Data-Gouv-ML/pcri-erc-participations-et-projets-laureats huggingface dataset:
Projet ERC : BacNanoMachine (Horizon 2020, appel 2019, Consolidator grants)
Domaine scientifique : Life Science
Panel : Integrative Biology: from Genes and Genomes to Systems
Entité participante : Humboldt-Universität zu Berlin — Pays : Allemagne — Rôle : PI
Acronyme de l'entité : HU
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1934950.0 €

Life has evolved diverse protein machines and bacteria provide many fascinating examples. Despite being unicellular organisms of relatively small size, bacteria produce sophisticated nanomachines with a high degree of self-organization. The motility organelle of bacteria, the flagellum, is a prime example of complex bacterial nanomachines. Flagella are by far the most prominent extracellular structures known in bacteria and made through self-assembly of several dozen different kinds of proteins and thus represents an ideal model system to study sub-cellular compartmentalization and self-organization. The flagellum can function as a macromolecular motility machine only if its many building blocks assemble in a coordinated manner. However, previous studies have focused on phenotypic and genetic analyses, or the characterization of isolated sub-components. Crucially, how bacteria orchestrate the many different cellular processes in time and space in order to construct a functional motility organelle remains enigmatic. The present proposal constitutes a comprehensive research program with the aim to obtain a holistic understanding of the underlying principles that allow bacteria to control and coordinate the simultaneous self-assembly processes of several multi-component nanomachines within a single cell. Towards this goal, we will combine for the first time the visualization of the dynamic self-assembly of individual flagella with quantitative single-cell gene expression analyses, re-engineering of the genetic network and biophysical modeling in order to develop a biophysical model of flagella self-assembly. This novel, integrative approach will allow us to move beyond the classical, descriptive characterization of protein complexes towards an engineering-type understanding of the extraordinarily robust and coordinated assembly of a multi-component molecular machine.

Mots-clés : bacterial flagellum,motility,self assembly,gene regulation,protein secretion,type iii secretion system,fluorescence microscopy,time lapse microscopy,salmonella enterica
Projet ERC : EcolMetabOrigin (Horizon 2020, appel 2020, Advanced grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
Entité participante : Heinrich Heine University Düsseldorf — Pays : Allemagne — Rôle : PI
Acronyme de l'entité : HHU
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2490000.0 €

Life is a chemical reaction. Over 1000 individual reactions are driven in the direction of cell growth by the coupling of biosyntheses to environmentally available exergonic reactions that are harnessed by a handful of enzymes in energy metabolism. How, where, and from what the chemical reaction of life arose, and how the primordial diversification of metabolism proceeded are the topics of this proposal. Evidence for the process of metabolic origin and traces from the very early course of microbial evolution should be preserved in the chemical reactions of metabolism itself. This concept, traditionally germane to thoughts on biochemical evolution, is (almost) self evident: Enzymes do not perform feats of magic, they just accelerate reactions that tend to occur anyway. Biochemical reactions can therefore themselves harbor relics of, or be holdovers from, metabolic origin. Yet not all reactions are equally old, metabolism has evolved — but how? In this proposal, the tools of comparative physiology, thermodynamics, and comparative genomics, will be applied to investigate the process of early metabolic evolution. Three kinds of data stand central to the work: i) thermodynamic properties of reactions that comprise modern metabolic networks, ii) information contained in the ability of H2 in the presence of Ni3Fe and magnetite catalysts to substitute for ferredoxin and enzymes in biochemical reactions, and iii) information about the evolutionary origin and phylogenetic spread of heme and cytochromes as well as the ecophysiological context of cytochrome origin. The proposed work will deliver groundbreaking insights into the chemical environment at the site of biochemical origins, inform about the pre-enzymatic nature of catalysts and reductants at the origin of metabolism, and offer insights into the course of bioenergetic evolution before and after heme as well as the ancestral function of cytochromes in accessing extracellular electron acceptors.

Mots-clés : anaerobes,autotrophes,comparative physiology,hydrogen,serpentinization,hydrothermal vents,heme,thermodynamics,metabolic networks,verticality
Projet ERC : CounterLIGHT (Horizon 2020, appel 2017, Starting grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Fundamental constituents of matter
Entité participante : National Physical Laboratory — Pays : Royaume-Uni — Rôle : Partner
Acronyme de l'entité : NPL
Type d'entité : Organismes privés (hors enseignement)
Financement ERC de l'entité : 218750.0 €

