Travel Report: Pau Farré, Physics

November 24, 2015

Pau Farré, a Doctoral student in Physics, received a Graduate International Research Travel Award (GIRTA) to further his research in Toulouse, France. His report:

Thanks to the Graduate International Research Travel Award (GIRTA), I was able to be in France during the summer of 2015 and work at "The National Centre for Scientific Research/Le Centre national de la recherche scientifique" (CNRS), in Toulouse. This was a great experience that allowed me to interact with a great number of research teams, and thus expand my knowledge about the biological system that I study, along with creating connections with scientists with similar research interests.

My research project consists of developing models that explain how the DNA of eukaryotic cells like ours generate and maintain complex structures inside their nuclei. In humans, almost two metres of DNA is tightly compacted into a volume smaller than the tip of a needle. This compaction is done in a highly organized manner, where parts of the DNA that are not used at the moment are tightly coiled up, while the ones in use stay in a looser configuration, allowing for DNA machinery to access it.

In addition, parts of the DNA that share common functionality are brought spatially close to each other, regardless of their genomic distance in the DNA strand, allowing for a better regulation. The nucleus of a cell is thus a highly complex system that accommodates the simultaneous activity of a great number of different mechanisms, analogous to the functioning of a busy city. With the help of physics, computer simulations, and big-data analysis, I generate hypotheses about the possible key-drivers of DNA configuration in the Emberly Group (SFU Physics). These ideas are then tested by the experimental biologist collaborators we continuously interact with.

The GIRTA offered me the opportunity to travel to the south of France, where I could actively collaborate with the Cuvier Lab (CNRS, Toulouse), a team of experts on the conformation of DNA. There, I learned the necessary tools to work with data on the genomic location of nucleosomes, protein complexes that DNA can wrap around. During my stay I developed novel tools that allowed for the identification of regions of the DNA where nucleosomes and other proteins attached to it differ in their configuration. This is an ongoing long-term collaboration that brings light onto how different biological mechanisms affect the positioning of nucleosomes under different genetic contexts.

In addition, I also had the chance to visit the Nollmann Lab (CNRS, Montpellier). This team uses super-resolution spectroscopy to observe in real time the different conformations that DNA adopts. This visit resulted in a research collaboration, and I am currently accompanying those measurements with simulations.

The experience of spending a semester abroad has been very positive, as I could learn more about my research interests and interact in person with our research collaborators, while experiencing another culture. The south of France is an amazing place, and I felt really connected to the city of Toulouse and its people from the very first moment. The only challenge was learning French, which turned out to be far more difficult than what I anticipated.

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