Degree Course: Cellular and Molecular Biology Syllabus for A.Y. 2021/2022

Percorso STANDARD

FIRST YEAR

First semester

Course	Credits	Scientific Disciplinary Sector Code	Contact Hours	Exercise Hours	Laboratory Hours	Personal Study Hours	Type of Activity	Optional materials and exam in a foreign language	Language
14800 - CELLULAR BIOCHEMISTRY (objectives) The course envisages the deepening of two themes of considerable scientific interest: 1) Protein engineering techniques that allow design, expression and purification of recombinant proteins in heterologous systems; 2) Deepening the biochemical and molecular mechanisms of cell cycle control in eukaryotes. EXPECTED LEARNING OUTCOMES Knowledge and  understanding: At the end of the training activities students will have in-depth knowledge of the biochemical and molecular basics of cell cycle control in eukaryotes. They will also learn the main techniques for the design and expression of recombinant proteins in heterologous systems. In general, they will have developed the ability to understand the pivotal experimental approaches for acquiring knowledge. Applying knowledge  and understanding: During the course, students will be encouraged to use the knowledge acquired for their application to specific problems, such as the design of new, more potent and / or more selective proteins for their use in various fields of interest (biomedical, agro-food, etc.). Making judgements: Students will be able to interpret and discuss the scientific papers presented during the course and be able to design and express new proteins with different characteristics. Communication skills: During the lessons students will be stimulated to discuss and compare different point of views in order to develop their communicative abilities that will be verified during the preliminary and final examinations at the end of training activities. Learning skills: Students will be able to describe scientific topics related to the course. This skill will be developed through the active involvement of students through oral class discussions and practical experiences during the hours dedicated to the experimental laboratory. - CARUSO Carla (syllabus) Proteic engineering fundamentals (2 CFU) Recombinant protein expression in prokaryotic systems: principles and applications. Recombinant protein expression in eukaryotic systems: -Expression in Saccharomyces cerevisiae and Pichia pastoris; -Expression in plants. Experimental laboratory (1 CFU) • Enzymatic digestion of pGEM-HEL plasmid and purification of the HEL gene from agarose gel; • Subcloning of the HEL gene in the expression vector pGEX-4T; • Transformation of competent BL-21 cells with the newly generated GST-HEL plasmid; • Expression of recombinant GST-HEL in BL-21 cells and analysis of the recombinant protein trough SDS-PAGE. The cell cycle (3 CFU) General strategy and cell cycle phases (M, G1(G0), S and G2. Experimental systems for the study of the cell cycle: Xenopus leavis eggs, mammalian cells and yeast. Molecular regulation of MPF and SPF: mitotic and G1 cyclins. Cdks and cyclins in mammalian cell cycle. Cell cycle checkpoints. Hereditary and sporadic retinoblastoma and role of Rb in cell cycle regulation. UV-damaged DNA and role of p53. Oncogenes and oncoproteines. (reference books) Cell Cycle Murray A & Hunt T, The cell cycle, an introduction, Oxford University Press, New York. Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts K & Walter P, Biologia Molecolare della Cellula, Zanichelli, 2016 (VI Edizione) Harvey Lodish, A Berk, C.A. Kaiser, M. Krieger, M.P. Scott, A. Bretscher, P. Ploegh, Paul Matsudaira Biologia Molecolare della Cellula, Zanichelli, 2009 (III edizione) Protein engineering Glick & Pasternak, Biotecnologia Molecolare, Zanichelli Primrose, Twyman & Old, Ingegneria Genetica, Zanichelli Watson, Caudy, Myers & Witkowski, DNA Ricombinante, Zanichelli 2008 (II Edizione) Brown, Biotecnologie molecolari, Zanichelli 2007	6	BIO/10	40	-	8	-	Core compulsory activities	-	ITA
14890 - CYTOGENETICS (objectives) LEARNING OBJECTIVES The course introduces the fundamental concepts and experimental approaches to the study of cytogenetics, a branch of genetics that analyzes the structure of the chromosomes to determine the relationship existing between the hereditary and specific karyotypes characters. The course aims to consolidate and expand the knowledge base on chromatin structure and its intranuclear organization, the metaphase chromosome as well as its specialized structures such as centromere, telomere and fragile sites and their role in maintaining genome stability. The course also aims to address the study of human chromosomal instability syndromes and the role of the biologist in their diagnosis using classical and molecular cytogenetics techniques. It also provides a basis for specialized studies such as the analysis of chromosomal aberrations in biological dosimetry and the use of the Comet test in genotoxicity. In particular, these issues are provided in the laboratory practice. - MESCHINI Roberta (syllabus) a) LEARNING OBJECTIVES The course introduces the fundamental concepts and experimental approaches to the study of cytogenetics, a branch of genetics that analyzes the structure of the chromosomes to determine the relationship