Data-Gouv-ML/pcri-actions-marie-curie-participations-et-projets-laureats huggingface dataset:
Projet NucLoc (Horizon 2020, appel à projets 2016)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

In eukaryotic cells mRNAs can be localized to specific places within a cell to achieve protein synthesis with spatiotemporal control. Recently, I and others have shown that prokaryotes can also target mRNAs to specific parts of the cell. However, these studies have been restricted to a limited number of mRNAs and were performed with Gram-negative bacteria, and due to the serendipitous nature of these discoveries and conflicting results, it is not clear how widespread mRNA localization is in a bacterial cell and what conserved mechanisms are playing a role. To investigate this, I will first employ a novel CLIP-seq-inspired deep-sequencing-based approach to gain an unbiased view of mRNAs enriched at the cell periphery and cell poles of the Gram-positive model bacterium Bacillus subtilis. This dataset will reveal the scope of mRNA targeting by the Signal Recognition Particle (SRP) and will reveal mRNAs that use another mechanism for cellular targeting. In addition, classic CLIP-seq experiments will be used to identify mRNAs that use the cytoskeleton and other morphological proteins for targeting. As a complementary approach, I will assess the localization of mRNAs coding for different classes of localized proteins (polar, cell division, cytoskeletal, membrane, secreted, motility, nucleoid and chaperone proteins) using the established fluorescence in situ hybridization (FISH) technique. Information obtained from these experiments will subsequently be used to investigate the role of protein translation, RNA sequences, genome location and cell morphology in mRNA localization, to gain functional insight into the mechanisms responsible for this basic morphogenetic process.

Mots clés : rna localization, cytoskeleton, rna binding proteins

Participants :
- University of Amsterdam (Pays-Bas) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 165598.8 €
Projet XPGCS (Horizon 2020, appel à projets 2015)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

In female mice, one of the two X chromosomes is inactivated during early development to ensure dosage compensation between genders. A long non-coding gene, Xist, plays a crucial role in the initiation of the X chromosome inactivation (XCI) process. Primordial germ cells (PGCs), the precursors of sperm and eggs, transmit genetic and epigenetic information to subsequent generations, following extensive reprogramming, erasure of methylation and genomic imprints, and X chromosome reactivation. The inactive X (Xi) then undergoes progressive reprogramming and reactivation in the germline of female embryos, through the loss of Xist RNA coating, followed by the erasure of the repressive H3K27me3 histone mark, and eventually biallelic expression of X-linked genes. Although the global dynamics of Xi reactivation have been mapped little is known about the gene-specific dynamics, or the mechanisms involved. To explore gene activity on the entire X chromosome during reprogramming in the germline, I will perform single-cell transcriptome analyses on PGCs from C57BL/6 X Castaneus F1 female hybrid embryos. The high rate of sequence polymorphisms between these strains provides allele-specific information for the activity of the Xp (paternal X) and the Xm (maternal X). I will investigate the kinetics of Xp and Xm gene reactivation chromosome-wide at the single cell level following PGC specification. Furthermore, I will study the dynamics of the expression of X-linked genes in conjunction with chromatin changes in PGCs by monitoring the loss of H3K27me3 enrichment on the inactive X chromosome. In parallel, I will study how the regulation of H3K27me3 affect Xi reactivation by using a conditional mutant mouse model of a H3K27me3 demethylase, UTX. Altogether, the innovative and multidisciplinary approach of this study will unravel important insights on germline reprogramming and the roles of chromatin changes associated with X chromosome reactivation.

Mots clés : primordial germ cells, x chromosome, histone marks, gene expression kinetics, mouse embryo

Participants :
- University of Cambridge (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 195454.8 €
Projet BioNetIllustration (Horizon 2020, appel à projets 2016)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Information Science and Engineering
Statut du projet : CLOSED

In living systems, one molecule is commonly involved in several distinct physiological functions. The roles of molecules are commonly summarized in pathway diagrams, which, however, are abstract, hierarchically nested and thus is difficult to comprehend especially by non-expert audience. The primary goal of this research in visualization is to intuitively support the comprehensive understanding of relationships among biological networks using interactively computed illustrations. Illustrations, especially in textbooks of biology are carefully designed to clearly present reactions between organs as well as interactions within cells. Automatic generation of illustrative visualizations of biological networks is thus the technical content of this proposal. Automatic generation of hand-drawn illustrations has been a challenging task due to the difficulty of algorithmically describing a human creative process such as evaluating and selecting significant information and composing meaningful explanations in a visually plausible manner. Our high-level idea in BioNetIllustration is to simulate this process by decomposing the entire problem into multiple steps including content-driven layout and illustration design as well as spatio-temporal event transitions across multiple representations. As a pioneer study on illustrations, a new visualization framework for these network illustrations will be developed. This study can be achieved by matching the unique competences of the researcher and the host research group and allows an innovative synthesis to produce hand-drawn like illustrations of biological networks. The project also involves experts from several disciplines including network and medical visualization, data mining, systems biology as well as perceptual psychology. The result will provide a new direction for physiological process analysis and accelerate the knowledge transfer not only within experts but also to the public.

