Comparative transcriptomics in Nematostella

Regeneration, as it restores missing tissue, is thought to employ processes originally used during embryonic development. If so, how does injury trigger those processes? Furthermore, are the ensuing genetic interactions similar to those of embryonic development ? This project explores the mechanistic basis of regeneration by comparing the gene regulatory networks (GRN) governing regeneration and development. To achieve this, we use the developmental model system Nematostella vectensis. This sea anemone can regrow half its body when bisected. Here we compare embryonic and regeneration RNAseq data sets to examine the global similarities and differences in transcription during these two processes.

The goals of this internship were to build a transcriptome based on RNAseq results and create a website to allow the team to quickly access, process and share their data with the research community.

Jan-Jul 2017, Team Dr. E. Röttinger under supervision of Dr. J. Warner, IRCAN, Nice, FRANCE.

Modelisation of mechanosensitive ion channels Piezo1 & 2

Piezo is a family of eukaryotic mechanosensitive non selective cation channels that was recently identified. Piezo1 was known to be involved in cell migration and vascular development and to act as a sensor of blood flow. It also has a role in human diseases such as hereditary xerocytosis and may be a key actor protein to fight malaria.

The goals of this internship were to build models of Piezo1 and Piezo2 proteins by using homology modelling and ab initio modelling. I also compared electrostatic potentials between both Piezo and looked for druggable pockets. I finally ran a molecular dynamic simulation of Piezo in a membrane.

Feb-Jul 2016, Team Dr. G. Lambeau under supervision of Dr. D. Douguet, IPMC, Sophia-Antipolis, FRANCE

Storing digital information in DNA

In recent years, the storage capacity of hard disk drives or USB flashdrives has grown exponentially. But long term data storage is still a challenge and few methods could survive more than a few decades. Furthermore, storing large amounts of data takes a lot of physical space. This is concerning as the total world data is expected to boom during the next few years. DNA could be the key to solve both problems. Indeed, DNA could easily last hundreds of years and a few kg of DNA could be sufficient to store today's world data.

This project aimed to develop a programm allowing us to convert digital information into a DNA sequence. Several problems were to be considered : errors could occur during synthesizing, decoding or storing the DNA and DNA fragments could not exceed 150bp length. The data was therefore cut into small fragments, then fragments were assigned a header with position information and encoded with an error correction algorithm (reed solomon allowing to correct until 10 mistakes/150 bp). Finally the data were encoded into DNA and stored. The original message (text or image) could be retrieved after translating the DNA, decoding the text with the reed-solomon key and sorting them with the positional information.

Summer 2015, supervised by Dr. P. Barbry and Dr. K. Robbe, IPMC, Sophia-Antipolis, FRANCE

22-23 octobre 2016 : project presentation, "fête de la sciences", Antibes