Corso di laurea: Bioinformatics Programmazione per l'A.A. 2019/2020

 

 

Lo studente espliciterà le proprie scelte al momento della presentazione, tramite INFOSTUD, del piano di completamento o del piano di studio individuale, secondo quanto stabilito dal regolamento didattico del corso di studio.

Primo anno

Primo semestre

Insegnamento	CFU	SSD	Ore Lezione	Ore Eserc.	Ore Lab	Ore Studio	Attività	Lingua
1049371 - PRINCIPLES OF MATHEMATICS (obiettivi) Principles of mathematics 1: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology. Principles of Mathematics 2: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered. Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.
- PRINCIPLES OF MATHEMATICS 1 (obiettivi) Principles of mathematics 1: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology. Principles of Mathematics 2: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered. Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology. - FACCHINEI FRANCISCO (programma) Sequences and Limits Functions of one real variable: basic definitions and properties, limits, derivatives, and integrals, Taylor formula. Vectors and Matrices: linear independence, dot product, linear system of equations, solution of a linear system, vector spaces and their basic properties Functions of several variables: partial derivatives, gradient, Taylor formula (Systems of) Linear Differential Equations: qualitative analysis and basic properties Optimization of functions of one or several variables Elements of graph theory   Course Material and Calculus for Biology and Medicine by Claudia Neuhauser Prentice Hall (Date degli appelli d'esame)	6	MAT/09	24	36	-	-	Attività formative di base	ENG
1049372 - ORGANIC AND INORGANIC CHEMISTRY (obiettivi) This course is an introduction to chemistry fundamentals addressed to students with limited chemistry background. The purpose of the course is to provide students with the knowledge of general chemistry principles, and with the tools to solve simple chemistry problems. At the end of the course the students are expected to know ho to apply the acquired chemical concepts to different fields, including pharmaceutical chemistry and biochemistry which are the subjects of further courses. The course aims to provide a correct knowledge of the fundamental principles of organic chemistry, proposing the contents into two distinct phases that are closely and logically linked. In the first phase the teaching is addressed to provide basic knowledge about classification and nomenclature of organic compounds, about the symbolism used to represent both structures and reactions, as well as over the chemical-physics, acid-base, nucleophilic-electrophilic properties of the considered compounds. In the second phase the teaching is instead focused on the description of the different reactivity involved by different classes of compounds, rationalizing the study through the analysis of the relevant mechanisms. In the context of the described methodology the objectives to be achieved are: 1) attainment of a suitable degree of specialized knowledge, understood as the ability to invoke theories, rules, nomenclature etc.; 2) capacity to properly interpret and process the reaction schemes and propose alternatives to the encountered syntheses; 3) establish connections between different studied subjects.
- ORGANIC AND INORGANIC CHEMISTRY 1 (obiettivi) This course is an introduction to chemistry fundamentals addressed to students with limited chemistry background. The purpose of the course is to provide students with the knowledge of general chemistry principles, and with the tools to solve simple chemistry problems. At the end of the course the students are expected to know ho to apply the acquired chemical concepts to different fields, including pharmaceutical chemistry and biochemistry which are the subjects of further courses. - FRASCHETTI CATERINA (programma) [3 hours] The scientific method. Matter: homogeneous and heterogeneous mixtures. Basic concepts of Stoichiometry: The atomic and mass number. Isotopes. The atomic mass and the atomic weight. Definition of molecule. The molecular weight. Ionic compounds. The mole. Empirical formula, molecular formula and structural formula. IUPAC nomenclature. [2 hours] Law of definite proportions. Law of conservation of mass. Chemical equations, stoichiometric coefficients. The limiting reactant concept. [2 hours] The atomic structure: The quantic numbers. The s, p, d, and f orbitals. The Aufbau principle. The ionization energy and the electron affinity. [4 hours] The chemical bonding: Octet rule. Ionic bond. Covalent bond. Electronegativity. Hybridization (sp3, sp2, sp, sp3d, sp3d2). Dative bond. VSEPR theory and molecular geometries. Intermolecular forces (Van der Waals, dispersion, hydrogen bond). [2 hours] The gaseous systems: The fundamental laws of gases: Boyle, Charles, gay-Lussac and Avogadro. The ideal gas law. Mixtures of not reactive gases. Dalton’s law. [4 hours] The oxidation number. Redox reactions and their balancing. [3 hours] Basic concepts of thermodynamics: Heat and work. The first thermodynamic law. Reversible and not reversible processes. Enthalpy. Hess’s law. Spontaneous processes and entropy. The second thermodynamic law. Free energy and Gibb’s Helmotz equation. [2 hours] Phase transitions: Phase transition. Vapor pressure. Clausius Clapeyron equation. Phase diagram. [4 hours] Solutions: Molarity, molality and molar fraction. Mass and volume percentages. Dilution and mixing. Themodynamics of solutions. The Raoult’s law. Colligative properties of solutions. Boiling point elevation, freezing point depression and osmotic pressure. Van’t Hoff coefficient. [3 hours] Chemical equilibrium: Mass action law. Le Chatelier principle. The concentration, pressure and temperature effects on the equilibrium. Homogeneous and heterogeneous equilibria. [4 hours] Acid-base equilibrium: Definitions of Bronsted-Lowry and Lewis. Acid halides and oxyacids. Acid strength. Autoionization of water. The pH scale. Calculation of the pH for a solution of: strong acid (base), weak acid (base). Alfa and dissociation degree. [3 hours] Acid-base properties of a salt solution. Buffered solution. [2 hours] Solubility equilibrium: Precipitation reaction. Common ion effect. [2 hours] Basic concepts of chemical kinetics: Reaction rate. Collision theory. Definition of transition state. Arrhenius equation. Catalysis. [10 hours] Numerical exercises   Chemistry, Zumdahl/Zumdahl	6	CHIM/03	48	-	-	-	Attività formative di base	ENG
1049251 - PRINCIPLES OF PHYSICS (obiettivi) The Physics course has several distinct aims. First, it aims to full the gap between school and university level physics. Second, it aims to provide a much logical and analytical framework for classical physics, which will be essential for the course. Third, it includes bio-medical themes generally underestimated in basic physics courses. Such topics will be selected among those that will be developed in the subsequent years of the course. Fourth, single lectures aim to broaden the student’s perspectives, so that he can begin to appreciate the great flexibility and generality of the laws of physics and their application in emerging biomedical fields of research. - CARACCIOLO GIULIO (programma) Rappresentare graficamente i fenomeni fisici, in particolare quelli che coinvolgono l'uomo e interpretarne le rappresentazioni grafiche. Definire le funzioni dimensionali e darne esempi semplici dal campo medico. Definire il concetto di forza e i principi della dinamica Definire i concetti di lavoro ed energia e le principali applicazioni in bio-medicina. Dare la definizione di deformazione e di elasticità con riferimento alle strutture corporee. Fornire la definizione di densità e descrivere le procedure per la sua misurazione. Dare la definizione di pressione e indicare le modalità per la sua misurazione. Fornire la definizione di viscosità e coefficiente di viscosità di un liquido reale. Descrivere sinteticamente il trasporto in regime viscoso, i processi di sedimentazione, elettroforesi, centrifugazione con esempi di applicazioni in campo medico-laboratoristico. Spiegare la distinzione tra moto laminare e moto turbolento e dare la definizione di numero di Reynolds. Definire i concetti di campo elettrico e magnetico e le principali applicazioni nell’organismo umano.   1) "Fisica Biomedica" - D. Scannicchio - Casa Editrice EdiSES 2) "Elementi di Fisica" - G. Capitani, E. De Sanctis - Editore: La Sapienza (Date degli appelli d'esame)	6	FIS/07	48	-	-	-	Attività formative di base	ENG
1049253 - PRINCIPLES OF COMPUTER SCIENCE I (obiettivi) The goal of this course is to teach students the basic programming skills needed to deal with bioinformatics data. At the end of the course the students will be able to: - model problems of medium difficulty and solve them by programming; - decompose complex programming problems into simpler problems; - design and implement programs; - test programs; - analyze programs in terms of their correctness and efficiency; - use Python and its libraries. - CHIERICHETTI FLAVIO (programma) Introduzione agli algoritmi, alla programmazione in Python, ed all'architettura dei computer. Input/Output, Sequenze, Iterazioni, Slice, Test (if, if-elif, if-elif-else), Funzioni, Oggetti, Stringhe, Codifica del Testo, File, Dizionari, Strutture dati per la Ricerca, Insiemi (Set), Liste di Liste, Strutture Dati per Immagini, Funzioni come argomenti, Classi.   Nessun libro di testo. Delle dispense saranno disponibili sul sito del corso. (Date degli appelli d'esame)	6	INF/01	24	36	-	-	Attività formative di base	ENG
1049373 - BIOLOGY OF THE CELL (obiettivi) Students acquire the knowledge and thinking skills necessary to understand biological problems in a evolutionary perspective. The course will provide students with understanding of the basic molecular mechanisms that operate in living cells, with a focus on the flow of genetic information.
- BIOLOGY OF THE CELL 1 (obiettivi) Students acquire the knowledge and thinking skills necessary to understand biological problems in a evolutionary perspective. The course will provide students with understanding of the basic molecular mechanisms that operate in living cells, with a focus on the flow of genetic information. - FULCI VALERIO (programma) 1. Definition of life. Darwinian evolution: variation, heritability and fitness. Origin of life: prebiotic chemistry, RNA world. Gene-centered view of evolution: replicators and vehicles. From molecules from the first cells. From single cells to multicellular organisms. The tree of life. The major transitions in evolution: mutualistic symbiosis and complexity 2. Proteins: structure and functions. Enzymes and biological reactions. 3. Bio-membranes: Structural Organization and Functions. Principles of membrane transport: active/passive transport, carrier proteins, ion channels, electrical properties of membranes. 4. Biological order and energy. Energy for cellular activities. Production of ATP. Structure and function of mitochondria. Glycolysis, Krebs cycle, electron transport chain. The mitochondrial ATP synthase. 5. RNA and DNA structures. DNA replication and repair. The cell nucleus: chromatin structure, epigenetic modifications. 6. Transcription and translation. RNA transcription in prokaryotes. RNA transcription and processing in eukaryotes: mRNA, tRNA, rRNA. The genetic code. Protein synthesis: initiation, elongation and termination . 7. Regulation of gene expression. Control of transcription in prokaryotes: bacterial operons. Control of transcription in eukaryotes. Post-transcriptional and translational regulation. Non-coding RNAs, microRNAs. 8. The genome organization in prokaryotic and eukaryotic organisms. Mobile elements. Genome evolution. 9. Endomembrane system: endoplasmic reticulum, Golgi. Protein sorting and glycosylation. Lysosomes. Phagocytosis and Endocytosis. 10. Principles of cell signaling: G Protein–Coupled Receptors. Effectors and second messengers. Receptor Tyrosine Kinases, MAP Kinase Pathways. 11. Eukaryotic cell cycle. Phases of cell cycle. Cyclin-dependent protein kinases (CdKs). Cell cycle checkpoints. S phase. Mitosis. Cytokinesis. Apoptosis. 12. Genetics of cancer. The hallmarks of cancer. Oncogenes and tumor suppressor genes. Somatic evolution in cancer.   Alberts et al,Essential cell Biology, Garland Science. (Date degli appelli d'esame)	6	BIO/13	40	-	12	-	Attività formative caratterizzanti	ENG

