Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Dissecting speciation using a genomics approach (RHINOSPEC)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Incoming Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2010-IIF, 2010)
Start date: 2012-03-20
End date: 2014-03-19
Duration (months): 24.0
Total project cost (EUR): 210092.8
EU funding (EUR): 210092.8
Participants: 1
Project status: CLOSED

Our proposal will tackle a central issue in biology: what is the genetic basis of species differentiation? Recent evidence of genetic exchange among species has led many to reject the traditional view that speciation requires complete reproductive isolation. Instead, the emerging new concept of so-called ‘genic speciation’ asserts that reproductive barriers can be established by divergence at only a few loci against a background of gene flow. We will combine novel and powerful analytical methods with new and traditional genetic technologies to investigate the genetic basis of species differences, and the process of divergence, in a model system of two co-distributed species of horseshoe bat (R. yunanensis and R. p. pearsoni). The Incoming Fellow has previously shown that, in these taxa, there is strong evidence of extensive past replacement of the nuclear genome in spite of clear phenotypic, acoustic and karyotypic differences. This unusual system provides an exceptional opportunity to identify and characterize genes that encode phenotypic differences among taxa, and also to determine the functional characteristics of ‘leaky genes’ versus ‘non-leaky genes’ (or ‘species genes’). Such knowledge of a natural mammalian system at a genome scale would take us beyond the current state-of-the art of research in this field, and would have impact in frontier science as well as potential benefits to conservation, genetics and evolutionary biologists. We will use Next Generation Sequencing and a highly novel statistical pipeline to identify key loci and larger ‘genomic islands’ that have resisted introgressive hybridization between our focal taxa. Our phylogenomic approach will then be extended to a larger sample to study whether these loci are under selection. Finally, we will apply chromosomal genetics methods to establish whether non-leaky loci and islands are influenced by the presence of chromosomal rearrangements, such as inversions.

Keywords: evolutionary biology,phylogeny,systematic zoology,genomics,population genetics
Moving Archaeological Knowledge Away from Neo-colonialism (MAKAN)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2012-01-09
End date: 2014-01-08
Duration (months): 24.0
Total project cost (EUR): 193349.6
EU funding (EUR): 193349.6
Participants: 1
Project status: CLOSED

The history of archaeology is tightly intertwined with colonialism. The archaeological rediscovery of ancient Middle Eastern civilizations, in particular, coincided, from the mid-19th century, with the process of colonial appropriation of the Ottoman Empire. For over two centuries the Middle East has been a resource both for ancient materials, enriching major Western collections, and for historical antecedents, and has itself remained disciplinarily excluded from the recovery of its own Past. Well after the acquisition of formal national independence by many countries colonial archaeology seems to have been followed, not by national, but by neo-colonial archaeological practices. In Egyptian Archaeology colonial rule resulted in a rigid exclusion of the local community, recreated by each subsequent generation of archaeologists, of all nationalities including Egyptian. The challenge of giving the local communities a primary role in developing and disseminating archaeological knowledge is of the outmost importance for the decolonization of Egyptology. Their involvement would end a traditional exclusion of local communities from their own Past and the Western control of knowledge. The MAKAN project objectives are: -to construct a self-critical history of Egyptian Archaeology, from the study of its formative phase and of so-called Neo-colonial Archaeology -to evaluate current strategies and proposing new approaches to the issue of the Decolonization of Egyptology, along the path of the World Archaeological Congress -the analysis of possible venues for the local community re-appropriation of its own Past, investigating whether local and distant museums can be accessible spaces for community expression and exchange -to implement a multi-site ethnography, designed from Petrie Museum proposed links and collection provenances, addressed to the production of a holistic evaluation report including guidelines for ethics in Egyptian Archaeology projects

Keywords: archaeology,history,egyptology,anthropology,self-critique history,reflexive archaeology,community archaeology,decolonization of egyptian archaeology
Towards a complete understanding of the roles of the Exon Junction Complex in Drosophila: Identification and functional characterization of the RNA targets and protein partners of the EJC (DROSEJCINRNAREG)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Germany
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2012-07-01
End date: 2014-06-30
Duration (months): 24.0
Total project cost (EUR): 169863.2
EU funding (EUR): 169863.2
Participants: 1
Project status: CLOSED

