Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
PHIDIAS: Phenotyping with a High-throughput, Intelligent, Distributed, and Interactive Analysis System (PHIDIAS)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Italy,Greece
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2011-09-01
End date: 2015-08-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 2
Project status: CLOSED

In this proposal we present PHIDIAS, with the objective to provide an affordable, high-throughput, distributed, knowledge-sharing platform for phenotype collection and analysis. PHIDIAS will incorporate lessons learned from prior phenotyping efforts and will be a simple to use platform for acquiring (non-destructively and continuously) and analyzing phenotypes from plant experiments. Its novelty arises from the fact that it combines distributed affordable sensors (cameras) to collect images and transmit them over the Internet for centralized processing. With slight modifications to their software, commercial cameras can become powerful image acquisition devices. To increase the fidelity of our data, we acquire multiple sequential images of different parameters (focus, zoom, exposure) to generate high resolution, fully focused composite images, using sophisticated algorithms borrowed from computational photography running in processing servers. The same servers also process the images and extract relevant phenotyping information. All the data are stored in databases and offered to the user for exploration through a modern web-based Graphical User Interface. The users can even edit and view images online through the web. PHIDIAS learns from the user’s inputs, for training continuously the learning-based image processing algorithms, in order to increase performance. We will provide an arena of constant development and evolution by adopting open source, open development and affordable hardware standards. Thus, users can help PHIDIAS evolve by contributing data and functionality. As the knowledge in PHIDIAS’s database increases, and more biological databases are connected, complex meta-analysis studies can be performed bringing us closer to both forward and reverse hypothesis formulations. To the best of our knowledge there is no tool combining the above qualities, with the potential of providing an evolvable and sustainable phenotyping platform.

Keywords: phenomics,plant,natural sciences,high-throughput
Peptide Crystal Engineering with Lanthanide Complexes (CEREPEP)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: European Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-09-01
End date: 2013-08-31
Duration (months): 36.0
Total project cost (EUR): 45000.0
EU funding (EUR): 45000.0
Participants: 1
Project status: CLOSED

Crystal engineering will be used to combine rare earth complex chemistry with peptide synthesis in order to prepare new crystalline supramolecular and polymeric materials. Rare earth containing metallopeptides with luminescent and magnetic properties will be targeted as model compounds for applications in medical and biochemical research (e.g. biological imaging, contrast agents, etc). This approach will involve interdisciplinary collaborations to produce and analyse new materials for medicinal or biological chemistry. The preparation of peptides as molecular building blocks for the synthesis of supramolecular compounds will demand specialist expertise in different sectors of chemistry, biology and physics. The solvent-less green synthesis of coordination polymers, supramolecular frameworks and materials will also be developed as a new direction in existing projects, which the applicant initiated during the Marie Curie Fellowship. New molecular solid-state synthesis will present the potential to initiate local and international collaborations with academia and industry.

Keywords: inorganic chemistry,molecular chemistry,structural chemistry,lanthanide chemistry,crystal engineering
Insulin/IGF-1 Signaling Regulates Novel Activities of the ER Stress Response Gene ire-1 (NEW IRE-1 ACTIVITY)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Israel
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-04-01
End date: 2014-03-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

The insulin/IGF-1 signaling pathway is a major conserved metabolic pathway that regulates aging and lifespan in worms, flies, and mammals. Using C.elegans as a model system, I discovered that ire-1, a highly conserved ER stress response gene, makes a big contribution to the longevity of animals with reduced insulin/IGF-1 signaling. I further discovered that inactivation of ire-1 results in a striking accumulation of DAF-28, an insulin-like peptide, in the body cavity of animals with reduced insulin/IGF1 signaling, but not in wild-type animals. ire-1’s most characterized mode of action is by activation of a downstream transcription factor XBP-1. A few recent studies have shown that ire-1 also has xbp-1 independent functions, however, these have not been characterized extensively. Interestingly, under conditions of reduced insulin/IGF-1 signaling, at least part of ire-1’s contribution to the extended lifespan is independent of xbp-1. Furthermore, the striking accumulation of the insulin-like peptide in the body cavity of animals with reduced insulin/IGF1 signaling is mediated by ire-1 completely independently of xbp-1. Thus, we identified novel xbp-1-independent activities of ire-1, which under conditions of reduced insulin/IGF-1 signaling alone, promote longevity and feedback to regulate insulin levels. I propose to combine molecular, genetic and biochemical approaches to further investigate the molecular mechanism that regulates the accumulation of the insulin/IGF-1 peptide, and investigate why this occurs specifically under conditions of reduced insulin/IGF-1 receptor signaling. These studies may be of particular importance and relevance in the context of diabetes, where insulin/IGF-1 signaling is dysfunctional, insulin levels are deregulated and insulin-secreting cells are over-loaded and suffer from ER stress.