existing between the hereditary and specific karyotypes characters. The course aims to consolidate and expand the knowledge base on chromatin structure and its intranuclear organization, the metaphase chromosome as well as its specialized structures such as centromere, telomere and fragile sites and their role in maintaining genome stability. The course also aims to address the study of human chromosomal instability syndromes and the role of the biologist in their diagnosis using classical and molecular cytogenetics techniques. It also provides a basis for specialized studies such as the analysis of chromosomal aberrations in biological dosimetry and the use of the Comet test in genotoxicity. In particular, these issues are provided in the laboratory practice. b) EXPECTED LEARNING RESULTS Knowledge and understanding At the end of the course students will have a thorough knowledge of the basic principles of cytogenetics such as organizing intranuclear chromatin, the chromosome structure and its specialized components. In addition, they will have learned the main classical and molecular cytogenetic techniques. Finally, they will have gained the ability to process the diagnostic protocols, the use of chromosomal aberrations as a biological dosimeter and the Comet assay as a tool for the study of genotoxicity. Applying knowledge and understanding Students will be encouraged to take advantage of the knowledge acquired during the course and during laboratory practice in order to apply them to specific issues such as, for example, the identification of a specific chromosomal instability syndrome or the genotoxic capacity of chemical or physical agent as well as the application potential of the techniques learned. Making judgements Students will be able to interpret and discuss scientific papers presented during class and be able to identify in them the highlights and key points. Communication skills During the lessons it will be stimulated students' ability to think and discuss about the topics covered as well as the comparison of opinions to develop their communication skills. These skills will then be tested in the examination. Learning skills Students will be able to expose and develop scientific issues related to the course. The active involvement of students through oral classroom discussions and experiences in the laboratory practices, will develop that skill. c) Program The structure of chromatin in eukaryotes: histones and histone proteins; The nucleosome; Chromatin fiber; Hints on histone modifications; Histone variants and specialized folding domains; The solenoid; The loop domains; Models of the metaphase chromosome; Mechanical properties of chromosomes. Chromosomal Territories: Their Dynamic Organization (Chromosomal Territories, Interchromatinic Domain, Nuclear Matrix); Experimental evidence and models; Chromosomal territories and cytogenetic damage. Evolution of the eukaryotic genome: organization in isochores; Compositional correlation; Distribution of genes and compartmentalization of the genome; Compositional transition in the vertebrates, their causes and their maintenance. Relationship between chromosomal territories and isochore content. The telomere: structure; function; Telomeric and accessory proteins; Replication (telomerase and recombination); Regulation of the elongation. The centromere: structure, function and accessory proteins in the lower eukaryotes; Structure, function and additional proteins in the higher eukaryotes; Epigenetic control of the centromere. The fragile sites: classification and structure; Genes at fragile sites; Fragile sites and cellular checkpoints; Repair at fragile sites; Instability of fragile sites in tumors; The X-fragile syndrome. Chromosome banding: differential banding techniques (bands G, R, Q); Selective banding techniques (bands C, NOR, G-11, restriction enzymes); Fluorochrome and counterstaining techniques; Replication banding; High resolution banding; Banding applications (karyotype study, chromosome aberration study, diagnostic and medical applications, etc.). Fluorescent in situ hybridization: basic concepts; The technique; Applications in classical and interfase cytogenetics, mutagenesis, diagnostic and medical fields, etc. The "Comet" assay: the technique and its applications. Chromosomal aberrations: classification. Theories. Molecular mechanisms of formation. Chromosomal instability syndromes. Biological dosimetry. Biological significance and consequences of chromosomal aberrations. Experimental laboratory (1 CFU) on induction and analysis of chromosomal aberrations and sister chromatid exchanges; Comet assay. (reference books) RECOMMENDED TEXTBOOKS The teaching materials and all the lessons in power-point format are provided by the teacher. Non-attending students are encouraged to contact the lecturer for information on the program, teaching materials and evaluation of the profit.	6	BIO/18	40	-	8	-	Core compulsory activities	-	ITA