Mots clés : information visualization, illustrations, graph, biological network

Participants :
- TU Wien (Autriche) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 166156.8 €
Projet MYO-DESMOPLASIA (Horizon 2020, appel à projets 2014)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Information Science and Engineering
Statut du projet : CLOSED

In many tumors a desmoplastic reaction takes place during progression, which results in extensive production of collagen by stromal cells of the tumor, mainly fibroblasts and myofibroblasts. Tumor desmoplasia determines in large part the patho-physiology of solid tumors and poses a major barrier to effective drug delivery, affecting the overall survival of cancer patients. Here, the applicant proposes to test the hypothesis that the increase in extracellular matrix (ECM) stiffness and transforming growth factor-beta (TGFβ) activation often observed during tumor progression have additive effects on tumor desmoplasia. Therefore, targeting any of these parameters alone or in combination can reduce the desmoplastic response of the stromal cells. To explore this hypothesis, a combination of cutting-edge techniques will be employed. Specifically, a collagen ECM model, with pre-determined topography and tunable stiffness will be developed. Subsequently, fibroblasts and myofibroblasts will be cultured in the ECM models. Cells nano-mechanical behavior and their morphodynamic alterations will be investigated with Atomic Force Microscopy and light/fluorescence microscopy under the presence or absence of TGFβ or anti-TGFβ agents. Finally, the effects of matrix stiffness along with different TGFβ concentrations in the expression pattern of genes encoding ECM components will be investigated using real-time PCR. The research results will elucidate the mechanisms of the interplay between matrix stiffness and TGFβ production in modulating the ability of fibroblasts and myofibroblasts to form tumor desmoplasia. In the proposed project, the fellow will acquire scientific and complementary skills according to his personalized career development plan and through advanced training, international and inter-sectoral mobility will reach a position of professional maturity in research.

Mots clés : tumor microenvironment, nanomechanics, collagen network models

Participants :
- University of Cyprus (Chypre) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 163648.8 €
Projet FLEXGENOME (Horizon 2020, appel à projets 2014)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Environment and Geosciences
Statut du projet : CLOSED

In multicellular animals, complex phenotypic traits such as behaviour, lifespan and diseases are not only determined by genetic factors but also in large part by the environment. Understanding how genes and the environment interact to produce fundamental traits is a major question in biology. Many organisms are capable of expressing multiple phenotypes from a single genome when exposed to different environments. This widespread phenomenon is termed phenotypic plasticity (PP). The genetic programs needed to produce alternative phenotypes are encoded within a single genome, and environmental stimuli determine which form is expressed. PP is highly relevant in nature as it allows organisms to survive and reproduce successfully in variable environments. Nevertheless, the molecular and genetic mechanisms responsible for this flexibility are surprisingly poorly understood. Here, I will investigate the genetic basis of PP by applying advanced genomic and computational techniques to an ecological model of PP, the butterfly Bicyclus anynana. In particular, I will 1) identify the genetic programs that produce alternative phenotypes from a single genome; and 2) assess the potential for evolutionary change in PP by characterising genetic variation in these programs. I will do this by applying RNA-Seq and gene co-expression networks to an ecologically well-characterised insect and developing and integrating methods and concepts across disciplines. Combining my significant expertise on the model system with the host laboratory’s outstanding track record in evolutionary genomics and bioinformatics, this project offers a unique opportunity for obtaining an unprecedented and long-desired insight into the genetic mechanisms of PP. This fellowship will train me in precisely the technical and analytical techniques that are critical for scientific progress in decades to come, and for my career development as a scientist within the European Research Area.

Mots clés : phenotypic plasticity, gene environment interaction, evolutionary ecology, evolutionary transcriptomics, bioinformatics, adaptation, life history, genetic architecture, climate change

Participants :
- University of London (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 183454.8 €
Projet NuMA_CyclinB1_EM (Horizon 2020, appel à projets 2020)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : SIGNED

In multicellular organisms, oriented cell divisions sustain tissue morphogenesis, tissue architecture and homeostasis by ensuring the correct positioning of daughter cell after mitosis. Accurate execution of oriented divisions and chromosome segregation relies on the positioning of an essential actor, the mitotic spindle. The consequence of spindle misorientation is drastic. Disruption of any of the spindle orientation factors could lead to genetic instability, tissue disorganization and tumorigenesis. However, cell division is controlled not only in orientation, but also in time. Indeed, spindle orientation is also very important for a wide range of developmental processes, ranging from germline stem cell division to epithelial tissue homeostasis and regeneration. A more complete understanding of how spindles are oriented will therefore require more extensive research, e.g. using CRISPR-based strategies to interrogate the proposed interactions in vivo, into how the spindle-orienting machinery is localized and regulated in multiple systems. The aim of this project is to advance knowledge on how cell cycle regulates spindle positioning and its contribution in epithelial morphogenesis in the intestinal tissues. This advance knowledge will serve to better understand the pathogenic mechanisms of important human diseases such as cancer.

