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BIOLOGY AND GENOMICS

Francesca RIZZO BIOLOGY AND GENOMICS

0623200003
DIPARTIMENTO DI INGEGNERIA DELL'INFORMAZIONE ED ELETTRICA E MATEMATICA APPLICATA
EQF7
INFORMATION ENGINEERING FOR DIGITAL MEDICINE
2022/2023



OBBLIGATORIO
YEAR OF COURSE 1
YEAR OF DIDACTIC SYSTEM 2022
AUTUMN SEMESTER
CFUHOURSACTIVITY
648LESSONS
324EXERCISES
FRANCESCA RIZZO T Curriculum
GIOVANNI NASSA Curriculum
Objectives
THE COURSE PROVIDES THE METHODOLOGICAL BASIS OF DOMAIN TO UNDERSTAND THE MAIN PROBLEMS OF BIOLOGICAL AND GENOMIC NATURE IN ORDER TO APPLY TYPICAL BIOINFORMATICS TOOLS FOR DATA ANALYSIS.
KNOWLEDGE AND UNDERSTANDING
CHARACTERISTICS OF CELLS AND CELL SYSTEMS; PROTEINS AND THEIR STRUCTURES. RELATIONSHIP BETWEEN STRUCTURE AND FUNCTION. CHARACTERISTICS OF NUCLEIC ACIDS (DNA, RNA) AND OF GENETIC INFORMATION TRANSFER. THE HUMAN GENOME. SEQUENCING TECHNIQUES. CLINICAL ANALYSIS AND INTERPRETATION OF THE GENOME FOR THE DIAGNOSIS OF DISEASES.
APPLYING KNOWLEDGE AND UNDERSTANDING
MATCH THE MAIN ISSUES OF BIOLOGY AND GENOMICS WITH DATA PROCESSING AND ANALYSIS PROCEDURES. USE KNOWLEDGE OF BIOLOGY AND GENOMICS TO UNDERSTAND THE REQUIREMENTS OF A BIOINFORMATICS SYSTEM OR DIGITAL HEALTH APPLICATION.
Prerequisites
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Contents
Didactic unit 1: STRUCTURE AND FUNCTION OF NUCLEIC ACIDS (LECTURE/PRACTICE/LABORATORY HOURS 6/0/0)
-1 (2 Hours Lecture): DNA AND RNA STRUCTURE AND FUNCTION: REPLICATION, TRANSCRIPTION AND TRANSLATION.
-2 (2 Hours Lecture): THE GENETIC CODE
-3 (2 Hours Lecture): STRUCTURAL GENOMICS

KNOWLEDGE AND UNDERSTANDING: Characterization of the molecular bases of the structure of nucleic acids and their regulation
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding the molecular differences in the gene structure and its specific characteristics


Didactic unit 2: MENDEL LAWS (LECTURE/PRACTICE/LABORATORY HOURS 4/2/0)
-4 (2 Hours Lecture): MENDEL, SINGLE HYBRID CROSSBREEDING, DIHYBRID, POLYHYBRID: ANALYSIS OF HEREDITARY TRANSMISSION MECHANISMS.
-5 (2 Hours Lecture): CHROMOSOMES, CELL DIVISIONS, GAMETOGENESIS: RELATIONSHIP WITH MENDELIAN PRINCIPLES.
-6 (2 Hours Practice): APPLICATION OF MENDEL’S LAWS

KNOWLEDGE AND UNDERSTANDING: Characterization of Mendel's laws
APPLYING KNOWLEDGE AND UNDERSTANDING: Application of Mendel's laws

Didactic unit 3: GENOMICS OF MICROORGANISMS (LECTURE/PRACTICE/LABORATORY HOURS 2/0/0)
-7 (2 Hours Lecture): GENETIC ANALYSIS TECHNIQUES OF ORGANISMS AND THEIR LIFE CYCLES.

KNOWLEDGE AND UNDERSTANDING: Characterization of the genome of microorganisms
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding and application of the techniques of genetics of microorganisms


Didactic unit 4: LINKAGE AND RECOMBINATION (LECTURE/PRACTICE/LABORATORY HOURS 2/1/0)
-8 (2 Hours Lecture): INHERITANCE LINKED TO SEX; GENETIC DETERMINATION OF SEX. ASSOCIATION, RECOMBINATION, CROSSING-OVER, ITS NATURE AND EVOLUTIONARY BIOLOGICAL SIGNIFICANCE. CHROMOSOME MAPPING, THREE-POINT CROSSING, INTERFERENCE;
-9 (2 Hours Practice): TETRAD ANALYSIS.

