHYSICAL PRINCIPLES UNDERLYING THE ANALYTICAL TECHNIQUES USED IN THE PROTEOMIC AND METABOLOMIC FIELDS
- WILL KNOW THE MAIN BIOINFORMATIC AND BIOSTATISTICAL TOOLS USED FOR THE PROCESSING OF PROTEOMICS, METABOLOMICS AND INTERACTOMICS DATA
- WILL UNDERSTAND THE THEORETICAL BASIS OF GENE-ONTOLOGY ANALYSIS AND WILL KNOW THE MOST USED TOOLS TO CARRY OUT THIS ANALYSIS
FURTHERMORE, THE STUDENT WILL BE ABLE TO:
- APPLY THE KNOWLEDGE ACQUIRED ON EXPERIMENTAL TECHNIQUES AND DATA ANALYSIS, ALSO THROUGH PRACTICAL APPLICATIONS CARRIED OUT DURING THE EXERCISES.
- UNDERSTAND THE BIOLOGICAL AND BIOCHEMICAL MEANING OF A SET OF RESULTS AND RELATE IT TO THE EXPERIMENTAL MODEL ANALYZED
- PROPOSE A SUITABLE EXPERIMENTAL STRATEGY FOR SOLVING BIOLOGICAL AND BIOCHEMICAL PROBLEMS OF INTEREST
- EVALUATE THE LIMITS OF CERTAIN APPROACHES IN SOLVING REAL PROBLEMS
- UNDERSTAND IN GENERAL THE IMPORTANCE OF CROSS-VALIDATING "OMICS" DATA THROUGH ORTHOGONAL APPROACHES AND THANKS TO
- COMMUNICATE, THROUGH ORAL PRESENTATION OR WITH THE HELP OF IT SUPPORTS, THE RESULTS OF OWN PROCESSING ON DATA USED FOR THE EXERCISES
- CLEARLY DESCRIBE TO COLLEAGUES THE EXPERIMENTAL PROTOCOLS USED, THE POST-ANALYTICAL PROCESSING PROCEDURES APPLIED AND THE BIOLOGICAL AND BIOCHEMICAL SIGNIFICANCE OF THE RESULTS OBTAINED
- PROPOSE USEFUL APPROACHES TO VALIDATE THE RESULTS OBTAINED THROUGH "OMICS" APPROACHES
- CRITICALLY EVALUATE THE RELIABILITY OF DATA OBTAINED THROUGH "OMICS" APPROACHES IN LIGHT OF THE KNOWLEDGE OF THE EXPERIMENTAL MODEL STUDIED
- OBTAIN FURTHER INFORMATION RELATING TO THE TOPICS COVERED THROUGH BIBLIOGRAPHIC AND/OR ON-LINE CHANNELS
Prerequisites
THE STUDENT MUST HAVE BASIC KNOWLEDGE RELATING TO THE STRUCTURE AND CHEMISTRY OF PROTEINS, THE BONDS AND INTERACTIONS THAT DETERMINE PROTEIN-LIGAND RECOGNITION, THE MAIN METABOLIC PATHWAYS AND THE STRUCTURE OF THE MAIN PRIMARY METABOLITES OF EUKARYOTIC CELLS

Contents
THE FOLLOWING TOPICS WILL BE COVERED AS PART OF THE COURSE

PROTEOMICS AND INTERACTOMICS MODULE (2 CFU LECTURES + 1 CFU OF EXERCISES):
CHEMISTRY OF AMINO ACIDS AND STRUCTURAL ORGANIZATION OF PROTEINS (2 HOURS), BONDS AND INTERACTIONS (1 HOUR), TURNOVER AND PROTEIN HOMEOSTASIS (1 HOUR), EXPERIMENTAL TECHNIQUES AND PROTOCOLS FOR PROTEOMIC ANALYSIS (ELECTROPHORESIS, SPECTROSCOPY, CHROMATOGRAPHY, MASS SPECTROMETRY, PEPTIDE MAPPING, WESTERN BLOTTING) (5 HOURS), PROCESSING OF INFORMATION FROM PROTEOMIC ANALYSIS (2 HOURS), ROLE OF PROTEIN INTERACTIONS IN BIOLOGICAL SYSTEMS (2 HOURS), STUDY OF INTERACTIONS USING BIOCHEMICAL AND BIOPHYSICAL METHODS (3 HOURS).
EXERCISE: ANALYSIS OF LC-MS/MS DATA FOR PROTEIN IDENTIFICATION (3 HOURS)
EXERCISE: ANALYSIS OF LC-MS/MS DATA FOR QUANTITATIVE ANALYSIS AND COMPARISON BETWEEN DIFFERENT SAMPLES (3 HOURS)
EXERCISE: BIOINFORMATIC PROCESSING USING GENE ONTOLOGY APPROACHES OF PROTEOMIC DATA (3 HOURS)
EXERCISE: STUDY OF PROTEIN COMPLEXES STARTING FROM PROTEOMICS AND INTERACTOMICS DATA (3 HOURS)