13688 - DEVELOPMENTAL GENETICS AND EPIGENETICS (objectives) The course will introduce students to the principles, experimental approaches and potentialities of the genetic analysis of animal development, with particular regard to that of Drosophila melanogaster; the panorama of epigenetic phenomena will be presented and the molecular mechanisms underlying the phenomena of epigenetic inheritance will be investigated; "genome wide" epigenetic analyzes and epigenomic synthesis will be addressed. Students will have to know how to apply the notions learned to the resolution of the questions that emerge from the analysis of development and epigenetic phenomena in complex organisms. Students will have to develop the ability to identify and address aspects related to development and epigenetics in the analysis of complex processes. They will also have to be able to learn independently by doing bibliographic research on the topics covered and communicate the results of their research. - PRANTERA Giorgio (syllabus) DEVELOPMENTAL GENETICS AND EPIGENETICS (6 cfu) Developmental Genetics (2 cfu) Genetic methods to dissect development Drosophila melanogaster as a model system Maternal effect genes and zygotic genes Anteroposterior coordinates Dorsoventral coordinates The terminal system Gap genes Pair rule genes Segment polarity genes Selector genes Genetic sex determination Drosophila X/A ratio Sex lethal gene Dosage compensation Mammals sxr gene (TDF) Dosage compensation Epigenetics (4 cfu) Epigenetic inheritance Genomic imprinting Insects Mammals Facultative heterochromatinization Insects Mammals Position effect variegation (PEV) Paramutation in plants Molecular mechanisms governing epigenetic phenomena Chromatin remodeling Heterochromatin proteins Histone modifications DNA methylation Non coding RNAs (reference books) P. Lawrence: “The making of a fly”. Blackwell editore Goldberg et al.: “Genetics - from genes to genomes”. McGraw-Hill. 7th ed. USA Allis, Jenuwein, Reinberg, Caparros: "Epigenetics". Cold Sprig Harbor press	6	BIO/18	48	-	-	-	Core compulsory activities	-	ITA
17461 - PROTEOMICS AND METABOLOMIES (objectives) FORMATIVE OBJECTIVES The course provides the theoretical bases of proteomics, interatomics and matabolomics as relevant scientific disciplines able to provide useful structural and dynamic information about the proteoma and metaboloma. The course will introduce students to the principles and the experimental approaches, and the learning objectives will be achieved by presenting students with the state of innovation in the specific field with a substantial presence in the laboratories. Particular attention will be given to the study of mass spectrometry techniques for the identification of proteins, metabolites and alterations of protein expression, thus enabling them to shed light on the biological complexity of a tissue in order to differentiate / identify a pathological state from the physiological one. b) EXPECTED LEARNING RESULTS 1) Knowledge and understanding The student will develop the knowledge of the principles of proteomics and metabolomics. Indispensable for experimental analysis and interpretation of results in biochemical and molecular biological disciplines. 2) Applyng knowledge and understanding. The student will also be introduced to the knowledge of the major classes of small biological molecules and metabolites and will learn the basic metabolic pathways through which these molecules are degraded and synthesized. It will be familiar with the main separation methods (2Dgel, HPLC) and will use instrumentation for the identification of high performance proteins and metabolites such as MALDI TOF / TOF, ESI-TRAP. 3) Making judgments Students will be able to independently carry out observations and experiments in the field of Proteomics or metabolomics. They will also have critical thinking and evaluation skills to rationalize them in an interpretative model. 4) Communicative skills. Students will be able to work in groups and communicate clearly their knowledge Or the results of your research, 5) Learning skills Students will need to learn autonomously by using advanced texts in Italian and English. English texts will be provided during the year. Students also be able to perform bibliographic research even at advanced level, selecting relevant topics; of proteomics and metabolomics - TIMPERIO Anna Maria (syllabus) PROGRAM Proteomics and metabolomics Proteomics: What is proteomics? Relationship between proteomics and other sciences post-genomic Sample preparation for the analysis of protein expression Analysis of protein expression using electrophoresis Analysis of protein expression by chromatographic techniques Quantitative analysis of protein expression Statistics: Programs and web sites for protein identification Subcellular fractionation Immunoprecipitation Posttranslational modifications The techniques used in proteomics: Two-dimensional electrophoresis Other electrophoretic techniques Chromatography of peptides and proteins Mass spectrometry Topographic distribution of proteins: MALDI Imaging The fingerprint: MALDI profiling The chemical fingerprint: Metabolomics METAOLOMICA Definition of metabolomics Workflow Untargeted metabolomics Sample preparation and methods of investigation Data analysis using "MAVEN" Targeted Metabolomics Lipidomics: sample preparation Data analysis using "Lipid search" (reference books) Since a specific text is not yet on the market, the teacher will take care to report appropriate articles and magazines during the year.	6	BIO/11	32	16	-	-	Core compulsory activities	-	ITA