Secondo semestre

Insegnamento	CFU	SSD	Ore Lezione	Ore Eserc.	Ore Lab	Ore Studio	Attività	Lingua
1049371 - PRINCIPLES OF MATHEMATICS (obiettivi) Principles of mathematics 1: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology. Principles of Mathematics 2: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered. Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology.
- PRINCIPLES OF MATHEMATICS 2 (obiettivi) Principles of mathematics 1: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The first semester (Principles of Mathematics 1) will be devoted mainly to the study of functions of one variables, including limits, derivative and integrals. Basic optimisation results for functions of one variable will also be considered Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology. Principles of Mathematics 2: The aim of this course is to give the student sound mathematical basis in calculus of one or several variables and optimization in a way appropriate for a student of bioinformatics. An emphasis is given to applications and intuitive understanding of the underlying concepts. The second semester (Principles of Mathematics 2) will be devoted mainly to the study of functions of several variables, linear algebra, and differential equations. Basic optimization results for functions of several variables will also be considered. Knowledge and understanding The aim of the course is to give students a basic understanding of calculus in a way appropriate to bioinformatics students. Students will also be exposed to mathematics proofs as an example of rigorous scientific reasoning. Applying knowledge and understanding By the end of the course, students will be able to use basic mathematical tools as applied to different environments. They will also be able to interpret in a critical way results obtained by applying mathematical modelling technique. Making judgements Lectures and practical exercises will provide students with the basic ability in assessing the main strengths and weaknesses of mathematical models when used to explain empirical evidence. Communication By the end of the course, students will have basic mathematical skills that will help them to talk in an appropriate way about quantitative models. Lifelong learning skills Students are expected to develop learning skills necessary to undertake additional and more advanced studies involving mathematics and mathematical modelling in biology. - CENTURIONI SANTE	6	MAT/09	48	-	-	-	Attività formative di base	ENG
1049372 - ORGANIC AND INORGANIC CHEMISTRY (obiettivi) This course is an introduction to chemistry fundamentals addressed to students with limited chemistry background. The purpose of the course is to provide students with the knowledge of general chemistry principles, and with the tools to solve simple chemistry problems. At the end of the course the students are expected to know ho to apply the acquired chemical concepts to different fields, including pharmaceutical chemistry and biochemistry which are the subjects of further courses. The course aims to provide a correct knowledge of the fundamental principles of organic chemistry, proposing the contents into two distinct phases that are closely and logically linked. In the first phase the teaching is addressed to provide basic knowledge about classification and nomenclature of organic compounds, about the symbolism used to represent both structures and reactions, as well as over the chemical-physics, acid-base, nucleophilic-electrophilic properties of the considered compounds. In the second phase the teaching is instead focused on the description of the different reactivity involved by different classes of compounds, rationalizing the study through the analysis of the relevant mechanisms. In the context of the described methodology the objectives to be achieved are: 1) attainment of a suitable degree of specialized knowledge, understood as the ability to invoke theories, rules, nomenclature etc.; 2) capacity to properly interpret and process the reaction schemes and propose alternatives to the encountered syntheses; 3) establish connections between different studied subjects.
- ORGANIC AND INORGANIC CHEMISTRY 2 (obiettivi) The course aims to provide a correct knowledge of the fundamental principles of organic chemistry, proposing the contents into two distinct phases that are closely and logically linked. In the first phase the teaching is addressed to provide basic knowledge about classification and nomenclature of organic compounds, about the symbolism used to represent both structures and reactions, as well as over the chemical-physics, acid-base, nucleophilic-electrophilic properties of the considered compounds. In the second phase the teaching is instead focused on the description of the different reactivity involved by different classes of compounds, rationalizing the study through the analysis of the relevant mechanisms. In the context of the described methodology the objectives to be achieved are: 1) attainment of a suitable degree of specialized knowledge, understood as the ability to invoke theories, rules, nomenclature etc.; 2) capacity to properly interpret and process the reaction schemes and propose alternatives to the encountered syntheses; 3) establish connections between different studied subjects. - BOTTA BRUNO (programma) Organic Chemistry Structure and properties Carbon compounds, Lewis structural formulas, types of bonds, functional groups, formal charge stereoisomer characteristics, identifies configuration of double bond cis (Z) /trans (E) identifies configuration of stereocenters (R)/(S), identifies rotation under plane-polarized light to determine whether molecule is (+) or (-), need to do laboratory tests where the molecule is put in plane-polarized light bonding and molecular structure atomic orbitals, covalent bond formation—molecular orbital (MO) method, hybridization of atomic orbitals, electronegativity and polarity, oxidation number, intermolecular forces, solvents, resonance and delocalized π electrons. Chemical reactivity and organic reactions. Reaction mechanism, carbon-containing intermediates, types of organic reactions, electrophilic and nucleophilic reagents, thermodynamics bond-dissociation energies, chemical equilibrium rates of reactions, transition-state theory and enthalpy diagrams, brönsted acids and bases basicity (acidity) and structure, Lewis acids and bases. Alkanes and cyclic hydrocarbons Definition, nomenclature of alkanes, preparation of alkanes, chemical properties of alkanes. Nomenclature and structure, geometric isomerism and chirality, conformations of cycloalkanes and chemical properties. Stereochemistry Stereoisomerism, optical isomerism, relative and absolute configuration, molecules with more than one chiral centre, synthesis and optical activity. Alkenes Nomenclature and structure, geometric (cis-trans) isomerism, preparation of alkenes, chemical properties of alkenes, substitution reactions at the allylic position, summary of alkene chemistry Alkyl halides Introduction, synthesis of alkyl halides and chemical properties. Alkynes and dienes Alkynes, chemical properties of acetylenes, alkadienes, MO theory and delocalized π systems. Addition reactions of conjugated dienes, polymerization of dienes, cycloaddition. Benzene and polynuclear aromatic compounds Introduction, aromaticity and Hückel's rule, polynuclear aromatic compounds, nomenclature chemical reactions. Alcohols and thiols Alcohols, nomenclature and H-bonding, preparation and chemical properties. Thiols, nomenclature and chemical properties. Ethers, epoxides, glycols, and thioethers Ethers, introduction and nomenclature, preparation, chemical properties. Cyclic ethers. Epoxides, introduction, nomenclature, chemical properties and synthesis. Glycols, nomenclature and chemical properties. Preparation of 1,2-glycols, unique reactions of glycols. Thioethers, introduction, nomenclature and chemical properties. Carbonyl compounds: aldehydes and ketones Introduction, nomenclature, preparation, and chemical properties. Oxidation and reduction of the carbonyl group. Carboxylic acids and their derivatives Introduction, nomenclature, preparation of carboxylic acids and carboxylic acid derivatives. Chemical properties of carboxylic acids and carboxylic acid derivatives. Amines Nomenclature and physical properties, preparation, chemical properties, reactions of quaternary ammonium salts, ring reactions of aromatic amines, spectral properties, reactions of aryl diazonium salts, summary of amine chemistry Phenolic compounds Introduction, Preparation, chemical properties, analytical detection of phenols, summary of phenolic chemistry, summary of phenolic ethers and esters Aromatic heterocyclic compounds Five-membered aromatic heterocycles with one heteroatom, six-membered, heterocycles with one heteroatom, compounds with two heteroatoms Carbohydrates and nucleic acids Introduction, classification of carbohydrates, the D and L notation, the configuration of aldoses and ketoses. The reactions of monosaccharides in basic solutions. The oxidation-reduction reactions of monosaccharides . lenghtening the chain: the kiliani-fisher synthesis. Shortening the chain: the Ruff degradation. chemical properties of monosaccharides, evidence for hemiacetal formations as exemplified with glucose, stereochemistry and structure proof , disaccharides Amino acids, peptides, proteins Introduction, preparation of α-amino acids, chemical properties of amino acids, peptides Reactivity and Reactions Radicals Radical stability. The reactivity-selectivity principle. The chlorination and bromination of alkanes. Radical addition to alkenes. The sterochemistry of radical substitution and radical addition reactions. Substitution and elimination reactions Mechanism and factors that affect reactions SN2. Mechanism and factors that affect reactions SN1. The stereochemistry of SN2 and SN1 reactions. Competition between SN2 and SN1. The E1 and E2 reactions. Competition between E1 and E2 reactions, and between SN2/E2and SN1/E1 reactions. Reactions of benzene and of substituted benzenes The general mechanism of electrophilic aromatic substitution reactions. Halogenation, nitration, sulfonation, Friedel-Crafts acylation and alkylation. The effect of substituents on reactivity and on orientation. Nucleophilic aromatic substitution: addition-elimination mechanism and elimination-addition mechanism. Carbonyl compounds: reaction of carboxylic acids and carboxylic acid derivatives General mechanism for nucleophilic addition-elimination reactions. Reactions of acyl halides, acid anhydrides, esters. Acid and basic catalyzed hydrolyses of esters, amides and nitriles. Carbonyl compounds: reactions of aldehydes, ketones and α,β-unsaturated carbonyl compounds Reactions of carbonyl compounds with: Grignard reagents, acetylide ions, hydride ions, hydrogen cyanide, amines and amines derivatives, water, alcohols, sulphur nucleophiles. The Wittig reaction. Nucleophilic addition to α,β-unsaturated aldehydes and ketones. α,β-unsaturated carboxylic acid derivatives. Carbonyl compounds: reactions at the α-carbon Keto-enol tautomerism. How enolate ions and enols react. Alkylating the α-carbon of carbonyl compounds. Alkylation of the α-carbon using an enamine intermediate. The Michael reaction. Aldol condensation and Claisen condensation. The Robinson annulation.   Testi: Graham Solomons, Craig Fryhle: Organic Chemistry Ed. Wiley Paula Bruice: Organic Chemistry Ed Pearson Chimica Organica: Bruno Botta Ed. Edi-Ermes (Date degli appelli d'esame)	6	CHIM/06	48	-	-	-	Attività formative di base	ENG
1049376 - INTRODUCTION TO BIOMEDICAL STATISTICS (obiettivi) This course provides an introduction to basic concepts of Statistics and Probability for students in the biosciences.
- INTRODUCTION TO BIOMEDICAL STATISTICS 1 (obiettivi) This course provides an introduction to basic concepts of Statistics and Probability for students in the biosciences. - ROCCI ROBERTO (Date degli appelli d'esame)	6	SECS-S/01	48	-	-	-	Attività formative di base	ENG
- INTRODUCTION TO BIOMEDICAL STATISTICS 2 (obiettivi) The main goal of the course is to give students the basis for a practical and mainly operational approach to the biological data sets focusing on the logical analysis of problems more than on theory. - FORDELLONE MARIO	6	MED/01	48	-	-	-	Attività formative di base	ENG
1049373 - BIOLOGY OF THE CELL (obiettivi) Students acquire the knowledge and thinking skills necessary to understand biological problems in a evolutionary perspective. The course will provide students with understanding of the basic molecular mechanisms that operate in living cells, with a focus on the flow of genetic information.
- BIOLOGY OF THE CELL 2 (obiettivi) Students acquire the knowledge and thinking skills necessary to understand biological problems in a evolutionary perspective. The course will provide students with understanding of the basic molecular mechanisms that operate in living cells, with a focus on the flow of genetic information. - FULCI VALERIO (programma) 1. Definition of life. Darwinian evolution: variation, heritability and fitness. Origin of life: prebiotic chemistry, RNA world. Gene-centered view of evolution: replicators and vehicles. From molecules from the first cells. From single cells to multicellular organisms. The tree of life. The major transitions in evolution: mutualistic symbiosis and complexity 2. Proteins: structure and functions. Enzymes and biological reactions. 3. Bio-membranes: Structural Organization and Functions. Principles of membrane transport: active/passive transport, carrier proteins, ion channels, electrical properties of membranes. 4. Biological order and energy. Energy for cellular activities. Production of ATP. Structure and function of mitochondria. Glycolysis, Krebs cycle, electron transport chain. The mitochondrial ATP synthase. 5. RNA and DNA structures. DNA replication and repair. The cell nucleus: chromatin structure, epigenetic modifications. 6. Transcription and translation. RNA transcription in prokaryotes. RNA transcription and processing in eukaryotes: mRNA, tRNA, rRNA. The genetic code. Protein synthesis: initiation, elongation and termination . 7. Regulation of gene expression. Control of transcription in prokaryotes: bacterial operons. Control of transcription in eukaryotes. Post-transcriptional and translational regulation. Non-coding RNAs, microRNAs. 8. The genome organization in prokaryotic and eukaryotic organisms. Mobile elements. Genome evolution. 9. Endomembrane system: endoplasmic reticulum, Golgi. Protein sorting and glycosylation. Lysosomes. Phagocytosis and Endocytosis. 10. Principles of cell signaling: G Protein–Coupled Receptors. Effectors and second messengers. Receptor Tyrosine Kinases, MAP Kinase Pathways. 11. Eukaryotic cell cycle. Phases of cell cycle. Cyclin-dependent protein kinases (CdKs). Cell cycle checkpoints. S phase. Mitosis. Cytokinesis. Apoptosis. 12. Genetics of cancer. The hallmarks of cancer. Oncogenes and tumor suppressor genes. Somatic evolution in cancer.   Alberts et al,Essential cell Biology, Garland Science. - COGONI CARLO (programma) 1. Definition of life. Darwinian evolution: variation, heritability and fitness. Origin of life: prebiotic chemistry, RNA world. Gene-centered view of evolution: replicators and vehicles. From molecules from the first cells. From single cells to multicellular organisms. The tree of life. The major transitions in evolution: mutualistic symbiosis and complexity 2. Proteins: structure and functions. Enzymes and biological reactions. 3. Bio-membranes: Structural Organization and Functions. Principles of membrane transport: active/passive transport, carrier proteins, ion channels, electrical properties of membranes. 4. Biological order and energy. Energy for cellular activities. Production of ATP. Structure and function of mitochondria. Glycolysis, Krebs cycle, electron transport chain. The mitochondrial ATP synthase. 5. RNA and DNA structures. DNA replication and repair. The cell nucleus: chromatin structure, epigenetic modifications. 6. Transcription and translation. RNA transcription in prokaryotes. RNA transcription and processing in eukaryotes: mRNA, tRNA, rRNA. The genetic code. Protein synthesis: initiation, elongation and termination . 7. Regulation of gene expression. Control of transcription in prokaryotes: bacterial operons. Control of transcription in eukaryotes. Post-transcriptional and translational regulation. Non-coding RNAs, microRNAs. 8. The genome organization in prokaryotic and eukaryotic organisms. Mobile elements. Genome evolution. 9. Endomembrane system: endoplasmic reticulum, Golgi. Protein sorting and glycosylation. Lysosomes. Phagocytosis and Endocytosis. 10. Principles of cell signaling: G Protein–Coupled Receptors. Effectors and second messengers. Receptor Tyrosine Kinases, MAP Kinase Pathways. 11. Eukaryotic cell cycle. Phases of cell cycle. Cyclin-dependent protein kinases (CdKs). Cell cycle checkpoints. S phase. Mitosis. Cytokinesis. Apoptosis. 12. Genetics of cancer. The hallmarks of cancer. Oncogenes and tumor suppressor genes. Somatic evolution in cancer.   Suggested Textbooks: Essential Cell Biology, Fourth Edition. Alberts B. et al. Garland Science.	6	BIO/13	48	-	-	-	Attività formative caratterizzanti	ENG