Light is generally expected to travel through media independent of its direction. Exceptions can be achieved eg. through polarization changes induced by magnetic fields (known as the Faraday effect) together with polarization-sensitive birefringent materials. However, light can also be influenced by the presence of a counterpropagating light wave. We have recently shown that this leads to the surprising consequence that light sent into tiny glass rings (microresonators) can only propagate in one direction, clockwise or counterclockwise, but not in both directions simultaneously. When sending exactly the same state of light (same power and polarization) into a microresonator, nonlinear interaction induces a spontaneous symmetry breaking in the propagation of light. In this proposal we plan to investigate the fundamental physics and a variety of ground-breaking applications of this effect. In one proposed application, this effect will be used for optical nonreciprocity and the realization of optical diodes in integrated photonic circuits that do not rely on magnetic fields (an important key element in integrated photonics). In another proposed experiment we plan to use the spontaneous symmetry breaking to demonstrate microresonator-based optical gyroscopes that have the potential to beat state-of-the-art sensors in both size and sensitivity. Additional research projects include experiments with all-optical logic gates, photonic memories, and near field sensors based on counterpropagating light states. Finally, we plan to demonstrate a microresonator-based system for the generation of dual-optical frequency combs that can be used for real-time precision spectroscopy in future lab-on-a-chip applications. On the fundamental physics side, our experiments investigate the interaction of counterpropagating light in a system with periodic boundary conditions. The fundamental nature of this system has the potential to impact other fields of science far beyond optical physics.

Mots-clés : microresonators,optical frequency combs,integrated photonics,nonlinear optics,laser,four wave mixing,kerr effect,ultra high q
Projet ERC : NanoEP (Horizon 2020, appel 2019, Starting grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Fundamental constituents of matter
Entité participante : Technion – Israel Institute of Technology — Pays : Israël — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1662923.0 €

Light-matter interactions are highly limited by strict fundamental rules. The commonly used dipole approximation enforces selection rules that prohibit many electronic transitions due to the mismatch between the wavelength of light and the scale of its emitter (e.g., atom, molecule, quantum dot). This mismatch even prevents access to many other light-matter interactions such as spin-flip transitions and multiphoton spontaneous emission. In the past four years, I have shown theoretically and experimentally how extreme confinement of light enables transitions that are otherwise forbidden. For example, transforming an unobservable multiphoton emission to be the dominant transition. The key to accessing such transitions is using nano-confined 2D plasmons or phonon-polaritons. I propose to go beyond my recent work and to study conventionally-forbidden light-matter interactions of free electrons, which have never been explored before. I will do this by utilizing polaritons in nanophotonic structures and in settings of 2D materials. Using both theory and experiments with an ultrafast transmission electron microscope (UEM), my group will develop and observe novel concepts of light emission such as double spontaneous emission of a polariton paired with a high energy photon. We will attempt to realize ultrastrong electron-polariton coupling in new systems, pushing the classical and quantum boundaries of electron-photon energy conversion that limit the efficiency of a wide range of processes. This project will challenge limits in electron-polariton interactions to enable novel polariton phenomena in nanostructures and settings of 2D materials.

Mots-clés : nanophotonics,2d plasmons,ultrafast electron microscopy,electron energy loss spectroscopy  eels,photon induced nearfield electron microscopy  pinem
Projet ERC : R2-TENSION (Horizon 2020, appel 2020, Synergy grants)
Entité participante : Board of the Swiss Federal Institutes of Technology — Pays : Suisse — Rôle : CO-PI
Acronyme de l'entité : ETH Zurich
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2498150.0 €

Lipid membranes compartmentalize and protect cells from the environment, and selectively permit transport. This functionality derives from unique membrane properties: 5 nm thick, yet fluid, deformable, resistant to stress and chemically complex. The physicochemical properties of membranes are expected to have a major impact on cell life, but the tools to measure the relevant multiscale and dynamic parameters in-vitro and, more importantly, in-vivo membranes are lacking. An essential property of membranes, their hydration and charge state, both needed for membrane integrity and playing a vital role in cell survival is not understood beyond the level of continuum theory. To enable quantitative physics, and physical chemistry for biology Roux and Roke, R^2, will join their expertise on molecular biology & biophysics and physics & interfacial chemistry & optics to create tools to measure membrane water and ion fluxes, and image 3D fields of electrostatic free energy, membrane tension and curvature. We will understand how molecular factors, such as the influence of the aqueous phase and interfacial electrostatics, are coupled to tension and curvature under dynamic conditions such as osmosis in artificial and cellular membranes. Obtaining the first temporally resolved, 3D maps of hydration, free energy, tension and curvature at the nanoscale in migrating cells and cells experiencing osmotic shocks we will quantify membrane physical parameters in two processes essential for cell survival, for which currently no data is available: Osmotic shock response and cell migration. Osmotic shock response plays an important role in infections, kidney and intestine function. Cell migration is essential to many cell processes, for example the spreading of cancer, wound repair and the immunological response, as well as food search in unicellular organisms.

