First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
BIOTECHNOLOGY
Course unit
INTRODUCTION TO OMICS: GENOMICS, TRANSCRIPTOMICS, PROTEOMICS
SCO2044012, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2015/16

Information on the course unit
Degree course First cycle degree in
BIOTECHNOLOGY
IF1839, Degree course structure A.Y. 2011/12, A.Y. 2017/18
N0
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Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination INTRODUCTION TO OMICS: GENOMICS, TRANSCRIPTOMICS, PROTEOMICS
Website of the academic structure http://biotecnologie.scienze.unipd.it/2017/laurea
Department of reference Department of Biology
E-Learning website https://elearning.unipd.it/biologia/course/view.php?idnumber=2017-IF1839-000ZZ-2015-SCO2044012-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 CRISTIANO DE PITTA' BIO/18

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses BIO/18 Genetics 6.0

Course unit organization
Period First semester
Year 3rd 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 02/10/2017
End of activities 19/01/2018

Examination board
Board From To Members of the board
6 INTRODUZIONE ALLE DISCIPLINE OMICHE: GENOMICA, TRASCRITTOMICA, PROTEOMICA 2018-2019 01/10/2018 30/11/2019 DE PITTA' CRISTIANO (Presidente)
CAGNIN STEFANO (Membro Effettivo)
MAZZOTTA GABRIELLA MARGHERITA (Supplente)
5 INTRODUZIONE ALLE DISCIPLINE OMICHE: GENOMICA, TRASCRITTOMICA, PROTEOMICA 2017/2018 01/10/2017 25/11/2018 DE PITTA' CRISTIANO (Presidente)
CAGNIN STEFANO (Membro Effettivo)
MAZZOTTA GABRIELLA MARGHERITA (Supplente)
4 INTRODUZIONE ALLE DISCIPLINE OMICHE: GENOMICA, TRASCRITTOMICA, PROTEOMICA 2016-2017 01/10/2016 30/11/2017 DE PITTA' CRISTIANO (Presidente)
CAGNIN STEFANO (Membro Effettivo)
MAZZOTTA GABRIELLA MARGHERITA (Supplente)

Syllabus
Prerequisites: Basic knowledge provided by Genetics , Molecular Biology and Genetic Engineering teachings are necessary to understand the "OMICS" course.
Target skills and knowledge: The genome science is the study of the structure, content and evolution of genomes. Today, the science of genomes, or " Genomics ", is no longer limited to the determination of DNA sequences, but also extends to the analysis of the expression and functions of the genes (Transcriptomics) and proteins (Proteomics). The main objective of this course is showing a different view of biology if the perspective has shifted from single genes to the whole genome. This course provides the fundamental basis for the understanding of the "Structural and functional genomics" teaching of the Master degree in Industrial Biotechnology .
Examination methods: Written exam . There are no partial exams ongoing .
(Multiple-choice and open questions and one exercise on restriction maps)
Assessment criteria: The exam will be assessed according to the answers given to each question, in terms of completeness of the information provided in each answer, links between different concepts (consequential logic) and for the presence of errors . The answer to each question will be evaluated numerically and the total score of the examination will be the sum of the scores obtained in each individual answer. In each exam there will be a question related to the practical laboratory.
Course unit contents: GENOMICS (18 hours):
• Definition of Genomics. What is a genome sequence?
• Isolation and purification of genomic DNA.
• DNA genomic libraries: partial digestion, redundancy information, relationship between frequency and probability, the high capacity cloning vectors (Cosmids, YAC, BAC). DNA library title and analysis of recombinant clones.
• Genetics and Physics mapping of a genome. Solving some exercises related to the mapping by restriction maps.
• Strategies of genome sequencing:
a) SHOTGUN Approach: Construction of a genomic library. The significance and importance of the genome coverage. Paired-end sequencing. Advantages and disadvantages of a shotgun approach.
b) CLONE by CLONE Approach: Construction of a primary library. Selecting the minimal tiling path (Chromosome walking, fingerprinting of clones). Construction of the secondary genomic library (BAC shotgun). Assembly of the genome sequence (END sequencing).
• Description of the phases that characterized the human genome project.
• Description of the DNA sequencing techniques:
a) Sanger method.
b) Next generation sequencing (NGS): Roche 454, Illumina, SOLiD, Helicos, Pacific Biosciences, Ion Torrent, Proton Torrent and Oxoford Nanopore.

TRANSCRIPTOMICS (16 hours):
• Introduction to gene expression: description of the RNA content in a cell (RNA coding and non-coding).
• How is processed and regulated RNA? (5'-Capping, lengthening of mRNA, polyadenylation, splicing mechanism and alternative splicing, editing, degradation of mRNA).
• Insights on microRNA: genomic location, biogenesis and mechanism of action (mRNA degradation and translational inhibition).
• The study of the transcriptome:
a) STATIC Approach: cDNA libraries, normalized, subtracted and large-scale sequencing of ESTs (Expressed Sequence Tag);
b) DYNAMIC Approach: SAGE, microarray technology and DNA chip (Affymetrix).
• bioinformatics and statistical methods used in the interpretation of the expression data.
• What biological questions can be answered through the analysis of gene expression?
• Quantitative Real-Time PCR (qRT-PCR).

PROTEOMICS (6 hours) :
• Definition of Proteome and Proteomics . What biological questions we can answer with proteomics?
• Relationship between transcriptome and proteome: the system biology .
• The two-dimensional electrophoresis: isoelectric focusing and SDS -PAGE .
• How to identify proteins in a proteome? Description of mass spectrometry ( MALDI - TOF ) .
• Analysis of differential proteome (SILAC method).
Planned learning activities and teaching methods: Lectures and experimental activities in the laboratory .
As regards the practical activity in the lab, the student will participate in the "Construction and screening of a full length cDNA library obtained by using the SMART technology ".
Additional notes about suggested reading: All resources (slides and scientific papers) used during the course will be available on the web site https://elearning.unipd.it/cmela/.
Textbooks (and optional supplementary readings)
  • Watson J.D, DNA Ricombinante. --: Zanichelli, 2008. II Edizione Cerca nel catalogo
  • Gibson G. & Muse S.V, Introduzione alla genomica. --: Zanichelli, 2004. Cerca nel catalogo
  • Brown T.A, Genomi 3. --: EdiSES, 2008. Cerca nel catalogo
  • Dale J.W., von Schantz M., Plant N., Dai geni ai genomi. --: EdiSES, 2013. III Edizione Cerca nel catalogo
  • Primrose S., Ingegneria genetica. --: Zanichelli, 2004. I Edizione Cerca nel catalogo
  • Hartwell L.H. et al., GENETICA dall'analisi formale alla genomica. --: McGraw-Hill, 2008. II Edizione Cerca nel catalogo
  • Strachan T. & Read A.P, Genetica Umana Molecolare. --: Zanichelli, 2012. III Edizione Cerca nel catalogo
  • Terry A. Brown, Biotecnologie molecolari. --: Zanichelli, 2017. II Edizione Cerca nel catalogo