RNA localization allows eukaryotic cells to control gene expression in space and time and contributes importantly to cell polarization, allowing asymmetry in events such as cell division, oogenesis and body patterning. Major contributions to our understanding of the functional aspects of RNA regulation control have come from studies in Drosophila. Investigation into oskar mRNA localization in the oocyte, which is essential for germ cell development in the embryo, has revealed a key role of the Exon Junction Complex (EJC) RNA transport. In contrast, in mammals the main role of the EJC shown to date is in RNA quality control, in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. However, recent reports have linked the EJC to development and cell polarization in mammals as well. The proposed project aims to determine the full spectrum of EJC functions in RNA regulation, using Drosophila as a model. This will be addressed by creating transgenic Drosophila strains expressing tagged-EJC fusions for use in biochemical assays. Purified EJC complexes will be analyzed by SOLEXA based deep-sequencing and SILAC based mass spectrometry following two major objectives: 1) to investigate the EJC associated transcriptome in the oocyte and selected tissues during development and 2) to define the oskar mRNA-associated EJC proteome and its composition at different exon-exon junctions and at different stages of its localization. The results obtained with this unbiased approach will constitute a major step forward in understanding EJC function, not only in the fly, but also in mammals. The project’s multidisciplinary nature, combining cutting-edge biochemical, genomic, and Drosophila genetic techniques, will provide a unique opportunity to generate new scientific knowledge and acquire novel experimental skills that will be essential bases for future research and an independent scientific career.

Keywords: developmental biology,biochemistry,histochemistry,genetic engineering,molecular genetics,proteomics,computational biology
The Many Kinds of Many: Pluralism about Properties (TMKM)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2011-10-03
End date: 2013-10-02
Duration (months): 24.0
Total project cost (EUR): 192349.6
EU funding (EUR): 192349.6
Participants: 1
Project status: CLOSED

In both ordinary and scientific inquiry we often seem to attribute properties to things, or to kinds of things: we say, for example, that grass is green, that the earth is spherical, that humans are animals, and that murder is wrong. We also seem to think that these properties are things in their own right: there is something that it is to be green, or spherical, or an animal, or wrong, and that scientific or normative projects are engaged in uncovering the essences of such properties. If we take these initial thoughts to amount to anything, an important question arises: what kind of things should we take properties to be? Perhaps we should take them to be those things in virtue of which one kind of thing is demarcated from another kind of thing. Or perhaps as those aspects of an object which ground the causal powers of that object. Alternatively, perhaps we should take properties to be just those things that are referred to by our predicates. These suggestions are all brief expressions of different ways of understanding properties, ranging from the thought that properties should only be those things that ground some genuine similarities between objects, thus rendering properties relatively sparse, to the thought that any predicate with consistent rules for its application can give rise to a corresponding property, thus rendering properties abundant. This project outlines and argues for pluralism about properties. It argues that we should take the existence of properties seriously, and aims to give a fully developed inventory of the various kinds of properties we should posit, why we should posit them, and what jobs each kind of property can do. It also aims to show why adopting a pluralist conception of properties over a monist conception of properties – which claims that there is only one kind of property – has significant theoretical benefits, and investigates the connections between properties and the closely related concepts of reference, truth and realism.

Keywords: humanities,philosophy,language,logic,metaphysics
Evaluation of the genetic response to climatic changes: the demographic history of the cottoid fish flock from Baikal. (GEN-RESP)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: France
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2011-06-01
End date: 2011-08-31
Duration (months): 3.0
Total project cost (EUR): 193564.0
EU funding (EUR): 193564.0
Participants: 1
Project status: CLOSED