Mots-clés : water,nonlinear optics,membranes,free energy,osmosis,osmotic shock response,cell migration
Projet ERC : BATMAN (Horizon 2020, appel 2015, Starting grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Products and processes engineering
Entité participante : Board of the Swiss Federal Institutes of Technology — Pays : Suisse — Rôle : PI
Acronyme de l'entité : ETH Zurich
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1500000.0 €

Lithium ion batteries offer tremendous potential as an enabling technology for sustainable transportation and development. However, their widespread usage as the energy storage solution for electric mobility and grid-level integration of renewables is impeded by the fact that current state-of-the-art lithium ion batteries have energy densities that are too small, charge- and discharge rates that are too low, and costs that are too high. Highly publicized instances of catastrophic failure of lithium ion batteries raise questions of safety. Understanding the limitations to battery performance and origins of the degradation and failure is highly complex due to the difficulties in studying interrelated processes that take place at different length and time scales in a corrosive environment. In the project, we will (1) develop and implement quantitative methods to study the complex interrelations between structure and electrochemistry occurring at the nano-, micron-, and milli-scales in lithium ion battery active materials and electrodes, (2) conduct systematic experimental studies with our new techniques to understand the origins of performance limitations and to develop design guidelines for achieving high performance and safe batteries, and (3) investigate economically viable engineering solutions based on these guidelines to achieve high performance and safe lithium ion batteries.

Mots-clés : electrochemistry,lithium ion batteries
Projet ERC : NoiseRobustEvo (Horizon 2020, appel 2016, Advanced grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
Entité participante : University of Zurich — Pays : Suisse — Rôle : PI
Acronyme de l'entité : UZH
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2383444.0 €

Living cells are constantly barraged by perturbations that originate within themselves. Especially abundant – far more than DNA mutations – are two kinds of such perturbations. The first is gene expression noise, pervasive stochastic variation of transcript and protein levels. The second is mistranslation noise, the misincorporation of amino acids by ribosomes during protein synthesis. Organisms and protein molecules can evolve robustness – the persistence of well-adapted phenotypes – to both kinds of noise. Theory predicts that noise and robustness can affect the adaptive evolution of new proteins, but we do not know whether they help or hinder adaptive evolution. We hypothesize that noise and robustness can accelerate protein evolution both separately and jointly. To validate this hypothesis, we will evolve light-emitting fluorescent proteins towards new color phenotypes via directed laboratory evolution in E.coli. During evolution, we will manipulate expression noise by driving FP expression from noisy or quiet promoters, and we will manipulate mistranslation via host strains with low and high mistranslation rates. We will manipulate protein robustness in three biologically important ways, chaperone overexpression, gene duplication, and stabilizing selection. We will study how fast FPs evolve new colors, and analyze protein evolutionary dynamics through a combination of high-throughput sequencing, engineering of selected adaptive mutations, and data-driven modeling. Our project will show how a ubiquitous but poorly understood source of phenotypic variation affects protein innovation. It will also help engineers discover new protein functions. Moreover, our work will help establish FPs as a major platform to study protein evolutionary dynamics. By revealing noise as a new and crucial factor in protein evolution, our observations have the potential to revolutionize molecular evolution research, much like earlier studies of noise have revolutionized cell biology.

Mots-clés : molecular evolution,protein adaptation,epistasis,fitness landscapes,fluorescent proteins
Projet ERC : FuelledLife (Horizon 2020, appel 2020, Starting grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Condensed matter physics
Entité participante : University of Augsburg — Pays : Allemagne — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1498852.0 €

Living cells rely on the compartmentalisation of thousands of different molecules and their chemical reactions. Remarkably, many of such compartments form by phase separation of heteropolymers controlled by sequence-specific interactions and fuel that drives reactions away from equilibrium. If we knew how such polymers with sequence-specific interactions evolve and compartmentalise in fuel-driven multi-component mixtures, we would better understand the role of phase separation in living cells and how synthetic or prebiotic cells emerge. I aim to study how fuel-driven phase separation can drive the selection and replication of hetero-polymers with sequence-specific interactions, the control of their chemical reactions and the emergence and selection of different compartments. My team and I will develop a theory for phase separation and chemical reactions in multi-component mixtures driven away from equilibrium by irreversible, fuel-driven reactions. This theory will provide a link between phenomena on the compartment scale and coarse-grained properties of sequences. First, we will use this theory to study how compartments control biochemical reactions, and how this control is determined by sequence. Second, we will investigate how sequences are selected, replicated and evolve under cyclic, non-equilibrium conditions. Third, we will use our theory to unravel how fuel-driven chemical reactions regulate formation and division of compartments, and affect selection of different compartments within a population. Our theoretical studies will elucidate the physical mechanisms and conditions which will be experimentally scrutinised by our collaborators. Our results will let us understand how living cells regulate phase separation, like the formation of stress granules by selecting RNA. Moreover, our results will elucidate the role of phase separation for the emergence of life by determining the prerequisites of a protocell to divide, replicate and undergo selection.

