MOLECULAR BIOLOGY WITH ELEMENTS OF BIOINFORMATICS
Academic Year 2022/2023 - Teacher: FRANCESCA MARIA GUARINOExpected Learning Outcomes
The graduate student, of this master course, through the teaching course “Molecular Biology with Bioinformatic elements”, will be able to apply the molecular biology basic knowledge acquired with the degree of the first level, to drive an experimental approach in research field. In the first part of the course, potentials and application of bioinformatics will be highlighted. In the second part of the course, taking inspiration from a biological topics addressed in the lab of the teacher, the progression of scientific knowledge, through the tools and the logic of biomolecular research, will be teached to the students. To the end of the course, the student will be able to utilize in full autonomy tools for bioinformatic analysis and to understand the potentiality of molecular biology techniques to answer the scientific questions.
Course Structure
The teaching is held with lectures using slides and practical lessons. Slides will be uploaded on Studium platform for students. Attendance of the course is mandatory to the extent provided by the study programme.
Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes with respect to previous statements, in line with the programme planned and outlined in the syllabus.
Required Prerequisites
Detailed Course Content
First part: Bioinformatic programs for global and local sequence alignment; biological significance of sequence alignment; databases screening by alignment programs: FASTA and BLAST; Multiple sequence alignment; Clustal W program; research of structural and functional patterns in nucleotidic and proteic sequences. Genomes projects: bioinformatic methods; sequencing approach; annotations; genomic results and goals. Protein classification; determination of 3D protein structure; protein databases PDB, MMDB, Expasy, Swiss-Prot; protein secondary structure prediction; classification of functional domains; databases SCOP and CATH; protein tertiary structure prediction; homology modelling; threading; Ab Initio prediction. Second part: Molecular Biology techniques application to study VDAC a protein of mitochondrial outer membrane: characterization of VDAC isoforms biological role and identification of aminoacid and protein domains involved in channel functionality. Techniques to study gene function: recombinant protein expression, production and application; site-directed mutagenesis, construction of chimeric proteins by PCR, gene assembly by PCR; generation of transgenic organisms, standard transgenesis, gene targeting. Gene expression regulation mediated by RNA and gene silencing; analysis of gene expression
Textbook Information
S. Pascarella, A. Paiardini -Bioinformatica; dalla sequenza alla struttura delle proteine- Zanichelli.
J.D.Watson, A.A.Caudy, R.M.Myers, J.A.Witkowski-DNA ricombinante-Geni e Genomi-Zanichelli.
J.W.Dale, M.v.Schantz, N.Plant-Dai Geni ai Genomi-principi e applicazioni della tecnologia del DNA ricombinante-EdiSES.
Other additional material will be uploaded on Studium platform.
Course Planning
Subjects | Text References | |
---|---|---|
1 | Progettazione e produzione di proteine ricombinanti | J.D.Watson et al.-DNA ricombinante-Geni e Genomi-Zanichelli. |
2 | Tecniche di mutagenesi per lo studio della funzione di un gene e/o di una proteina | J.D.Watson et al.-DNA ricombinante-Geni e Genomi-Zanichelli. |
3 | Caratteristiche strutturali e funzionali della proteina VDAC. Metodi di studio della funzione di canale della proteina mediante l’utilizzo di membrane artificiali | materiale didattico fornito dal docente |
4 | Produzione di proteine VDAC ricombinanti wild-type e mutanti | materiale didattico fornito dal docente |
5 | Generazione di cellule e organismi transgenici mediante ricombinazione omologa, sito-specifica, trasposizione | J.D.Watson et al.-DNA ricombinante-Geni e Genomi-Zanichelli. |
6 | Identificazione del ruolo biologico delle proteine VDACs mediante lo studio in organismi transgenici | materiale didattico fornito dal docente |
7 | RNA regolatori dell’espressione genica: significato biologico, evidenze sperimentali, meccanismi d’azione e applicazioni | J.D.Watson et al.-DNA ricombinante-Geni e Genomi-Zanichelli |
8 | Tecniche per lo studio e l'analisi dell'espressione genica | J.D.Watson et al.-DNA ricombinante-Geni e Genomi-Zanichelli |
9 | Studio dell'espressione delle isoforme VDACs e del loro ruolo biologico in modelli di colture cellulari | materiale didattico fornito dal docente |
10 | Banche dati e sistemi di retrieval | S. Pascarella et al. -Bioinformatica; dalla sequenza alla struttura delle proteine- Zanichelli |
11 | Matrici per lo studio di sequenze. Allineamenti tra sequenze e programmi usati | S. Pascarella et al. -Bioinformatica; dalla sequenza alla struttura delle proteine- Zanichelli |
12 | Metodi e programmi per lo studio e l'analisi della struttura secondaria delle proteine | S. Pascarella et al. -Bioinformatica; dalla sequenza alla struttura delle proteine- Zanichelli |
13 | Metodi e programmi per lo studio e l'analisi della struttura tridimensionale delle proteine | S. Pascarella et al. -Bioinformatica; dalla sequenza alla struttura delle proteine- Zanichelli |
Learning Assessment
Learning Assessment Procedures
The learning assessment may also be conducted electronically, should conditions require it.