Keywords: molecular genetics,cell biology,er stress,insulin,aging,ire-1,c. elegans,upr,unfolded protein response,signaling,metabolsim,daf-2,endoplasmic reticulum,genetics,model organism
The Molecular Mechanisms of Stem Cell Self Renewal (MMSR)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Netherlands
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-08-01
End date: 2014-07-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Over the past few years, a view has emerged that pluripotency in mouse embryonic stem cells (ESCs) is cell-autonomous and does not depend on external signals. This was based on work that showed that a combination of a small molecule ERK inhibitor with a GSK3 kinase inhibitor was sufficient to maintain self-renewal, in absence of any growth factors. I have now discovered that autocrine or paracrine signalling via the Wnt pathway plays an essential role in ESC self-renewal, and is required to inhibit their differentiation towards primitive ectoderm. Moreover, I have discovered that the combination of Wnt protein with the cytokine LIF is sufficient to support the maintenance and derivation of germ-line competent ES cells in fully defined conditions not containing any other growth factor. Thus, two different fully defined conditions both maintain self-renewal, but do so in different ways. However, the intracellular events downstream of those conditions must both converge on the self-renewal machinery. By analyzing and comparing these events in both systems, unmatched synergy in zooming in on the relevant entrances into the self-renewal machinery can be obtained. I propose to analyze the events downstream of these two sets of self-renewal stimuli, in an effort to identify novel self-renewal genes. The downstream effects of the self-renewal stimuli will be analyzed using gene expression profiling, ChIP-Seq, and phosphoproteomic approaches. Combining and comparing the different data sets will identify candidate genes that will be screened in a self-renewal assay designed for high sensitivity and throughput. Genes that pass this test will be further analyzed for their roles in proliferation, survival, and differentiation in an effort to compartmentalize the self-renewal machinery into functional blocks. This analysis will provide the first comprehensive resource documenting the molecular workings of self-renewal.

Keywords: stem cells,self-renewal,wnt,gene regulation,embryonic stem cell,phosphoproteome
Reconstruction and understanding of molecular networks (RAUMN)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Israel
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-04-01
End date: 2014-03-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

A major challenge for current biology is to understand how bio-molecules interact and cooperate to achieve their joint cellular functions. Understanding a pathway requires that we first reconstruct the network - identify what molecules participate in a given pathway and how they interact, and then characterize its functional modes. Following the explosion of genome wide assays, network reconstruction became a central task in molecular biology, spanning signaling, metabolic, and regulatory pathways. However, despite intensive research, many fundamental cellular pathways are only partially known, and not well understood. For instance, in the metabolic pathways of S. cerevisiae, perhaps the best understood biochemical network, 20 percent of enzymes and transporters are unidentified. In the same organism, only 30 percent of the interactions in the signaling pathways are known. The goal of the research proposed here is to develop computational and statistical methods for completing partially known biological pathways and use these methods to reconstruct and understand two important molecular pathways: metabolic pathways and signal transduction pathways. This will be achieved by learning how diverse functional data maps onto known networks, identifying recurring patterns of this mapping, and use them to predict unknown network components. We have recently showed how these patterns, which we call “activity motifs”, can be identified from data, and reveal organization principles of metabolic and signaling pathways1-2.

Keywords: technological sciences
The birth of the first stars and galaxies (GALAXIES BIRTH)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: European Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Germany
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-04-01
End date: 2013-03-31
Duration (months): 36.0
Total project cost (EUR): 45000.0
EU funding (EUR): 45000.0
Participants: 1
Project status: CLOSED

The aim of this proposal is to simulate the formation and evolution of galaxies within the first billion years of the Universe by using unprecedented high-resolution simulations. The hydrodynamical, cosmological simulations are designed to evolve the Universe, focusing on the sites of star and galaxy formation. They include all the relevant physics: radiative cooling and formation of molecular hydrogen, star formation and feedback from supernovae, metal enrichment of the inter-stellar material, black hole formation and feedback. In particular, the theory of population III (POP III) star formation will be tested within a cosmological framework. The reseracher would like to address the following questions: (i) what is the luminosity function of galaxies at redshift six and larger; (ii) how the transition from metal poor POP III to metal enriched POP II star formation happens; (iii) what is the role of the turbulence from cold accretion in mod ifying star formation at early times; (iv) where seed black holes from POP III stars form and how they grow. Answering these questions will deepen the understanding of the formation of the first galactic structures in the Universe, and will provide direct predictions for upcoming space-based satellite missions like the James Webb Space Telescope.

