MOLECULAR BIOLOGY WITH ELEMENTS OF BIOINFORMATICS

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 experimental research, will be teached to the students. At the end of the course, the students' ability to apply their knowledge and understanding will emerge from their ability to use many of the bioinformatic analysis tools available on the web independently, and from their ability to design and develop an experimental approach in the field of Molecular Biology in order to answer the scientific questions. To this end, students will be stimulated in their autonomy of judgement and communication skills through discussion with other colleagues and interlocution with the teacher during lectures and exercises.

The teaching is held with lectures using slides and practical lessons.

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.

Knowledge of Molecular Biology

Attendance of at least 60% of the lectures is mandatory, as required by the degree course in which the course is included.

First part of the course: Bioinformatics. Primary and secondary databases. Organization of entries in databases. NCBI and EMBL and the Entrez and SRS retrieval systems. Principles of sequence alignment techniques. Concept of homology and similarity. Scoring a sequence alignment using PAM and BLOSUM matrices. Sequence alignment methods: dot matrix method, exhaustive and heuristic algorithms. Global and local sequence alignment programs. Biological significance of alignment. Alignment programs for BD screening: FASTA and BLAST. A measure of the statistical significance of an alignment. Biological significance of multialignment. Sequence multialignment methods and programs: ClustalW/Ω program, T-coffe. Definition and meaning of protein functional motifs: consensus sequences, patterns and profiles. Methods for profile generation. Pattern databases (Pfam, Smart, PROSITE). Prediction of the secondary structure of proteins: methods based on chemical-physical characteristics (DSSP, STRIDE), statistical methods (Chou and Fasman), methods using neural networks (PHD, PSIPRED, JPRED). Methods for determining the 3D structure of proteins. PDB and protein analysis databases such as Expasy and Swiss-Prot. Protein secondary structure predictions. 3D protein structure predictions: Homology modeling, Threading, Ab Initio prediction. Introduction to Molecular Dynamics. Second part of the course: Application of Molecular Biology techniques in the study of the VDAC family of mitochondrial proteins in vitro and in vivo. Design and production of recombinant proteins for use in research and industrial applications: prokaryotic and eukaryotic host cells and organisms, expression vectors, DNA manipulation, mutagenesis techniques, use of functional tags and fluorescent proteins, transfer of recombinant DNA in host cells. Study of the regulatory regions of DNA using reporter gene systems and interaction techniques between regulators and specific recognition elements on DNA. RNA regulators of gene expression: biological significance, experimental evidence, mechanisms of action. Generation of transgenic organisms: meaning and usefulness in the field of biotechnology and in the study of gene and protein function. Generation of transgenic plants: use of binary vector and cointegrated vector. Generation of transgenic Drosophila: P element-mediated transposition and GAL4/UAS-mediated regulation. Methods of generating transgenic animals: use of retroviral vectors, gene targeting by homologous recombination, use of the cre-lox site-specific recombination system.

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.

 

The examination mode consists of a written test at the end of the course that will be followed by an oral examination. This mode will be carried out only for the first available examination call after the course of lectures and for students who have regularly attended and reached the minimum attendance threshold. For subsequent calls, learning will be assessed exclusively oral examination.

The learning assessment may also be conducted electronically, should conditions require it.

The questions will focus on the topics and exercises carried out during the lessons.

Example: Given the protein x, identify the amino acid and nucleotide sequence of the corresponding mRNA through the use of databases