Università degli Studi di Perugia

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Unit FUNCTIONAL AND STRUCTURAL GENOMICS

Course
Biotechnology
Study-unit Code
GP004130
Curriculum
In all curricula
Teacher
Manlio Di Cristina
Teachers
  • Manlio Di Cristina - Didattica Ufficiale
Hours
  • 47 ore - Didattica Ufficiale - Manlio Di Cristina
CFU
6
Course Regulation
Coorte 2018
Offered
2019/20
Learning activities
Affine/integrativa
Area
Attività formative affini o integrative
Sector
BIO/11
Type of study-unit
Opzionale (Optional)
Type of learning activities
Attività formativa monodisciplinare
Language of instruction
English
Contents
Definition of structural and functional genomics.
Structural organization of prokaryotic and eukaryotic genomes: chromosomes, heterochromatin and euchromatin, nucleosomes. Epigenetic modification of the genome.
Genome content: genes and gene related sequences (pseudogenes, miRNA), intergenic DNA (satellite DNA, transposable elements).
Human genome sequencing: cloning vectors, shotgun and "clone by clone" sequencing ; EST; automatic sequencing. Gene Expression Profile analysis: DNA microarrays; SAGE (Serial Analysis of Gene Expression); Chromatin Immunoprecipitation (ChIP) Assays. Genome and diseases.
Practical programme: Cloning of a gene encoding a human protein in bacteria: preparation of the insert and the vector, bacterial transformation and analysis of the colonies
Reference texts
J.D. Watson, T.A. Baker,S.P.Bell, A.G.Gann, M. Levine, R. Losick: Biologia Molecolare del Gene 6a Ed. Zanichelli
Craig et al.: Biologia Molecolare: Principi di funzionamento del genoma, Pearson
Lesk: Introduzione alla genomica, Zanichelli
Educational objectives
Biotechnology competence - understanding and knowledge of: i) the structure and biological properties of either virus or bacteria, including genetic modified organisms; ii) molecular methods of analysis; iv) techniques of genomic manipulation. In addition to this common knowledge, students can study in depth further knowledge based on the curriculum selected from those available (agriculture and environment, pharmaceutics, medical, molecular and veterinary curricula): genomics, proteomics, lipidomics, metabolomics.
Capability to apply knowledge and understanding of: 1) molecular biology and bioinformatics methods to proteome, metabolome and genome characterization of organisms ii) the main methods to analyze biological and pharmacological matrices.
Prerequisites
Basic knowledge in the field of organic chemistry, biology, biochemistry and spectrophotometry represent a prerequisite for student planing to follow the course with profit
Teaching methods
Lectures will be made by using slides and movies. Some lessons could be dedicated to revision and depth of issues also proposed by the students and that could involve students themselves. Practical lessons will be taught in the laboratory of Molecular Biology equipped to carry out nucleic acids analysis and purification, were the student will work autonomously, under the supervision of the teacher and the tutor. Some lessons will be taught in the laboratory of bioinformatics.
Other information
Attending classes Optional but strongly advised.
Learning verification modality
The exam consists in written and oral examination. The written examinations are designed at evaluating the student's knowledge and understanding of the topics proposed, the ability to work in laboratory and to solve problems. Since the course is constitued by three units, the examination will consist in a unique evaluation covering all the unit topics. As for the present unit, the written exam consists in fifteen multiple-choice questions followed by an essay to evaluate the ability to communicate in written form. The students have the possibility to integrate the written exam with oral examination provided they have optained at least the minimum mark 18/30.
Extended program
Genome structure and composition of prokaryotic and eukaryotic organisms
- Genetic and physical maps
- Genome size: C value
- C value paradox
- Phenotype—genotype complexities
- Structure and composition of Euchromatin and heterochromatin
- Structure and organization of eukaryotic genes
- Alternative Splicing
- Gene families
- Repeated DNA elements
- Site-Specific Recombination and Transposition of DNA
- LINE and SINE elements
- Banding pattern of chromosomes
- Cytogenetics (FISH)
- Chromosome Abnormalities: trisomy, Turner syndrome, Klinefelter syndrome, XYY syndrome.
- Polytechnic chromosomes
- Isocores
- Epigenetics
- Genome epigenetic modifications: genome acetylation, methylation and phosphorylation: histone code
- Genomic Imprinting: Beckwith–Wiedemann, Angelman, Prader-Willi syndromes
- X Chromosome: X Inactivation
- Polycomb e Trithorax groups
- Gene regulation in stem cells
- Epigenetics and cancer
- Methods for chromatin analysis: DNA and whole-genome sequencing (next generation sequencing); DNA microarrays; chromatin immunoprecipitation (ChIP)
- microRNA e RNA interference
- Lab Practical: Cloning of a human cDNA in bacteria: Preparation of competent E. coli cells. Human RNA purification, cDNA synthesis, tubulin cDNA amplification by PCR, restriction digestion of plasmidic vector and tubulin PCR product and cloning into E. coli by heat shock transformation. Colony screening by PCR. Minipreparation of plasmids and restriciton analysis
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