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Second cycle
degree courses
Single cycle
degree courses
School of Science
INDUSTRIAL BIOTECHNOLOGY
Course unit
STRUCTURAL AND FUNCTIONAL GENOMICS
SCN1037597, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
INDUSTRIAL BIOTECHNOLOGY
SC1731, Degree course structure A.Y. 2014/15, A.Y. 2017/18
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Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination STRUCTURAL AND FUNCTIONAL GENOMICS
Website of the academic structure http://biotecnologie.scienze.unipd.it/2017/laurea_magistrale
Department of reference Department of Biology
E-Learning website https://elearning.unipd.it/biologia/course/view.php?idnumber=2017-SC1731-000ZZ-2017-SCN1037597-N0
Mandatory attendance
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge STEFANO CAGNIN BIO/18

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/18 Genetics 6.0

Course unit organization
Period Second semester
Year 1st Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Laboratory 1.0 16 9.0 No turn
Lecture 5.0 40 85.0 No turn

Calendar
Start of activities 26/02/2018
End of activities 01/06/2018
Show course schedule 2019/20 Reg.2014 course timetable

Examination board
Board From To Members of the board
7 GENOMICA STRUTTURALE E FUNZIONALE 2018-2019 01/10/2018 30/11/2019 CAGNIN STEFANO (Presidente)
DE PITTA' CRISTIANO (Membro Effettivo)
LANFRANCHI GEROLAMO (Supplente)
6 GENOMICA STRUTTURALE E FUNZIONALE 2017/2018 01/10/2017 25/11/2018 CAGNIN STEFANO (Presidente)
DE PITTA' CRISTIANO (Membro Effettivo)
LANFRANCHI GEROLAMO (Supplente)
5 GENOMICA STRUTTURALE E FUNZIONALE 01/10/2016 30/11/2017 CAGNIN STEFANO (Presidente)
DE PITTA' CRISTIANO (Membro Effettivo)
LANFRANCHI GEROLAMO (Supplente)