Mots-clés : phase separation in cells,synthetic cells,non equlibrium thermodynamics,physics of emulsions,statistical physics of living systems,cell biophysics,biophysics of the origin of life
Projet ERC : RIDING (Horizon 2020, appel 2020, Consolidator grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Products and processes engineering
Entité participante : University of Genoa — Pays : Italie — Rôle : PI
Acronyme de l'entité : UniGe
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1973485.0 €

Living systems developed dramatically efficient strategies to sense and navigate turbulent environments. Understanding these strategies is key to many real world applications required to function in the presence of turbulence: from search and rescue to demining and patrolling. While much is known on navigation in smooth environments, these approaches fail in the presence of turbulence. RIDING aims at elucidating the computations organisms use to extract useful information from turbulent stimuli and navigate to a target. A key observation is that organisms rely on multiple sensory cues, despite the distortions due to turbulence. Explaining this puzzle requires blending fluid dynamics with biological behavior. I will achieve this goal by developing physics-based algorithms elucidating the computations that support three fundamental pillars of biological behavior: 1) combine navigation with sensing, 2) balance multiple senses, 3) adapt to different environments. The result will be a comprehensive theory integrating biological behavior in a computational framework based on fluid dynamics. Predictions will be tested via experiments on fishes, known to routinely perform turbulent navigation combining multiple senses across distinct sensory environments. This multidisciplinary project leverages methods from physics, computer science and biology. In summary, the objectives of RIDING are to: O1. Assemble a massive dataset of chemical and mechanical signals emitted by a target using computational fluid mechanics and asymptotic methods. O2. Develop algorithmic approaches for sensing and navigation using tools from machine learning trained on multiple sensory signals from O1. O3. Examine how sensory signals from O1 and algorithms from O2 vary in different environments. O4. Test predictions by recording prey capture in the laboratory using three species of fish. Analysis includes a fascinating species which evolved unique sensory “legs” to catch prey in different environment

Mots-clés : turbulence,decision making,biological behavior,data driven methods
Projet ERC : LocomotorIntegration (Horizon 2020, appel 2015, Advanced grants)
Domaine scientifique : Life Science
Panel : Neuroscience and Disorders of the Nervous System
Entité participante : Karolinska Institutet — Pays : Suède — Rôle : PI
Acronyme de l'entité : KI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1125130.1 €

Locomotion is a complex motor act that is used in many daily life activities and is the output measures of a plethora of brain behaviors. The planning and initiation of locomotion take place in the brain and brainstem, while the execution is accomplished by activity in neuronal networks in the spinal cord itself. Recent experiments have provided significant insight to the organization of the executive spinal locomotor networks. However, little is known about the brainstem control of these networks. Here, I propose to provide a unified understanding of the functional connectome of the key brainstem networks that control locomotion in mammals needed to select appropriate locomotor outputs. To obtain these goals we will develop a suite of transgenic mouse models with optogenetic or chemogenetic switches in defined populations of brainstem neurons combined with the possibility to use state-of-the-art cell-specific electrophysiological and anatomical connectivity studies. We will reveal the functional organization of ‘go’ and ‘stop’ command systems in the brainstem that are directly upstream from the spinal locomotor networks and the mechanisms for how spinal networks are selected. We will further functionally deconstruct the next network layer in midbrain structures that control the ‘go’ and ‘stop’ command systems. Our research takes a specific approach to provide mechanistic insight to the integrated movement function by building the motor matrix in a functional chain from the locomotor–related spinal cord neurons that have been identified to midbrain neurons. A segment of our research will link these networks to locomotor impairments after basal ganglia dysfunction. The work has the potential to make a breakthrough in our understanding of how complex movements are generated by the brain and has translational implications for patients with movement disorders. It will push boundaries in the universal effort that aims to comprehend how brain networks create behaviors.

Mots-clés : motor control,brainstem,spinal cord,basal ganglia,neurons,optogenetics