Secondo anno

Primo semestre

Insegnamento	CFU	SSD	Ore Lezione	Ore Eserc.	Ore Lab	Ore Studio	Attività	Lingua
1052115 - GENETICS AND COMPUTATIONAL GENOMICS (obiettivi) General skills The course of Genetics and computational genomics provides students with a basic knowledge of Genetics aimed at understanding the rules of inheritance, their molecular bases, their main applications and their implications for evolution. In addition, the course will allow students to understand how genetic information is encoded at the DNA level and how it contribute to phenotypic variability. Fundamentals concepts in functional genetics and evolution will be reconsidered in light of the sequencing and re-sequencing projects. The student will be also provided of practical and theoretical tools to solve genetic problems and to use databases for storage, management, analysis, and visualization of genetic data. Specific skills A) Knowledge and understanding -Knowledge and understanding of the characteristics of the genetic material -Knowledge and understanding of the rules of genetic transmission -Knowledge and understanding of mutations and their implications -Basic knowledge on the dynamics of genes in populations as well as on the genetic mechanisms underlying evolution - Knowledge and understanding of informatic methods used for genomic analyses B) Applying knowledge and understanding - Usage of a proper genetic terminology - Identification of the right procedures to solve genetic problems - Formulation of hypotheses on the hereditary transmission of characters - Constructing and interpreting genetic maps and genealogical trees - Acquisition of conceptual tools for the genetic dissection of biological systems - Management of genomic browsers and programs for storage, management analysis, and visualization of “big data” C) Making judgements - Acquisition of a critical judgment capacity on solving problems of formal genetics, through the study of the evolution of the gene concept from Mendel to the present day and the detailed analysis of some fundamental experiments - Addressing questions for the elaboration and deepening of the gained information D) Communication skills - Communicating the genetic concepts acquired during the course with appropriate terminology E) Learning skills - Logically connecting the acquired knowledge - Identification of the most relevant topics of the issues discussed during the course - TROMBETTA BENIAMINO (programma) Human population genetics • Hardy-Weinberg equilibrium. • Genetic effects of inbreeding, calculation of the inbreeding coefficient from pedigrees. • Genetic drift and natural selection. Human genetic diversity in health and disease: • Classes of genetic variants/ polymorphisms. De novo mutation rates. • International projects on the human genetic diversity: "1,000 genomes" and "UK10K" projects. Genetics of multifactorial characters and complex pathologies: • Decomposition of phenotypic variance: environmental and genetic variance; heritability. • Polygenic theory of quantitative and discontinuous characters. • The polygenic threshold model. The "infinitesimal" and the "rare allele" models. Human gene mapping • Linkage analysis, lod score calculation. • Haplotypes and linkage disequilibrium, linkage disequilibrium-based mapping methods. Storage, management, analysis, and visualization of data • Use of genome browsers: theoretical aspects and practical exercises. • Use of genome viewer programs: theoretical aspects and practical exercises on NGS data. • Structure, feature and handling of the main files used in NGS analysis. • Storage and analysis of genetic raw data. • Mining information from databases acquired knowledge: Students will acquire a deep understanding of the theoretical and practical tools to solve genetic problems. Fundamentals concepts in genetics, functioning and evolution will be reconsidered in light of the sequencing and re-sequencing projects. Acquired skills: During the course, students will learn to rely on computational and data science tools for the storage, management, analysis, and visualization of genetic data.   “Human Molecular Genetics” 4th Edition, Strachan & Read "Genetics of population" Hedrick 3th edition Jones and Bartlett - CIAPPONI LAURA (programma) L’insegnamento prevede 48 ore di didattica frontale, suddivise in due MODULI (Modulo I e Modulo II) di 24 ore ciascuno. Modulo I La prima parte del corso è un’introduzione alla Genetica. Il modulo si propone di fornire allo studente una conoscenza delle leggi che regolano l’ereditarietà e di come queste possano essere applicate per la soluzione di problematiche biologiche Argomenti: • Le leggi dell’ereditarietà di Mendel e loro estensioni (6 ore) • La teoria cromosomica dell’ereditarietà (2 ore) • Struttura e funzione del gene (2 ore) • Strategie di mappatura genica (4 ore). • Mutazioni geniche, cromosomiche e del genoma (2 ore) • Codice genetico e sua decifrazione (2 ore) • Regolazione genica nei procarioti e concetto di operone (4 ore) • Genetica della determinazione del sesso (2 ore). Modulo II La seconda parte del corso è una introduzione alla genomica computazionale. Il modulo si propone di applicare le leggi dell’ereditarietà a popolazioni e di risolvere problemi complessi di genomica utilizzando supporti informatici. Argomenti: • Struttura e variabilità del genoma umano (6 ore) • Modelli matematici di evoluzione genetica (8 ore) • Alberi genealogici mappature e associazione (4 ore) • Genomica comparativa e modelli di filogenesi (2 ore) • Analisi informatiche (4 ore)   • “Genetics: From Genes to Genomes” Hartwell- • “Human molecular genetics” Strachan Il materiale didattico è disponibile sulla pagina web del corso: https://elearning2.uniroma1.it (Date degli appelli d'esame)	6	BIO/18	48	-	-	-	Attività formative caratterizzanti	ENG
1049261 - PRINCIPLES OF COMPUTER SCIENCE II (obiettivi) The course aim to introduce the algorithmic approach to solving problems correctly and efficiently. Algorithms are ubiquitous in bioinformatics and are often at the interface of computer science and biology. Well established algorithmic techniques will be studied as well as ways to encode them in a computer programme using python. - CHATZIGIANNAKIS IOANNIS (programma) We will introduce the algorithmic approach and the theory of algorithms for studying correctness and efficiency, understanding what makes a good algorithm and how to classify them. We will study characteristic algorithmic techniques and the related computational ideas that are relevant to the field of biology and how to select the most suitable to solve a given task. Topics covered include - Searching algorithms - Dynamic programming algorithms - Graph-based algorithms - Divide-and-Conquer algorithms - Clustering and Tree-based algorithms - Randomized Algorithms We will work with Python and how to write a computer programme encoding a given algorithm.   NEIL C. JONES AND PAVEL A. PEVZNER: An Introduction to Bioinformatics Algorithms A Bradford Book, The MIT Press, Cambridge, Massachusetts, London, England, 2004. (Date degli appelli d'esame)	6	ING-INF/05	48	-	-	-	Attività formative affini ed integrative	ENG
1049256 - MICROBIOLOGY (obiettivi) Microorganisms play a key role in the environment, in human health and in biotechnological research. The course of Microbiology aims to provide the basic principles of structure, function and evolution of microbial cells, with particular regard to bacterial cells. The knowledge and skills acquired during this course will represent a framework for the study of bioinformatics and biotechnological applications of microorganisms, and for the analysis of their impact on human health and the environment. Students who have passed the exam will know and understand (acquired knowledge) - The structural and functional diversity which is present in the microbial world; - The mechanisms responsible for the structure and functioning of bacterial cells; - The mechanisms responsible for the evolution of bacterial species; - The structure and life cycles of viruses; - The methods and strategies for the control of microbial growth. Students who have passed the exam will be able to (acquired skills): - Understand and analyse microbiological data; - Critically analyze the issues related to the evolution and diffusion of multi-resistant antibiotic bacteria; - Understand and design experimental and bioinformatics approaches for the study and exploitation of bacteria for biotechnological and environmental purposes; - Identify and develop key themes to build educational paths in microbiology. - PROSSEDA GIANNI (programma) Introduzione alla microbiologia, la sua portata e la rilevanza. Ultrastruttura e caratteristiche dei microrganismi e delle cellule procariote. Una panoramica della morfologia della cellula batterica: la parete cellulare batterica, il nucleoide, la membrana cellulare, la matrice citoplasmatica. Confronto delle cellule Prokaryotic ed eucariotica. Secrezione dielle proteine nei procarioti. Strutture esterne alla parete cellulare. Genetica microbica: genomi, plasmidi e trasposoni; mutazione, ricombinazione e trasferimento genetico orizzontale; regolazione trascrizionale dei geni. Nutrizione microbica , crescita e metabolismo. Gli antibiotici Breve profilo di virus con particolare attenzione ai batteriofagi: termini e definizione, nomenclatura e classificazione, proprietà distintive, morfologia, simmetria e ultrastruttura. Identificazione dei batteri.   - Madigan M.T. and Martinko J.M. : Brock, Biology of Microorganisms. Vol. 1. optional: Snyder L. and Champness W. Molecular Genetics of Bacteria. (Date degli appelli d'esame)	6	BIO/19	40	-	12	-	Attività formative caratterizzanti	ENG
1049375 - MOLECULAR BIOLOGY (obiettivi) General goals The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis. Specific goals 1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology. 2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches. 3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions. 4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach.
- MOLECULAR BIOLOGY 1 (obiettivi) General goals The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis. Specific goals 1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology. 2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches. 3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions. 4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach. - NEGRI RODOLFO (programma) Main goal of the course is to give to the students a general view of the molecular mechanisms which are at the base of the biological processes. For each argument a methodological section will introduce the students to the main technical approaches used at the state of the art. Practical training (2 CFU) will make the students to breath the atmosphere of a molecular biology laboratory. Particular attention will be given to the high throughput methods utilized in “Omic” approaches to the comprehension of biological processes which will be further illustrated in the course of Molecular Biology and Genomics. General aims: The course is focused on the deep connection between DNA structure and functions. The student will learn the molecular mechanisms which are at the base of the processes of Replication, Recombination, Transcription and DNA repair and their regulatory circuits. Specific aims: 1. Knowledge and understanding: The student should learn the basic molecular mechanisms of the cellular omeostasis and gene regulation and the most used techniques of Molecular Biology. 2. Ability to apply Knowledge and understanding: The student should be able to apply this knowledge in the discussion of recent arguments of general interest in Molecular Biology research. 3. Critical Judgement abilities: The student should demonstrate critical judgement abilities in solving problems related to theoretical and practical Molecular Biology projects and should communicate its conclusions to the colleagues and to the teacher in an effective way. 4. the student should demonstrate to be able to apply the learned concepts to his future work in molecular biology. Molecular Biology I The polimorphic DNA – Chemical components of DNA: bases, sugars and phosphodiesteric backbone (0.1 cfu). DNA B basic structure (0.2). Alternative DNA conformations, unusual structures (crucifiorms, triple helix) (0.2) – Conformational variability of structural parameters, curvature and bendability (0.2). DNA topology, winding and unwinding; linking number; DNA topoisomerases (0.2). The Genetic Code - the code decrypting; the structure and function of the code (0.1). DNA replication: machinery and mechanisms in prokaryotes and eukaryotes (0.2). Replicons organization; topological and end-replication problems (0.1). DNA mutability and repair; damage checkpoints (0.1). DNA transcription: transcription in bacteria and bacteriophages; transcriptional machinery and RNA polymerase positioning signals (0.2). Methodological approach to the study of transcription: in vitro transcription systems (0.2). Transcription regulation in prokaryotic systems: activation and repressions; operon structures and function (0.2). Transcription in eukaryotic systems (0.1); transcriptional machinery and RNA polymerase positioning signals (0.2). Methodological approaches to the study of transcription: eukaryotic in vitro transcription systems. Coordinate regulation of the three eukaryotic RNA polymerases (0.2). Transcription factors and transcription regulation in eukaryotes (0.2). The RNA molecule (chemical and structural features) (0.2); structure and function of tRNA, rRNA, pre- and mRNA, snRNA e snoRNA (0.2); mRNA capping and polyadenilation and their regulative role (0.2). Chromatin basic structure in eukaryotes and prokaryotes (0.2). The structure of nucleosomes and further organization levels (0.2). Histone modifications and their regulatory effects; the histone code. (0.2). DNA methylation and its regulatory role (0.2). Histone variants and their regulatory role. Chromatin structure and chromatin remodelling at promoters (0.2). Chromosomes structure: centromers, telomers and origin of replication (0.1). Molecular Biology Techniques (0.5 cfu): Nucleic acids purification, quantization, labeling and sequencing (introduction to NGS); PCR, RT-PCR, Southern and Northern blot; basic cloning techniques Techniques for analysis of protein-DNA interactions. Practical training (1 cfu).   James D. Watson, Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Losick: Molecular Biology of the Gene Suggested lectures: selected chapters from: C.R. CALLADINE and H.R. DREW "UNDERSTANDING DNA" - ACADEMIC PRESS ADDITIONAL MATERIALS (SLIDES AND REVIEWS) WILL BE AVAILABLE ON MOODLE2 PLATFORM (Date degli appelli d'esame) - SABATINI SABRINA	6	BIO/11	48	-	-	-	Attività formative di base	ENG