KNOWLEDGE AND UNDERSTANDING: Characterization of chromosomal recombination.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding and application of chromosomal recombination analysis

Didactic unit 5: CHROMOSOMIC ALTERATIONS (LECTURE/PRACTICE/LABORATORY HOURS 6/1/0)
-10 (2 Hours Lecture): ALTERATIONS OF CHROMOSOMES STRUCTURES: DELETIONS, DUPLICATIONS, INVERSIONS, TRANSLOCATIONS: THEIR PHENOTYPIC EFFECT AND BIOLOGICAL EVOLUTIONARY SIGNIFICANCE.
-11 (2 Hours Lecture): ALTERATIONS IN THE NUMBER OF CHROMOSOMES: ANEUPLOIDY: CASES IN HUMANS.
-12 (2 Hours Lecture): VARIATION OF PLOIDY NUMBER: ITS PHENOTYPIC EFFECT AND BIOLOGICAL EVOLUTIONARY SIGNIFICANCE.
-13 (1 Hour Practice): PRACTICAL EVALUATION OF CHROMOSOMIC ALTERATIONS


KNOWLEDGE AND UNDERSTANDING: Characterization of chromosomal alterations.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of chromosomal alterations and their biological and evolutionary significance



Didactic unit 6: MUTATIONS (LECTURE/PRACTICE/LABORATORY HOURS 4/1/0)
-14 (2 Hours Lecture): MUTATION DETECTION TECHNIQUES. MOLECULAR BASIS OF MUTATIONS; PHYSICAL AND CHEMICAL MUTAGENS; MUTAGENICITY TESTS.
-15 (2 Hours Lecture): MECHANISMS FOR REPAIRING DNA DAMAGE AND THEIR CONTRIBUTION TO MUTAGENESIS.
-16 (1 Hour Practice): EVALUATION OF MUTATIONS

KNOWLEDGE AND UNDERSTANDING: Characterization of gene mutations.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of gene mutations and their identification.


Didactic unit 7: BACTERIAL GENETICS AND HUMAN GENETICS (LECTURE/PRACTICE/LABORATORY HOURS 6/1/0)
-17 (2 Hours Lecture): TRANSFORMATION, CONJUGATION, TRANSDUCTION, MAPPING OF THE BACTERIAL CHROMOSOME.
-18 (2 Hours Lecture): GENETICS OF BLOOD GROUPS, IMMUNITY AND INBORN ERRORS OF METABOLISM.
-19 (2 Hours Lecture): EXTRANUCLEAR GENETICS AND MATERNAL INHERITANCE: MITOCHONDRIAL GENOME AND CHLOROPLASTS, THEIR BIOLOGICAL-EVOLUTIONARY SIGNIFICANCE.
-20 (1 Hour Practice): GENERAL PRINCIPLES OF POPULATION GENETICS.

KNOWLEDGE AND UNDERSTANDING: Characterization of bacterial and human genetics.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of Similarities and Differences in Bacterial and Human Genetics.


Didactic unit 8: MAIN TECHNOLOGIES OF DNA ANALYSIS AND MANIPULATION (LECTURE/PRACTICE/LABORATORY HOURS 10/2/2)
-21 (2 Hours Lecture): ELEMENTARY CYTOGENETIC TECHNIQUES.
-22 (2 Hours Lecture): DNA MICROARRAYS TECHNOLOGY.
-23 (2 Hours Lecture): GENOME SEQUENCING TECHNOLOGIES. HIGH-THROUGHPUT TECHNOLOGIES. SHOTGUN SEQUENCING.
-24 (2 Hours Lecture): THE FIRST GENERATION SEQUENCING. SECOND-GENERATION SEQUENCING OR NEXT-GENERATION SEQUENCING (NGS).
-25 (2 Hours Lecture): THIRD-GENERATION SEQUENCING.
-26 (2 Hours Practice): TUTORIAL ON SEQUENCING TECHNIQUES
-27 (2 Hours Laboratory): FUNCTIONAL GENOMICS LABORATORY EXPERIENCE

KNOWLEDGE AND UNDERSTANDING: Characterization of DNA analysis and manipulation techniques.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of the main sequencing techniques and their application.


Didactic unit 9: PROTEOGENOMICS (LECTURE/PRACTICE/LABORATORY HOURS 2/0/0)
-28 (2 Hours Lecture): COMBINATION OF PROTEOMICS, GENOMICS AND TRANSCRIPTOMICS; ONTOLOGICAL ANALYSIS

KNOWLEDGE AND UNDERSTANDING: Characterization of proteomics and its combination with transcriptomics.
APPLYING KNOWLEDGE AND UNDERSTANDING: Comprensione delle principali tecniche di proteogenomica e loro applicazione.


Didactic unit 10: THE GENOME PROJECTS (LECTURE/PRACTICE/LABORATORY HOURS 8/1/0)
-29 (2 Hours Lecture): GENETIC POLYMORPHISMS AND GENE IDENTIFICATION MEDIATED BY GENOMIC MARKERS.
-30 (2 Hours Lecture): MUTATIONS AND GENETIC VARIABILITY. GENETIC POLYMORPHISMS. POLYMORPHISMS OF SINGLE NUCLEOTIDES (SNPS).
-31 (2 Hours Lecture): HAPLOTYPES AND GENOTYPING. SNP MARKERS, THE LINKAGE DISEQUILIBRIUM.
-32 (2 Hours Lecture): THE CONCEPT OF "ODDS RATIO". MINISATELLITES AND MICROSATELLITES. DNA FINGERPRINTING AND ITS APPLICATIONS
-33 (1 Hour Practice): APPLICATION OF FINGERPRINTING TECHNIQUES

KNOWLEDGE AND UNDERSTANDING: Characterization of human genome completion projects.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of the main techniques of characterization of the human genome and their application.