Mots clés : numa, cyclinb1, spindle orientation, epithelial morphogenesis

Participants :
- Spanish National Research Council (Espagne) — Coordinator, beneficiary, Recherche, subvention : 160932.48 €
Projet MultisensoryIntegration (Horizon 2020, appel à projets 2015)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

In natural environments, the brain is typically bombarded with multisensory information. Animals must continually evaluate which of these multimodal cues should be associated with a single physical object, and which are separate. For example, when a rabbit hears footsteps and sees a blur, is the blur responsible for the footsteps, or are there two separate sources of danger? Animals use two types of information to make this decision: spatial correlations (are the footsteps and blur localized together) and temporal correlations (does the blur move in sync with the footsteps). Humans constantly perform these same operations. We use lip movements to help identify the words spoken by a friend, a subconscious process which becomes painfully apparent when watching a poorly dubbed movie. This may explain why psychological conditions such as autistic spectrum disorder and schizophrenia often present with deficits in audiovisual integration. Despite the ethological and medical significance of multisensory integration, little is known about the underlying neural mechanisms. However, I believe the behavioral repertoire of the mouse, combined with new technological advances, provides an unprecedented opportunity to answer this fundamental research question. With recent developments in calcium imaging and optogenetic techniques, it is now possible to record and manipulate neural activity across the majority of mouse cortex. I will develop novel behavioral tasks for the mouse which require multisensory integration in space or time. By recording or perturbing cortical activity during these behaviors, I will determine the roles of individual neurons, neural populations, and cortical regions in multisensory integration. I will perform these experiments in the Cortical Processing Laboratory at University College London, led by Professors Kenneth Harris and Matteo Carandini.

Mots clés : multisensory integration, cortex, vision, audition, behavior, two photon imaging, optogenetics

Participants :
- University of London (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 183454.8 €
Projet CHERI (Horizon 2020, appel à projets 2015)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

In nature, plants are challenged by disease-causing pathogens such as viruses, bacteria and fungi. Understanding mechanisms of plant disease and disease resistance is of fundamental importance to sustainable agriculture and human health. Unlike mammals, plants lack a circulating immune system. Plants instead rely on the innate immune capacity of each cell and systemic signals that disseminate from infection sites. Successful pathogens use effectors to suppress plant immunity and cause disease. Plants have evolved disease resistance genes encoding immune receptors that perceive specific pathogen effectors to mount effector-triggered immunity. In Arabidopsis, a heteromeric pair of intracellular immune receptors forms a functional recognition complex which senses virulence activities of two structurally unrelated bacterial effectors at the nuclear chromatin. Results suggest that effector targeting of histone modifications and chromatin remodelling interferes with host basal immunity and that this is transduced by the receptor pair to activation of defence pathways. The underlying molecular mechanisms remain unclear. We have found that the two bacterial effectors interact with an overlapping set of chromatin-associated proteins and with certain immune receptor domains. We hypothesize that the effectors converge on the same chromatin machinery for promoting disease and that their actions are intercepted by the immune receptor system which is physically connected to basal immunity signalling components. By using the effectors as molecular probes, this proposal aims to elucidate how the chromatin environment is modulated during infection and how effector perturbations are converted to effective immunity.

Mots clés : innate immunity, pathogen effectors, nlr receptors, chromatin dynamics, transcriptional, regulation

Participants :
- Max Planck Society (Allemagne) — Coordinator, beneficiary, Recherche, subvention : 159460.8 €
Projet NanoSyNNets (Horizon 2020, appel à projets 2014)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