1049377 - BIOCHEMISTRY (obiettivi) Educational aims i.e what is the purpose of the course and general statements about the learning that takes place over the duration of the course 1. To give students a good understanding of the major areas of Biochemistry 2. To develop students’ understanding of the application of biochemical principles to other areas of biology and biomedical sciences 3. To develop students’ awareness of the role of Biochemistry both as a research discipline and its applications 4. Develop the key skills required for independent evaluation of data, critical appraisal of scientific literature. 5. Develop confidence in oral presentation skills to specialized audiences, and the ability to write scientific reports. Knowledge and understanding The course provides a knowledge and understanding of the following: 1. Key concepts in areas of direct relevance to biochemistry 2. Structure and function of proteins 3. Key concepts in enzymology, metabolic pathways and their regulation 4. Mechanisms of enzymatic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids and connections between the metabolic pathways 5. Relevance of the knowledge of enzymic mechanisms, the metabolic pathways for research in metabolomics applied to human health issues and to pharmaceutical chemistry. 6. 7. Role of hormones in cellular communications and signal transduction 8. Theoretical basis of key biochemical and immunological practical techniques 9. Theoretical basis of the determination of protein structure 10. Basis of bioinformatics and sequence/structure analysis 11. Awareness of major issues currently at the forefront of Biochemistry research Teaching/learning methods and strategies The above mentioned points are achieved through lectures, group work and formative assessments, and are reviewed and reinforced in tutorials. Intellectual/Communication skills and Judgements 1. Interpret and analyze biochemical data with a critical understanding of the appropriate contexts for their use 2. Integrate subject knowledge and understanding to explore and solve familiar and unfamiliar problems 3. Understand Biochemistry literature 4. Produce critical and original pieces of written work on biochemical topics 5. Think critically about their own work/research and to input into the formulation of future hypotheses and experiments 7. Ability to present Biochemistry to audiences of differing scientific knowledge 8. Computer skills, to include molecular viewers, data analysis/presentation, spreadsheets and statistical analysis.
- BIOCHEMISTRY 1 (obiettivi) KNOWLEDGE AND UNDERSTANDING The students will acquire the knowledge necessary for the understanding of the structures and functions of the living matter in molecular terms. Structures and functions of proteins, lipids, phospholipids. Structure-function relationship of protein and folding. Fibrous and globular proteins. Antibodies and their applications in analytical biochemistry. Importance of kinetics and thermodynamics in biochemistry. Biological membranes and transport systems. Mechanisms of enzymic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids. Mechanisms of regulation of metabolic pathways, production and conservation of energy. Connections between the metabolic pathways. Some aspects of the forefront research in biochemistry and, in particular, in metabolomic research, will also be illustrated, supported by advanced textbooks and scientific articles. APPLYING KNOWLEDGE AND UNDERSTANDING The students will gain an insight into the relevance of the knowledge of biochemistry for pharmaceutical chemistry, biotechnology and, in particular, metabolomic research applied to human health. The knowledge acquired during the lectures will be consolidated by exercises regarding the single topics. Also, examples of problems which can be solved only by applying the knowledge on the enzymic mechanisms, metabolic pathways and their connections, will be proposed. The students will be encouraged to tackle the problems and to put forward the ideas on the possible solutions. The importance of the constant updating on the progress in the research will also be highlighted. MAKING JUDGEMENTS The knowledge and the understanding of the single topics will be consolidated through discussions regarding the conceptual and methodological approaches used in the studies on the metabolic reactions and on the connections among the metabolic pathways. The students will be encouraged to apply the acquired knowledge to new problems. The discussions on the topics regarding the programme, presented in an interdisciplinary framework, together with the acquired knowledge, will help to develop the ability to make autonomous judgements, to gather and interpret relevant data regarding issues in biochemistry. In particular, examples of metabolomic research will be presented and the students will be encouraged to tackle the problems and put forward the ideas on the possible solutions. COMMUNICATION The knowledge of the biochemical bases of biological processes oriented towards applications in medicine and pharmaceutical research and framed in an interdisciplinary context, as well as the correct use of the biochemical terminology, contributes to develop the ability to communicate with specialist and nonspecialist interlocutors. LEARNING SKILLS The knowledge of the fundamentals of biochemistry and the ability to interpret the data, as well as the insight gained into the strategies of biochemical research, will enable the students to develop those skills needed to undertake further studies requiring a higher level of autonomy, such as the Master degree - GRGURINA INGEBORG (programma) BACHELOR DEGREE IN BIOINFORMATICS COURSE OF BIOCHEMISTRY 1 Prof. Ingeborg Grgurina (2018-2019) INTRODUCTION TO PROTEINS Basic Concepts of Thermodynamics and Kinetics. Enthalpy, the First Law of Thermodynamics. Entropy, the Second Law of Thermodynamics. Free Energy and Useful Work. Chemical Reaction Rates and the Effects of Catalysts. Transition States and Reaction Rates. (4 hours) The Primary Level of Protein Structure. Structure, Stereochemistry and Acid-Base Properties of Amino Acids. The Peptide Bond. The Three-Dimensional Structure of Proteins. Secondary Structure. Regular Ways to Fold the Polypeptide Chain. α-Helices and β-Sheets. Ramachandran Plots. Tertiary Structure. Globular Proteins. Functional Diversity. The Interactions Stabilizing the Tertiary Structure: Charge–Charge Interactions, Internal Hydrogen Bonds Van der Waals Interactions, The Hydrophobic Effect, Disulfide Bonds. The Thermodynamics of Folding. Dynamics of Globular Protein Structure. Protein Misfolding and Disease. Prediction of Protein Secondary and Tertiary Structure. Collagen: Example of a Fibrous Protein (4 hours). Quaternary Structure of Proteins. Multisubunit Proteins: Hemoglobin, Structure and Function. Oxygen Transport from Lungs to Tissues: Protein Conformational Change Enhances Function. The Oxygen-Binding Sites in Myoglobin and Hemoglobin. Analysis of Oxygen Binding by Myoglobin. The Role of Conformational Change in Oxygen Transport. Cooperative Binding and Allostery. Models for the Allosteric Change in Hemoglobin. Changes in Hemoglobin Structure Accompanying Oxygen Binding. Allosteric Effectors of Hemoglobin. The Bohr Effect. Hemoglobin Variants and Their Inheritance: Genetic Diseases (Sickle Cell Disease). Antibody Structure and Function. The Adaptive Immune Response. The Structure of Antibodies. Antibody-Antigen Interactions. Shape and Charge Complementarity Interactions. Production of monoclonal antibodies. Production of antibodies which can recognize small molecules.( 6 hours). ENZYMES AS BIOLOGICAL CATALYSTS The Diversity of Enzyme Function. Reaction Rates, Rate Constants, and Reaction Order. Transition State Theory Applied to Enzymatic Catalysis. Mechanisms for Achieving Rate Acceleration: Principles and Examples (Serine Proteases). Models for Substrate Binding and Catalysis. Michaelis-Menten Kinetics. Interpreting KM, kcat and kcat/KM. Enzyme Inhibition. Competitive, Uncompetitive and Mixed Inhibition. Irreversible Inhibition. The Regulation of Enzyme Activity. Substrate-level Control. Feedback Control. Allosteric Enzymes. Covalent Modifications. (6 hours). METABOLISM (20 hours) Introduction Overview and Chemical Logic of Metabolism. Catabolic and Anabolic Pathways. Distinct Pathways for Biosynthesis and Degradation. Compartmentation. ATP as a Free Energy Currency. Major Metabolic Control Mechanisms. Control of Enzyme Levels, Control of Enzyme Activity, Hormonal Regulation. Experimental Analysis of Metabolism. Levels of Organization at Which Metabolism is Studied (Whole Organisms, Organs, Whole Cells, Cell-free Systems, Purified Components, Metabolic Probes. Metabolomics: Experimental Approaches and Fields of Application. Carbohydrate Metabolism Glycolysis. Chemical Strategy of Glycolysis. Reactions Leading from Glucose to Pyruvate. The Energy Investment Phase and Energy Generation Phase. Main Control Points. Regulation of Phosphofructokinase. Relation of Glycolysis to Other Pathways. Metabolic Fates of Pyruvate. Lactate Metabolism. Ethanol Metabolism. Acetyl-CoA Formation: Pyruvate Dehydrogenase Complex. The Pentose Phosphate Pathway. Oxidative and Nonoxidative Phase. Gluconeogenesis: Reactions and Relation to Glycolysis. Coordinated Regulation of Glycolysis and Gluconeogenesis. Glycogen: Structure and Function: Reactions Involved in the Breakdown and Biosynthesis of Glycogen. Coordinated Regulation of Glycogen Metabolism. Lipids Metabolism Triacylglycerol and Fatty Acid Metabolism: Degradation and Biosynthesis. Fatty acid oxidation: Fatty Acid Activation and Transport into Mitochondria. The β-Oxidation Pathway. Fatty Acid Biosynthesis by Multifunctional Proteins. Formation and Degradation of Triacylglycerols. Citric Acid Cycle Chemical Strategy, Reactions and Energetics of the Citric Acid Cycle. Malfunctions of the Citric Acid Cycle as a Cause of Human Disease. Anaplerotic Sequences. Electron Transport, Oxidative Phosphorylation Free Energy Changes in Biological Oxidation. Mitochondrial Transport Systems. Respiratory Complexes, Electron Carriers in the Respiratory Chain. Chemioosmotic Coupling. The Structure of Mitochondrial ATP-Synthase Enzyme and Mechanism of ATP Synthesis. Amino Acid Metabolism Degradation and Biosynthesis of Amino Acids: Selected Examples. Transamination Reactions, Glutamate Dehydrogenase. Urea Cycle. Problems and Exercices, Examples of metabolomic studies. (The role of metabolomic profiling in the identification of metabolic alterations in disease, of the metabolic pathways involved and in the detection of disease-specific biomarkers.) Analytical aspects (isotope labelling, protein purification, immunochemical techniques).   TEXTBOOK BIOCHEMISTRY: CONCEPTS AND CONNECTIONS, Global Edition Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews, ISBN-13: 9781292112008 2016 • Pearson •	6	BIO/10	40	12	-	-	Attività formative caratterizzanti	ENG

