3. CRISPR WARS: The Gene Strikes Back

Luis Povoas (Gene Translation Laboratory) 

Some years ago, during the process of constructing a fly model to study human diseases our lab found a very interesting protein that seems to be responsible for many different processes in the cell. This protein is a derivate of a group of proteins responsible to introduce amino acids in tRNA, to enable protein synthesis. We called it SLIMP (seryl-tRNA synthetase-like insect mitochondrial protein). Past studies suggest that this new protein has acquired an essential function in insects, being one of the most interesting results obtained so far, the role of SLIMP in cell cycle progression. To uncover more of SLIMP’s functions, our lab is using a revolutionary technology that changed the way we make science. This technology is the CRISPR editing system. This tool enables us to precisely edit the genome of live cells. With it, we can remove genes (knock-out), introduce genes (knock- in), introduce markers to follow a specific protein (tags) and others. Therefore, with this technology, we expect to uncover SLIMP intracellular location, protein-protein interactions and try to understand the SLIMP knockdown phenotypes in relation to DNA damage and cell cycle checkpoints. During this workshop, you will be introduced to concepts of molecular cloning, cell culture and CRISPR technology. May the science be with you!

The budding yeast Saccharomyces cerevisiae, a well-established eukaryotic model organism, has several advantages: ease of manipulation, short life span, ability to produce a large number of offspring and a sequenced genome. We use S. cerevisiae to study the adaptive eukaryotic responses to a variety of environmental stresses. Remarkably, many processes initially discovered and studied in yeast, are conserved in higher eukaryotes, such as transcription regulation, stress-signaling transduction and cell cycle regulation. 

Yeast and mammals share a conserved family of proteins that sense and respond to environmental changes known as Stress-Activated Protein Kinases (SAPKs). The activation of SAPKs leads to a set of adaptive responses that involve the modulation of several physiological processes like changes in gene transcription, cell metabolism, protein translation and cell cycle progression.

In this practical course, we will learn how to manipulate and work with S. cerevisiae to understand how cells detect and respond to external signals in order to ensure survival. For this purpose, we will study at the protein level the activation of Hog1 SAPK upon different stress conditions and examine the cell fitness of different mutant strains when subjected to environmental insults.

4. An omics complex puzzle? Let’s decipher it by using Bioinformatics!

Olfat Khannous (Comparative Genomics) & Marina Murillo (Gene Translation Laboratory)

Complex biological diseases such as cancer and Alzheimer are caused by a combination of genetic and environmental factors, and in many cases, we have not yet identified or established a relationship between them to shed light to the understanding of the origin and progression of such biological problems.

Multi-omics profiling and integration combines different types of data for a better understanding of these complex diseases. 

One of the branches of the ‘Omics’ sciences is transcriptomics which involves the study of all the RNA molecules (including mRNA, tRNA, rRNA, and other non-coding RNAs) within a cell, otherwise known as the transcriptome. Consequently, by analyzing the transcriptome researchers can determine if a gene is turned on or off in the cells and tissues of an organism.

On the other hand, metagenomics is the study of the genetic material (genomes) from a mixed community of organisms of a sample. It allows us to describe which microbial communities are living within each individual (microbiome) and its relationship with host genetics, diet and environment can reveal links with disease or health.

In our workshop you will be immersed in the computational world (dry lab) understanding its synergy with the experimental lab (wet lab), and you will learn how to obtain transcriptomics and metagenomics data and also how to use bioinformatics tools to analyze them and to add missing pieces to these mentioned complex puzzles.

5. CRISPR/Cas9 to generate a KO

Camilla Bertani (Translational Control of Cell Cycle and Differentiation)

Our laboratory is focused on studying a family of proteins called Cytoplasmic Polyadenylation Element Binding Proteins (CPEBs), which are sequence-specific mRNA- binding proteins that control translation in development, health and diseases, such as cancer. A useful approach to evaluate the role of these proteins in cancer cells is to induce their deletion (knockout (KO)) and to evaluate the resulting phenotype.

For this reason, in the laboratory we have designed a possible genomic editing approach, based on the CRISPR / Cas9 technique. Our aim is to induce the deletion of an exon present in the genomic sequence of these proteins in order to block their functionality. Before being able to evaluate the final phenotype, it is necessary to evaluate which clones obtained presents the deletion of the exon. Thus, in this workshop, we will analyze the DNA of these clones using a technique called PCR.