Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
New Methods to Reconstruct Phylogenetic Networks (NETWORK PHYLOGENIES)

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-2009-IEF, 2009)
Start date: 2010-07-14
End date: 2012-07-13
Duration (months): 24.0
Total project cost (EUR): 158445.6
EU funding (EUR): 158445.6
Participants: 1
Project status: CLOSED

Phylogenies are used to describe the history of evolutionarily related biological entities (e.g. genes, individuals, species) and are central in many biological applications, including functional genomics, epidemiology and biodiversity assessment. Many methods for reconstructing and studying phylogenies have been proposed, almost all of which use trees to represent them. Although in many cases this is reasonable, in many others phylogenies should be represented as networks (more precisely directed acyclic graphs). This is due to a number of biological phenomena collectively known as recombination, which are common in viruses (e.g. HIV and influenza), bacteria and sexual populations. Unfortunately recently proposed methods to reconstruct network phylogenies have not yet found many applications in evolutionary biology. I believe that this is due to the fact that many of these methods aim to explain all conflicting signal in the data with recombination, thus inferring far more recombination events than what is actually needed. I therefore propose a number of techniques whose goal is to explore the gap that is left between classical tree reconstruction, where no recombination is allowed, and the new network-based methods, where too many recombinations are allowed. The methods I propose are simple extensions of well-known approaches for tree reconstruction: maximum parsimony and distance methods. The two approaches differ for the optimality criterion used to score networks, but they have in common the fact that they impose a constraint on the number of recombinations allowed. Maximum parsimony scores networks on the basis of the number of sequence changes needed to explain the input sequences. On the other hand, distance methods score networks on the basis of how well they fit a collection of distance matrices given in input. In both cases, the optimization problems involved are likely to be computationally hard and therefore I plan to attack them using heuristics.

Keywords: evolution,computational biology,bioinformatics,algorithms,phylogenetic reconstruction,recombination,phylogenetic network,hiv,influenza,virus,parsimony,distance methods.
The cradle of flowering plants: biogeographical investigations in the most paleogeographically complex region on Earth, South-East Asia (CRADLE)

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-2009-IEF, 2009)
Start date: 2010-12-01
End date: 2012-11-30
Duration (months): 24.0
Total project cost (EUR): 172240.8
EU funding (EUR): 172240.8
Participants: 1
Project status: CLOSED

Since Darwin suggested that the cradle of flowering plants was found in an isolated southern continent now vanished, the spatial aspect of their origin has been neglected. In this project conducted with the support of Dr F. Forest from the Royal Botanic Gardens, Kew (UK), the applicant wish to address the following questions pertaining to the spatial origin of angiosperms: 1) Was the proto-South-East (SE) Asian continent, formed by landmasses that rifted from the southern Gondwana during the Paleozoic-Mesozoic, the birthplace of angiosperms?; 2) Has SE Asia acted as a centre of diversification for many angiosperm families through time?; 3) Has SE Asia been an important source of dispersal into other geographic regions?; and 4) How different dispersal modes will affect the ability of taxa to colonize other geographic regions and the resulting biogeographic patterns? To investigate these issues, the innovative full Bayesian framework approach (that simultaneously integrates phylogenetic, dating and biogeographic inferences) will be applied to DNA-sequence datasets compiled for several families from published and newly produced data. This project will also contribute to the development of novel biogeographic methods by providing a protocol to integrate paleogeographic connections through times and estimate specific dispersal rates per lineage. This will be implemented in MrBayes 4.0 with the collaboration of Prof. I. Sanmartin (Spain) and Prof. F. Ronquist (Sweden). Through this project, the applicant will have the opportunity to develop his skills in many aspects of biology and bioinformatics, which will provide him with the necessary expertise and experience to become one of the leaders in this field in Europe. Moreover, his immersion in an extremely active research environment at Kew and the establishment of links with other institutions will strengthen the applicant’s network and increase his potential to reach a position of professional maturity.