Second semester

Course	Credits	Scientific Disciplinary Sector Code	Contact Hours	Exercise Hours	Laboratory Hours	Personal Study Hours	Type of Activity	Optional materials and exam in a foreign language	Language
13700 - DIETETICS AND FUNCTIONAL FOOD (objectives) Educational objectives The aim of the course is to provide students with the information needed to understand the theoretical / practical bases of food science and, in particular, the evolution that this subject has undergone over the years. In fact it no longer deals only with satisfying the nutritional needs of the individual but tends to be a means for the prevention and treatment of some diseases. In this course then it will be about functional foods pointing out that part of the classic and modern diet and the experimental approaches that have allowed its evolution. Students will have to learn the meaning of functional foods and novel foods as well as learn which criteria and which technological approaches to use to improve food quality. Finally, the course aims to provide the basis for further in-depth studies in the field of foods and their effect on the human organism. The topics concerning nutrigenetics and nutrigenomics will also be addressed. Expected learning outcomes Knowledge and understanding: To have developed the knowledge of the principles of classic food science and some dietary principles. Furthermore, the relationship between diet and health should be clear in order to bring this knowledge into the process of food transformation and improvement. Have communication skills in the field of Food Science Ability to apply knowledge and understanding: the student should be able to use the knowledge acquired to work in the food industry and in particular in the field of functional foods. Making judgements: Being able to improve the quality of food and to identify new ingredients for the development and food with high health properties. Communication skills: The students' ability to talk, reason and discuss the questions raised during the lessons on the topics discussed will be stimulated. Learning skills: Being able to discuss scientific topics concerning food science also in its bio-medical applications and its implications in the food industry. This skill will be developed and tested by involving students in oral discussions in the classroom. - MERENDINO Nicolo' (syllabus) -The main nutrients: lipids * proteins * carbohydrates * vitamins * mineral salts * - Calorimetry; measurement of energy expenditure (direct and indirect calorimetry), energy needs and its evaluation, respiratory quotient; basal and total metabolism; - Diet induced thermogenesis; - Energy and nutrient requirements; - Nutrigenomics; - Cellular oxidation and antioxidants; - Applications of dietetics as a preventive tool for some pathologists; -Applications of dietetics as a support for some pathologies; - Immunology and nutrition; Adverse reactions to food (food intolerances and allergies); -Functional foods: classification, study method and new knowledge in this sector; * These topics are treated only from the point of view of food science, leaving out the biochemical, molecular and microbiological aspects that are treated in other courses. (reference books) Lecture notes. Siliprandi & Tettamanti; Biochimica Medica; Piccin Editori A. Mariani –Costantini; C. Cannella; G Tomassi/ Alimentazione e Nutrizione Umana. Il Pensiero Scientifico Editore Roma, 2006. Nino Carlo Battistini, Patrizia Pedrazzi Monica Prampolini, Curare con il cibo: Gli alimenti funzionali nella dietetica e nella dietoterapia. Livelli di Assunzione Raccomandati di Energia e Nutrienti, Società Italiana di Nutrizione Umana.	6	MED/49	48	-	-	-	Core compulsory activities	-	ITA
118999 - BIOINFORMATICS AND APPLICATIONS (objectives) Aim of the course is to train students in various fields of Bioinformatics, with particular regard to the knowledge of state-of-the-art tools used to support biological research. In detail, training objectives are: 1) Basic knowledge in Informatics/Bioinformatics 2) Biological databases: inquiry and programmatic access 3) Alignment of nucleotide and amino acid sequences 4) In silico structural and functional characterization of genes and proteins 5) Bioinformatic analysis applied to Next-Generation-Sequencing data. EXPECTED LEARNING OUTCOMES: KNOWLEDGE AND UNDERSTANDING. At the end of the course the students will get the following: the basic principles of bioinformatics, how biological databases are designed, managed, and queried, how sequences similarity search are performed, how to perform in silico characterization of genes and proteins and of how to analyse data from Next-Generation-Sequencing platforms. APPLYING KNOWLEDGE AND UNDERSTANDING. Understanding the computational approaches discussed in the lessons and their applications to specific problems. MAKING JUDGEMENTS. Be able to critically interpret the results obtained through the bioinformatics tools discussed during