Data-Gouv-ML/pcri-erc-participations-et-projets-laureats huggingface dataset:
Projet ERC : SuperGenE (Horizon 2020, appel 2017, Starting grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
Entité participante : Stockholm University — Pays : Suède — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1475636.0 €

Understanding how adaptive combinations of traits are maintained is a central question in evolutionary biology. Supergenes are clusters of genes that can maintain favorable trait combinations because they are inherited as a unit. Studying supergenes allows us to address fundamental questions on the origin and evolution of complex adaptations and the effects of suppressed recombination, and is therefore of broad significance. Distylous plants offer a particularly promising opportunity to study supergene evolution. In distylous plants there are two floral morphs that differ reciprocally in the placement of stigma and anthers. These character combinations are maintained by a supergene, the distyly S-locus. While distyly has interested many generations of biologists, we still know little about the origin and evolution of this supergene, and progress on this front has been hampered by the lack of molecular genetic data on the S-locus. Here, we aim to make full use of the latest advances in genome sequencing technology to bring the study of distyly into the genomic era. Specifically, we will develop the classic Linum genus as a model for supergene evolution. We will first combine de novo assembly of the genomes of six Linum species with genetic studies to identify S-linked regions. Then, we will test whether the S-locus exhibits similarities to sex chromosomes with respect to recombination suppression, genetic degeneration and gene expression evolution. Finally, we will investigate the genetic causes and population genetic consequences of recurrent loss of distyly in Linum. The high-quality genome assemblies produced during this project will pave the way for future studies of the molecular basis of adaptive floral differences first identified by Darwin. The results from this project are of great general importance for our understanding of the evolution of coadapted gene complexes and will shed new light on the important and fascinating phenomenon of supergenes.
Projet ERC : DeCRyPT (Horizon 2020, appel 2017, Advanced grants)
Domaine scientifique : Life Science
Panel : Integrative Biology: from Genes and Genomes to Systems
Entité participante : European Molecular Biology Laboratory — Pays : Allemagne — Rôle : PI
Acronyme de l'entité : EMBL
Type d'entité : Recherche
Financement ERC de l'entité : 2499675.0 €

Understanding how genomic information is organised and interpreted to give rise to robust patterns of gene expression is a long-standing problem in genome biology, with direct implications for development, evolution and disease. Despite recent advances in locating regulatory elements in animal genomes, there is a general lack of functional data on elements in their endogenous setting – the bulk of our current knowledge comes from reporter assays examining elements out of context, giving insights on sufficiency but not necessity. The functional requirement of very few individual enhancers, and other elements, has been assessed by deletion, with even less known about how the action of multiple elements is integrated. To understand the functional effects of genetic variants, and how they are buffered during embryogenesis, it is imperative to genetically dissect regulatory domains to uncover functional rules of genome regulation within a well-characterised animal model. Here, by combining Drosophila population genetics, developmental genetics, and novel multiplexed genomic methods we will perform the first large-scale functional dissection of cis-regulatory landscapes during embryogenesis. Extensive resources make Drosophila a unique model organism for this task, including (a) 500 fully sequenced inbred wild isolates for population genetics, (b) over 20,000 fly strains custom-built for genome engineering & (c) a wealth of cis-regulatory information on the location of enhancers. The proposal has three Aims: 1) Use population genetics as a perturbation tool to functionally link regulatory elements to their target genes; 2) Systematically delete cis-regulatory elements to dissect their role in gene expression and genome topology; 3) Manipulate cis-regulatory domains to generate new regulatory environments for developmental genes.These Aims will provide unique functional insights, enabling us to move from correlation to causation in our understanding of genome regulation.
Projet ERC : SUExp (Horizon 2020, appel 2018, Starting grants)
Domaine scientifique : Social Sciences and Humanities
Panel : Individuals, Markets and Organisations
Entité participante : University of London — Pays : Royaume-Uni — Rôle : PI
Acronyme de l'entité : U. London
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1357946.0 €

