Data-Gouv-ML/pcri-erc-participations-et-projets-laureats huggingface dataset:
Projet ERC : ELFBAD (Horizon 2020, appel 2014, Advanced grants)
Domaine scientifique : Life Science
Panel : Immunity, Infection and Immunotherapy
Entité participante : Newcastle University — Pays : Royaume-Uni — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2428621.0 €

Despite the clear importance and multiple functions of the bacterial cell wall, many bacteria appear to be able to switch into a cell wall deficient or “L-form” state. L-forms are very heterogeneous in size and shape and generally require osmotic stabilisers, such as 0.5 M sucrose, for viability. However, by lacking the requirement for a cell wall, L-forms are completely resistant to common cell wall antibiotics, such as β-lactams, and they are probably protected from some elements of innate immune recognition. L-forms are therefore of potential interest in relation to their possible involvement in human disease. They have often been reported in clinical specimens obtained from patients with recurrent or persistent infections or on long term prophylaxis with β-lactam antibiotics. Unfortunately, until recently, most of the work on L-forms had been done in the pre-molecular era, when it was difficult to characterise the L-forms and particularly to identify their origins and relationship with other resident pathogenic bacteria. Recently, several labs have revisited the L-form issue and started to apply modern molecular and cell biological methods. The proposal is divided into three Themes: • Improve our understanding of key features of the L-forms of our best characterised model system, B. subtilis, including both basic science and possible biotechnological applications. • Extend our analysis of basic L-form biology into several diverse bacterial systems, of relevance to both biotechnology and infectious disease. • Explore in detail the possible clinical relevance of L-forms, aiming to identify specific clinical situations in which they are relevant or, at least, to establish model systems in which the interactions between L-form and mammalian systems can be studied.

Mots-clés : l forms,membrane synthesis,infectious disease,bacterial cell wall,bacterial cell division,bacterial cell biology
Projet ERC : DyNET (Horizon 2020, appel 2017, Consolidator grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Earth system science
Entité participante : University of Padua — Pays : Italie — Rôle : PI
Acronyme de l'entité : UNIPD
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1999758.0 €

Despite the ubiquity of expansion and retraction dynamics of flowing streams, the large majority of biogeochemical and hydrological studies conceive river networks as static elements of the landscape, and a coherent framework to quantify nature and extent of drainage network dynamics is lacking. The implications of this phenomenon extend far beyond hydrology and involve key ecological and biogeochemical function of riparian corridors. The proposed research project will move beyond the traditional paradigm of static river networks by unravelling, for the first time, physical causes and biogeochemical consequences of stream dynamics. In particular, the project will undertake the following overarching scientific questions: 1) what are the climatic and geomorphic controls on the expansion/contraction of river networks? 2) what is the length of temporary streams and what is their impact on catchment-scale biogeochemical processes and stream water quality across scales? These challenging issues will be addressed by developing a novel theoretical framework complemented by extensive field observations within four representative sites along a climatic gradient in the EU. Field measurements will include long-term weekly mapping of the active drainage network and daily hydro-chemical data across scales. The experimental dataset will be used to develop and inform a set of innovative modelling tools, including an analytical framework for the description of spatially explicit hydrologic dynamics driven by stochastic rainfall and a modular hydro-chemical model based on the concept of water age, able to account for the variable connectivity among soil, groundwater and channels as induced by stream network dynamics. The project will open new avenues to quantify freshwater carbon emissions - crucially dependent on the extent of ephemeral streams - and it will provide a robust basis to identify temporary rivers and maintain their biogeochemical function in times of global change.

Mots-clés : river networks,catchments,transport processes,modeling
Projet ERC : VIBRANT-BIO (Horizon 2020, appel 2015, Consolidator grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Systems and communication 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 : 2562325.0 €

Devastating diseases such as Alzheimer’s, Parkinson’s and various cancers are still without cures, continue to undermine the quality of life for millions of people and impose significant economic burdens. Misfolded toxic proteins constitute the microscopic basis of these diseases, but little is understood about their structure and biological function. This is due the fact that current technologies are severely limited for molecular-level identification of protein structures and high-throughput analysis of biomolecular interactions. VIBRANT-BIO aims to introduce breakthrough mid-infrared spectroscopy technologies, including the first spectroscopic microarray, to overcome the limitations of current methods by enabling complete profiling of biomolecules from identification of their structure and composition to their biological function. To achieve its ambitious goals, VIBRANT-BIO will exploit plasmonics and newly discovered two-dimensional nanomaterials such as graphene and explore the ultimate limits of light-matter interaction to demonstrate biosensors with extreme sensitivity, throughput and functionality, well beyond the state-of the art. It will innovatively integrate nanoplasmonics with advanced photonics and bioanalytical tools to dramatically enhance sensor performance and introduce new functionalities. The proposed technologies will be applied to study toxic amyloid-beta proteins and their interaction with lipid membranes for understanding the molecular mechanisms underlying Alzheimer’s disease. VIBRANT-BIO will contribute to define the road-map for next generation biosensor and spectroscopy technologies through interdisciplinary research covering physics, engineering, chemistry and biology. The capability of the proposed systems to analyze a broad range and ultra-low quantities of molecules and chemicals provides a general-purpose toolkit that can impact numerous fields such as bioscience, material science, pharmaceutical industry, and homeland security.
Projet ERC : CisTune (Horizon 2020, appel 2020, Starting grants)
Domaine scientifique : Life Science
Panel : Integrative Biology: from Genes and Genomes to Systems
Entité participante : Max Planck Society — Pays : Allemagne — Rôle : PI
Acronyme de l'entité : MPG
Type d'entité : Recherche
Financement ERC de l'entité : 1494375.0 €

