In living organisms, gene expression is finely regulated by the joint action of regulatory proteins. Among these proteins, transcription factors (TFs hereafter) play a key role since they bind specific sequences in the promoters of genes to initiate their regulation. TFs can combine to form complexes and regulate the expression of new genes or to alter the direction or level of regulation of genes already targeted by one of the two TFs alone. The complexes thus diversify the repertoire and regulatory levels of genes targeted by the transcription factors. Little is known about the extent of this phenomenon, the number of complexes, the identity of the partners and the way they bind to DNA. This project proposes to develop a bioinformatics model to predict the existence of protein complexes formed by transcription factors and likely to regulate gene expression in the plant Arabidopsis thaliana. In a second phase, the project will explore the predictions of the model to verify the existence of the predicted complexes, and to characterize their DNA binding mode and their target genes. The discovery of new complexes will be done by developing a model that integrates clues scattered in different types of genomic data. These clues are (i) the common binding of the TFs on promoter regions, the motifs and combinations of DNA motifs bound by the TFs on these bound regions, (i) the co-expression of the TFs, (iii) the target genes common to both TFs, and (iv) the co-evolution of amino acid residues between the two TFs forming a complex. The model will be obtained by machine learning on these data: the model will be built and its parameters adjusted to optimize the predictions against a set of TFs known to form complexes. Newly predicted interactions, in particular those between transcription factors studied in our lab and new partners, will be explored in detail to understand how these complexes form (interaction surface), how they bind DNA and to know which genes and functions they regulate. The results of the model will be represented in the form of an interaction network for all Arabidopsis thaliana TFs.. This network will be made available to the community so that biologists can in turn explore the potential partners of their favorite TFs. In the medium term, the model could be applied to other plant species such as rice and maize, two species characterized by extensive genomic data. This approach represents a considerable time saving compared to the genetic method and works even in the case where several TFs play a redundant role.

The aim of the EXCALYB project is to develop the processes, material stacks and CMOS integration for new types of high density, highly scalable non-volatile memories. This will allow for high density (feature size <20nm corresponding to 1 Tbit/in²) with high data rates, as well as a very significant reduction of power consumption of electronic circuits in standby mode. EXCALYB project aims to establish an innovative sub-20nm technology platform to be used in the evaluation of magnetic tunnel junction based spintronic devices at nanoscale dimensions. The developed process flow will not be specific only to MRAM cells, and could be used to evaluate any device based on magnetic tunnel junctions, such as spin-torque oscillators, magnetic field sensors and generally any electrically connected pillar device having magnetic materials. A successful integration will provide an alternative approach for the evaluation of integrated hybrid circuits, using CMOS and magnetic elements. This low-cost platform unique in France is complementary with ongoing efforts to create 200/300mm magnetic backend lines. The proposed alternative significantly reduces the costs associated with evaluating circuit designs that include magnetic tunnel junctions. The cost reduction comes from the fact that the 3 to 4 backend mask levels are not required each time a new design needs to be evaluated. Mask reticles for 200/300mm magnetic backend process can account for significant initial costs, becoming the major roadblock to use emergent technology used in new applications. The EXCALYB project aims to provide the technology missing for these applications, requiring the availability of high performance non-volatile memory with associated non-volatility for very low-power consumption. The project will allow demonstrate these devices and explore their scalability in future generations, by reducing the cell size for extreme integration low power operation. EXCALYB will leverage the existing knowledge of each partner to achieve a significant scientific and technological breakthrough. Magnetic memory cell concept breakthroughs pursued in this project could be used directly in novel MRAM memory implementations by Crocus Technology. The explored concepts provide a clear technology roadmap for MRAM below 20nm cell sizes. This will allow strengthening the intellectual property and know-how enabling the deposition of devices with important industrial applications. It will strengthen the position of Crocus Technology as a French/European contender in the high performance non-volatile arena. The research involves in particular bringing to maturity a perpendicular MTJ stack for sub-20 dimensions using thermal assistance for the spin torque writing process. Our own initial results have shown the world best figure of merit between thermal stability and writing current. There is considerable improvement to expect from the first demonstration, especially in terms of TMR amplitude, leading to even higher values of thermal stability to STT switching current ratio. Establishing a process flow to sub-20nm dimensions will allow experimental validation of the expected scalability. It will be a significant breakthrough to validate ultimate density perpendicular cells, in both standalone cells and in integrated hybrid circuits. The concept of hybrid non-volatile circuits is extremely appealing due to the stand-by power savings that it can achieve. The in-plane self-reference cells represent a low-density high value application for embedded high temperature applications MRAM that could quickly find market acceptance. The project will test the scalability of current cells, and provide the material research necessary to scale these cells down to 45nm, corresponding to 3 additional technology generations from the current 130nm cell size.