Secondo semestre

Insegnamento	CFU	SSD	Ore Lezione	Ore Eserc.	Ore Lab	Ore Studio	Attività	Lingua
1049260 - IMMUNOLOGY AND MOLECULAR PATHOLOGIES (obiettivi) Learning results This course is aimed at providing an overview of the most important cellular and molecular mechanisms involved in the regulation of the immune response. The factors regulating immune system will be put in relation to the molecular mechanisms governing resistance against pathogens and promoting pathologies related to a defective immune response. Specific aims Student will acquire fundamental knowledge on - how immune cells function and interplay to participate to immune responses - how immune system protects us from pathogens and how mechanisms that inhibit immune responses lead to disease state. - how interpretation of transcriptomic and proteomic data helps to elucidate mechanisms of development of the immune response. At the end of the course, students will be able to explain how immune system works and to understand and explain data obtained from multiparametric analysis of immune cell function at transcriptional and post-transcriptional levels. The use of bioinformatics tools to clarify the molecular processes underlying pathologies and their use in diagnosis and treatment of diseases will be discussed. At the end of the course, students will be able to perform bibliographic searches in public scientific data banks (i.e. PubMed) to develop the topics covered in the course. This will be instrumental to identify the most recent methods of bioinformatic analysis used to approach immunology issues. The independent ability of the student to propose solutions to solve immunological questions is and aim of the course. Communication skills will be verified during the course by stimulating discussion and implemented by suggestions and the critical analysis of the slides presented during the course - BERNARDINI GIOVANNI (programma) - Introduction to cells, organs and function of immune system - Role of innate immunity in generating specific immune responses. - The antigen-presenting cells to T lymphocytes (dendritic cells and macrophages). - T cell maturation and activation - B cell maturation and activation - Epigenetic modifications in immune cells. Mechanisms and analysis. Role in maturation and differentiation to effector cells. - Effector cell-mediated mechanisms. The role of helper T cells in determining the nature of the immune response. - The activation of macrophages: phagocytosis and cytolysis - Humoral immunity effector mechanisms. - Molecules involved in immunity to infection and mechanisms of viral immune evasion - Molecules involved in immunity to tumors and mechanisms of tumor immune evasion - Molecular oncology in the diagnosis and development of targeted therapies Learning results This course is aimed at providing an overview of the most important cellular and molecular mechanisms involved in the regulation of the immune response in order to comprehend their specific role in the resistance against pathologies. More in detail, students will learn: Student will acquire fundamental knowledge on - how immune cells function and interplay to participate to immune responses - how immune system protects us from pathogens and how mechanisms that inhibit immune responses lead to disease state. - how interpretation of transcriptomic and proteomic data helps to elucidate mechanisms of development of the immune response. At the end of the course, students will be able to explain how immune system works and to understand and explain data obtained from multiparametric analysis of immune cell function at transcriptional and post-transcriptional levels. The use of bioinformatics tools to clarify the molecular processes underlying pathologies and their use in diagnosis and treatment of diseases will be discussed.   A.K. Abbas, A.H. Lichtman, S. Pillai. BASIC IMMUNOLOGY. Function and disorders of the Immune System 5TH edition, Masson. C.A. Janeway, K. Murphy, P. Travers, M. Walport. IMMUNOBIOLOGY, Piccin. (Date degli appelli d'esame)	6	MED/04	48	-	-	-	Attività formative caratterizzanti	ENG
1049375 - MOLECULAR BIOLOGY (obiettivi) General goals The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis. Specific goals 1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology. 2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches. 3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions. 4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach.
- MOLECULAR BIOLOGY 2 (obiettivi) General goals The course aims to introduce the students to the links between DNA, RNA and protein structure and their relevant biological functions with particular emphasis on the bioinformatic approaches to their analysis. Specific goals: 1. Knowledge and comprehension: the students will have to know the molecular mechanisms which regulate cellular homeostasis and gene expression and the most utilized methodologies in Molecular Biology. 2. Ability in applying Knowledge and comprehension: the students will have to be able to apply this knowledge in the discussion of specific arguments of recent and general interest with a particular focus on the bioinformatic approaches. 3. Abilities in judging methodologic approaches and communication skill: The students will have to show skills in judging strategies in biological problems solving and to communicate their conclusions to the teacher and to the colleagues. This is also applicable to the practical training sessions. 4. The students will have to show skill in applying what they have learned in molecular biology to specific problems to be solved with a bioinformatic approach. - SABATINI SABRINA - NEGRI RODOLFO (programma) Main goal of the course is to give to the students a general view of the molecular mechanisms which are at the base of the biological processes. For each argument a methodological section will introduce the students to the main technical approaches used at the state of the art. Practical training (2 CFU) will make the students to breath the atmosphere of a molecular biology laboratory. Particular attention will be given to the high throughput methods utilized in “Omic” approaches to the comprehension of biological processes which will be further illustrated in the course of Molecular Biology and Genomics. General aims: The course is focused on the deep connection between DNA structure and functions. The student will learn the molecular mechanisms which are at the base of the processes of Replication, Recombination, Transcription and DNA repair and their regulatory circuits. Specific aims: 1. Knowledge and understanding: The student should learn the basic molecular mechanisms of the cellular omeostasis and gene regulation and the most used techniques of Molecular Biology. 2. Ability to apply Knowledge and understanding: The student should be able to apply this knowledge in the discussion of recent arguments of general interest in Molecular Biology research. 3. Critical Judgement abilities: The student should demonstrate critical judgement abilities in solving problems related to theoretical and practical Molecular Biology projects and should communicate its conclusions to the colleagues and to the teacher in an effective way. 4. the student should demonstrate to be able to apply the learned concepts to his future work in molecular biology. Molecular Biology II RNA Splicing (0.3): role of small nuclear RNAs; RNA/RNA interactions and structural modifications in active splicesosome formation; protein/protein interactions and the role of SR proteins; alternative splicing regulation, self-splicing (0.2); mRNA transport; RNA stability and its regulation (0.3 Cfu); ribozymes and their applications (0.2): RNAi (interference) and its applications, synthesis and regulative role of miRNA and other classes of noncoding RNAs (0.4). Protein biosyntesis (0.6): general principles; structure and functions of the ribosome; comparison between procariotic and eukaryotic protein biosynthetic systems; translation initiation, elongation and termination. Protein biosynthesis inhibitors; protein folding and stability; role of molecular chaperones; protein transport and targeting (0.3). Control of protein homeostasis (0.4): ubiquitin and proteasome systems. Principles of protein engineering (0.2). Systems of signal transduction systems and their role in cellular regulation (0.4). The molecular mechanisms of hormone action (0.3). Genome structure. The structure of the genomes: coding and non coding DNA (0.3), transposable elements and genome variability (0.2); the evolution of the genomes the paradox of DNA content (0.2); the exon shuffling theory (0.2). Necessity of information compaction in the genomes. Molecular Biology Techniques (0.5 cfu): The multiple uses of reporter genes; techniques for analysing protein localization in the genome (chIP, ChIP on chip end ChIPSeq); techniques for analysing protein-protein interactions (Co-IP; two-hybrid systems). Practical training (1Cfu)   James D. Watson, Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Losick: Molecular Biology of the Gene	6	BIO/11	32	-	24	-	Attività formative di base	ENG
1049377 - BIOCHEMISTRY (obiettivi) Educational aims i.e what is the purpose of the course and general statements about the learning that takes place over the duration of the course 1. To give students a good understanding of the major areas of Biochemistry 2. To develop students’ understanding of the application of biochemical principles to other areas of biology and biomedical sciences 3. To develop students’ awareness of the role of Biochemistry both as a research discipline and its applications 4. Develop the key skills required for independent evaluation of data, critical appraisal of scientific literature. 5. Develop confidence in oral presentation skills to specialized audiences, and the ability to write scientific reports. Knowledge and understanding The course provides a knowledge and understanding of the following: 1. Key concepts in areas of direct relevance to biochemistry 2. Structure and function of proteins 3. Key concepts in enzymology, metabolic pathways and their regulation 4. Mechanisms of enzymatic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids and connections between the metabolic pathways 5. Relevance of the knowledge of enzymic mechanisms, the metabolic pathways for research in metabolomics applied to human health issues and to pharmaceutical chemistry. 6. 7. Role of hormones in cellular communications and signal transduction 8. Theoretical basis of key biochemical and immunological practical techniques 9. Theoretical basis of the determination of protein structure 10. Basis of bioinformatics and sequence/structure analysis 11. Awareness of major issues currently at the forefront of Biochemistry research Teaching/learning methods and strategies The above mentioned points are achieved through lectures, group work and formative assessments, and are reviewed and reinforced in tutorials. Intellectual/Communication skills and Judgements 1. Interpret and analyze biochemical data with a critical understanding of the appropriate contexts for their use 2. Integrate subject knowledge and understanding to explore and solve familiar and unfamiliar problems 3. Understand Biochemistry literature 4. Produce critical and original pieces of written work on biochemical topics 5. Think critically about their own work/research and to input into the formulation of future hypotheses and experiments 7. Ability to present Biochemistry to audiences of differing scientific knowledge 8. Computer skills, to include molecular viewers, data analysis/presentation, spreadsheets and statistical analysis.
- BIOCHEMISTRY 2 (obiettivi) Educational aims i.e what is the purpose of the course and general statements about the learning that takes place over the duration of the course 1. To give students a good understanding of the major areas of Biochemistry 2. To develop students’ understanding of the application of biochemical principles to other areas of biology and biomedical sciences 3. To develop students’ awareness of the role of Biochemistry both as a research discipline and its applications 4. Develop the key skills required for independent evaluation of data, critical appraisal of scientific literature. 5. Develop confidence in oral presentation skills to specialized audiences, and the ability to write scientific reports. Knowledge and understanding The course provides a knowledge and understanding of the following: 1. Key concepts in areas of direct relevance to biochemistry 2. Structure and function of proteins 3. Key concepts in enzymology, metabolic pathways and their regulation 4. Mechanisms of enzymatic reactions, Michaelis-Menten kinetics. The most important metabolic pathways of carbohydrates, lipids, fatty acids and amino acids and connections between the metabolic pathways 5. Relevance of the knowledge of enzymic mechanisms, the metabolic pathways for research in metabolomics applied to human health issues and to pharmaceutical chemistry. 6. 7. Role of hormones in cellular communications and signal transduction 8. Theoretical basis of key biochemical and immunological practical techniques 9. Theoretical basis of the determination of protein structure 10. Basis of bioinformatics and sequence/structure analysis 11. Awareness of major issues currently at the forefront of Biochemistry research Teaching/learning methods and strategies The above mentioned points are achieved through lectures, group work and formative assessments, and are reviewed and reinforced in tutorials. Intellectual/Communication skills and Judgements 1. Interpret and analyze biochemical data with a critical understanding of the appropriate contexts for their use 2. Integrate subject knowledge and understanding to explore and solve familiar and unfamiliar problems 3. Understand Biochemistry literature 4. Produce critical and original pieces of written work on biochemical topics 5. Think critically about their own work/research and to input into the formulation of future hypotheses and experiments 7. Ability to present Biochemistry to audiences of differing scientific knowledge 8. Computer skills, to include molecular viewers, data analysis/presentation, spreadsheets and statistical analysis. - PAIARDINI ALESSANDRO (programma) Aminoacidi: proprietà e struttura chimico-fisiche Visualizzazione di macromolecole con visualizzatori molecolari Database di sequenze proteiche Allineamenti di sequenza proteica Il legame peptidico in vitro e in vivo Struttura secondaria Struttura terziaria - Stabilità proteica e folding Domini, motivi, moduli e ripetizioni - Struttura quaternaria Microscopia elettronica e cristallografia a raggi X. Risonanza magnetica nucleare delle proteine Predizione della struttura proteica Dinamica molecolare e drug design Esempi selezionati di meccanismi proteici   C. I. Branden, J. Tooze. Introduction to protein structure. Garland science David Whitford, PROTEINS STRUCTURE AND FUNCTION (Wiley) http://books.google.it/books?id=qbHLkxbXY4YC Fondamenti di Biochimica Voet D & Voet JG. (Zanichelli) "Struttura e Funzione delle Proteine” Petsko & Ringe (Date degli appelli d'esame)	6	BIO/10	40	-	12	-	Attività formative caratterizzanti	ENG
1055572 - BIOINFORMATICS I (obiettivi) L'obiettivo del corso è fornire agli studenti un'introduzione alle tecniche pratiche e alle risorse disponibili sul web per la bioinformatica. Sarà data enfasi alla familiarizzazione degli studenti con l'applicazione di un'ampia varietà di strumenti bioinformatici e database biologici per svolgere attività di ricerca di base (compreso l'accesso ai principali database pubblici di sequenze, ricerca avanzata e recupero di set di dati di espressioni specifici, analisi di espressione differenziale, allineamento di sequenze proteiche) attraverso un ampio uso di tutorial e sessioni di allenamento pratico. - LICURSI VALERIO (Date degli appelli d'esame)	6	INF/01	48	-	-	-	Attività formative affini ed integrative	ENG
1049264 - PHARMACEUTICAL CHEMISTRY (obiettivi) During the course the student will learn the basics to design a drug through computational methods. The aim of the course is to impart an understanding of what medicinal chemists consider when attempting to design new pharmaceuticals. The course is twofold: a theoretical part and practical section. In the first part the course will describe the principles involved in modern drug design and drug discovery, usually with reference to compounds in current clinical usage. In the second part practical sections will be set up to teach the student some computational methods to apply in the drug design process. - RAGNO RINO (programma) 1. Introduction to Medicinal Chemistry 1A. History 1B. Drugs and Drug Targets 1C. Drug Discovery Screening Techniques 2. Drug Targets 2A. Proteins 2B. Lipids 2C. Sugars 3. Farmacodinamics 3A. Drug-Target interactions 3B. Drug Mechanisms of Action with Receptors and Enzymes 4. Farmacokinetics 4A. ADME Properties 4B. Metabolism 5. Drug Discovery 5A. Hit and Lead 5B. Structure Activity Relationships 6. Drug Design 6A. The computer in Drug Design 6B. Introduction toLigand-Based Drug Design 6C. QSAR 6D. Introduction to 3-D QSAR 6E. Introduction to Structure-Based Drug Design 7. Practical Exercizes on General Med Chem 7A. How to draw molecules in 2-D and 3-D 7B. Analysis of three-dimensional Drug/Target interactions 7C. Ligand-Based Methods: basics approaches on how to build a QSAR model 7D. Ligand-Based Methods: basics approaches on how to build a 3-D QSAR model 7E. Structure-Based Methods: basics approaches on how to perform molecular docking of a small molecule in a macromolecule   - Foye. Principles of medicinal chemistry. - Patrick. An Introduction to Medicinal Chemistry. - Burger. Drug Discovery. - Wermuth. The Practice of Medicinal Chemistry. - Comprehensive Medicinal Chemistry II. - Lectures available from e-learning web platform. (https://elearning.uniroma1.it/course/view.php?id=4523) (Date degli appelli d'esame)	6	CHIM/08	32	40	-	-	Attività formative caratterizzanti	ENG

