Ateneo - UPO

The course aims to provide adequate knowledge of the molecular basis of biological systems, the structure and functions of biological macromolecules and the cellular processes in which they intervene; technological and biotechnological platforms of omics analysis (genomics, transcriptomics, proteomics); bioinformatics analysis tools and omics data; IT methods for biomolecular data management and analysis.
Case studies and practical exercises are proposed, focusing on the analysis of the interaction between food, environment, and human health.
Students will receive a theoretical and practical introduction to genomic and protein sequence databases and computer tools for data retrieval, mining, visualisation, and analysis.

The teaching material will be represented by the material used in class and by scientific articles and manuals, the references of which will be provided during the lessons themselves.
The following texts are then recommended:
Arthur Lesk, “Introduction to Bioinformatics”, Oxford University Press
Arthur Lesk, “Introduction to Genomics”, Oxford University Press

To provide a basic overview of the most commonly used bioinformatics tools in the field of research on the interaction between food, environment and human health. To provide basic skills in reading and interpreting scientific articles with bioinformatics content.

Basic knowledge in molecular biology and genetics.

Lectures, analysis of case studies, computer lab exercises and lessons using application software and online tools.

Classes are designed to be very interactive. Students work in groups and carry out analytical projects by putting into practise the principles learned in class.

There will be continuous oral presentations on the work done by the groups and a final oral examination. The final oral exam will consist of about three questions on the development of the group experiences and on the general topics covered.

Introduction to bioinformatics: definition, objectives, terminology, applications, and limitations.

Implication of genomics/bioinformatics for health and nutrition: understanding the molecular mechanisms underlying the relationships between food and health, from basic nutrient actions to the interactions between food microorganisms and the human intestinal system.

How to explore the knowledge: the use of PubMed to search the Medline scientific literature database, how to build an efficient and specific research string, how to plan a literature search.

The sequencing process: Sanger chain-termination method and automated fluorescence sequencing, the Next-generation sequencing method.

The sequencing data: Bioinformatics databases and tools, how to explore the main repository of genomic data:
• Genome browsers and analysis platforms: NCBI Genome (organises NCBI’s information on genomes including sequences, maps, chromosomes, assemblies, and annotations), ENSEMBL (the European eukaryotic genome resource web server), UCSC Genome Browser (the site for the genomic programme at the University of California, Santa Cruz), and Gramene genome browser (as part of the Gramene project that aggregates tools for Comparative plant genomics for crops and model organisms). Learn how they are structured, how to personalise the data displayed and how to extract information from them and. how to use them efficiently.
• The NCBI’s Blast tool: how to use it to determine the putative role of a DNA or protein sequence that are newly identified; and to find out whether a genome (or the other large sequence database) has a comparable sequence with a recognised gene.
• Gene expression database: the example of Human Protein Atlas.

How gene expression is epigenetically regulated, the example of DNA methylation. How do the laboratory analysis work, the Illumina Infinium method and the NGS method.
• The EWAS Toolkit a web toolkit for epigenome-wide association study, how to use it and understand the results.

Looking for a meaning: metabolic pathway and network of protein interaction, tools for visualization, and integrated discovery.
• The gene ontology and the food ontology, how they work and how to use them.
• Pathway analysis: learn how to integrate the extensive information on metabolic pathways available in the literature and databases, explore the protein function and interaction using the Kegg database, String, and Reactome.
• How to query the Database for Annotation, Visualization and Integrated Discovery (DAVID). this website provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes.

How to report the results, presentation and discussion of the projects conducted by students over the course.

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 visualise, analyse and interpret biological data. They will learn how to obtain information on the internet to build background knowledge on a topic related to the interaction between food, the environment and human health. They will also improve their critical thinking, learn to collaborate and carry out a research project.