the course, as well as choose the ones most suitable to achieve a specific goal. COMMUNICATION SKILLS. Students should acquire the ability to transfer the acquired knowledge in a clear and comprehensible manner, even to people who are not in the field, and must demonstrate the ability to present the acquired information. LEARNING SKILLS. Be able to describe the topics of Bioinformatics in oral form. This ability will be developed by the active involvement of the students through class discussions and practical activities organized in the Informatics room on specific topics. - CASTRIGNANO' TIZIANA (syllabus) Basic concepts of computer science. Essential concepts on genomes. Primary and secondary databases. Sequence alignment algorithms. Phylogenetic trees. Next Generetion Sequencing platforms. Reconstruction and annotation of genomes. The big genomic projects. Transcriptome analysis. Proteins and proteomes. Bioinformatic methods for the analysis of protein sequences. Structural bioinformatics. Protein interactions. Big data projects. Scientific competitions. (reference books) Manuela Helmer Citterich Fabrizio Ferrè Giulio Pavesi Graziano Pesole Chiara Romualdi First principles of bioinformatics 2018 Stefano Pascarella Alessandro Paiardini Bioinformatics From sequence to protein structure 2011	6	BIO/11	48	-	-	-	Core compulsory activities	-	ITA
17449 - CELL BIOLOGY AND DEVELOPMENT (objectives) TRAINING OBJECTIVES The course introduces the rapidly evolving principles and approaches to cellular biology and developmental biology. The course aims to consolidate and widen the basic knowledge of cellular functioning (how cells interact with each other and with the tissue environment, how they differentiate and how they develop in tissues and how they can regenerate the complexity of an organ). It provides a framework for understanding the several issues into currently sciences up to date (eg stem cells and cancer cells and their biomedical application potential, translational study models) and it provides the basis for further deepen studies in cellular biology and development. • knowledge and understanding: Knowledge of cell biology principles applied to developmental biology. Knowledge of the principles of inter- and intra-cellular communication; of the molecular mechanisms of the regulation of the expression of genes related to development, differentiation, de-differentiation, migration, cell survival. Embryonic and adult stem cells, regeneration. • applying knowledge and understanding: In addition to the knowledge acquired through the study of cell biology and development, students will understand and explore the applicative potential of the subject in the sector of organ and tissue regeneration, the control of stem and tumor cell differentiation in the field of biomedical disciplines and translational medicine. • making judgments: The course offers connections with other disciplines of the Degree course (molecular biology, biochemistry, bioinformatics, genetics, and epigenetics) providing an integrated, current and dynamic knowledge, capable of specific insights such as 1) reading of scientific material found through keyword research and also provided and shared with learners on the google-drive website; 2) organized seminars; 3) further integration of knowledge with exams of your choice in the second year of the course. These three points represent strength for achieving an interpretation of experimental results of cell biology and development similar to those discussed in class. • communication skills: During the lessons students are invited to give their opinion and to study in a group to develop their communication skills. These skills are then verified during the exam tests at the end of the training activities. • learning skills: Students will be able to describe scientific topics related to cell biology and development. Such restitution skills will be developed through the active involvement of students in the in-depth study of the course topics. The learners will thus be encouraged to report in-class (also in a group) in-depth topics related to the course. The involvement of students in the improvement of the course content represents a fundamental growth point of training for the learner, but also for the teacher. - ROMANO Nicla (syllabus) Overview of the fundamental aspects of cell and developmental biology, biological model sused. The differentiated stateof the cells: characterization. Function of genes in the processes of determination and differentiation: Equivalence of the genome of the different cell types. Development control at the level of chromatin organization, transcription, RNA maturation, maturation and transport of RNA, translation, maturation of proteins. Morphogenetic factors and their influence on gene expression: transcription factors and growth factors. Cellular interactions in development: embryonic induction, the role of the cell surface, the extracellular matrix and soluble