Little is known about the evolutionary response of species to climate changes because time scales are too long to be directly studied; however recent phylogenetic studies on ancient lakes taxa suggest that climate- and/or geological-induced environmental changes can be reconstructed by analyzing genetic patterns within and among species. Lake Baikal is the most voluminous and deepest freshwater lake in the world. Therefore population genetics patterns can be compared between populations over a latitudinal range from the northern to the Southern basin (650 km) but as well over a large bathymetric range (1600m). Very little population genetics researches have been conducted on endemic Baikal species probably due to geopolitics and sampling difficulties. The endemic cottoid fishes flock contains only 33 described species. Our project attempts to combine population genetics, demographic and paleoclimatic data to investigate the effects of major climatic and geological changes on the Baikal endemic ichtyofauna given the various cottoid fishes habitats (e.g. benthic/pelagic species, shallow water/deep water species, latitudinal differences). We will genotype populations of 6 target sculpin species from different habitat types using 15 microsatellites. For the analytic part of the project we will use the Approximate Bayesian Computation methods, recent model-based methods used in very diverse fields. To reconstruct the recent evolutionary history of species or populations these methods use genetic data to test alternative models of speciation and genetic divergence. One of the main advantages of these methods is their flexibility; there is indeed no a priori limitation on the demographic models that can be built in terms of number of species involved, population structure, and demographic events. Our project will help elucidating the effects of global climatic changes on the general dynamics of diversification, loss of variation, adaptive radiations and speciation events.

Keywords: population genetics,phylogeography,climatic changes,baikal,abc methods,endemism,cottoid fish
Role of plasmacytoid dendritic cells in the orchestration of in vivo immune responses (ORCHESTRATE)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: France
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2012-12-01
End date: 2014-11-30
Duration (months): 24.0
Total project cost (EUR): 185748.0
EU funding (EUR): 185748.0
Participants: 1
Project status: CLOSED

Plasmacytoid dendritic cells (pDCs) which are professional type I IFN producing cells modulate phenotype and function of conventional dendritic cells (cDCs) triggering maturation and enhancing priming of cytotoxic T lymphocytes (CTLs). It is widely accepted that type I IFNs offer a link between innate and adaptive immune responses, but there are contrasting data regarding their immunoregulatory effects. It has been shown that pDC derived IFNs modulate the phenotype and function of conventional DCs. Moreover, pDCs and cDCs contribute to the activation of NK cells. Ability of pDC to function as APC for T cells is also demonstrated. Thus pDC appear specialized for initiation of innate response, but also have certain capabilities of inducing and modulating adaptive immune responses. Recent work from Albert group provided a first-generation multi-analyte profile (MAP) of how pDCs serve to bridge innate and adaptive immune responses in the context of TLR7 and TLR9 agonists analysing in vitro human isolated pDCs. Four distinct cytokine/chemokine loops by wich pDCs contribute to the initiation of an inflammatory response were identified, what helped to provide a foundation for understanding the functional status of pDCs in different disease states. To understand the impact of inflammatory response on the coordination of immune responses, to define the mechanism by which innate effector molecules influence adaptive immunity at a fundamental level, in vivo research on mouse models is required. Thusfar mice strain that permit control of gene expression in pDCs has not been used. The Albert lab developed Siglec-H-CreERT2 knock-in mice with pDC specific inducible Cre expression. A second knock-in was developed in order to control the production of type I IFNs – Siglec-H-IRF-7. By using new mice mutants it will be possible to determine the role of pDCs and pDC-derived type I IFNs in the orchestration of cDC activation of CD8+ T cell and NK cell responses in vivo.

Keywords: plasmacytoid dendritic cells,type i ifns,siglec-h-creert2,siglec-h-irf-7,pdc-dta,pdcs-yfp,pdcs-dcred,conventional dendritic cells,nk cells,cd8+ t cells
Coordinated regulation of transcription and pre-mRNA splicing at gene promoters (PRE-MRNA SPLICING)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Germany
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2011-05-01
End date: 2013-04-30
Duration (months): 24.0
Total project cost (EUR): 162742.4
EU funding (EUR): 162742.4
Participants: 1
Project status: CLOSED

Accurate pre-mRNA splicing is a fundamental step for gene expression. SR proteins, a protein family of splicing regulators, play an essential role in the process by defining intron-exon boundaries and recruiting the spliceosome to carry out splicing. Pre-mRNA splicing occurs co-transcriptionally and it is now emerging that promoter identity modulates alternative splicing, possibly through the recruitment of SR proteins or through kinetic coupling by altering Pol II elongation rates. The aim of the present proposal is to investigate the relationship between promoter elements, differential SR protein recruitment to genes and splicing outcome. The genome-wide recruitment of SR proteins to promoter elements will be investigated resorting to innovative approaches. SR proteins tagged with LAP-tag and expressed in "BAC cell lines" will be isolated with associated DNA sequences (ChIP) which will then be used to interrogate a genome-wide promoter microarray (ChIP-on-CHIP). This will reveal similarities and differences in recruitment to genes and gene regions among SR protein family. To test how promoter elements influence spliceosome assembly and splicing outcome, model-genes containing alternative and constitutively spliced exons will be created. The focus will be on genes relevant for neuronal differentiation. Model genes will be introduced in cells already expressing individual SR proteins BACs, creating "Double-BAC cell lines". The results expected from this project will provide a global view of SR protein role in regulating and coupling transcription and pre-mRNA splicing. Elucidating these regulatory mechanisms is key for the understanding of genomic and proteomic diversity.

