Background:
Infectious diseases continue to be a major public health problem. Diverse infections from bacteria, fungi, parasites, virus, etc… continue to be a worldwide burden. Indeed, the current spread of infectious diseases from the first to the third world countries rise an important public health concerns. The need for better infrastructures and prevention strategies is joint to a better understanding of the host-pathogen interaction. This knowledge is fundamental to identify prognostic, diagnostic and predictive biomarkers and to identify molecular targets for better therapies and patients stratification. Indeed, the current mass drug administration for most of the infectious diseases irrespective of the disease status, patient response and drug-resistance calls for better elucidation of the pathology. The twentieth century has seen a revolution in the way we study infectious diseases. Nowadays, biological systems are considered as “systems” where the total is more than the sum of the individual parts requiring a complete understanding of the connection between the parts to have a comprehensive knowledge. This understanding is possible due to the joint forces of multi-omics sciences such as genomics, transcriptomics, proteomics, lipidomics and metabolomics. These sciences are used to connect each biomolecule and build networks that are perturbed by the pathogen and to build a predictive model to prioritize biomolecules for therapy. Indeed, the knowledge of gene mutations, mRNA expression, splicing variants, miRNA, differential protein and PTMs expression, changes in lipid and metabolites quantity… require an interdisciplinary task force that works on the acquisition and interpretation of the data to better understand the biological system. The course entitled: Omics Sciences in Infectious Diseases” will focus on the theory of the Genomic, Transcriptomic, Lipidomic and Proteomic sciences explaining the methodological and technological developments along the years. Moreover, several hands-on classes will be given to put in practice the theoretical principles. These practical classes will be given in the form of laboratory experiments and instrument acquisition on biological samples and bioinformatics sessions. The practical part constitutes the differential of this course since every student will learn not only the principles of each discipline but also the tips and tricks of large-scale omics experiments. Several classes from professors and postdocs working with infectious diseases and omics disciplines will be given to see the application of these disciplines to real life samples. Moreover, each student will have the possibility to visit mass spectrometry core facilities and laboratories of companies to have the possibility to actually perform the experiments taught in the course.
Teaching program:
- Introduction to the course (Prof. Dr. Giuseppe Palmisano)
- Genomics (Prof. Dr. Joao M.P. Alves)
- What is genomics and why do we need genomics?
- Explanation of the genomic principles;
- Experimental approaches to genomics;
- Algorithms;
- Genomics data handling with the freely available and open source platforms;
- Lectures from researchers working with infectious diseases and genomics;
- Online and command line software and available genomic databases (practical part);
- Transcriptomic (Prof. Dr. Helder Nakaya)
- What is transcriptomics and why do we need transcriptomics?
- Explanation of the transcriptomic principles;
- Old and Next generation sequencing;
- Algorithms;
- Transcriptomics data handling with the freely available and open sources platforms;
- Lectures from researchers working with infectious diseases and transcriptomics;
- Available bioinformatics tools and databases for transcriptomic data analysis (practical part);
- Proteomics (Prof. Dr. Giuseppe Palmisano)
- Mass spectrometry: principles and instrumentation;
- What is proteomics and why do we need proteomics?
- Explanation of the proteomics principles from sample preparation to analysis;
- Quantitative proteomics and PTMs;
- Software for protein analysis;
- Lectures from researchers working with infectious diseases and proteomics;
- Protein extraction, digestion and desalting (practical part);
- Database search (practical part);
- Lipidomics/Metabolomics (Prof. Dr. Sayuri Miyamoto)
- What is lipidomics and why do we need lipidomics?