Development of multicellular organisms relies on differential gene activation in a single genome. In response to multiple quantitative signals, cell-type specific transcriptional programs are established that determine cell identify. Their perturbation can result in pathologies such as cancer. Large cis-regulatory landscapes integrate information on cell state, space and time to precisely tune the activity of developmental genes. How cis-regulatory landscapes decode multiple quantitative signals remains poorly understood. CisTune aims at gaining a functional and mechanistic understanding of how regulator levels are sensed, how the input from multiple regulators is integrated and how information is processed by cis-regulatory landscapes. CisTune will use the Xist locus as a model, which controls X-chromosome inactivation, an essential developmental process in mammals. Xist's cis-regulatory landscape integrates multiple quantitative input signals that transmit information on sex and developmental time, to ensure up-regulation from one X chromosome in each female cell. In CisTune we will thus study an essential process in great depth to identify regulatory principles that control activity of the mammalian genome during development. CisTune will use an interdisciplinary approach at the intersection of systems biology, epigenetics and gene regulation, where highly multiplexed perturbation experiments of endogenous genes are interpreted with the help of mathematical models. We will build on recent technological breakthroughs, including single-cell genomics and high-throughput CRISPR screens, which we will complement with a new approach to functionally link sequence elements to their input signals. CisTune has the potential to overcome challenges that have prevented mammalian quantitative biology of gene regulation to becoming more broadly applied and will set the stage for investigating gene regulation across multiple layers of complexity.

Mots-clés : x chromosome inactivation,quantitative biology,gene regulatory networks,single cell genomics,crispr screens,mathematical modelling
Projet ERC : RadioClick (Horizon 2020, appel 2017, Proof of concept grants)
Entité participante : Johannes Gutenberg University Mainz — Pays : Allemagne — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 75000.0 €

Diagnosing cancer as early as possible is one of the most powerful strategies in modern medicine to improve human well-being. Antibodies (Abs) are excellent molecules that can be used to target specific tumors. As Abs require hours to days for accumulating on tumor surfaces, the use of Abs for nuclear imaging (such as PET imaging) is limited by the short half-lives of popular radioisotopes. Therefore, we plan to move the step of radiolabeling from the bench to the tumor itself. However, the entanglement of Abs with an artificial chemical probe is one of the most promising but at the same time one of the most technically challenging developmental areas in biotechnology. Our unique approach is based on the production of “hybrid-Abs”, which combine in only one “click” step the power of synthetic chemistry with the best of biology (“custom-biologics”). Our unique selling points are ultra-fast, exceptional bioorthogonal and specific labeling reactions in living organism as well as a both-sided modularity of the connection between Abs and chemical probe. By doing so, high contrast visualization of the cancer will become possible.

Mots-clés : noncanonical amino acid,labeling,radiomarker,site specific,click chemistry,tetrazine
Projet ERC : RadioClick (Horizon 2020, appel 2017, Proof of concept grants)
Entité participante : Johannes Gutenberg University Mainz — Pays : Allemagne — Rôle : Partner
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 12500.0 €

Diagnosing cancer as early as possible is one of the most powerful strategies in modern medicine to improve human well-being. Antibodies (Abs) are excellent molecules that can be used to target specific tumors. As Abs require hours to days for accumulating on tumor surfaces, the use of Abs for nuclear imaging (such as PET imaging) is limited by the short half-lives of popular radioisotopes. Therefore, we plan to move the step of radiolabeling from the bench to the tumor itself. However, the entanglement of Abs with an artificial chemical probe is one of the most promising but at the same time one of the most technically challenging developmental areas in biotechnology. Our unique approach is based on the production of “hybrid-Abs”, which combine in only one “click” step the power of synthetic chemistry with the best of biology (“custom-biologics”). Our unique selling points are ultra-fast, exceptional bioorthogonal and specific labeling reactions in living organism as well as a both-sided modularity of the connection between Abs and chemical probe. By doing so, high contrast visualization of the cancer will become possible.

