Ateneo - UPO

The course provides a comprehensive overview of the molecular basis of biological systems, the structure and function of biological macromolecules, and the cellular processes in which they participate. It introduces students to biotechnological omics platforms (genomics, transcriptomics, proteomics) along with specialized bioinformatic tools and computational methods for biological data management. Practical case studies and hands-on computer lab sessions focus specifically on the interaction between food, environment, and human health. Students receive a comprehensive introduction to genomic and proteomic databases as well as software tools for data retrieval, visual mapping, critical interpretation, and functional analysis. 

The educational material will consist of the material used in class, as well as scientific articles and manuals, the references for which will be provided during the lessons.
Students who need to deepen their understanding of the biological aspects are recommended the following text: Arthur Lesk, 'Introduction to Genomics,' Oxford University Press.

The course aims to deliver the fundamental theoretical concepts and practical methodologies of bioinformatics, specifically applied to studying the complex interplay between diet, environment, and human health. It focuses on empowering students to independently search, analyze, and interpret scientific literature with a bioinformatics component, as well as establishing the technical foundations needed to model and investigate molecular networks and pathways.

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 will complete practical exercises designed to apply the core concepts addressed during lectures.

Students with physical disabilities, Learning Disabilities or Special Education Needs can request
specific services and tools via the
, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities

Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination
modalities, concerning academic aspects.

Student evaluation is continuous and based on:
1. In-course assignments: Regular practical exercises to evaluate the steady acquisition of practical skills.
2. Final Project: A practical case study analyzed during the final lab session, testing analytical independence, critical evaluation, and cooperative work.
3. Oral Exam: A final interview covering the defense of the project report and general theoretical topics, specifically verifying critical analysis, communication capacity, and proper terminology.
The final grade is a synthesis of the oral interview, the quality/timeliness of assignments, and the final project report.

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 are expected to achieve the following learning outcomes: 1. Knowledge and understanding: Describe the structure and purpose of major biological databases and genome browsers (NCBI, Ensembl, UCSC, Gramene). Explain the theoretical principles of sequence alignment (BLAST) and statistical parameters of significance. Understand epigenetic regulation mechanisms (DNA methylation) and functional annotation systems (Gene Ontology, Food Ontology). 2. Applying knowledge and understanding: Query genomic repositories to retrieve target DNA or protein sequences in standard formats. Run BLAST searches to identify unknown sequences and map variants/mutations. Use tools such as EWAS Toolkit, DAVID, and pathway resources (KEGG, Reactome, STRING) to model biological networks and interpret omics datasets. 3. Making judgements: Critically evaluate qualitative and quantitative outputs from computational and epigenetic modeling software. Integrate heterogeneous biological data to formulate hypotheses on molecular mechanisms linking dietary/environmental exposures to human pathological outcomes. 4. Communication skills: Present, illustrate, and defend the results of their final bioinformatics projects using accurate scientific, biological, and computational terminology. Collaborate effectively in teams to convey complex findings to peer groups and instructors. 5. Learning skills: Acquire the academic independence required to query online databases and research literature databases (PubMed) to build foundational knowledge on novel topics in human health and nutrition. Develop the methodological flexibility to adapt to and utilize newly emerging web platforms and bioinformatics technologies.