Keywords: genomics,molecular genetics,pre-mrna splicing,gene transcription,neuronal development
The Approximation Problem in Computational ElectroMagnetics (APPROCEM)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: France
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2011-05-01
End date: 2013-04-30
Duration (months): 24.0
Total project cost (EUR): 179548.0
EU funding (EUR): 179548.0
Participants: 1
Project status: CLOSED

The proposal is focused on computational electromagnetics (CEM) with emphasis on the moment method (MoM) and its application to the numerical solution of integral equations (IEs) arising in electromagnetic (EM) scattering by either perfectly-conducting or homogeneous dielectric objects in both 2-D and 3-D geometries. Particularly it addresses four research objectives (ROs). RO1 concerns a priori and a posteriori error analyses for the Reduced Basis Method on account of its application to popular IEs in EM scattering theory (i.e. EFIE, MFIE, and CFIE). RO2 is aimed to shed light on the intimate (but quite involved) relationship between properties of the relevant integral operators underlying our preferred EM models and analogous properties of finite ranked operators resulting from their MoM discretization. This is expected to provide insights for performance and reliability improvements of common iterative techniques used to solve the corresponding MoM system (i.e. CG, BiCG, and GMRES). RO3 points to contribute to the development and further understanding of the approximation problem in the light of Enflo’s and subsequent work on the existence of Banach spaces lacking Grothendieck’s approximation property. This will be done in regard to the sole EFIE. The issue seems almost completely unexplored, yet, it may be useful to know if and when MoM intrinsically fails to represent certain classes of operators, commonly encountered in EM scattering, by finite ranked operators (e.g. depending on the smoothness of scatterers). This is the deepest theoretical theme addressed by the proposal and represents one of the strongest motivations that has led the fellow to apply at LJLL on the consideration of its researchers’ expertise on foundations of numerical methods. Finally RO4 regards numerical experimentation. It will aid the fellow in the development and testing of novel MoM-based schemes for EM scattering problems, but also in the refinement of existing analog techniques.

Keywords: computational electromagnetics,moment method,integral equations,electromagnetic scattering,approximation property,a priori and a posteriori estimates,reduced basis method,iterative methods
Bright attosecond x-rays in the water-window using phase-matched high-harmonic generation (BAXHHG)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Spain
Call:  (FP7-PEOPLE-2010-IEF, 2010)
Start date: 2011-04-01
End date: 2013-03-31
Duration (months): 24.0
Total project cost (EUR): 166565.6
EU funding (EUR): 166565.6
Participants: 1
Project status: CLOSED

We propose to develop a compact source of x-rays, with sub-femtosecond duration, near-perfect spatial coherence, and photon energy approaching 500 eV. Such a source will be an essential tool for attoscience and nanometre-resolution microscopy. In particular, the importance of sub-femtosecond dynamics is being appreciated in a rapidly growing range of contexts, including nanoplasmonics and charge migration in biomolecules. The transparency window of water (280 eV to 530 eV) is particularly attractive for structural and dynamical imaging of biological samples. We shall use high-harmonic generation driven by mid-infrared (2 micron) light. The principle advantage of a long-wavelength drive over the visible (800 nm) drive fields which currently receive much attention is the higher energy of the emitted x-rays photons, which scale with the square of the drive wavelength. There are also numerous potential technical advantages, including greater robustness through the use of intrinsically phase-stable mid-infrared sources based on difference-frequency generation, and greater brightness at high photon energies through improved phase matching.

Keywords: experimental physics,microscopy,applied optics,atomic physics,radiation physics,molecular physics,x-ray science