METABOLOMICS MODULE (2 CFU LECTURES + 1 CFU OF EXERCISES):
INTRODUCTION TO METABOLOMICS, DEFINITIONS AND ROLE IN SYSTEMS BIOLOGY (2 HOURS) COLLECTION AND PREPARATION OF BIOLOGICAL SAMPLES FOR METABOLOMICS INVESTIGATIONS (2 HOURS) MASS SPECTROMETRY IN METABOLOMICS STUDIES (2 HOURS) CHROMATOGRAPHY IN METABOLOMICS STUDIES METABOLOMICS (2 HOURS)
DATABASES FOR METABOLOMICS INVESTIGATIONS (PRE-TREATMENTS) (2 HOURS: 1 LECTURE + 1 EXERCISE) CHEMOMETRIC METHODS AND STRATEGIES IN THE ANALYSIS OF METABOLOMICS DATA - PART I (EXPLORATORY ANALYSES) (2 HOURS: 1 LECTURE + 1 EXERCISE ) CHEMOMETRIC METHODS AND STRATEGIES IN THE ANALYSIS OF METABOLOMICS DATA - PART II (UNSUPERVISED LEARNING METHODS) (2 HOURS: 1 LECTURE + 1 EXERCISE) CHEMOMETRIC METHODS AND STRATEGIES IN THE ANALYSIS OF METABOLOMICS DATA - PART III (SUPERVISED METHODS ) (2 HOURS: 1 LECTURE + 1 EXERCISE)
HYPERPARAMETER OPTIMIZATION AND VALIDATION STRATEGY (2 HOURS EXERCISE) FEATURES SELECTION IN METABOLOMICS (2 HOURS EXERCISE)
APPLICATIONS
TARGETED METABOLOMICS - EXPANDED METABOLIC SCREENING (1 HOUR) UNTARGETED METABOLOMICS (1 HOUR EXERCISE)
DERIVED OMICS - LIPIDOMICS, FLOWOMICS AND EXPOSOMICS (1 HOUR) PATHWAY ANALYSIS (1 HOUR EXERCISE)
SINGLE CELL METABOLOMICS (1 HOUR)
METABOLOMICS IN THE STUDY OF ONCOLOGICAL PATHOLOGIES (1 HOUR)
METABOLOMICS AS A PRECISION MEDICINE TOOL (1 HOUR EXERCISE) DIAGNOSTIC PERSPECTIVES OF METABOLOMICS (1 HOUR EXERCISE)
Teaching Methods
PROTEOMICS AND INTERACTOMICS MODULE:
THE COURSE IS DIVIDED INTO LECTURES (16 HOURS IN TOTAL) AND PRACTICE MEETINGS (12 HOURS IN TOTAL).
THE LECTURES ARE HELD USING SLIDES, WITH CONTINUOUS REFERENCES TO THE TEXTBOOK AND THE STUDY MATERIAL MADE AVAILABLE, WITH PRACTICAL EXAMPLES FROM SCIENTIFIC ARTICLES ON RESEARCH PROJECTS IN WHICH THE TECHNIQUES DESCRIBED IN THE LESSONS WERE USED.
PRACTICAL EXERCISES INCLUDE COMPUTER DEMONSTRATIONS AND APPLICATIONS USING ONLINE SOFTWARE.