co-factors, differential affinity of the cells in the development, intercellular recognition, receptors, cadherins. Inductors embryogenesis for primary, secondary, tertiary, etc. Control of the development for the distribution of gradients of morphogenetic factors in vertebrates. Grid’s development and activation of homeotic genes and differential gene expression. The homeotic selector genes in Drosophila and vertebrates, differentiated cells and maintenance of the differentiated state of tissue stem cells and differentiation potential. Examples of organogenesis and organ regeneration: development and differentiation of the axis and the limb, limb regeneration, development and regeneration of the tegument, regeneration and new medical technologies (medical aesthetics); development and regeneration of the eye, development and regeneration of the digestive system. Development and evolution of the hematopoietic system, heart and regeneration. Cloning procedures. Organization of tissue and stem cells: primary oocytes as cellular source for the treatment of infertility and tissue regeneration. Oncogenes, oncogenes, tumor suppressor cancer gene. The tumor cell migration through the tissues. Immunotherapies as new avantaments for cancer cure. (reference books) S.F. Gilbert, "Developmental Biology", Zanichelli (most recent edition) - C. Lewin "Cellule", Zanichelli further lectures: CITOLOGIA ed ISTOLOGIA Dini & Romano et al (2021), Idelson-Gnocchi	6	BIO/06	48	-	-	-	Core compulsory activities	-	ITA
17451 - MOLECULAR BIOLOGY II (objectives) COURSE OBJECTIVES. The course aims to provide adequate knowledge for the understanding of the biochemical and molecular mechanisms responsible for extracellular signal transduction and possible connections between these events and nuclear dynamics. In addition, the mechanisms of regulation of gene expression in some model systems (lambda bacteriophage, GAL genes in S. cerevisiae, HIV virus, human beta-interferon gene) will be thoroughly analyzed, paying attention to possible evolutionary implications. Particular emphasis will be given to the post-transcriptional regulatory strategies in which non-coding RNAs are involved. KNOWLEDGE AND UNDERSTANDING. To acquire in-depth knowledge of protein-protein interactions (the basis of intracellular communication), and between nucleic acids and proteins (the basis of gene expression control). Owning up-to-date information on the role of catalytic and regulatory RNAs. APPLYING KNOWLEDGE AND UNDERSTANDING. Being able to correlate the three-dimensional structure of proteins and nucleic acids with their biological functions. To possess the ability to translate the latest knowledge of molecular biology into some application areas, such as the medical one. MAKING JUDGEMENTS. To achieve a fuller understanding of the molecular mechanisms at the basis of life, along with the ability to discuss their role. To acquire the autonomy needed to align the gained scientific knowledge with advances in biological research. COMMUNICATION SKILLS. To demonstrate mastery of skills and knowing how to convey them adequately. To develop the ability to use the correct terminology. LEARNING SKILLS. To be able to grasp, rework and discuss the scientific issues dealt with in the lesson, including their applications. - RINALDUCCI Sara (syllabus) SIGNAL TRANSDUCTION: PATHWAYS REGULATING GENE EXPRESSION. Single-pass transmembrane receptors. Tyr-kinases. Adaptor proteins. Protein interaction domains (SH2, SH3, PTB, WW, PH, PDZ etc.). Transduction pathways from the membrane to the nucleus: Src, Ras, MAPKs, PI-3K proteins. TGF-beta/Smad signaling. Cytokine receptors and JAK/STAT pathway. Cell surface receptors with multiple membrane spanning segments. CREB activation, PKA and AMPc. Wnt/beta-catenin signaling. NFkB. CONTROL OF GENE EXPRESSION. Details on gene regulation in bacteriophage lambda. Nucleosomes, histones and post-translational modifications (HATs, HDACs, HKMTs, PRMTs). Bromodomains, Chromodomains, PHD finger and TUDOR domains. Chromatin remodeling complexes. Repressors, activators: structural domains. The yeast GAL regulon. Sir proteins. Combinatorial control of the mating-type genes from yeast. HMG, nuclear non-histone proteins. IFN-beta gene and assembly of the enhanceosome. Molecular biology of HIV. CATALYTIC AND REGULATORY RNAs. Introns of type I and II. Ribozymes and Riboswitches. RNA interference. siRNAs. The biogenesis and function of microRNAs. Drosha, Pasha, Dicer, the Argonaute proteins, RISC. rasiRNAs. Gene silencing, RITS. mirMASA technology. (reference books) Advised books: Biologia Molecolare della Cellula, Lodish et al., 2009-Zanichelli. Biologia Molecolare del Gene, Watson J.D. et al., sesta edizione, 2009-Zanichelli Geni e Segnali, Ptashne-Gann, 2004-Zanichelli Regolazione genica, Ptashne, 2006-Zanichelli Il Gene, Lewin et al., 2011-Zanichelli.	6	BIO/11	48	-	-	-	Core compulsory activities	-	ITA
118993 - STAGE	4		-	-	-	-	Other activities		ITA