- Explanation of a lipidomic experiment;
- Sample preparation and analysis of a lipid extract;
- Software and databases;
- Lectures from researchers working with infectious diseases and lipidomics/metabolomics;
- Lipid extraction from a biological source and mass spectrometry-based analysis (practical part);
- Data analysis (practical part);
Coordinator:
Prof. Dr. Giuseppe Palmisano (ICB-USP), GP
Teachers of the course:
Prof. Dr. Joao M. P. Alves (ICB-USP), JMP
Prof. Dr. Helder Nakaya (FCF-USP), HN
Prof. Dr. Sayuri Miyamoto (IQ-USP), SM
Course assistants:
Dr. Claudia Blanes Angeli (ICB-USP)
Dr. Rebeca Kawahara (ICB-USP)
Gilberto Santos de Oliveira (ICB-USP)
Joyce Silva Saad (ICB-USP)
Victoria Rocha (ICB-USP)
Sayuri Miyamoto laboratory (IQ-USP)
Objectives:
This course will provide a multi-disciplinary environment to learn the theoretical principles and apply them in the practical sessions. The theoretical classes will be given in order to introduce the subject and show the latest developments in the field. The practical sessions will be focused on applying to different biological systems the different analyses. Lectures from several researchers working with infectious diseases and omics sciences. Moreover, each student will visit core facilities and companies to run their samples for their own projects. Each professor is highly qualified to give this course offering her/his knowledge to each student. Due to that, a large forum to discuss the latest developments of the omics sciences and to apply them to each project will be possible.
At the end of the course each student will be able to:
- critically read a paper involving omics sciences;
- understand the principles and methodologies of omics sciences;
- reproduce an experiment involving omics sciences;
- search in publically available databases the large-scale experiments performed by other researchers;
- transfer the information of existing facilities and companies to other researchers;
Along with sharing new approaches and insights, we hope to generate new collaborative research, and the schedule will be designed to allow plenty of time for interactions beyond the lectures.
Language:
The course will be taught in Portuguese. However, if one English-speaking student is enrolled, the course will be taught in English.
Teaching Methods and Course Materials
The course consists of a theoretical and practical part. The theoretical part of the course will consist in lectures. The practical part will consist in computer sessions, presented in a computing laboratory and experimental session performed in specific laboratories. All materials will be provided as pdf files. The software and links used will be provided. A laptop will be needed; however, the computer session could be performed in small groups. The course is limited to 30 participants. If more than 30 students will be subscribed to the course, the teachers will select based on the following rules: 1) the order of subscription; 2) one person per laboratory; 3) academic degree and 4) motivation letter.
Assessment:
The formal assessment will be the formulation of several questions for the researchers working with infectious diseases that will present dedicated lectures during the course. The name and the lecture title of each researcher will be given at the beginning of the course so each student will have the possibility to read the latest papers of that research group and formulate questions. A certificate of attendance will be provided if needed.
| Time | Monday 03/07 | Tuesday 04/07 | Wednesday 05/07 | Thursday 06/07 | Friday 07/07 | Saturday/Sunday |
|---|---|---|---|---|---|---|
| 9:00-12:30 | GP (Prot) | GP (Prot) | GP (Prot) | HN (RNA) | HN (RNA) | |
| 12:00-14:00 | Lunch | Lunch | Lunch | Lunch | Lunch | |
| 14:00-17:00 | GP (Prot) | GP (Prot) | GP (Prot) | HN (RNA) | HN (RNA) |
| Time | Monday 10/07 | Tuesday 11/07 | Wednesday 12/07 | Thursday 13/07 | Friday 14/07 | Saturday/Sunday |
|---|---|---|---|---|---|---|
| 9:00-12:30 | JMP (Gene) | JMP (Gene) | GP (Prot) | GP (Prot) | Visits | |
| 12:00-14:00 | Lunch | Lunch | Lunch | Lunch | Lunch | |
| 14:00-17:00 | JMP (Gene) | JMP (Gene) | GP (Prot) | GP (Prot) | Visits |
| Time | Monday 17/07 | Tuesday 18/07 | Wednesday | Thursday | Friday | Saturday/Sunday |
|---|---|---|---|---|---|---|
| 9:00-12:30 | SM (Lipid) | SM (Lipid) | ||||
| 12:00-14:00 | Lunch | Lunch | ||||
| 14:00-17:00 | SM (Lipid) | SM (Lipid) Concluding remarks |
*Some days the time indicated in the calendar might be subjected to variations due to the practical part and the time for visits and discussion forum.