In neuronal networks of the brain, synapses are the connection points between neurons. The dynamics (or plasticity) of these synapses allow us to think, learn and memorize. A deeper understanding of these phenomena requires investigations of single synapses. Synapses have been intensively studied in vivo but in such studies the physiological complexity limits the investigations at the single synapses level. Despite tremendous technical and conceptual advances of in vivo studies, we miss (1) a better understanding of the mechanics of synapses formation; (2) observing directly the chemical activity at single synapses; (3) investigating the role of neuronal network topology in synaptic plasticity. These classical limitations can now be overcome by alternative in vitro approaches, using recent technological advances in microfluidics and nano-technologies. The aim of NANOSYNNETS is to use vertical arrays of NANOwires (aNWs) to study in vitro the formation and plasticity of single SYnapses in Neuronal NETworkS with controlled topologies. With my expertise in growing controlled neuronal networks in microfluidic chips, I decided to join the one of the leading group in bio-nanotechnologies, lead by Karen Martinez (KM) and based at the NanoScience Center (NSC) of the University of Copenhagen (UCPH), to exploit novel technologies for the investigation of in vitro single synapse formation, activity and plasticity. This novel approach will give a complementary and cutting-edge point of view to classical in vivo studies of synapses and will thereby provide unmatched insights into neurobiology and will shed new lights on unanswered questions in learning mechanisms or neuronal communication.

Mots clés : nanowires, synapses, neuronal networks, synaptic plasticity

Participants :
- University of Copenhagen (Danemark) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 212194.8 €
Projet GOLD-ICE (Horizon 2020, appel à projets 2017)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Environment and Geosciences
Statut du projet : CLOSED

In order to prepare for future climate changes we need to understand the fundamental dynamics of our climate system. To this end it is crucial to understand the role of greenhouse gases in the past shift some 1.2 million years ago from 40k to 100k year periodicities dominating our climate system. Only studying the deepest, and oldest ice layers of Antarctica can provide us with an answer. However, the deepest layers are inevitably highly thinned, thus calling for ice core analysis at unprecedented detail. Succeeding where conventional cm-resolution melting techniques fail, Laser-Ablation Inductively-Coupled Plasma Mass Spectrometry (LA-ICP-MS) has recently started to emerge for glaciochemical analysis at sub-millimeter depth resolution. The project proposed here takes a novel approach to establish LA-ICP-MS for ice core analysis at the Università Ca' Foscari Venezia. Unique synergy exists for this purpose, based on the leading expertise in trace element ice core analysis of Professor Carlo Barbante at the Institute for the Dynamics of Environmental Processes and the state-of-the-art know-how in applying LA-ICP-MS to ice cores recently obtained by the proposer. LA-ICP-MS is an essentially non-destructive technique, and offers the opportunity to re-visit existing archive pieces from previous ice core drillings. In so doing, the project targets a two-fold application to investigate previously untapped paleoclimatic signals stored in the highly thinned deep layers of Antarctic ice cores. At the same time, a comprehensive view on potential limitations arising on this fine is integrated in its unique approach to avoid misinterpretation of the novel LA-ICP-MS signals. By this means, the project will fully unfold the potential of LA-ICP-MS for ice core analysis, opening new avenues of research in Europe at the forefront of future prestigious ice coring projects.


Participants :
- Ca' Foscari University of Venice (Italie) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 180277.2 €
Projet NH-DEHAZE (Horizon 2020, appel à projets 2019)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Information Science and Engineering
Statut du projet : SIGNED

In presence of haze, small floating particles absorb and scatter the light from its propagation direction. This results in selective and significant attenuation of the light spectrum, and causes hazy scenes to be subject to a loss of contrast and sharpness for distant objects. Besides, most computer vision and image processing algorithms (e.g., from feature extraction to objects/scene detection and recognition) usually assume that the input image is the scene radiance (haze-free image), and therefore strongly suffer from the color-shift, and low-contrast induced by hazy conditions. For instance, in normal visibility conditions the Traffic Sign Detection and Recognition (TSDR) module of the existing ADAS systems reaches a detection rate averaging around 90%, but drops below 40% in case of haze or poor illumination conditions1. Therefore, many recent works have explored inverse problem formulations and have designed dedicated image enhancement methods to address the dehazing problem. However, to estimate their key internal parameters (e.g. airlight in Koschmieder’s light transmission model), most of those solutions assume homogeneous distribution of light and haze, which is rarely the case in practice (e.g. lighting is non-uniform in space and frequency during the night, attenuation caused by haze depends on the light frequency). Image dehazing thus remains a largely unsolved problem in case of dense and non-homogeneous haze scenes. As a federating objective, our project aims at implementing dehazing methods that are suited to dense and non-homogeneous hazy scenes. This implies the following tasks: (O1) build up the first (world-wide) image dataset including pairs of hazy and haze-free scenes, for which hazy scenes include real, dense, and non-homogeneous haze; (O2) develop and train deep dehazing neural networks to derive the dehazed images from hazy inputs. (O3) train deep image interpretation models that are suited to images captured in adverse conditions.

Mots clés : image dehazing, non homogeneous haze, neural networks

Participants :
- Université Catholique de Louvain (Belgique) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 178320.0 €