Understanding how individuals or groups interact is at the core of virtually every economic and social problem. A central difficulty in studying such interactions is the fact that in practice, players face strategic uncertainty. This uncertainty – uncertainty about how others play the game – is important for determining one’s own behaviour. This proposal is a broad attempt to bring strategic uncertainty to bear on game theory. The basic premise of this proposal is that, in a wide variety of situations, actors reason under direct forms of strategic uncertainty – forms of strategic uncertainty that are not properly captured by standard equilibrium analysis. While there is a strong theoretical tradition geared towards the investigation of strategic uncertainty (Epistemic Game Theory), there have been few attempts to empirically investigate the role of strategic uncertainty on behaviour. This research will deliver the first comprehensive empirical study of direct strategic uncertainty. This research program will use the tools of Experimental Economics to investigate the sources of direct strategic uncertainty, how players reason under strategic uncertainty, and the implications for game theoretic models. My proposal will provide evidence and theory on five research themes: i) Is uncertainty about the bounded reasoning of others a source of direct strategic uncertainty? ii) Are there are other sources of strategic uncertainty in bounded reasoning models? What happens if you believe others are more sophisticated than you? iii) How do people reason when facing strategic uncertainty? Does stochastic choice play a role in uncertain situations? iv) How do we incorporate strategic uncertainty into game theoretic models? Can we develop models that are predictive as well as explanatory? And, v) What is the role of strategic uncertainty in dynamic games? In particular, does direct strategic uncertainty cause delays in bargaining?

Mots-clés : strategic uncertainty,behavioral game theory,epistemic game theory,bounded reasoning bounded rationality,level k,cognitive hierarchy
Projet ERC : CODE4Vision (Horizon 2020, appel 2016, Consolidator grants)
Domaine scientifique : Life Science
Panel : Neuroscience and Disorders of the Nervous System
Entité participante : Universitätsmedizin Göttingen — Pays : Allemagne — Rôle : PI
Acronyme de l'entité : UMG
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1991445.0 €

Understanding how neural circuits process and encode information is a fundamental goal in neuroscience. For the neural network of the retina, such knowledge is also of concrete importance for the development of vision restoration therapies for patients suffering from degeneration of photoreceptors. Artificial stimulation of retinal neurons through electronic implants or inserted light-sensitive proteins (“optogenetics”) aims at reconstructing natural transmission of visual information to the brain. Recreating natural retinal activity, however, will require a thorough understanding of the complex and diverse neural code of the retina. The challenge lies in deciphering the various nonlinear operations and dynamics in the around 30 parallel signalling streams that emerge from the retina, represented by as many types of ganglion cells, the retina’s output neurons. The CODE4Vision project will tackle this challenge by identifying the effective connectivity between the different types of retinal ganglion cells and their excitatory presynaptic partners, bipolar cells, and by determining the features of information processing between these neuronal layers. We will characterize the layout of bipolar cell inputs to large populations of ganglion cells with novel analyses that we derive from computational statistics and machine learning. We will then study the nonlinear and dynamical features of these connections by designing closed-loop experiments that automatically adjust visual stimuli to the identified layout of bipolar cells. These analyses will be supplemented by direct measurements of connections through simultaneous bipolar and ganglion cell recordings. The results will pave the way towards new models of how the retina encodes natural visual stimuli. Finally, we will apply this knowledge to mouse models of optogenetic vision restoration in order to develop stimulation schemes that emulate natural retinal stimulus encoding.

Mots-clés : neural coding,functional connectivity,retina
Projet ERC : DROSADAPTATION (Horizon 2020, appel 2014, Consolidator grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
Entité participante : Spanish National Research Council — Pays : Espagne — Rôle : PI
Acronyme de l'entité : CSIC
Type d'entité : Recherche
Financement ERC de l'entité : 2392521.0 €

Understanding how organisms adapt to their environments is a long-standing problem in Biology with far-reaching implications: adaptation affects the ability of species to survive in changing environments, host-pathogen interactions, and resistance to pesticides and drugs. Despite recent progress, adaptation is to date a poorly understood process largely due to limitations of current approaches that focus (i) on a priori candidate genes, (ii) on signals of selection at the DNA level without functional validation of the identified candidates, and (iii) on small sets of adaptive mutations that do not represent the variability present in natural populations. As a result, major questions such as what is the relative importance of different types of mutations in adaptation?, and what is the importance of epigenetic changes in adaptive evolution?, remain largely unanswered. To gain a deep understanding of adaptation, we need to systematically identify adaptive mutations across space and time, pinpoint their molecular mechanisms and discover their fitness effects. To this end, Drosophila melanogaster has proven to be an ideal organism. Besides the battery of genetic tools and resources available, D. melanogaster has recently adapted to live in out of Africa environments. We and others have already shown that transposable elements (TEs) have substantially contributed to the adaptation of D. melanogaster to different environmental challenges. Here, we propose to use state-of-the-art techniques, such as Illumina TruSeq sequencing and CRISPR/Cas9 genome editing, to systematically identify and characterize in detail adaptive TE insertions in D. melanogaster natural populations. Only by moving from gathering anecdotic evidence to applying global approaches, we will be able to start constructing a quantitative and predictive theory of adaptation that will be relevant for other species as well.