Keywords: angiosperms,biogeography,cradle,dispersal rate,diversification,mrbayes 4.0,paleogeography,south-east asia,spatial origin
Basal ganglia and the control of locomotion (BASALGANGLIANETWORKS)

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: France,Spain
Call:  (FP7-PEOPLE-2009-IIF, 2009)
Start date: 2010-12-13
End date: 2012-12-12
Duration (months): 24.0
Total project cost (EUR): 161293.0
EU funding (EUR): 161293.0
Participants: 2
Project status: CLOSED

The goal of this project is to understand of the mechanisms, at the neuronal network level, by which the basal ganglia control locomotor activity. The rational beyond this objective is twofold. First, altered locomotor activity is a hallmark of motor and psychiatric disorders. Second, the basal ganglia, a group of subcortical nuclei that connects the entire neocortex to locomotor brain centers, are known to control locomotion, but the network mechanisms responsible for this function are still unclear. Overall this project will have a strong impact on the understanding of an essential brain function (the control of locomotion by basal ganglia) and has direct implication for widespread human diseases such as Parkinson Disease, schizophrenia and drug addiction To reach this goal we will use an experimental strategy that combines state-of-art large-scale electrophysiological tools (silicon-based electrode arrays) and pharmacological manipulations of the locomotion, using rats as experimental model. Specifically the applicant proposes to investigate the mechanism by which low dose of cannabinoids increase spontaneous locomotor activity. The highest level of cannabinoid receptors in the brain have been reported in basal ganglia nuclei that belong to two pathways (the so called direct and indirect pathways) which are classically believed to have antagonistically impact on locomotor activity. How low doses of cannabinoid can affect both direct and indirect pathways and result in increased locomotor activity is therefore puzzling. We hypothesize that solving this apparent contradiction will significantly advance the understanding of the neuronal mechanisms that control locomotion. Moreover as the endocannabinoid system has been implicated in numerous basal ganglia-related diseases, the insight generated by this project will provide new therapeutic strategies to treat widespread diseases such as drug addiction and Parkinson’s disease.

Keywords: basal ganglia,locomotion,network dynamics,cannabinergic system,rats
Interferometry in the near-infrared: a very high angular resolution insight into the accretion/ejection process in young stars (ACCRETION/EJECTION)

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-2009-IEF, 2009)
Start date: 2011-12-01
End date: 2013-11-30
Duration (months): 24.0
Total project cost (EUR): 158945.6
EU funding (EUR): 158945.6
Participants: 1
Project status: CLOSED

A crucial problem in star formation is to understand the physical mechanism by which mass is ejected by young stars and collimated into stellar jets and the nature of the link with the accretion process. The interaction of outflowing material with the parental cloud is observable on scales from hundreds of astronomical units (AU) up to parsec scales and is relatively well understood. Conversely, both accretion and ejection take place on very small scales, from a few down to fractions of AU (i.e. milliarcsecond scales for the nearest star forming regions). Thus direct observations of the critical regions has been long hindered by the lack of high angular resolution facilities. The goal of this project is to probe the accretion/ejection region for the first time, by means of very high angular resolution near-infrared interferometric observations (~0.001&quot;). In particular, it is proposed to exploit the unique capabilities of the AMBER instrument at the Very Large Telescope Interferometer to observe the inner region of the accretion disk and the base of the jet down to sub-AU scales in young accreting stars. The analysis of complementary observations at ~0.1&quot; angular resolution will trace the jet collimation/acceleration region and the accretion/ejection interplay on larger scales (tens of AU). These observations, as well as dedicated models of the emission in both permitted and forbidden lines, are crucial for a proper interpretation of interferometric data. The proposed multifaceted approach will provide long-awaited critical observational constraints to test the proposed models of jet launching and magnetospheric accretion, which are central to both star and planet formation. Moreover, the accretion/ejection mechanism is at work in a large range of astrophysical objects from active galactic nuclei to brown dwarfs. Hence, the results of this project will have repercussions for several astrophysical disciplines from extragalactic astronomy to planetary science.

Keywords: physical sciences,star formation,stellar jets,accretion/ejection,near-infrared interferometry,high angular resolution techniques
Dissecting cGMP- and calcium-dependent signalling pathways that control gliding of a malaria zoite (PLASMODIUM MOTILITY)

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-2009-IEF, 2009)
Start date: 2011-07-01
End date: 2013-06-30
Duration (months): 24.0
Total project cost (EUR): 179603.2
EU funding (EUR): 179603.2
Participants: 1
Project status: CLOSED