Mots-clés : noncanonical amino acid,labeling,radiomarker,site specific,click chemistry,tetrazine
Projet ERC : DIATOMIC (Horizon 2020, appel 2018, Advanced grants)
Domaine scientifique : Life Science
Panel : Environmental Biology, Ecology and Evolution
Entité participante : École normale supérieure PSL — Pays : France — Rôle : Partner
Acronyme de l'entité : ENS PSL
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 72000.0 €

Diatoms are major contributors of primary production in the ocean and participate in carbon sequestration over geologically relevant timescales. As key components of the Earth’s carbon cycle and marine food webs we need to understand the eco-evolutionary underpinnings of their ecological success to forecast their fate in a future ocean impacted by anthropogenic change. Genomes and epigenomes from model diatoms, as well as hundreds of transcriptomes from multiple species, have revealed genetic and epigenetic processes regulating gene expression in response to changing environments. The Tara Oceans survey has in parallel generated resources to explore diatom abundance, diversity and gene expression in the world’s ocean in widely contrasting conditions. DIATOMIC will build on these resources to understand how evolutionary and ecological processes combine to influence diatom adaptations to their environment at unprecedented spatiotemporal scales. To examine these processes over timescales relevant to current climate change, DIATOMIC includes the pioneering exploration of ancient diatom DNA from the sub-seafloor to reveal the genetic and epigenetic bases of speciation and adaptation that have impacted their ecological success during the last 100,000 years, when Earth experienced major climatological events and an increase in anthropogenic impacts. As a model for exploring eco-evolutionary processes in the past and contemporary ocean we will focus primarily on Chaetoceros because this diatom genus is ancient, ubiquitous, abundant and contributes significantly to carbon export. Key findings will be additionally supported by lab-based studies using the diatom Phaeodactylum for which exemplar molecular tools exist. Specifically, the project will address: 1. What molecular features characterize genome evolution in diatoms? 2. Which processes determine diatom metapopulation structure? 3. What can ancient DNA tell us about diatom adaptations to environmental change in the past?

Mots-clés : micro eukaryotes,diatoms,paleogenomics,phytoplankton
Projet ERC : FastBio (Horizon 2020, appel 2016, Starting grants)
Domaine scientifique : Life Science
Panel : Integrative Biology: from Genes and Genomes to Systems
Entité participante : Alexander Fleming Biomedical Sciences Research Center — Pays : Grèce — Rôle : PI
Type d'entité : Recherche
Financement ERC de l'entité : 1500000.0 €

Dietary intake has an enormous impact on aspects of human health, yet scientific consensus about how what we eat affects our biology remains elusive. To address the complex biological impact of diet, I propose to apply an unconventional, ‘humans-as-model-organisms’ approach to compare the molecular and functional effects of a highly structured dietary regime, specified by the Eastern Orthodox Christian Church (EOCC), to the unstructured diet followed by the general population. Individuals who follow the EOCC regime abstain from meat, dairy products and eggs for 180-200 days annually, in a temporally-structured manner initiated in childhood. I aim to explore the biological signatures of structured vs. unstructured diet by addressing three objectives. First I will investigate the effects of the two regimes, and of genetic variation, on higher-level phenotypes including anthropometric, physiological and biomarker traits. Second, I will carry out a comprehensive set of omics assays (metabolomics, transcriptomics, epigenomics and investigation of the gut microbiome), will associate omics phenotypes with genetic variation, and will integrate data across biological levels to uncover complex molecular signatures. Third, I will interrogate the functional consequences of dietary regimes at the cellular level through primary cell culture. Acute and long-term effects of dietary intake will be explored for all objectives through a two timepoint sampling strategy. This proposal therefore comprises a unique opportunity to study a specific perturbation (EOCC structured diet) introduced to a steady-state system (unstructured diet followed by the general population) in a ground-breaking human systems biology type of study. This approach brings together expertise from genomics, computational biology, statistics, medicine and epidemiology. It will lead to novel insights regarding the potent signalling nature of nutrients and is likely to yield results of high translational value.
Projet ERC : RMGPP (Horizon 2020, appel 2014, Advanced grants)
Domaine scientifique : Social Sciences and Humanities
Panel : Individuals, Markets and Organisations
Entité participante : University of Warwick — Pays : Royaume-Uni — Rôle : Partner
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 243294.56 €