SECOND YEAR

First semester

Course

Credits

Scientific Disciplinary Sector Code

Contact Hours

Exercise Hours

Laboratory Hours

Personal Study Hours

Type of Activity

Optional materials and exam in a foreign language

Language

119000 - ENGLISH B2 (objectives)

- HOBSON Julie anne (syllabus) (reference books)

Other activities

ITA

Optional group: OPZIONALI II ANNO - (show)

15406 - INSTRUMENTAL DIAGNOSTICS, BIOPHYSICS AND NANOSCIENCE (objectives) The Course would achieve the following principal targets: i) To describe the fundamentals of molecular biophysics which are at the basis of the variuos biological phenomena. ii) To describe the theoretical and experimental fundamentals of the different, advanced techniques and methodologies (even of nanotechnological content) available in the Biophysics and Nanoscience Centre, to investigate the structural, dynamic and of interaction properties of biological systems; also in connection with the detection of biological/biomedical markers with possible diagnostic relevance. iii) To guide the students in performing, with scientific awareness and critical spirit, individual experiments on every biophysical/nanotechnological technique, as studied theoretically before. - BIZZARRI Anna Rita (syllabus) Elements of Molecular Biophysics, Instrumental diagnostics, for applications in Biology, Bio-engineering and Bioelectronics. Theory and applications of different spectroscopic techniques for using in research and in diagnostic labs ( UV/Vis Absorption, static and time-resolved Fluorescence, FRET, Raman, Surface Plasmon Resonance) to various biological systems. Nanoscopic techniques on biomolecules with exercitations on Scanning Probe microscopies (STM/AFM) in air and in buffers. For each experimental technique, individual practical exercitation will be done. Molecular Dynamics Simulation of proteins and DNA with elements of Bioinformatics Docking e Drug Design ( with practical exercitations). (reference books) The slides of the course and -W. Hoppe, W. Lohmann, H. Markl, H. Ziegler (Eds.): “Biophysics”. Springer-Verlag - D. Freifelder: “Physical biochemistry”. Freeman and Company	6	FIS/07	24	-	24	-	Related or supplementary learning activities	-	ITA
118995 - GENETICS AND PHARMACOGENOMICS OF AGING AND ASSOCIATED DISEASES (objectives) TRAINING OBJECTIVES The teaching is aimed at providing students with the basic notions for understanding the genetic and molecular bases of aging and longevity, the pathogenetic bases of diseases associated with aging and finally the basics of pharmacogenetics and pharmacogenomics, this last the disciplines that aim to identify the genes and gene variants that determine the inter-individual variability in the response to drugs .. EXPECTED LEARNING RESULTS 1) Having developed knowledge of the genetic basis of the biology of aging and longevity; 2) Have an understanding of the experimental approaches of aging genetics; 3) have gained knowledge of drug-organism interactions (molecular and cellular) that determine the efficacy or toxicity of drug treatment and the role of interindividual genetic variability (primarily genetic polymorphisms) in determining the variability of response to the drug; 4) Being able to apply the knowledge developed in points 1, 2 and 3 to understand specific cases; 4) Being able to express oneself with appropriate scientific terminology 5) Having developed the ability to understand and describe experiments, which contributed to the understanding of the genetic basis of aging, of the associated pathologies and of their possible pharmacological treatment but which had not been treated during the course. - PROIETTI DE SANTIS Luca (syllabus) Definition and Measurement of Aging: Definition of aging and senescence processes. Identification of the characters associated with the aging process. Measurement of inter and intra-individual age-related changes. Theories of aging. Genetic approaches to the study of aging and longevity: Gerontogens and longevity promoters. Human studies: genealogical, population, twins, sex, healthy centenarians, longitudinal studies. Animal experimental models: mouse and other rodents, saccharomices cerevisiae, caernorhabditis elegans, drosophila melanogaster. Cellular aging: Cellular senescence and apoptosis. Telomeres and telomerase. Damage to the DNA molecule: endogenous and exogenous nature. DNA repair systems. Decline of repair systems during aging. The pleiotropic effect of the p53 protein in the aging process and carcinogenesis. Protein synthesis, post-translational modifications. DNA helicase. Progeroid syndromes: Cockayne syndrome, trichothioodystrophy, Bloom syndrome, Werner syndrome, Alzheimer's syndrome. Molecular dysfunctions and therapeutic targets. Genetics