Malaria parasites critically depend on an unusual form of gliding motility to colonize their hosts and to invade cells. Transmission of malaria to the mosquito, for instance, relies on the ability of the motile zygote, the ookinete, to glide towards and invade the midgut epithelium. Results obtained in the host team have revealed a central role of cGMP- and calcium-dependent signalling in ookinete motility. Nevertheless, how these pathways control gliding is unknown. I therefore propose to combine real-time quantitative imaging approaches with molecular phenotyping of parasite phosphoproteins to identify and distinguish molecular targets of signalling through calcium and cGMP-dependent pathways in Plasmodium berghei ookinetes. For this purpose, I will use transgenic parasites in which cGMP- and/or calcium-dependent signalling pathways are either inactivated and/or deregulated. The impact of genetically inhibiting or over-stimulating specific protein kinases on motility will be analysed in an automated quantitative imaging assay, allowing signalling pathways to be linked with specific changes in motility phenotypes. I will then use shotgun phosphoproteomics on enriched populations of selected mutants to identify candidate substrates. Phenotyping of stage-specific mutants in candidate substrates will allow the molecular targets of signalling cascades to be verified.

Keywords: malaria,cell biology,signal transduction,protein kinase,motility,quantitative imaging,phosphoproteome,ookinete,plasmodium berghei,cell invasion,mosquito
Method of Osteo-fracture Study through Automatic Identification and Classification: biomechanical analysis of bone trabecular structure (MOSAIC)

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: Greece
Call:  (FP7-PEOPLE-2009-IEF, 2009)
Start date: 2010-10-15
End date: 2012-10-14
Duration (months): 24.0
Total project cost (EUR): 146497.4
EU funding (EUR): 146497.4
Participants: 1
Project status: CLOSED

Bone fractures represent a major health problem in the increasingly elder population. The correct prediction of bone fracture risk in bone disease, e.g. osteoporosis, is a mandatory issue for the prevention of traumatic events and related medical efforts. The assessment of the fracture risk is based on the clinical evaluation of bone mineral density, but with an estimation error ranging from 20% to 40%. Trabecular structure is known to play an important role in the mechanical behaviour of bone, but clinical imaging does not provide sufficient information. In order to perform a systematic and in depth analysis of the trabecular framework, and its relation with the mechanical properties, micro-tomographic devices are required. Using these devices, structural analysis of bone specimens could be performed by investigating the structure of the broken region, in order to examine the differences between broken and unbroken regions on specimens that were mechanically tested. The aim of the proposed project is the development of a system that will permit the prediction of in-vitro trabecular mechanical behaviour with possible applications on clinical meso-level x-ray images. The presented system will be comprised mainly of a classifier that will identify the fracture probability of bones’ regions using estimated mechanical parameters. In order to define the classifier, a fracture identification module, based on image processing, will be also developed with the aim to locate firstly broken and unbroken regions of mechanically tested specimens, and then estimate specific mechanical parameters related to the different regions. This initial knowledge will be used to train the classifier and to predict the broken region of not tested bone specimens.

Keywords: bone fracture,trabecular bone,micro-ct,bmd,meso-level,mechanical parameters,image processing,registration,classification.
Gravity duals of inhomogeneous strongly correlated fermions (GDISCF)

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: Italy
Call:  (FP7-PEOPLE-2009-IEF, 2009)
Start date: 2010-09-01
End date: 2012-12-31
Duration (months): 28.0
Total project cost (EUR): 221553.2
EU funding (EUR): 221553.2
Participants: 1
Project status: CLOSED

The string/gauge theory correspondence is a powerful tool to study strongly coupled quantum field theories. Recently it has been proposed to use its computational framework to address non perturbative problems in condensed matter physics. Holographic models of quantum critical theories and homogeneous unconventional superconductors and superfluids have been considered. The present project aims to extend this line of research to models of strongly correlated fermionic systems which are expected to develop phases with inhomogeneous and anisotropic condensates. Realistic examples include polarized ultracold Fermi gases at unitarity, unconventional superconductors in the presence of a strong external magnetic field and high density quark matter at the core of neutron stars.

Keywords: quantum field theory,string theory,qcd,relativity,condensed matter properties,superconductors
Function of centromeres during meiotic bouquet stage and protein composition of telomeres (MEIOTIC CENTROMERES)

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-2009-IEF, 2009)
Start date: 2012-07-31
End date: 2014-07-30
Duration (months): 24.0
Total project cost (EUR): 182103.2
EU funding (EUR): 182103.2
Participants: 1
Project status: CLOSED

Meiosis is a fundamental process in cell biology. During meiosis several unique features events occur such as segregation of homologs rather than sister chromatids and repair of double strand breaks by recombination of the homologs happen. During the first reductional meiotic division, the telomeres cluster in a formation called &quot;bouquet&quot;. The bouquet is important for the establishment and maturation of the spindle during meiosis, and is conserved in evolution. Initial results lead us to suspect that the bouquet might affect chromosome segregation through effect on meiotic centromeres. In my this project I intend to study the effect of bouquet disruption on the protein composition and microtubules attachment of centromeres during S. pombe meiosis. I plan to investigate the possibility that a cis effect is mediated between the telomeres and the centromere of the same chromosome. This study will be conductedwill be accomplished by live cell imaging using fluorescent microscopy, together with advanced genetic techniques available in fission yeast. In addition, I intend to isolate all the proteins associated with a pombe telomere. This will be accomplished by using the newly developed PICh technique, and by careful quantification of the yield and use of a unique control without telomeres available only in fission yeast.

