Educational offer - University of Padova

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 . (5 multiple-choice, 10 open questions, one exercise on restriction maps and one question about the practical laboratory)
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.
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 Gibson G. & Muse S.V, Introduzione alla genomica. --: Zanichelli, 2004. Brown T.A, Genomi 4. --: EdiSES, 2018. Dale J.W., von Schantz M., Plant N., Dai geni ai genomi. --: EdiSES, 2013. III Edizione Primrose S., Ingegneria genetica. --: Zanichelli, 2004. I Edizione Binelli G. & Ghisotti D., GENETICA. --: EdiSES, 2018. I Edizione Strachan T. & Read A.P, Genetica Umana Molecolare. --: Zanichelli, 2012. III Edizione Terry A. Brown, Biotecnologie molecolari. --: Zanichelli, 2017. II Edizione Amaldi F., Benedetti P., Pesole G., Plevani P., Biologia molecolare. --: Casa Editrice Ambrosiana, 2018. III Edizione Helmer Citterich M., Ferrè F., Pavesi G., Romualdi C., Pesole G., Fondamenti di bioinformatica. --: Zanichelli, 2018. I edizione