Syllabus
Prerequisites: To understand the content of teaching are necessary basic knowledge provided by the teachings of 'Introduzione alle discipline omiche', 'Bioninformatica e statistica', 'Biologia molecolare e cellulare' e 'Ingegneria genetica'.
Target skills and knowledge: The course aims to introduce the strategies developed for the sequencing of whole genomes, from the simplest (bacteria) to complex (eukaryotes: D. melanogaster, C. elegans, A. thaliana), with special emphasis on the human genome . The traditional concept of the gene will be revised in the light of the latest findings. It then goes on to describe in detail the latest technologies for transcriptome analysis, such as the setting up of specialized libraries for next generation sequencing, analysis of gene expression profiles by microarray and qRT-PCR. Finally, we will describe the main techniques used for the analysis of the epigenome.
The student will have the opportunity to apply one of the technologies addressed in the laboratory and interpret critically the results obtained.
Examination methods: ORAL interview.
Assessment criteria: The exam will be evaluated on the basis of the answers given for each question, in terms of correctness and completeness of the information provided in each answer and concerning the capacity of connection between different concepts (consequential logic). In addition, students must demonstrate to be able to design simple experimental designs. During the interview will also assess the understanding of the practical exercises.
Course unit contents: STRUCTURAL GENOMICS (20 hours):
• Definition of Genomics.
• Brief Review on strategies for sequencing a genome and techniques of Next Generation Sequencing (NGS).
• Organization of the genome of a few model organisms: S. cerevisiae, D. melanogaster, A. thaliana, M. musculus.
• Organization of the Human Genome:
a. The mitochondrion and the mitochondrial genome.
b. The NUCLEAR genome:
• The protein-coding genes: genes overlapped and internal gene families, pseudogenes.
• The genes for RNA: rRNA and tRNA, snRNA and snoRNA, snRNA in Cajal bodies, miRNA and piwiRNA; lncRNA and circularRNA.
• transposable elements in the human genome:
a. Transposable elements in prokaryotes: Transposons simple (Tn3) and Transposons compounds (TN10).
b. Transposable elements in eukaryotes:
• Class 1: LTR retrotransposons and non-LTR retrotransposons (LINE, SINE, Alu).
• Class 2: DNA transposons.
c. Discovering of P elements
d. Molecular explanation of hybrid dysgenesis in Drosophila. The UAS-GAL4 system in D. melanogaster.
• Pharmacogenetics and Pharmacogenomics:
a. Basic Concepts of Pharmacology: Pharmacokinetics and Pharmacodynamics.
b. The Pharmacokinetics: Reactions of Phase 1 and Phase 2 reactions.
c. The Pharmacodynamics: Example angiotensin converting enzyme (ACE) inhibitors.
d. The Personalized Medicine: the example of warfarin and certain medications genotype-specific.
e. Gene expression profiling and personalized medicine: the example of the classification of breast cancer.
• Metagenomics
FUNCTIONAL GENOMICS (20 hours):
• Introduction to gene expression: the study of the transcriptome: static and dynamic approach. How NGS techniques have revolutionized the analysis of the transcriptome?
• Quantification of the levels of expression of a single gene (qRT-PCR):
a. The Northern blot.
b. The semi-quantitative PCR.
c. the technology of Real Time Quantitative PCR: the threshold cycle Ct; system of fluorescence detection; total RNA extraction, cDNA synthesis; design of primers for qRT-PCR.
d. Methods of marking and fluorescence detection: SYBR Green, TaqMan probes, Molecular Beacons, Scorpion probes; Hybridization primers.
e. miRNA qRT-PCR.
f. Applications of qRT-PCR.
g. Analysis of the data obtained by qRT-PCR: Determination of the threshold cycle (Ct). Absolute and relative quantification. Determination of the efficiency of reaction. Method of ΔΔCt
• Microarrays and DNA chips
a. Introduction to microarray technology.
b. Microarray platforms are available: The macroarray; Microarray deposition, photolithography (Affymetrix and Nimblegene); Inkjet technology; Combimatrix.
c. Description of the various stages of a microarray experiment:
1. Production of the target marked: description of the various methods of marking.
2. Hybridize to the target marked.
3. The washes.
4. Scanning and image analysis.
5. Normalization of expression data.
d. Data representation of expression and analysis of differentially expressed genes;
e. Comparison: microarray Vs. next generation sequencing.
f. Description of some microarray studies from the literature.
• Epigenomics:
a. Structure and function of chromosomes;
b. Association between histone modifications and chromatin structure;
c. The chromatin remodeling;
d. DNA methylation;
e. Techniques for the analysis of DNA methylation: sodium bisulfite, MS-PCR; MeDIP; Methyl-MAPS; MethyIC-Seq, microarray.
f. Chromatin immunoprecipitation: Formaldehyde cross-linking, ChIP-chip and ChIP-Seq.
g. Chromosome Conformation Capture: ChIP-loop protocol of 3C, 4C and 5C.
• The importance of PATHWAY ANALYSIS for understanding the biological phenomena.
Planned learning activities and teaching methods: Lectures and experimental activities in the educational workshops.
As regards the practical exercises, the student will set up an experiment of qRT-PCR to determine the gene expression of specific target genes.
Additional notes about suggested reading: The slides used by the teacher and scientific articles useful for the understanding of the various topics will be made available on e-learning web site
Textbooks (and optional supplementary readings)
  • Gibson G., Muse S.V., Introduzione alla genomica. --: Zanichelli, 2004. Cerca nel catalogo
  • Strachan T., Read A.P., Genetica Umana Molecolare. --: Zanichelli, 2012. III edizione Cerca nel catalogo
  • Meneely P., Analisi genetica avanzata. --: McGraw-Hill, 2012. I edizione Cerca nel catalogo
  • Watson J.D., --. DNA Ricombinante: Zanichelli, 2008. II edizione Cerca nel catalogo
  • Brown T.A., Genomi 3. --: EdiSES, 2008. III edizione Cerca nel catalogo