Keywords: cell biology,molecular design,de novo design
Systematic analysis and modeling of the gene regulatory network underlying neural tube patterning (NEURAL TUBE NETWORK)

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-2009-IEF, 2009)
Start date: 2011-05-01
End date: 2013-10-28
Duration (months): 24.0
Total project cost (EUR): 172240.8
EU funding (EUR): 172240.8
Participants: 1
Project status: CLOSED

In many developing tissues, initially equipotent cells acquire their intended identity by exposure to extrinsic, graded signals termed morphogens, such as Sonic Hedgehog (Shh). In the ventral neural tube, Shh induces 5 progenitor domains in a precise spatial order along the dorsoventral axis of the developing spinal cord. These domains can be distinguished by the expression of different combinations of transcription factors (TFs). During their specification, the progenitors transit through several metastable states, exhibited by the expression of different combinations of TFs. In network analysis terminology these states define so-called attractors – states of equilibrium towards which global gene expression profile tends to move. We predict that ventral neural tube progenitor states correspond to such attractor states that are generated by a gene regulatory network (GRN) controlled by graded Shh signalling. We will use a series of experimental and in silico approaches to systematically decipher and model this GRN. We will perturb the GRN in the developing chick neural tube using in ovo electroporation of constructs that change the level of Shh signalling and/or the expression of specific TFs. The consequences on the transcriptome of neural cells will be assayed systematically. Factors newly identified in this analysis will be examined and their function in the transcriptional response of neural cells assessed. We will use this approach iteratively to build, challenge and refine our model, and progressively understand the principles of the network. This will define the attractor states of the system and identify the TFs that contribute to the establishment of these states. By extending our knowledge of basic mechanisms of neural tube development we hope to provide new insight that will guide therapeutic approaches to the diseased or damaged spinal cord.

Keywords: developmental biology,molecular biology,computational biology,genomics,neurobiology
Cancer associated glycan epitopes via Ionic Catch and Release Oligosaccharide Synthesis (ICROS) (ICROS)

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-2009-IEF, 2009)
Start date: 2010-03-01
End date: 2012-02-29
Duration (months): 24.0
Total project cost (EUR): 172740.8
EU funding (EUR): 172740.8
Participants: 1
Project status: CLOSED

The quest for an effective cancer vaccine was initiated over 100 years ago from the moment vaccines against infectious diseases were successfully applied, and despite the many advances to date, the search for therapeutic vaccines derived from carbohydrate antigens is still an ongoing challenge. Carbohydrate antigens of tumour cells are uniquely effective targets for antibody-mediated active and passive cancer immunotherapy and have also proven to be effective targets for immune recognition and attack. The gastrointestinal tract posses a protective epithelial barrier as part of the basic innate protective system, which produces a secreted mucus layer that contains hundreds of different mucin type O-linked oligosaccharides known to be connected with diseases such as breast and colon cancers. However, little is known about the specific role of this family of oligosaccharides in disease due to the lack of tools for study. Access to structurally defined complex carbohydrates is still a very laborious process and combinatorial approaches to prepare diverse libraries of oligosaccharides remain limited. A general automated method for oligosaccharide assembly will allow rapid preparation of structures of interest. This programme’s long term aim is to develop carbohydrate-based cancer vaccines that elicit both a strong humoral- and cellular immune response against colon and breast cancers. To achieve our objectives, we plan to apply a novel and improved methodology (ICROS) to the synthesis of mucin type carbohydrate fragments, which are otherwise not available, ready to be immobilized onto nanocarrier systems for initial biological (antibody screening) and immunogenic assays. The understanding of these glycosylation patterns at both molecular and functional level will help us identify mucin oligosaccharide based antigens that will pave the way to the development of target specific anti cancer vaccines.

Keywords: organic chemistry,oligosaccharide synthesis,glycoarray preparation,glycobiology