Didactic unit 11: TRANSCRIPTOMICS (LECTURE/PRACTICE/LABORATORY HOURS 2/1/0)
-34 (2 Hours Lecture): THE TRANSCRIPTOME AND HIGH-THROUGHPUT ANALYSIS OF GENE EXPRESSION. RNA – SEQ. FUNCTIONAL GENOMICS
-35 (1 Hour Practice): RNA – SEQ LIBRARY PREPARATION.

KNOWLEDGE AND UNDERSTANDING: Characterization of the main aspects of functional genomics.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of the main transcriptome analysis techniques and their application



Didactic unit 12: EPIGENETICS (LECTURE/PRACTICE/LABORATORY HOURS 6/2/0)
-36 (2 Hours Lecture): DEFINITION OF EPIGENETICS. THE DISCOVERY OF EPIGENETIC PHENOMENA, HELEN CROUSE'S EXPERIMENTS. GENOMIC IMPRINTING IN INSECTS AND MAMMALS. GENOMIC IMPRINTING AND HUMAN DISEASES. AN OVERVIEW OF EPIGENETIC PHENOMENA.
-37 (2 Hours Lecture): THE MOLECULAR MECHANISMS OF EPIGENETIC PHENOMENA. DNA METHYLATION, THE CPG ISLANDS. THE MODIFICATIONS OF THE HISTONES. NON-CODING RNA. EPIGENOMICS. THE GENOMIC DISTRIBUTION OF EPIGENETIC FACTORS.
-38 (2 Hours Lecture): CHROMATIN IMMUNO PRECIPITATION (CHIP) –SEQ. METHYL-SEQ.
-39 (2 Hours Practice): CHIP – SEQ LIBRARY PREPARATION.

KNOWLEDGE AND UNDERSTANDING: Characterization of epigenetic mechanisms and their molecular basis.
APPLYING KNOWLEDGE AND UNDERSTANDING: Understanding of the main epigenome analysis techniques and their application.

TOTAL LECTURE/PRACTICE/LABORATORY HOURS 58/12/02
Teaching Methods
THE COURSE IS CARRIED OUT THROUGH LECTURES (58 HOURS), CLASSROOM EXERCISES (12 HOURS), AND LABORATORY EXPERIENCES (2 HOURS). LECTURES TAKE ADVANTAGE OF THE USE OF VIDEO-PROJECTION SYSTEMS FOR VIEWING POWERPOINT PRESENTATIONS. THE LECTURES WILL INTRODUCE SUBJECTS WITH GRADUAL COMPLEXITY ADEQUATELY TO THE DEVELOPMENT OF THE TRAINING PATH AND WILL BE SUPPORTED BY DIFFERENT TEACHING METHODOLOGIES INCLUDING SEMINAR LESSONS BUT ALWAYS PROVIDING THE STUDENT IN THE FOREGROUND, WHO WILL BE ACTIVELY INVOLVED BY INTERVENING WITH PROPOSALS AND QUESTIONS.
Verification of learning
THE ASSESSMENT OF LEARNING BY THE STUDENT IS CARRIED OUT THROUGH A WRITTEN TEST THAT IS HELD AFTER THE END OF THE COURSE FOLLOWED BY AN ORAL TEST. THE WRITTEN TEST IS PROPOSED WITH MULTIPLE CHOICE QUESTIONS FROM ALL THE TOPICS COVERED IN THE COURSE. IN THE EVENT OF A NEGATIVE OUTCOME OF THE WRITTEN TEST, THE STUDENT CAN NOT TAKE THE ORAL EXAM BUT CAN TAKE THE EXAM AGAIN DURING THE SUBSEQUENT APPEALS. THE FINAL EVALUATION WILL TAKE INTO CONSIDERATION THE OUTCOME OF THE WRITTEN AND ORAL TESTS AND WILL, THEREFORE, PROVIDE A MARK OUT OF THIRTY.
Texts
GENETICS: FROM GENES TO GENOMES (HARTWELL, GENETICS) 4TH EDITION
GENETICS, PETER J. RUSSELL. REED COLLEGE. 5TH EDITION

TEXTS FOR THE STUDY OF SPECIFIC TOPICS

GENETICS: A CONCEPTUAL APPROACH. BENJAMIN A. PIERCE
GENETICS IN MEDICINE. NUSSBAUM, ET AL. THOMPSON & THOMPSON. PHILADELPHIA: SAUNDERS/ELSEVIER.
EPIGENETICS. ALLIS ET AL. COLD SPRIG HARBOR LABORATORY PRESS

SUPPLEMENTARY TEACHING MATERIAL WILL BE AVAILABLE ON THE UNIVERSITY E-LEARNING PLATFORM (HTTP://ELEARNING.UNISA.IT) ACCESSIBLE TO STUDENTS USING THEIR OWN UNIVERSITY CREDENTIALS.
More Information
THE COURSE IS HELD IN ENGLISH.
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