Differences in productivity explain much of differences in income levels across countries, yet little is known about how to improve productivity of manufacturing in the developing world. Recent research reveals very high dispersion in productivity in low-income countries. We examine firm productivity at a uniquely detailed level, collecting sub-factory production and survey data from hundreds of garment manufacturers in several countries. The data, coupled with a new method for comparing productivity, allow us to measure physical productivity in and across firms and among heterogeneous products. Initial results from nearly 100 factories in Bangladesh show significant dispersion of productivity within factories; production lines at the 90th percentile are 50% more efficient than those at the 10th percentile. Differences are highly persistent – puzzling given that the lines are often on the same production floor. Capital and the quality of the buyer explains a small part of the dispersion: lines producing goods for higher-end buyers are significantly more efficient. Shocks and interventions allows us to examine the challenges of increasing productivity in volatile conditions characteristic of low-income countries. Our data span a period including general strikes and a 67% minimum wage increase. We have conducted 2 RCTs on line supervisor training. We are designing data collection and analysis tools for use by factories and a program to address issues related to worker stress. We have collected data from 10 factories in Pakistan to benchmark productivity across countries. We are also working with the garment association in Myanmar. Relationships with large European-based buyers have led to discussions on linking with their suppliers in other countries. Our goal over the next 2 years is to collect data from at least 6 to 8 countries in Asia and Africa allowing cross-country analysis of productivity in lower-income countries at an unprecedented level of detail.

Mots-clés : productivity dispersion,productivity and growth,persistent productivity differences,private sector development,management practices,social compliance
Projet ERC : CerQuS (Horizon 2020, appel 2018, Consolidator grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Computer science and informatics
Entité participante : University of Tartu — Pays : Estonie — Rôle : PI
Acronyme de l'entité : UT
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1716475.0 €

Digital communication permeates all areas of today's daily life. Cryptographic protocols are used to secure that communication. Quantum communication and the advent of quantum computers both threaten existing cryptographic solutions, and create new opportunities for secure protocols. The security of cryptographic systems is normally ensured by mathematical proofs. Due to human error, however, these proofs often contain errors, limiting the usefulness of said proofs. This is especially true in the case of quantum protocols since human intuition is well-adapted to the classical world, but not to quantum mechanics. To resolve this problem, methods for verifying cryptographic security proofs using computers (i.e., for "certifying" the security) have been developed. Yet, all existing verification approaches handle classical cryptography only - for quantum protocols, no approaches exist. This project will lay the foundations for the verification of quantum cryptography. We will design logics and software tools for developing and verifying security proofs on the computer, both for classical protocols secure against quantum computer (post-quantum security) and for protocols that use quantum communication. Our main approach is the design of a logic (quantum relational Hoare logic, qRHL) for reasoning about the relationship between pairs of quantum programs, together with an ecosystem of manual and automated reasoning tools, culminating in fully certified security proofs for real-world quantum protocols. As a final result, the project will improve the security of protocols in the quantum age, by removing one possible source of human error. In addition, the project directly impacts the research community, by providing new foundations in program verification, and by providing cryptographers with new tools for the verification of their protocols.

Mots-clés : quantum cryptography,formal verification
Projet ERC : AlgoHex (Horizon 2020, appel 2019, Starting grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Computer science and informatics
Entité participante : University of Bern — Pays : Suisse — Rôle : PI
Acronyme de l'entité : UB
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 1482156.0 €

Digital geometry representations are nowadays a fundamental ingredient of many applications, as for instance CAD/CAM, fabrication, shape optimization, bio-medical engineering and numerical simulation. Among volumetric discretizations, the "holy grail" are hexahedral meshes, i.e. a decomposition of the domain into conforming cube-like elements. For simulations they offer accuracy and efficiency that cannot be obtained with alternatives like tetrahedral meshes, specifically when dealing with higher-order PDEs. So far, automatic hexahedral meshing of general volumetric domains is a long-standing, notoriously difficult and open problem. Our main goal is to develop algorithms for automatic hexahedral meshing of general volumetric domains that are (i) robust, (ii) scalable and (iii) offer precise control on regularity, approximation error and element sizing/anisotropy. Our approach is designed to replicate the success story of recent integer-grid map based algorithms for 2D quadrilateral meshing. The underlying methodology offers the essential global view on the problem that was lacking in previous attempts. Preliminary results of integer-grid map hexahedral meshing are promising and a breakthrough is in reach. We identified five challenges that need to be addressed in order to reach practically sufficient hexahedral mesh generation. These challenges have partly been resolved in 2D, however, the solutions do not generalize to 3D due to the increased mathematical complexity of 3D manifolds. Nevertheless, with our experience in developing and evaluating the 2D techniques, we identified the key properties that are necessary for success and accordingly propose novel volumetric counterparts that will be developed in the AlgoHex project.

Mots-clés : hexahedral mesh generation,geometry processing,differential geometry,volumetric mappings,finite element method,simulation,mixed integer optimization