Terzo anno

Primo semestre

Insegnamento	CFU	SSD	Ore Lezione	Ore Eserc.	Ore Lab	Ore Studio	Attività	Lingua
1049266 - BIOINFORMATICS II (obiettivi) The course aims to provide some bioinformatics tools to analyze and visualize data produce from next generation sequencing technologies. In particular the attendee will be to perform differential expression analysis of RNA-sequencing data and then integrate the results with other data coming from high-throughput technologies - PALLOCCA MATTEO (Date degli appelli d'esame)	6	ING-INF/06	24	-	36	-	Attività formative affini ed integrative	ENG
1049265 - BIOETHICS (obiettivi) The course will introduce to the main historical and theoretical knowledge needed to understand the cultural and political relevance that in the western and democratic societies has taken the reflection on the ethical dimensions of biological and medical research. The course objectives are to provide students with the cognitive tools to understand the terms of the discussions on the various controversial bioethical issues, and to enable him to develop a personal and critical view on the various issues addressed in the lessons. - SIRGIOVANNI ELISABETTA (programma) Il corso copre i seguenti argomenti: introduzione generale all'etica per bioscienziati; fondamenti di logica e psicologia del ragionamento per la bioetica; storia della bioetica; teoria etiche per la bioetica, naturalismo/anti-naturalismo e pragmatismo in bioetica; approcci su principi e su casi; etica della ricerca e integrità della ricerca; etica della genetica; potenziamento genetico e cerebrale; biobanche e uso dei dati genetici nei contesti giuridici; etica delle information technologies e nuove sfide dall'Intelligenza Artificiale; neuroetica; etica delle neurotecnologie; basi biologiche della moralità. Esempi, casi studio e attività pratiche riguarderanno argomenti popolari nei dibattiti bioetici contemporanei (cellule staminali, clonazione, GMOs, fine vita, vaccini, privacy (genetica), sperimentazione animale, protesi, riproduzione assistita, ecc.). Alcune questioni innovative nelle biotecnologie verranno presentate e discusse da un punto di vista etico: organoidi cerebrali, macchine morali, chimere, interfaccia uomo-macchina, editing genetico, ecc.   Testi richiesti: - slide del docente - lista bibliografica obbligatoria (vedere sotto). Le letture (articoli, capitoli di libro in lingua inglese) vengono fornite agli studenti prima, durante o al termine delle lezioni. Le slide e tutta la bibliografia obbligatoria viene caricata dal docente in pdf sulla pagina E-learning Sapienza (Moodle) al termine di ogni lezione. (Date degli appelli d'esame)	6	MED/02	48	-	-	-	Attività formative caratterizzanti	ENG
1049258 - MOLECULAR BIOLOGY AND GENOMICS (obiettivi) The new generation of sequencing technologies offered extraordinary opportunities for high-throughput functional genomic studies. These tools have been applied in a variety of contexts, including whole-genome sequencing, discovery of transcription factor binding loci, mapping out DNA accessibility and RNA expression profiling. Intriguingly, recent efforts in annotation led to the discovery of novel noncoding RNA genes that control temporal and/or spatial gene expression along cell differentiation. Aim of the course is the integration of the knowledge of the modern molecular biology with high-throughput technologies. Besides RNA metabolism and noncoding content, the course will introduce NGS technologies, highlight different applications of these new tools and show ways to analyse data in the context of completed genome sequences of different model organisms. The course will also feature methods to assist the study and the prioritization of gene lists from large-scale gene expression data. - BALLARINO MONICA (programma) Il corso prevede 48 ore di lezioni teoriche, esercizi al computer e seminari. Biologia Molecolare (24 ore) Introduzione al Genoma ed alla complessità funzionale dei sistemi eucarioti. Cenni sui meccanismi di maturazione dell’RNA: capping, splicing e poliadenilazione. Splicing alternativo e regolazione dello splicing; Elementi di terapia genica (Distrofia Muscolare di Duchenne); Esporto e stabilità dell’RNA; Struttura della cromatina e modificazioni istoniche; Il modello dell’mRNA Factory: RNA non codificanti (ncRNA); RNA interference: scoperta, meccanismi di azione e fattori coinvolti; microRNA (miRNA): biogenesi, meccanismi di azione e ruolo nel differenziamento e nella proliferazione; long non-coding RNA (lncRNA); RNA circolari RNA (circRNAs); RNAi e cromatina. Genomica Strutturale (12 ore). Evoluzione del concetto di gene: dalle teorie di Darwin sull’ereditarietà all’Era post-genomica; il Progetto Genoma Umano; il Progetto Encode. Tecnologie di sequenziamento del DNA e del genoma (Sanger, Maxam-Gilbert, BAC). Sequenziamento automatizzato e Next-Generation Sequencing (NGS). La tecnologia "Illumina". Anatomia dei genomi, grandezza del genoma e numero di geni. Il DNA non codificante (ncDNA). Tecnologie di sequenziamento dell’RNA. Il trascrittoma e l’analisi high-throughput dell’espressione genica; WET lab e DRYLAB applicati all’analisi di un tipico esperimento di RNA-seq (FASTQ, PHRED quality score, FASTQC). Identification de-novo e analisi dell’espressione differenziale di mRNA e RNAs non-codificanti (ncRNA). Approcci genetici e biochimici per lo studio dell’interattoma. Il sistema del “two-hybrid”; Immunoprecipitazione, Co-immunoprecipitazione, Protein tagging e saggi di pull-down. Studio delle interazioni tra PROTEINE (ChIP) e RNA (ChIRP) con la cromatina: le tecniche di i) Chromatin Immunoprecipitation (ChIP) e di ii) Chromatin Isolation by RNA Purification (ChIRP). Identificazione e studio di domini topologici (TADs). 3C, 5C, Hi-C e ChIA-PET. Genomica Funzionale (6 ore). Approcci di genetica Forward e Reverse. Sistemi modello: pros e cons. Editing Genomico: il sistema CRISPR/CAS9. Screening omici basati su RNAi e CRISPR. Analisi funzionale di mRNA e non-coding RNA (ncRNA) in sistemi di differenziamento muscolari e neuronali (topo e uomo). Risorse web per l’analisi in silico di dati genomici (6 ore). Esercizi in aula informatizzata. Elaborazione ed interpretazione di dati genomici. Database biologici (primari, secondari, specializzati); il formato FLAT; NCBI: accesso via Taxonomy, Gene; Protein Map Viewer, Pubmed and Pubmed MeSH, Entrez; Genome browsers (UCSC), Ensembl, DDBJ, UniProt; Elementi di gene ontology (GO). miRBase, TargetScan e miRTARBASE.   Un libro di testo scelto tra i seguenti: R.F. Weaver Molecular Biology, Mc Graw Hill, V Edition Watson J. D et al Molecular Biology of the Gene, Zanichelli VII Edition Arthur M. Lesk 2009, “INTRODUZIONE ALLA GENOMICA”, Zanichelli Greg Gibson, Spencer V. Muse 2004, “INTRODUZIONE ALLA GENOMICA”, Zanichelli Tom Strachan, Judith Goodship, Patrick Chinnery 2016, “GENETICA E GENOMICA”, Zanichelli Per un immediato aggiornamento dei testi o del materiale didattico distribuiti dai docenti consultare la pagina web del corso: https://elearning2.uniroma1.it (Date degli appelli d'esame)	6	BIO/11	48	-	-	-	Attività formative caratterizzanti	ENG
Gruppo opzionale: Gruppo OPZIONALE - (visualizza) 12                1049267 - MODELLING AND SIMULATION OF BIOMOLECULAR DYNAMICAL SYSTEMS (obiettivi) This course aims to provide students with a practical and hands-on experience with common modeling and simulation tools in molecular biology. It would be expected that after completing this course a student would be able to model and simulate using Matlab a biomolecular systems like, for example, a gene regulatory network using the appropriate methodology. Further, students will understand the basic theory behind these modeling tecniques and critically analyze the results of their analysis. - FARINA LORENZO (programma) Introduzione alla modellistica matematica. Elementi di teoria dei sistemi. Modelli di interazione genica e reti. Identificazione di geni regolati dal ciclo cellulare.   Materiale didattico fornito dal docente (Date degli appelli d'esame) 6  ING-INF/06  48  -  -  -  Attività formative affini ed integrative  ENG 1049268 - SIGNAL PROCESSING AND INFORMATION THEORY - COLONNESE STEFANIA (programma) Rappresentazione, misura ed estrazione dell’informazione contenuta nei dati. Sorgenti di informazioni, entropia, informazione mutua. Fondamenti di codifica di canale. Decodifica di codici senza memoria e con memoria. Acquisizione di segnali ed immagini, campionamento e quantizzazione. Il rumore di osservazione. Filtraggio. Rappresentazione di segnali ed immagini nel dominio di Fourier. Rappresentazione compatta di segnali ed immagini: Trasformata di Karounen Loewe, analisi a componenti principali (PCA). Principi di rivelazione e stima di segnale. Riconoscimento di pattern mediante correlazione per stima di ritardo e spostamento.   DISPENSE: DISPONIBILI SULLA PAGINA MOODLE DEL CORSO TESTO: GAETANO SCARANO ELABORAZIONE STATISTICA DEI SEGNALI (VOL.I) (Date degli appelli d'esame) 6  ING-INF/03  48  -  -  -  Attività formative affini ed integrative  ENG 1049269 - ALGORITHMS (obiettivi) this course is an introduction to algorithms with special emphasis given to those algorithmic problems and techniques that have the greatest impact for bioinformatics. - RODOLA' EMANUELE (programma) - Algoritmi e strutture dati: generalità ed esempi. Introduzione alla nozione di costo (tempo e spazio di memoria). - Notazioni asintotiche per le funzioni di costo e metodi di analisi (caso peggiore, medio, migliore). - Metodi di analisi di algoritmi ricorsivi: albero della ricorsione, iterazione, sostituzione, Master Theorem. - Tipi di dato astratto (pile, code, alberi) e loro implementazioni. Algoritmi di visita di un albero. - Algoritmi di ordinamento incrementali (descrizione, implementazione e analisi): SelectionSort, InsertionSort, BubbleSort, HeapSort, MergeSort, QuickSort. Lower bound sul costo dell'ordinamento per modello basato su confronti. - Algoritmi di ordinamento di interi (descrizione, implementazione e analisi): IntegerSort, BucketSort, RadixSort. - Tipo di dato Dizionario. Alberi di ricerca binari. Alberi AVL. - Tavole Hash. - Grafi e loro rappresentazione. Algoritmi di visita (descrizione, implementazione e costo). - Tecnica algoritmica greedy. Minimo albero ricoprente e rispettivo calcolo basato su algoritmo greedy. Algoritmi di Kruskal, di Prim e di Boruvka. - Cammini minimi su grafi e relativi algoritmi (descrizione, implementazione e analisi): calcolo delle distanze, algoritmo di Bellman e Ford, calcolo dei cammini minimi a sorgente singola su grafi aciclici, algoritmo di Dijkstra.   Il materiale di studio viene fornito completamente sul sito di riferimento del corso. Come materiale integrativo vengono suggeriti di volta in volta capitoli selezionati dai seguenti testi: T.H. Cormen, C.Papadimitriou, U. Vazirani. Introduzione agli algoritmi J. Kleinberg, E. Tardos Algorithm Design S. Dasgupta, C. Papadimitriou, U. Vazirani Algorithms C. Demetrescu, I. Finocchi, G.F. Italiano Algoritmi e strutture dati (Date degli appelli d'esame) 6  INF/01  48  -  -  -  Attività formative affini ed integrative  ENG 1049270 - COMPLEX BIOMOLECULAR NETWORKS (obiettivi) The course aims to provide basics concepts and tools for complex networks analysis. The attendee will be able to apply complex networks concepts to biological networks and explore the underlying process and molecular related issues. - MARCHETTI SPACCAMELA ALBERTO (programma) 1.Algorithms and Complexity Computational complexity of algorithms and programs - Fast versus Slow Algorithms - Big-O Notation - Algorithm Design Techniques – Tractable versus Intractable Problems - NP-complete problems. 2. Algoritmic Techniques Greedy Algorithms - Dynamic Programming - Exhaustive Search - Branch-and-Bound Algorithms - Heuristics – Branch and Bound (these techniques are introduced when they are applied in solving problems considered in sections 4-6). 3. Graph Algorithms Basic definition on Graphs – Memory representation – Connectivity - Shortest path, Eulerian path, Traveling Salesmna problem, Hamiltonia path. 4. DNA Assembling Shortest Superstring Problem - DNA Arrays as an Alternative Sequencing Technique - Sequencing by Hybridization - SBH as a Hamiltonian Path Problem - SBH as an Eulerian Path Problem - Fragment Assembly in DNA Sequencing – Overlap-Layout-Consensus assembly- De Bruijn graph assembly – Scaffolding. 5. HiddenMarkovModels CG-Islands and the “Fair Bet Casino” – Definition of Hidden Markov Models - Decoding Algorithm - HMM Parameter Estimation. 6. Clustering and Trees Gene Expression Analysis - Hierarchical Clustering - k-Means Clustering - Clustering and Corrupted Cliques - Evolutionary Trees - Distance-Based Tree Reconstruction - Reconstructing Trees from Additive Matrices - Evolutionary Trees and Hierarchical Clustering - Character-Based Tree Reconstruction - Small Parsimony Problem - Large Parsimony Problem. 7. Advanced topics in large networks and phylogenetic recontructions.   