METABOLOMICS MODULE:
THE COURSE IS DIVIDED INTO 14 LESSONS (28 HOURS IN TOTAL OF WHICH 16 ARE LECTURES AND 12 ARE EXERCISES). DURING THE LECTURES, THE ANALYTICAL PRINCIPLES AND MAIN TECHNOLOGIES USED IN METABOLOMICS INVESTIGATIONS ARE DESCRIBED, AS ARE THE STRATEGIES, ALGORITHMS AND BIOINFORMATIC TOOLS NECESSARY FOR THE ANALYSIS OF THE DATA PRODUCED, AS WELL AS THE MAIN APPLICATIONS OF METABOLOMICS IN THE STUDY OF HUMAN PATHOLOGIES.
THE LECTURES ARE ACCOMPANIED BY CLASSROOM EXERCISES AIMED AT SIMULATING SOME "TYPICAL" EXPERIMENTS THROUGH THE DEFINITION OF THE MOST APPROPRIATE EXPERIMENTAL DESIGN AND THE CORRECT IDENTIFICATION OF ANALYTICAL AND BIOINFORMATIC STRATEGIES. FURTHERMORE, A PHASE OF ANALYSIS OF DATA FROM REAL EXPERIMENTS IS FORESEEN.

Verification of learning
THE ACHIEVEMENT OF THE TEACHING OBJECTIVES IS VERIFIED THROUGH AN EXAM WITH A GRADE OUT OF THIRTY. THE EXAM TAKES PLACE AFTER THE END OF THE COURSE, THROUGH AN INTERVIEW IN TWO PARTS, ONE FOR EACH OF THE TWO TEACHING MODULES, AIMED AT ASCERTAINING AND EVALUATING THE LEVEL OF KNOWLEDGE AND UNDERSTANDING ACHIEVED ON THE THEORETICAL AND PRACTICAL CONTENTS OF THE PROGRAM. THE EVALUATION TAKES INTO ACCOUNT THE LANGUAGE SKILLS, THE AUTONOMY OF ORGANIZING THE PRESENTATION, THE ABILITY TO ELABORATE ANSWERS TO THE QUESTIONS ALSO ASKED ON THE PRACTICAL ACTIVITIES CARRIED OUT DURING THE EXERCISES.

THE FINAL GRADE, RELATING TO BOTH MODULES AND WITH EQUAL WEIGHT, TAKES INTO ACCOUNT THE KNOWLEDGE ACQUIRED, THE LANGUAGE SKILLS, THE QUALITY OF THE PRESENTATION AND THE ABILITY TO FIND SOLUTIONS IN PRACTICAL ACTIVITIES. THE MINIMUM GRADE (18/30) IS REACHED WHEN THE EXAM DEMONSTRATES THE ACHIEVEMENT OF A SUFFICIENT LEVEL IN KNOWLEDGE, LANGUAGE ABILITY AND QUALITY OF PRESENTATION. THE MAXIMUM GRADE (30/30) IS ACHIEVED WHEN THE STUDENT DEMONSTRATES, WITH THE EXAM, FULL AND COMPLETE KNOWLEDGE AND OWNERSHIP OF LANGUAGE ON THE TOPICS ADDRESSED, WITH MAXIMUM QUALITY OF PRESENTATION AND ABILITY TO APPLY KNOWLEDGE IN PRACTICAL ACTIVITIES. HONORS ARE AWARDED WHEN THE EXAM DEMONSTRATES, IN ADDITION TO THE HIGHEST POSSIBLE RESULT, A PARTICULAR QUALITY OF PRESENTATION WITH CRITICAL ANALYSIS SKILLS.

Texts
T. ALBERIO, M. FASANO, P. ROCADA. PROTEOMICA. EDITORE: EDISES EDIZIONI SRL NAPOLI, 2021.

J. TROISI, METABOLOMICS PERSPECTIVES: FROM THEORY TO PRATICAL APPLICATIONS. ACADEMIC PRESS, ELVEVIER, 2022

FURTHERMORE, LECTURE NOTES, RELEVANT SCIENTIFIC ARTICLES AND MATERIALS PROVIDED BY THE TEACHERS

More Information
PARTICULAR ATTENTION WILL BE PAID TO THE COORDINATION BETWEEN THE COURSE MODULES AND THE INTEGRATION BETWEEN THE CONTENTS OF THIS TEACHING AND THE OTHERS OF THE COS.
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