Mots-clés : next generation sequencing,genome editing,epigenetics,environment,positive selection,genotype phenotype map
Projet ERC : NEUROFISH (Horizon 2020, appel 2017, Consolidator grants)
Domaine scientifique : Life Science
Panel : Neuroscience and Disorders of the Nervous System
Entité participante : Champalimaud Foundation — Pays : Portugal — Rôle : PI
Type d'entité : Recherche
Financement ERC de l'entité : 1694063.0 €

Understanding how our brains extract relevant features of sensory input to select and guide appropriate actions is a fundamental goal of neuroscience. Yet even relatively simple sensorimotor reflexes can depend on activity within complex networks of neurons that are distributed across the brain, presenting a challenge for traditional neuroscience approaches. Our recent work has demonstrated the capacity to image neural activity with single cell resolution throughout the small transparent brain of behaving zebrafish. Here we will trace, from sensory input to motor output, the neural circuits that allow zebrafish to select and execute distinct swimming patterns in response to varying visual input. Through comprehensive whole-brain functional imaging in combination with optical and genetic circuit tracing, we aim to determine the principles on which these sensorimotor circuits are organised and reveal how activity dynamics unfold throughout the whole brain during behaviour. We will take a systematic approach to this problem, based on a thorough quantitative analysis of swim kinematics and the sensory stimuli that drive them. We will: 1) Use whole-brain functional imaging of genetically defined neural populations to reveal the neural circuit organization and activity dynamics during visuomotor behaviour. 2) Establish how motor commands are encoded at the single-cell and population level by brainstem reticulospinal neurons, through imaging and ablation studies and 3) Systematically map the functional organisation of retinal inputs into the brain. Taken together, these experiments will provide an unprecedented, single-cell resolution view of the organization of complete circuits that transform retinal inputs to motor outputs in the vertebrate brain.

Mots-clés : circuit neuroscience,zebrafish,sensorimotor integration,locomotion,vision,calcium imaging
Projet ERC : EngineeringPercepts (Horizon 2020, appel 2014, Starting grants)
Domaine scientifique : Life Science
Panel : Neuroscience and Disorders of the Nervous System
Entité participante : Max Planck Society — Pays : Allemagne — Rôle : PI
Acronyme de l'entité : MPG
Type d'entité : Recherche
Financement ERC de l'entité : 1219000.0 €

Understanding how the brain is able to transform sensory input into decisions is one of the major challenges of systems neuroscience. While recording/imaging during sensory-motor tasks identified neural substrates of sensation and action in various cortical areas, the crucial questions of 1) how these correlates are implemented within the underlying neural networks and 2) how their output triggers decisions, will only be answered when the individual functional measurements are integrated into a coherent model of all task-related circuits. The goal of my proposal is to use the rodent vibrissal system for building such a model in the context of how a tactile-mediated percept is encoded by the interplay between biophysical, cellular and network mechanisms. Specifically, rodents decide to cross a gap when detecting its far side with a single facial whisker. This suggests that whisker contact with the platform, if synchronized with an internal motor signal, triggers the decision. My key hypothesis is that in sensory cortex layer 5 thick-tufted (L5tt) neurons receive touch and motor information via specific pathways that target basal and apical tuft dendrites, respectively. When localizing the far side of the gap, the two inputs coincide and result in burst spiking output to (sub)cortical areas, triggering the gap cross. To test this hypothesis, I will determine all sensory/motor-related local and long-range inputs/outputs to/from L5tt neurons, measure whisker-evoked responses of these populations and use the data to constrain network simulations of active whisker touch. Using a multidisciplinary approach, combining in vivo electrophysiology, virus injections, custom imaging/reconstruction tools and Monte Carlo simulations, my reverse engineering strategy will provide unmatched mechanistic insight to perceptual decision making and will function as a show case – generalizable across sensory modalities and species – of how to derive computations that underlie behavior.

Mots-clés : gap cross behavior,barrel cortex,connectome,monte carlo simulations,coincidence detection
Projet ERC : PICOMETRICS (Horizon 2020, appel 2017, Consolidator grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Condensed matter physics
Entité participante : University of Antwerp — Pays : Belgique — Rôle : PI
Acronyme de l'entité : UAntwerp
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1998750.0 €