Libro di Testo Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, MIT Press (capp. 2,5.1-5.3, 6, 8,10, 11) Altri testi distribuiti in classe e disponibili sulla piattaforma e-learning Martin Vingron, Jens Stoye, Hannes Luz Algorithms for Phylogenetic Reconstructions, Notes Slides delle lezioni Materiale (suggerito) per i seminari (Date degli appelli d'esame) 6  ING-INF/05  48  -  -  -  Attività formative affini ed integrative  ENG 1049271 - PLANT FUNCTIONAL GENOMICS (obiettivi) The aim of the course is to provide a theoretical knowledge of plant genomes, and practical explanation of the techniques used in plant functional genomics, i.e. a large-scale analysis of the function of the different gene products to understand how the genome generates the phenotype of the plant. Insights will be given into the new information that will be generated from whole genome-/proteome-/metabolome analysis. The course will cover the following concepts: array and sequencing based methods; reverse and forward genetics; comparison of plant genomes; epigenomics; proteomics and metabolomics. Also covered are robotization, miniaturization (single-cell studies) and high-throughput-screenings. Finally, the course will introduce methods for visualization and analysis of high-density data. - FERRARI SIMONE (programma) Module I (3 cfu) INTRODUCTORY CONCEPTS - Plant organisms. The plant cell. Nuclear, mitochondrial and plastid genome of plants. Reproduction of plant organisms. -Basic concepts of genetics. Genetic polymorphisms. Genetic and molecular markers. Genetic and physical maps. Backcross and inbreeding. Heterosis. Recombinant Inbred Lines. Quantitative Trait Loci. ANALYSIS OF PLANT GENOMES AND USE OF GENOMICS IN PLANT BREEDING - Evolution of plant genomes. Repetitive DNA; polyploidy; sequencing of genomes; the genome of Arabidopsis thaliana. - Comparative genomics; identification of orthologous genes in different species, synteny. Databases of plant genomes. Genome-wide association studies. Development of new plant varieties through marker assisted selection. PLANT EPIGENETICS AND EPIGENOMICS - Epigenetic modifications: DNA methylation; histone changes; Non-coding RNAs: siRNA, microRNA; transcriptional and post-transcriptional gene silencing; role of silencing in maintaining the integrity of the genome. - Generation and maintenance of epigenetic modifications; epialleles; large-scale analysis of the epigenome; transposons. Module II (3 cfu) DIRECT AND REVERSE GENETICS - Analysis of gene function: direct and reverse genetic approaches in plants. Mutagenesis by insertion in plants. Overexpression and silencing. Map-based and deep sequence-based identification of mutations. (4 h). - From mutants to transgenic plants of biotechnological interest. Natural genetic variability as a source of characteristics of biotechnological interest. TILLING and ecoTILLING. Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype. (4 h) - Genome editing: CRISPR/Cas9 (2 h) - Chemical genomics in plant biology. "Click" chemistry. Single cell genomics. (2 h) TRANSCRIPTOME AND INTERACTOME ANALYSES IN PLANTS - ESTs, cDNA-AFLPs, Microarrays, DNA Chips, SAGE. RNA sequencing, sequence analysis and their applications (4 h) -Transcriptomic analysis on a single cell or individual tissues: laser capture; FACS on protoplasts labeled with fluorescent proteins. Databases of plant transcriptomes. (4 h) - Examples of networks and correlation analysis of the expression of multiple genes. (2 h) - Interactomics (2 h)   - Teaching material provided through E-Learning (articles, reviews, lectures slides); - Biotecnologie Sostenibili - Galbiati et al. – EDAGRICOLE - Biotecnologie e Genomica delle Piante - Rao e Leone - Idelson-Gnocchi (acronimo BGP) - Biochemistry and Molecular Biology of Plants, - Buchanan, Gruissem e Jones, 2° ed., Wiley Blackwell (Date degli appelli d'esame) - DE LORENZO GIULIA (programma) Module I (3 cfu) INTRODUCTORY CONCEPTS - Plant organisms. The plant cell. Nuclear, mitochondrial and plastid genome of plants. Reproduction of plant organisms. -Basic concepts of genetics. Genetic polymorphisms. Genetic and molecular markers. Genetic and physical maps. Backcross and inbreeding. Heterosis. Recombinant Inbred Lines. Quantitative Trait Loci. ANALYSIS OF PLANT GENOMES AND USE OF GENOMICS IN PLANT BREEDING - Evolution of plant genomes. Repetitive DNA; polyploidy; sequencing of genomes; the genome of Arabidopsis thaliana. - Comparative genomics; identification of orthologous genes in different species, synteny. Databases of plant genomes. Genome-wide association studies. Development of new plant varieties through marker assisted selection. PLANT EPIGENETICS AND EPIGENOMICS - Epigenetic modifications: DNA methylation; histone changes; Non-coding RNAs: siRNA, microRNA; transcriptional and post-transcriptional gene silencing; role of silencing in maintaining the integrity of the genome. - Generation and maintenance of epigenetic modifications; epialleles; large-scale analysis of the epigenome; transposons. Module II (3 cfu) DIRECT AND REVERSE GENETICS - Analysis of gene function: direct and reverse genetic approaches in plants. Mutagenesis by insertion in plants. Overexpression and silencing. Map-based and deep sequence-based identification of mutations. (4 h). - From mutants to transgenic plants of biotechnological interest. Natural genetic variability as a source of characteristics of biotechnological interest. TILLING and ecoTILLING.. Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype. (4 h) - Genome editing: CRISPR/Cas9 (2 h) - Chemical genomics in plant biology. "Click" chemistry. Single cell genomics. (2 h) TRANSCRIPTOME AND INTERACTOME ANALYSES IN PLANTS - ESTs, cDNA-AFLPs, Microarrays, DNA Chips, SAGE. RNA sequencing, sequence analysis and their applications (4 h) -Transcriptomic analysis on a single cell or individual tissues: laser capture; FACS on protoplasts labeled with fluorescent proteins. Databases of plant transcriptomes. (4 h) - Examples of networks and correlation analysis of the expression of multiple genes. (2 h) - Interactomics (2 h)   - Teaching material provided through E-Learning (articles, reviews, lectures slides); - Biotecnologie Sostenibili - Galbiati et al. – EDAGRICOLE - Biotecnologie e Genomica delle Piante - Rao e Leone - Idelson-Gnocchi (acronimo BGP) - Biochemistry and Molecular Biology of Plants, - Buchanan, Gruissem e Jones, 2° ed., Wiley Blackwell 6  BIO/04  48  -  -  -  Attività formative affini ed integrative  ENG 1049272 - PRINCIPLES OF GENERAL PATHOLOGY - CAMPESE ANTONIO FRANCESCO (programma) -Scopi, vantaggi e limiti della generazione e dell’utilizzo dei modelli murini geneticamente modificati per lo studio e la cura delle patologie umane (2 ore) -Aspetti legislativi della sperimentazione animale (Regola delle 3R, dLGS 26/2014) e relative ricadute sulla bioinformatica: i metodi alternativi; i protocolli di sperimentazione animale; i registri e i database informatici (3 ore); -Mantenimento delle colonie di animali geneticamente modificati e relativi strumenti bioinformatici (2 ore) -Metodologie e strumenti informatici per la generazione di modelli murini geneticamente modificati ‘convenzionali’: topi transgenici e topi ‘knock-out’ (4 ore) e ‘condizionali’ e/o inducibili: il sistema Cre/LoxP; topi ‘knock-in’ condizionali; geni ‘reporter’ (4 ore) -Esempi di modelli murini per lo studio di patologie umane: leucemie, tumori solidi, malattie autoimmuni (3 ore) -Strumenti bioinformatici per la potenziale validazione di modelli murini di patologia umana (2 ore) -Seminari sulle applicazioni bioinformatiche nell'utilizzo dei modelli murini di patologie umane (4 ore)   Materiale didattico e pubblicazioni scientifiche segnalate durante il corso. - PO AGNESE (programma) The topics will be: 1) Getting started and general aspects of molecular and cellular pathology. Concept and causes of alteration in the cell, cellular and tissue homeostasis, Cellular damage: causes, molecular mechanisms, responses and adaptations, Cell death and its manifestations: necrosis and apoptosis 2) Next generation Sequencing (NGS): introduction to NGS tecniques. Illumina platform, Ion Torrent. Applications: Genome Sequencing, Whole exome sequencing, Targeted sequencing, NGS-based comprehensive genomics: DNA methylation, chromatin accessibility and modifications. Analysis of NGS derived data: bioinformatics analysis, analysis of the transcriptome and of the mirnome. Examples of the use of NGS for biomedical research. Data mining on available databases. 3) Molecular and cellular pathology of cancer: Definition and classification of tumors, Stages of tumor progression: initiation, promotion, progression, invasiveness and metastasis, Dominant and recessive mutations: oncogenes and tumor suppressor, molecular basis of neoplastic transformation, invasiveness, metastasization, Identification of tumor markers. Significance of tumor markers in the prevention and staging/classification of tumors 4) Chronic degenerative diseases: diabetes mellitus, metabolic diseases 5) Pathogenetic mechanisms of non-coding RNAs: microRNAs and long non-coding RNAs. microRNA: biogenesis, deregulation mechanisms in pathologies, circulating microRNAs; long non-coding RNA: biogenesis, mechanisms of action, examples of long non-coding deregulated in pathologies. Circular RNAs. 6) Stem cells: embryonic stem cells, adult stem cells. Therapeutic applications of stem cells. Cancer stem cells: biological features and epigenetic regulation. 7) Circulating nucleic acids as markers for diseases. The discovery, challenges an approaches for the identification and evaluation of circulating RNAs and DNAs.   notes and scientific papers given by the teacher (Date degli appelli d'esame) 6  MED/46  48  -  -  -  Attività formative affini ed integrative  ENG 1049273 - OPTIMIZATION METHODS FOR COMPUTATIONAL BIOLOGY (obiettivi) We aim to introduce students to the analysis of decision problems that arise in bioinformatics and health management. Students would be able to: model as mathematical programming problem to be used as a support to the decision maker, use algorithm suitable to each model for the solution, make post-optimality analysis. - SAGRATELLA SIMONE (programma) Part 1: Mathematical programming Things to know: - structure of an optimization problem - feasiblility, unboundedness, and optimality - active, satisfied, violated, and redundant constraints Abilities to acquire: - recast a model as a problem in general form - understand if an optimization problem is an LP, an ILP, or an NLP Part 2: Linear Programming Things to know: - properties of linear functions - convex sets and polyhedra - vertices of a polyhedron and their properties - fundamental theorem of LP - solution set properties Abilities to acquire: - graphical solution - computation of all the vertices of a polyhedron - (graphical) simplex algorithm Part 3: Integer Linear Programming Things to know: - linear formulations and their properties - optimal linear formulations Abilities to acquire: - computation of an optimal linear formulation - branch and bound method for knapsack problems and graphical solution Part 4: NonLinear Programming Things to know: - local and global solutions - feasiblility, unboundedness, and optimality in nonlinear programming - convex problems and their properties Abilities to acquire: - understand if a problem is (strictly) convex   lecture notes of the teacher (Date degli appelli d'esame) 6  MAT/09  48  -  -  -  Attività formative affini ed integrative  ENG 1049285 - BIOINFORMATICS IN PLANT PATHOLOGY (obiettivi) Recent advances in -omics technology, namely genomics, proteomics and metabolomics allow to go deeper into the understanding of the subtle mechanism underlying host-pathogen interactions. This is made possible by next generation sequencers that uncover entire genome or exome of host and pathogens while interacting, skipping complicate procedures for separating the two challengers. Moreover, we are moving faster in re-shaping plant pathology from the one disease-one pathogen dogma, as embodied in Koch's postulate, to the pathobiome concept. Meta-omic tools shed light on the inter-reign network originating the disease of the host in its complexity. The analysis and understanding of the huge amount of data generated by a single experiment represents currently the classical bottleneck. In relation to this, bioinformatics plays a crucial role in data capture, analysis and integration. Plant pathologists have to answer to very concrete and problematic question, today, more, and more in the next future: food security, food safety and food quality. Actually, plant disease burden current food production, accounting for more than 40% of food losses. Climate change and globalization enhance pathogens ability and mobility worldwide. Nevertheless, for environmental as well as political reasons, pathogens cannot be controlled anymore by using pesticides and/or GMO plants. A more sustainable, "green" and integrated pest management is needed. A modern plant pathologist has to face this complex reality, plan experiments at real scale, "sucks the marrow out of -omics" (par. Walt Whitman) by using bioinformatics tools, individuate biocontrol agents and stimulate plant self-defences. In relation to this, the main aim of this course is forming young scientists in managing plant diseases tout court by the mean of the -omics plus bioinformatics tools. - FAINO LUIGI   Per la prima parte, dispense e articoli saranno i testi da cui studiare mentre per la prate del progetto, siti specifici all bionformatica tipo stackoverflow saranno usati (Date degli appelli d'esame) - REVERBERI MASSIMO (programma) MODULO 1: PATOLOGIA vegetale (12 ORE) 1. Introduzione alla patologia vegetale: il concetto di malattia 2. Gli agenti patogeni: dal virus ai funghi, diverse strategie per diversi patogeni 3. Gestione integrata delle malattie: come coniugare la sicurezza alimentare con la salubrità alimentare MODULO 2: PATOLOGIA VEGETALE MOLECOLARE (12 ORE) 1. Il concetto di Patobioma 2. PATOGENOMICA; come la genomica incontra il patogeno MODULO 3: IDENTIFICAZIONE DI EFFETTORI (12 ore) 1. organizzazione dei genomi fungini 2. caratteristiche degli effettori 3. metodi di identificazione MODULO 4: IDENTIFICAZIONE DI GENI DI RESISTENZA (12 ore) 1. i genomi delle piante 2. organizzazione dei genomi delle piante e cluster dei geni R 3. identificazione dei geni di resistenza   MODULO 1: PATOLOGIA VEGETALE GENERALE 1 testo a scelta tra i seguenti: Fondamenti di patologia vegetale, Editore: Pàtron, Edizione:2; A cura di:F. Favaron, F. Scala; Data di Pubblicazione:2017; EAN:9788855533829; ISBN:8855533827 Elementi di Patologia Vegetale, di Belli G, Editore Piccin-Nuona Libraria. Edizione: 2; Data di Pubblicazione: 2011. ISBN: 9788829921294 Fisiologia Vegetale; AUTORI: Taiz Zeiger, ISBN: 978-88-299-2157-7; CODICE PICCIN: 2001230 MODULO 2: PATOLOGIA VEGETALE MOLECOLARE 1 testo a scelta tra i seguenti: • Plant Pathology, Authors: George Agrios; ISBN: 9780120445653; eBook ISBN: 9780080473789; Imprint: Academic Press Per un immediato aggiornamento dei testi o del materiale didattico distribuito dal docente consultare la pagina web del corso: https://elearning2.uniroma1.it 6  AGR/12  48  -  -  -  Attività formative affini ed integrative  ENG