of Cancer Cells: The Clonal Origin of Cancer Cells. Genetic defects that interfere with genome stability, DNA repair and cell cycle regulation. Introduction to pharmacogenetics and pharmacogenomics. Human genome sequencing and inter-individual variability. Individual variability in responses to drug therapy (efficacy and tolerability). Genes that influence drug response: genes coding for proteins involved in drug bioavailability (pharmacokinetics); genes that code for the therapeutic target of the drug (pharmacodynamics). Allelic variants in the human population. Polymorphisms of enzymes responsible for drug metabolism. Polymorphisms / mutations of the genes coding for the therapeutic target of the drug. Polygenic complexity and modulators of the action of a drug. Predictive Medicine and Personalized Therapy. Sequencing of tumor genomes and selection of tumor inhibitors. Identification of biological targets with diagnostic, prognostic and therapeutic value. (reference books) The course does not have a single reference text as it is not available. Therefore the teacher to deepen the topics covered on the following texts:- Chimica farmaceutica (Patrick) di Edises - Le basi farmacologiche della terapia (Goodman & Gilman) - Principles of Pharmacogenetics and Pharmacogenomics, Edited by Russ B. Altman, Stanford University, California, David Flockhart, Indiana University, David B. Goldstein, Duke University, North Carolina, Cambridge University Press. In addition the teacher will provide specific scientific articles during the course	6	BIO/18	40	-	8	-	Related or supplementary learning activities	-	ITA
17467 - BIOMOLECOLAR TECHNIQUE (objectives) The course Biomolecular Techniques aims to provide the students with theoretical and practical knowledge of the major molecular biology and biochemical techniques applied to the study of genes, genomes, proteins and proteomes, as well as the rational basis for designing an experiment and knowledge for the analysis of the results and their description. Specifically, it is intended to provide students with specific skills for the manipulation and analysis of nucleic acids and proteins (mutagenesis and genome editing techniques, differential proteomic), for the analysis of gene expression levels (qPCR, microarrays, differential transcriptomic) and gene expression regulation (study of epigenetic modifications and protein-DNA interactions), for the study of transduction signal pathways by protein-protein interaction analysis. The advances in the field of the sequencing of whole genomes and the application of biomolecular techniques in the field of forensic genetics will be also discussed. - PROIETTI Silvia (syllabus) Theoretical part (32 hours) Introduction to nucleic acids and proteins handling: Methods for DNA, RNA and proteins isolation from biological samples and related analysis. Comparison between protein samples: differential-in-gel electrophoresis (DIGE). Methods for gene expression analysis: RT-PCR. DNA microarray technology. RNA-Seq. Methods for protein-protein interaction analysis: Far-Western, Pull-down, yeast-two/three hybrid assay, Co-Immunoprecipitation, Tandem Affinity Purification (TAP) system, Phage Display, Bimolecular Fluorescent Complementation (BiFC), FRET. Methods for DNA/RNA-protein interaction analysis: Chromatin Immunoprecipitation assay (ChIP and ChIP-on-chip). Electrophoretic Mobility Shift Assay (EMSA). DNA pull-down. Southwestern. Yeast three-hybrid system. Methods for epigenetic modifications analysis : DNA Methylation analysis: Methylation-Sensitive Amplification Polymorphism (MSAP). Bisulfite (non methylation)-specific PCR and Methylation-specific PCR (MSP). Methods for histone modifications analysis by ChiP. Mutagenesis techniques and genome editing: Site-directed mutagenesis and CRISPR-Cas9 System. Diagnostic application of PCR. Next Generation Sequencing: second and third generation sequencing platforms. Practical part (16 hours) Total RNA extraction, RT-qPCR. Genomic DNA extraction. DNA methylation analysis. Total protein isolation and protein-protein interaction assays. (reference books) Brown T.A. Gene cloning and DNA analysis: an introduction. 7th ed., 2016, Wiley-Blackwell. Watson J.D., Caudy A.A., Myers R.M., Witkowski J.A. Recombinant DNA, genes and genomes – a short course. 3rd ed., 2007, W.H. Freeman & Co. Lesk A.M. Introduction to Genomics. 3rd ed., 2017, Oxford University press. Slides are available in the teaching platform. Handouts are provided by the teacher for practical activities. Non-attending students are encouraged to contact the teacher for information about the program, teaching materials, and the examination mode.	6	BIO/10	32	-	16	-	Related or supplementary learning activities	-	ITA