Drug resistance is still a daunting challenge in patient treatment, and can dramatically impact prognosis. It can be found in many clinical settings and can originate from many causes. In this proposal we focus on the first line of defense, which is the drug extrusion out of the cell by ABC transporters; they harness the energy of ATP binding and hydrolysis to expel drugs out of the cell, thereby decreasing their intracellular concentration below cytotoxic levels. They undergo such expulsion by changing conformation as a response of ATP binding, moving from inward-facing where they accept substrates to outward-facing where they expel them. Often, ABC transporters are able to transport a wide range of substrates, thus protecting the organism against many drugs and leading to the multidrug resistance phenotype. How these transporters are able to handle many drugs is still widely discussed and is the core of this proposal. We focus on the ABC transporter BmrA from B. subtilis for which we have a lot of structural data. We were able to first capture it in the outward-facing conformation in complex with its substrate Rhodamine 6G (R6G), the only structure like this today. We are now characterizing the transition from Inward- to outward-facing, through many cryoEM datasets at key concentration points; notably, the transporter binds ATP the Michaelian way in absence of R6G, but changes to Allosteric when in complex. During this proposal, the consortium will study this transition via 3 main Tasks; 1/ at steady state, to observe changes of population in response to drug binding or in different amphipathic environments. 2/ The conformational change will be investigated in a time-resolved manner (biochemistry + tr-cryoEM). 3/ We will explore intermediates using in-silico simulations to reconcile the experimental data. Ultimately, we wish to understand the mechanic of BmrA and how it is able to use plastic deformations to transport and adapt to multiple substrates.

Photosynthesis is a fascinating source of inspiration to design innovative molecular devices for the conversion and storage of solar energy. Applications of interest however rely on multielectronic catalytic processes whereas light-driven processes are single-electron events in essence. Nature perfectly masters this apparent mismatch thanks to specific cofactors, able to accumulate and then to relay two electrons at a time by coupling these processes with proton transfers. PhotoAcc thus aims at developing novel charge photoaccumulation systems, by taking inspiration from such biological cofactors, flavins in particular. The project will benefit from the complementary expertise of the four internationally recognized research groups to (i) undertake their synthesis supported by a (TD)DFT-predictive approach to allow tailormade optoelectronic properties, (ii) to decipher their electronic properties by virtue of various electrochemical and spectroscopic characterizations, including advanced EPR techniques to identify the electron storage sites, and (iii) to assess their activity in light-driven multielectron/multiproton redox processes.

Linear motifs are short sequence stretches that occur in intrinsically disordered protein regions (IDRs) lacking stable secondary and tertiary structure, and mediate vital interactions within various biological systems. An exemplary system for the presence of IDRs and a high concentration of linear motifs is the clathrin mediated endocytosis machinery of the eukaryotic cell, where a complex interaction network of IDR-rich adaptor proteins enables both protein and lipid interactions. The molecular mechanism of such interactions, especially when multiple motifs act in concert, is however only poorly understood particularly since the dynamic and flexible nature of IDRs makes them a very difficult object to study. I aim to develop an integrative approach based on single molecule fluorescence and NMR spectroscopies to characterize the molecular principles of IDRs in clathrin mediated endocytosis. A systematic analysis of IDRs with different types of motifs and various interaction partners will not only shed light on the molecular functions of linear motifs within endocytosis, but also on how multiplicities of linear motifs may work in various biological processes in general. In vitro structural studies will be connected with single molecule imaging to relate molecular conformation with function within the cell.