ANR RNAGRIMP

Participants : Florence Besse [PI] , Xavier Descombes, Eric Debreuve, Djampa Kozlowski, Nicolas Cedilnik.

Here, we propose to study the molecular bases underlying the assembly and regulation of RNA granules, using the highly conserved IMP-containing granules as a paradigm. Specifically, we propose to perform an unbiased genome-wide RNAi screen on Drosophila cultured cells to identify mutant conditions in which the organization and/or distribution of IMP-containing granules is altered. To quantitatively and statistically analyze mutant conditions, and to define precise and coherent classes of mutants, we will combine high throughput microscopy with the development of a computational pipeline optimized for automatic analysis and classification of images. The function of positive hits isolated in the screen will then be validated in vivo in Drosophila neurons using fly genetics and imaging techniques, and characterized at the molecular and cellular levels using biochemical assays, in vitro phase transition experiments and live-imaging. Finally, the functional conservation of identified regulators will be tested in zebrafish embryos combining gene inactivation and live-imaging techniques. This integrative study will provide the first comprehensive analysis of the functional network that regulates the properties of the conserved IMP RNA granules. Our characterization of the identified regulators in vivo in neuronal cells will be of particular significance in the light of recent evidence linking the progression of several degenerative human diseases to the accumulation of non-functional RNA/protein aggregates.

This 4-years project started january, 2016 and is leaded by F. Besse (iBV, Nice). Participants are iBV, institut de biologie Paris Seine (IBPS, Paris), and Morpheme.

ANR HMOVE

Participants : Xavier Descombes, Eric Debreuve.

Among the signaling molecules involved in animal morphogenesis are the Hedgehog (Hh) family proteins which act at distance to direct cell fate decisions in invertebrate and vertebrate tissues. To study the underlying process we will develop accurate tracking algorithm to compare trajectories of different Hh pools transportation in live animals. This will allow us to analyze the contribution of the different carriers in the establishment of the Hh gradient. Moreover, we will develop new methods to modify the spatio-temporal and dynamical properties of the extra-cellular Hh gradient and separate the contribution of the apical versus basal Hh pools. We will complete this study with a genome-wide screen to identify genes and related cellular processes responsible for Hh release. The particular interest of this collaboration lies in the combination of development of tracking algorithm to analyze Hh distribution and trajectories with extremely powerful genetics, ease of in vivo manipulation and lack of genetic redundancy of Drosophila.

This 4-years project started january, 2016 and is leaded by P. Thérond (iBV, Nice). Participants are iBV and Morpheme.

ANR DIG-EM

Participants : Grégoire Malandain, Xavier Descombes, Gaël Michelin.

Morphogenesis controls the proper spatial organization of the various cell types. While the comparatively simple process of patterning and cell differentiation has received considerable attention, the genetic and evolutionary drivers of morphogenesis are much less understood. In particular, we very poorly understand why some morphogenetic processes evolve very rapidly, while others show remarkable evolutionary stability.

This research program aims at developing a high-throughput computational framework to analyze and formalize high-throughput 4D imaging data, in order to quantify and formally represent with cellular resolution the average development of an organism and its variations within and between species. In addition to its biological interest, a major output of the project will thus be the development of robust general computational methods for the analysis, visualization and representation of massive high-throughput light-sheet data sets.

This 4-years project started october the 1st, 2014 and is leaded by P. Lemaire (CRBM, Montpellier). Participants are the CRBM, and two Inria project-team, Morpheme and Virtual Plants.

ANR PhaseQuant

Participants : Grégoire Malandain, Eric Debreuve.

The PhaseQuantHD project aims at developing a high-content imaging system using quadriwave lateral shearing interferometry as a quantitative phase imaging modality. Automated analysis methods will be developed and optimized for this modality. Finally an open biological study question will be treated with the system.

This 3-years project started october the 1st, 2014 and is leaded by B. Wattelier (Phasics, Palaiseau). Participants are Phasics, and three academic teams TIRO (UNS/CEA/CAL), Nice, Mediacoding (I3S, Sophia-Antipolis), and Morpheme.

Inria Large-scale initiative Morphogenetics

Participants : Grégoire Malandain, Xavier Descombes, Gaël Michelin.

This action gathers the expertise of three Inria research teams (Virtual Plants, Morpheme, and Evasion) and other groups (RDP (ENS-CNRS–INRA, Lyon), RFD (CEA-INRA-CNRS, Grenoble)) and aimed at understanding how shape and architecture in plants are controlled by genes during development. To do so, we will study the spatio-temporal relationship between genetic regulation and plant shape utilizing recently developed imaging techniques together with molecular genetics and computational modeling. Rather than concentrating on the molecular networks, the project will study plant development across scales. In this context we will focus on the Arabidopsis flower, currently one of the best-characterized plant systems.

Octopus Project

Participant : Eric Debreuve.

The Octopus project deals with automatic classification of images of zooplankton. It is conducted in collaboration with the Laboratoire d'Océanographie de Villefranche-sur-mer (LOV) et l'ENSTA Paris. The kickoff meeting took place in May 2015 and a 3-day brainstorming meeting on Deep Learning took place in December 2015. Participants are I3S (Frédéric Precioso and Mélanie Ducoffe), LOV (Marc Picheral and Jean-Olivier Irisson), and ENSTA Paris (Antoine Manzanera).