Ateneo - UPO

The module aims to provide the basic methodological skills required to use the main web-based bioinformatics platforms. Students will acquire the ability to query primary biological databases, extract nucleotide and protein sequences, perform sequence alignments for the identification of homologies and mutations, and utilize computational prediction tools to study post-transcriptional regulation, in close synergy with the theoretical contents of the Molecular Biology course.

The module aims to provide students with the theoretical and practical skills required to use the main web-based bioinformatics platforms. 

The module aims to provide students with the essential methodological and practical skills required to use the main web-based bioinformatics platforms. The primary objective is to bridge the gap between biological theory and computational analysis, working in close synergy with the theoretical contents of the Molecular Biology course. Through interactive lectures and practical exercises based on detailed analytical protocols, the course aims to enable students to independently retrieve biological information from databases, perform mutational analysis on genes of clinical interest, and study the post-transcriptional regulation of gene expression.
By the end of the course, students are expected to achieve the following objectives:
- Knowledge and understanding: Understand the structure of key biological databases (NCBI, UniProt) and the theoretical principles behind alignment algorithms (BLAST) and computational prediction.
- Practical skills: Develop independence in extracting gene and protein sequences, performing alignments to identify homologies and mutations, and using computational tools to study post-transcriptional regulation (TargetScan).
- Judgment skills: Develop the ability to critically interpret qualitative and quantitative data from the analyzed software outputs.

The Molecular Biology lecture course will provide the essential background and foundational knowledge necessary to undertake the laboratory work.

Assessment for this module is Pass/Fail (Idoneo/Non idoneo) and is based on the quality and completion of the practical exercises completed during laboratory hours.

The final assessment to obtain the laboratory credit consists of a 30-minute computer-based test. The exam will feature a multiple-choice quiz (12–15 questions) focused on the critical interpretation of graphical and tabular outputs generated by the tools analyzed during the course (e.g., BLAST alignment screens, NCBI records, microRNA targeting tables). This test aims to assess the student's ability to navigate web interfaces and extract the required biological data.

Lectures (8 Hours)

• Unit 1 (2 hours): Architecture of Primary Biological Databases and Sequence Extraction. Introduction to the NCBI (National Center for Biotechnology Information) portal. Structure of gene records: annotation of exons, introns, regulatory regions, and splicing variants. The FASTA standard format for nucleic acids and proteins. Introduction to the UniProt database for protein domain analysis.
• Unit 2 (2 hours): Local Sequence Alignment Algorithms (BLAST). Theoretical principles of local alignment. Use of the NCBI BLAST tool (BLASTn) for the identification of unknown sequences. Interpretation of macroscopic output parameters (percent identity, query coverage) for the characterization of nucleotide variants and point mutations.
• Unit 3 (2 hours): Comparative Genomics and Applied Molecular Phylogeny. Pairwise Sequence Alignment of orthologous sequences. Analysis of evolutionary conservation between different organisms (e.g., Homo sapiens vs Mus musculus), supporting the understanding of transgenic animal models and gene targeting.
• Unit 4 (2 hours): Post-Transcriptional Regulation and microRNA Target Prediction. MicroRNAs as modulators of gene expression. Introduction to computational prediction databases based on thermodynamic pairing and phylogenetic conservation of the 3'-UTR region of transcripts (TargetScan). Analysis of the combinatorial nature of microRNA-target interactions.

Practical Exercises (2 sessions of 4 Hours each)

• Laboratory 1 (4 hours): Mutational Analysis and Structural Characterization of Oncogenes and Tumor Suppressors
• Phase A: Querying the NCBI Gene database to extract reference sequences of tumor suppressors (e.g., TP53) in FASTA format and analyzing their exonic architecture.
• Phase B: Alignment of simulated clinical sequences (healthy vs. oncological patient) using BLASTn to identify single nucleotide mutations (gain of function in oncogenes like KRAS or loss of function in TP53). Mapping of the mutation to the corresponding protein domain via UniProt.
• Laboratory 2 (4 hours): Comparative Genomics and Post-Transcriptional Regulatory Networks
• Phase A: Alignment of homologous sequences to determine the evolutionary conservation index of cell cycle target genes between humans and murine models.
• Phase B: Use of the TargetScan portal to identify microRNA-mediated regulatory networks on the previously analyzed oncogenic or tumor suppressor transcripts, verifying the specificity and density of the binding sites.

By the end of the course, students will have a deeper understanding of the principles of bioinformatics and will be able to use basic bioinformatics tools and techniques to visualize, analyze, and interpret biological data. 

Specifically, the expected learning outcomes are structured as follows:

• Knowledge and understanding: Understand the organization of primary biological databases (NCBI, UniProt) and the structure of gene annotations (exons, introns, splicing variants). Learn the theoretical principles of local alignment algorithms (BLAST) and their statistical significance parameters (percent identity, query coverage). Understand the computational and thermodynamic mechanisms underlying the prediction of microRNA-target transcript interactions. 
• Applying knowledge and understanding: Ability to independently query bioinformatics web portals and extract sequences in FASTA format. Ability to perform nucleotide alignments (BLASTn) to identify point mutations in clinical sequences and map their effects onto protein domains. Ability to conduct comparative genomics analyses (pairwise alignments) to evaluate target gene conservation between humans and murine models. Ability to use predictive databases (TargetScan) to map post-transcriptional regulatory networks on genes of interest. 
• Making judgements: Develop the ability to critically interpret graphical and tabular outputs generated by the analyzed tools (BLAST screens, NCBI records, targeting tables). Ability to correlate a bioinformatics data point (e.g., the presence of a mutation or a microRNA binding site) to its potential biological, functional, or clinical impact. 
• Communication and learning skills: Use correct scientific and computational terminology to describe the results of bioinformatics analyses. Develop the methodological flexibility and operational independence required to successfully navigate and utilize new web interfaces and emerging biological databases.