Seeing to understand
Understanding living systems requires an acute knowledge of anatomic details of cells like bacteria. Given their small size below 1 micrometer, only electronic microscopy can access these structures. In collaboration with the Max Planck Institute in Munich, a cryo-microscopy project enabled to observe ribosomes distribution inside E. coli bacteria. (Florian Brandt, Stephanie A. Etchells, Julio O. Ortiz, Adrian H. Elcock, F. Ulrich Hartl, and Wolfgang Baumeister – The Native 3D Organization of Bacterial Polysomes)
Tools for discovery and conception: LifeExplorer project
The Foundation initiated the LifeExplorer project aiming at reconstructing a full E. coli bacterial cell in 3D. The construction of an interactive atlas would allow understanding bacterial cells metabolism and exploit their potential as nano factories. The Graphite-LifeExplorer software was developed by INRIA to enable researchers to assemble various molecular building blocks into macromolécule assemblies. (Samuel Hornus, Bruno Lévy, Damien Larivière, and Eric Fourmentin – Easy DNA Modeling and More with GraphiteLifeExplorer)
Tools for discovery and conception: DeepFinder tool
In collaboration between INRIA Rennes and Max Planck Institute in Munich, a software tool was conceived to identified known molecular parts inside a 3D cryo tomogram of a full bacteria. The DeepFinder software is built upon artificial intelligence techniques and is recognized as a reference tool for image analysis. (Moebel, E., Martinez-Sanchez, A., Lamm, L. et al. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nat Methods 18, 1386–1394 (2021))
New concepts : I2CELL Initiative
The idea that living systems could be understood and described as information-processing systems has been around even before the first computers were built. The initial Alan Turing’s paper in 1936 to Erwin Schrödinger’s work in 1944 and John von Neumann in 1948, opened the topic which were confirmed by the recent works of C. Lartigue on genome transplantation. I2CELL initiative aims at building a community of biologists around the use of concepts and tools from Information Technology. This initiative started by a seminar in 2018 and by a grant in 2019 which was attributed to Professor Wallace Marshall for new work on protists. Site I2CELL