Understanding nanostructures down to the atomic level is the key to optimise the design of advanced materials with revolutionary novel properties. This requires characterisation methods enabling one to quantify atomic structures with high precision. The strong interaction of accelerated electrons with matter makes that transmission electron microscopy is one of the most powerful techniques for this purpose. However, beam damage, induced by the high energy electrons, strongly hampers a detailed interpretation. To overcome this problem, I will usher electron microscopy in a new era of non-destructive picometer metrology. This is an extremely challenging goal in modern technology because of the increasing complexity of nanostructures and the role of light elements such as lithium or hydrogen. Non-destructive picometer metrology will allow us to answer the question: what is the position, composition and bonding of every single atom in a nanomaterial even for light elements? There has been significant progress with electron microscopy to study beam-hard materials. Yet, major problems exist for radiation-sensitive nanostructures because of the lack of physics-based models, detailed statistical analyses, and optimal design of experiments in a self-consistent computational framework. In this project, novel data-driven methods will be combined with the latest experimental capabilities to locate and identify atoms, to detect light elements, to determine the three-dimensional ordering, and to measure the oxidation state from single low-dose recordings. The required electron dose is envisaged to be four orders of magnitude lower than what is nowadays used. In this manner, beam damage will be drastically reduced or even be ruled out completely. The results of my programme will enable precise characterisation of nanostructures in their native state; a prerequisite for understanding their properties. Clearly this is important for the design of a broad range of nanomaterials.

Mots-clés : electron microscopy,metrology,statistical parameter estimation theory,signal processing,quantitative structure determination,nanostructures
Projet ERC : PhyMo (Horizon 2020, appel 2014, Advanced grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
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 : 2499980.0 €

Understanding processes in microbial communities is a crucial task given the impact of microbial communities on environmental systems, including plants and animals. There is a rapidly increasing number of microbial communities whose collective genomes have been determined; however, it is important to uncover their collective function and to understand how community properties emerge from the properties of individual microbial types and their interactions. One habitat that has been gaining growing interest is the phyllosphere, or the aerial parts of plants, which carry out the majority of terrestrial carbon dioxide fixation. There is a urgent need to better understand the microorganisms living in the phyllosphere and an increasing awareness of the importance of indigenous microbiota and their role in microbe-microbe and host-microbe interactions for both plant growth and protection. This project aims to uncover the molecular basis shaping microbial communities in the phyllosphere in order to improve our functional understanding of microbial interaction in the context of the plant host and to unravel the principles of the formation of community pattern and function in situ. To reach these objectives, a reductionist approach will be used to generate and test new hypotheses regarding microbial interactions in phyllosphere communities. Synthetic, tractable microbial communities will be formulated and analyzed under gnotobiotic conditions. In situ community approaches will be developed and applied, while community genetics and experimental evolution will provide complementary perspectives on the community structure and function. These approaches will be mirrored by manipulating interactions on the host side through the use of plant mutants and ecotypes. Taken together, using multifaceted perspectives on microbial interactions in situ will allow unprecedented insights into the biology of bacteria living in the phyllosphere and their individual and collective function.

Mots-clés : plant microbiome,microbial interactions,bacterial community,single cell,genetics,metabolomics,proteomics,mass spectrometry,fish,fluidfm,experimental evolution
Projet ERC : IceAGenT (Horizon 2020, appel 2018, Consolidator grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
Entité participante : UiT The Arctic University of Norway — Pays : Norvège — Rôle : PI
Acronyme de l'entité : UiT
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2189775.75 €

Understanding rates of migration and resilience to climate change is important for explaining both the distribution of single species and anticipate how ecosystems may respond to climate change. There are two vigorously debated questions about the response of NW European biota to past climate changes: 1) glacial survival vs tabula rasa and 2) Reid´s paradox of rapid plant migration through seed dispersal vs. survival in cryptic refugia just south or east of the ice sheet. These are related as survival in any northern refugia would suggest local dispersal rather than the rapid dispersal rates that are needed from southern refugia. While we have learned a lot about dispersal routes from phylogeography and about glacial refugia from macrofossils, pollen and, more recently, ancient DNA (aDNA), we have never been able to trace plant migration routes back in time. Our lab is at a step-change in answering these questions as we now have a full genome reference library for the entire flora of Norway and adjacent regions (>2000 species), which will allow us to develop genomic markers identifying not only species, but genetic variation within species, in ancient sediment samples. In addition, we have >20 sediment cores already analysed for vascular plant aDNA using metabarcoding, and a further 20 are in the pipeline. Based on these and 12 new cores, we will select samples that contain key species representing different bioclimatic zones (boreal trees, dwarf shrubs, arctic herbs), and re-analyse them for within-species genetic variation. This will be complemented by analyses of contemporary phylogeography of the same species. This will allow us to identify refugia areas and trace migration routes back in time by different components of the ecosystems. The results of this study will open a new era in studies of species abilities to respond to climate changes (palaeo-phytogeography) and enable us to model the effects of current global warming more accurately than before.