Secondo semestre

Insegnamento	CFU	SSD	Ore Lezione	Ore Eserc.	Ore Lab	Ore Studio	Attività	Lingua
Gruppo opzionale: Gruppo OPZIONALE - (visualizza) 12                1049267 - MODELLING AND SIMULATION OF BIOMOLECULAR DYNAMICAL SYSTEMS (obiettivi) This course aims to provide students with a practical and hands-on experience with common modeling and simulation tools in molecular biology. It would be expected that after completing this course a student would be able to model and simulate using Matlab a biomolecular systems like, for example, a gene regulatory network using the appropriate methodology. Further, students will understand the basic theory behind these modeling tecniques and critically analyze the results of their analysis. - FARINA LORENZO (programma) Introduzione alla modellistica matematica. Elementi di teoria dei sistemi. Modelli di interazione genica e reti. Identificazione di geni regolati dal ciclo cellulare.   Materiale didattico fornito dal docente (Date degli appelli d'esame) 6  ING-INF/06  48  -  -  -  Attività formative affini ed integrative  ENG 1049268 - SIGNAL PROCESSING AND INFORMATION THEORY - COLONNESE STEFANIA (programma) Rappresentazione, misura ed estrazione dell’informazione contenuta nei dati. Sorgenti di informazioni, entropia, informazione mutua. Fondamenti di codifica di canale. Decodifica di codici senza memoria e con memoria. Acquisizione di segnali ed immagini, campionamento e quantizzazione. Il rumore di osservazione. Filtraggio. Rappresentazione di segnali ed immagini nel dominio di Fourier. Rappresentazione compatta di segnali ed immagini: Trasformata di Karounen Loewe, analisi a componenti principali (PCA). Principi di rivelazione e stima di segnale. Riconoscimento di pattern mediante correlazione per stima di ritardo e spostamento.   DISPENSE: DISPONIBILI SULLA PAGINA MOODLE DEL CORSO TESTO: GAETANO SCARANO ELABORAZIONE STATISTICA DEI SEGNALI (VOL.I) (Date degli appelli d'esame) 6  ING-INF/03  48  -  -  -  Attività formative affini ed integrative  ENG 1049269 - ALGORITHMS (obiettivi) this course is an introduction to algorithms with special emphasis given to those algorithmic problems and techniques that have the greatest impact for bioinformatics. - RODOLA' EMANUELE (programma) - Algoritmi e strutture dati: generalità ed esempi. Introduzione alla nozione di costo (tempo e spazio di memoria). - Notazioni asintotiche per le funzioni di costo e metodi di analisi (caso peggiore, medio, migliore). - Metodi di analisi di algoritmi ricorsivi: albero della ricorsione, iterazione, sostituzione, Master Theorem. - Tipi di dato astratto (pile, code, alberi) e loro implementazioni. Algoritmi di visita di un albero. - Algoritmi di ordinamento incrementali (descrizione, implementazione e analisi): SelectionSort, InsertionSort, BubbleSort, HeapSort, MergeSort, QuickSort. Lower bound sul costo dell'ordinamento per modello basato su confronti. - Algoritmi di ordinamento di interi (descrizione, implementazione e analisi): IntegerSort, BucketSort, RadixSort. - Tipo di dato Dizionario. Alberi di ricerca binari. Alberi AVL. - Tavole Hash. - Grafi e loro rappresentazione. Algoritmi di visita (descrizione, implementazione e costo). - Tecnica algoritmica greedy. Minimo albero ricoprente e rispettivo calcolo basato su algoritmo greedy. Algoritmi di Kruskal, di Prim e di Boruvka. - Cammini minimi su grafi e relativi algoritmi (descrizione, implementazione e analisi): calcolo delle distanze, algoritmo di Bellman e Ford, calcolo dei cammini minimi a sorgente singola su grafi aciclici, algoritmo di Dijkstra.   Il materiale di studio viene fornito completamente sul sito di riferimento del corso. Come materiale integrativo vengono suggeriti di volta in volta capitoli selezionati dai seguenti testi: T.H. Cormen, C.Papadimitriou, U. Vazirani. Introduzione agli algoritmi J. Kleinberg, E. Tardos Algorithm Design S. Dasgupta, C. Papadimitriou, U. Vazirani Algorithms C. Demetrescu, I. Finocchi, G.F. Italiano Algoritmi e strutture dati (Date degli appelli d'esame) 6  INF/01  48  -  -  -  Attività formative affini ed integrative  ENG 1049270 - COMPLEX BIOMOLECULAR NETWORKS (obiettivi) The course aims to provide basics concepts and tools for complex networks analysis. The attendee will be able to apply complex networks concepts to biological networks and explore the underlying process and molecular related issues. - MARCHETTI SPACCAMELA ALBERTO (programma) 1.Algorithms and Complexity Computational complexity of algorithms and programs - Fast versus Slow Algorithms - Big-O Notation - Algorithm Design Techniques – Tractable versus Intractable Problems - NP-complete problems. 2. Algoritmic Techniques Greedy Algorithms - Dynamic Programming - Exhaustive Search - Branch-and-Bound Algorithms - Heuristics – Branch and Bound (these techniques are introduced when they are applied in solving problems considered in sections 4-6). 3. Graph Algorithms Basic definition on Graphs – Memory representation – Connectivity - Shortest path, Eulerian path, Traveling Salesmna problem, Hamiltonia path. 4. DNA Assembling Shortest Superstring Problem - DNA Arrays as an Alternative Sequencing Technique - Sequencing by Hybridization - SBH as a Hamiltonian Path Problem - SBH as an Eulerian Path Problem - Fragment Assembly in DNA Sequencing – Overlap-Layout-Consensus assembly- De Bruijn graph assembly – Scaffolding. 5. HiddenMarkovModels CG-Islands and the “Fair Bet Casino” – Definition of Hidden Markov Models - Decoding Algorithm - HMM Parameter Estimation. 6. Clustering and Trees Gene Expression Analysis - Hierarchical Clustering - k-Means Clustering - Clustering and Corrupted Cliques - Evolutionary Trees - Distance-Based Tree Reconstruction - Reconstructing Trees from Additive Matrices - Evolutionary Trees and Hierarchical Clustering - Character-Based Tree Reconstruction - Small Parsimony Problem - Large Parsimony Problem. 7. Advanced topics in large networks and phylogenetic recontructions.   Libro di Testo Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, MIT Press (capp. 2,5.1-5.3, 6, 8,10, 11) Altri testi distribuiti in classe e disponibili sulla piattaforma e-learning Martin Vingron, Jens Stoye, Hannes Luz Algorithms for Phylogenetic Reconstructions, Notes Slides delle lezioni Materiale (suggerito) per i seminari (Date degli appelli d'esame) 6  ING-INF/05  48  -  -  -  Attività formative affini ed integrative  ENG 1049271 - PLANT FUNCTIONAL GENOMICS (obiettivi) The aim of the course is to provide a theoretical knowledge of plant genomes, and practical explanation of the techniques used in plant functional genomics, i.e. a large-scale analysis of the function of the different gene products to understand how the genome generates the phenotype of the plant. Insights will be given into the new information that will be generated from whole genome-/proteome-/metabolome analysis. The course will cover the following concepts: array and sequencing based methods; reverse and forward genetics; comparison of plant genomes; epigenomics; proteomics and metabolomics. Also covered are robotization, miniaturization (single-cell studies) and high-throughput-screenings. Finally, the course will introduce methods for visualization and analysis of high-density data. - FERRARI SIMONE (programma) Module I (3 cfu) INTRODUCTORY CONCEPTS - Plant organisms. The plant cell. Nuclear, mitochondrial and plastid genome of plants. Reproduction of plant organisms. -Basic concepts of genetics. Genetic polymorphisms. Genetic and molecular markers. Genetic and physical maps. Backcross and inbreeding. Heterosis. Recombinant Inbred Lines. Quantitative Trait Loci. ANALYSIS OF PLANT GENOMES AND USE OF GENOMICS IN PLANT BREEDING - Evolution of plant genomes. Repetitive DNA; polyploidy; sequencing of genomes; the genome of Arabidopsis thaliana. - Comparative genomics; identification of orthologous genes in different species, synteny. Databases of plant genomes. Genome-wide association studies. Development of new plant varieties through marker assisted selection. PLANT EPIGENETICS AND EPIGENOMICS - Epigenetic modifications: DNA methylation; histone changes; Non-coding RNAs: siRNA, microRNA; transcriptional and post-transcriptional gene silencing; role of silencing in maintaining the integrity of the genome. - Generation and maintenance of epigenetic modifications; epialleles; large-scale analysis of the epigenome; transposons. Module II (3 cfu) DIRECT AND REVERSE GENETICS - Analysis of gene function: direct and reverse genetic approaches in plants. Mutagenesis by insertion in plants. Overexpression and silencing. Map-based and deep sequence-based identification of mutations. (4 h). - From mutants to transgenic plants of biotechnological interest. Natural genetic variability as a source of characteristics of biotechnological interest. TILLING and ecoTILLING. Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype. (4 h) - Genome editing: CRISPR/Cas9 (2 h) - Chemical genomics in plant biology. "Click" chemistry. Single cell genomics. (2 h) TRANSCRIPTOME AND INTERACTOME ANALYSES IN PLANTS - ESTs, cDNA-AFLPs, Microarrays, DNA Chips, SAGE. RNA sequencing, sequence analysis and their applications (4 h) -Transcriptomic analysis on a single cell or individual tissues: laser capture; FACS on protoplasts labeled with fluorescent proteins. Databases of plant transcriptomes. (4 h) - Examples of networks and correlation analysis of the expression of multiple genes. (2 h) - Interactomics (2 h)   - Teaching material provided through E-Learning (articles, reviews, lectures slides); - Biotecnologie Sostenibili - Galbiati et al. – EDAGRICOLE - Biotecnologie e Genomica delle Piante - Rao e Leone - Idelson-Gnocchi (acronimo BGP) - Biochemistry and Molecular Biology of Plants, - Buchanan, Gruissem e Jones, 2° ed., Wiley Blackwell (Date degli appelli d'esame) - DE LORENZO GIULIA (programma) Module I (3 cfu) INTRODUCTORY CONCEPTS - Plant organisms. The plant cell. Nuclear, mitochondrial and plastid genome of plants. Reproduction of plant organisms. -Basic concepts of genetics. Genetic polymorphisms. Genetic and molecular markers. Genetic and physical maps. Backcross and inbreeding. Heterosis. Recombinant Inbred Lines. Quantitative Trait Loci. ANALYSIS OF PLANT GENOMES AND USE OF GENOMICS IN PLANT BREEDING - Evolution of plant genomes. Repetitive DNA; polyploidy; sequencing of genomes; the genome of Arabidopsis thaliana. - Comparative genomics; identification of orthologous genes in different species, synteny. Databases of plant genomes. Genome-wide association studies. Development of new plant varieties through marker assisted selection. PLANT EPIGENETICS AND EPIGENOMICS - Epigenetic modifications: DNA methylation; histone changes; Non-coding RNAs: siRNA, microRNA; transcriptional and post-transcriptional gene silencing; role of silencing in maintaining the integrity of the genome. - Generation and maintenance of epigenetic modifications; epialleles; large-scale analysis of the epigenome; transposons. Module II (3 cfu) DIRECT AND REVERSE GENETICS - Analysis of gene function: direct and reverse genetic approaches in plants. Mutagenesis by insertion in plants. Overexpression and silencing. Map-based and deep sequence-based identification of mutations. (4 h). - From mutants to transgenic plants of biotechnological interest. Natural genetic variability as a source of characteristics of biotechnological interest. TILLING and ecoTILLING.. Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype. (4 h) - Genome editing: CRISPR/Cas9 (2 h) - Chemical genomics in plant biology. "Click" chemistry. Single cell genomics. (2 h) TRANSCRIPTOME AND INTERACTOME ANALYSES IN PLANTS - ESTs, cDNA-AFLPs, Microarrays, DNA Chips, SAGE. RNA sequencing, sequence analysis and their applications (4 h) -Transcriptomic analysis on a single cell or individual tissues: laser capture; FACS on protoplasts labeled with fluorescent proteins. Databases of plant transcriptomes. (4 h) - Examples of networks and correlation analysis of the expression of multiple genes. (2 h) - Interactomics (2 h)   - Teaching material provided through E-Learning (articles, reviews, lectures slides); - Biotecnologie Sostenibili - Galbiati et al. – EDAGRICOLE - Biotecnologie e Genomica delle Piante - Rao e Leone - Idelson-Gnocchi (acronimo BGP) - Biochemistry and Molecular Biology of Plants, - Buchanan, Gruissem e Jones, 2° ed., Wiley Blackwell 6  BIO/04  48  -  -  -  Attività formative affini ed integrative  ENG 1049272 - PRINCIPLES OF GENERAL PATHOLOGY - CAMPESE ANTONIO FRANCESCO (programma) -Scopi, vantaggi e limiti della generazione e dell’utilizzo dei modelli murini geneticamente modificati per lo studio e la cura delle patologie umane (2 ore) -Aspetti legislativi della sperimentazione animale (Regola delle 3R, dLGS 26/2014) e relative ricadute sulla bioinformatica: i metodi alternativi; i protocolli di sperimentazione animale; i registri e i database informatici (3 ore); -Mantenimento delle colonie di animali geneticamente modificati e relativi strumenti bioinformatici (2 ore) -Metodologie e strumenti informatici per la generazione di modelli murini geneticamente modificati ‘convenzionali’: topi transgenici e topi ‘knock-out’ (4 ore) e ‘condizionali’ e/o inducibili: il sistema Cre/LoxP; topi ‘knock-in’ condizionali; geni ‘reporter’ (4 ore) -Esempi di modelli murini per lo studio di patologie umane: leucemie, tumori solidi, malattie autoimmuni (3 ore) -Strumenti bioinformatici per la potenziale validazione di modelli murini di patologia umana (2 ore) -Seminari sulle applicazioni bioinformatiche nell'utilizzo dei modelli murini di patologie umane (4 ore)   Materiale didattico e pubblicazioni scientifiche segnalate durante il corso. - PO AGNESE (programma) The topics will be: 1) Getting started and general aspects of molecular and cellular pathology. Concept and causes of alteration in the cell, cellular and tissue homeostasis, Cellular damage: causes, molecular mechanisms, responses and adaptations, Cell death and its manifestations: necrosis and apoptosis 2) Next generation Sequencing (NGS): introduction to NGS tecniques. Illumina platform, Ion Torrent. Applications: Genome Sequencing, Whole exome sequencing, Targeted sequencing, NGS-based comprehensive genomics: DNA methylation, chromatin accessibility and modifications. Analysis of NGS derived data: bioinformatics analysis, analysis of the transcriptome and of the mirnome. Examples of the use of NGS for biomedical research. Data mining on available databases. 3) Molecular and cellular pathology of cancer: Definition and classification of tumors, Stages of tumor progression: initiation, promotion, progression, invasiveness and metastasis, Dominant and recessive mutations: oncogenes and tumor suppressor, molecular basis of neoplastic transformation, invasiveness, metastasization, Identification of tumor markers. Significance of tumor markers in the prevention and staging/classification of tumors 4) Chronic degenerative diseases: diabetes mellitus, metabolic diseases 5) Pathogenetic mechanisms of non-coding RNAs: microRNAs and long non-coding RNAs. microRNA: biogenesis, deregulation mechanisms in pathologies, circulating microRNAs; long non-coding RNA: biogenesis, mechanisms of action, examples of long non-coding deregulated in pathologies. Circular RNAs. 6) Stem cells: embryonic stem cells, adult stem cells. Therapeutic applications of stem cells. Cancer stem cells: biological features and epigenetic regulation. 7) Circulating nucleic acids as markers for diseases. The discovery, challenges an approaches for the identification and evaluation of circulating RNAs and DNAs.   notes and scientific papers given by the teacher (Date degli appelli d'esame) 6  MED/46  48  -  -  -  Attività formative affini ed integrative  ENG 1049273 - OPTIMIZATION METHODS FOR COMPUTATIONAL BIOLOGY (obiettivi) We aim to introduce students to the analysis of decision problems that arise in bioinformatics and health management. Students would be able to: model as mathematical programming problem to be used as a support to the decision maker, use algorithm suitable to each model for the solution, make post-optimality analysis. - SAGRATELLA SIMONE (programma) Part 1: Mathematical programming Things to know: - structure of an optimization problem - feasiblility, unboundedness, and optimality - active, satisfied, violated, and redundant constraints Abilities to acquire: - recast a model as a problem in general form - understand if an optimization problem is an LP, an ILP, or an NLP Part 2: Linear Programming Things to know: - properties of linear functions - convex sets and polyhedra - vertices of a polyhedron and their properties - fundamental theorem of LP - solution set properties Abilities to acquire: - graphical solution - computation of all the vertices of a polyhedron - (graphical) simplex algorithm Part 3: Integer Linear Programming Things to know: - linear formulations and their properties - optimal linear formulations Abilities to acquire: - computation of an optimal linear formulation - branch and bound method for knapsack problems and graphical solution Part 4: NonLinear Programming Things to know: - local and global solutions - feasiblility, unboundedness, and optimality in nonlinear programming - convex problems and their properties Abilities to acquire: - understand if a problem is (strictly) convex   lecture notes of the teacher (Date degli appelli d'esame) 6  MAT/09  48  -  -  -  Attività formative affini ed integrative  ENG 1049285 - BIOINFORMATICS IN PLANT PATHOLOGY (obiettivi) Recent advances in -omics technology, namely genomics, proteomics and metabolomics allow to go deeper into the understanding of the subtle mechanism underlying host-pathogen interactions. This is made possible by next generation sequencers that uncover entire genome or exome of host and pathogens while interacting, skipping complicate procedures for separating the two challengers. Moreover, we are moving faster in re-shaping plant pathology from the one disease-one pathogen dogma, as embodied in Koch's postulate, to the pathobiome concept. Meta-omic tools shed light on the inter-reign network originating the disease of the host in its complexity. The analysis and understanding of the huge amount of data generated by a single experiment represents currently the classical bottleneck. In relation to this, bioinformatics plays a crucial role in data capture, analysis and integration. Plant pathologists have to answer to very concrete and problematic question, today, more, and more in the next future: food security, food safety and food quality. Actually, plant disease burden current food production, accounting for more than 40% of food losses. Climate change and globalization enhance pathogens ability and mobility worldwide. Nevertheless, for environmental as well as political reasons, pathogens cannot be controlled anymore by using pesticides and/or GMO plants. A more sustainable, "green" and integrated pest management is needed. A modern plant pathologist has to face this complex reality, plan experiments at real scale, "sucks the marrow out of -omics" (par. Walt Whitman) by using bioinformatics tools, individuate biocontrol agents and stimulate plant self-defences. In relation to this, the main aim of this course is forming young scientists in managing plant diseases tout court by the mean of the -omics plus bioinformatics tools. - FAINO LUIGI   Per la prima parte, dispense e articoli saranno i testi da cui studiare mentre per la prate del progetto, siti specifici all bionformatica tipo stackoverflow saranno usati (Date degli appelli d'esame) - REVERBERI MASSIMO (programma) MODULO 1: PATOLOGIA vegetale (12 ORE) 1. Introduzione alla patologia vegetale: il concetto di malattia 2. Gli agenti patogeni: dal virus ai funghi, diverse strategie per diversi patogeni 3. Gestione integrata delle malattie: come coniugare la sicurezza alimentare con la salubrità alimentare MODULO 2: PATOLOGIA VEGETALE MOLECOLARE (12 ORE) 1. Il concetto di Patobioma 2. PATOGENOMICA; come la genomica incontra il patogeno MODULO 3: IDENTIFICAZIONE DI EFFETTORI (12 ore) 1. organizzazione dei genomi fungini 2. caratteristiche degli effettori 3. metodi di identificazione MODULO 4: IDENTIFICAZIONE DI GENI DI RESISTENZA (12 ore) 1. i genomi delle piante 2. organizzazione dei genomi delle piante e cluster dei geni R 3. identificazione dei geni di resistenza   MODULO 1: PATOLOGIA VEGETALE GENERALE 1 testo a scelta tra i seguenti: Fondamenti di patologia vegetale, Editore: Pàtron, Edizione:2; A cura di:F. Favaron, F. Scala; Data di Pubblicazione:2017; EAN:9788855533829; ISBN:8855533827 Elementi di Patologia Vegetale, di Belli G, Editore Piccin-Nuona Libraria. Edizione: 2; Data di Pubblicazione: 2011. ISBN: 9788829921294 Fisiologia Vegetale; AUTORI: Taiz Zeiger, ISBN: 978-88-299-2157-7; CODICE PICCIN: 2001230 MODULO 2: PATOLOGIA VEGETALE MOLECOLARE 1 testo a scelta tra i seguenti: • Plant Pathology, Authors: George Agrios; ISBN: 9780120445653; eBook ISBN: 9780080473789; Imprint: Academic Press Per un immediato aggiornamento dei testi o del materiale didattico distribuito dal docente consultare la pagina web del corso: https://elearning2.uniroma1.it 6  AGR/12  48  -  -  -  Attività formative affini ed integrative  ENG
AAF1749 - FOR THE FINAL TEST (obiettivi) The final exams consists of writing, presenting and discussing a thesis, developed autonomously by the students, which illustrates in a coherent and detailed manner the problem tackled during the practical training and all the activities carried out to develop its solution.	9		72	-	-	-	Per la prova finale e la lingua straniera (art.10, comma 5, lettera c)	ENG
AAF1750 - FURTHER LINGUISTIC KNOWLEDGE	3		24	-	-	-	Ulteriori attività formative (art.10, comma 5, lettera d)	ENG
AAF1752 - STAGES AND PROFESSIONAL TRAINING (obiettivi) Acquisition of manual, methodological and organizational skills aimed at the elaboration of technical-scientific issues.	3		24	-	-	-	Ulteriori attività formative (art.10, comma 5, lettera d)	ENG
AAF1753 - OTHER KNOWLEDGE USEFUL FOR ENTERING INTO THE WORK MARKET (obiettivi) Basic training in laboratorytechniques aimed to improve professionalization.	3		24	-	-	-	Ulteriori attività formative (art.10, comma 5, lettera d)	ENG
- - Elective course	12		96	-	-	-	Attività formative a scelta dello studente (art.10, comma 5, lettera a)	ENG

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