Keywords: physical sciences,astrophysics,cosmology
Uncovering conserved proliferation pathways between plants and animals (ARABIGANS)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Spain
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-09-01
End date: 2014-08-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

The study of plant biology is useful in two ways. Under a basic research perspective, it yields basic knowledge on processes that are specific to plants and distinguish them from animals. From an applied perspective, this knowledge can lead to an improvement in the quality or the productivity of crops. Any given aspect of plant biology can be considered to be fully dissected only after the genes that control it have been identified, which makes its eventual controlled perturbation possible. Plant genetic research can also help to understand the conserved functions of such genes in different organisms as well as to establish their biotechnological potential. In this proposal, I aim (1) to identify genes important for leaf morphogenesis in the model plant Arabidopsis thaliana, as inferred from the effects of their loss of function on cell size and cell number; (2) to characterize the effects of their constitutive expression in Arabidopsis thaliana, in order to assess their potential application as plant growth modulators; (3) to characterize the effects of their heterologous expression in an animal model system (Caenorhabditis elegans), in order to assess their potential pharmacological use and the eventual conservation of their functions in the control of cell proliferation; and (4) to knock down the putative orthologs of these genes in Caenorhabditis, in an attempt to establish their potential use as regulators of cell proliferation.

Keywords: genetics,cell biology,arabidopsis,caenorhabditis,leaf development,germline,proliferation
Development and Neuromodulation of Intrinsic Cortical Activity (INTRICA)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Greece
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-07-01
End date: 2014-06-30
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

We propose to study intrinsic cortical network activity in-vitro. It is already known that the cerebral cortex, both in-vivo and in-vitro, produces spontaneous patterns of electrical activity independently of extrinsic inputs. These consist of network-induced prolonged depolarizations &amp; action potentials (UP states), alternating with periods of synaptic withdrawal, membrane hyperpolarization and cessation of firing (DOWN states). It is precisely on such endogenous activity that all external inputs act, namely sensory information and/or neuromodulation. It is also increasingly evident that certain mental disorders are associated, not with specific brain lesions or cellular degeneration, but with abnormal cortical activity. Hence, this endogenous activity is crucial for our understanding of cortical information processing. To present, the generation and development of intrinsic discharge patterns and their interaction with external inputs are poorly understood. Here we propose to use brain slices to study the ontogeny and susceptibility to neuromodulation of spontaneous slow oscillations (UP/DOWN states) and persistent activity (evoked UP states) of different cortical regions. We will first compare the development of spontaneous slow oscillations in distinct cortical areas, from prenatal ages to adulthood. This is a novel and essential first step towards understanding the functional differentiation of the cortex, and identifying the possible onset of abnormal network activity during disease. We will then examine how neuromodulators, that gate distinct information processing brain states, affect spontaneous and evoked UP states in thalamocortical slices from adult animals. These data will help clarify how behaviourally distinct brain states affect intrinsic cortical dynamics. This grant will enable the applicant, a worldwide expert in this in-vitro model, to bring the know-how to Europe and continue his training and research in the European Community.

Keywords: up states,development,neuromodulation,slow oscillations,persistent activity,cortical dynamics,in vitro model,brain slices,prefrontal,somatosensory,piriform,motor cortex,thalamocortical
Dissecting the role of a novel transcriptional regulator in microbial-host interactomes. (MEXT REGULATION)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: European Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Ireland
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-04-01
End date: 2013-03-31
Duration (months): 36.0
Total project cost (EUR): 45000.0
EU funding (EUR): 45000.0
Participants: 1
Project status: CLOSED

Pseudomonas aeruginosa is a versatile bacterium that can inhabit many environments. In its natural environments, Pseudomonas predominantly grows in organized communities called biofilms. Growth as a biofilm is also an important requirement for the colonization of human tissues. For instance, P. aeruginosa grows as a biofilm in the lungs of cystic fibrosis (CF) patients. Previously, it has been shown that nfxC-phenotypic isolates of P. aeruginosa associated with decreased early attachment - the first phase of biofilm formation. This chloramphenicol resistant nfxC-phenotype is thought to be caused by the activation of a LysR-type transcriptional regulator, MexT, which regulates the expression of the MexEF-oprN efflux-system. Recently, we have shown that this biofilm phenotype is a result of the activation of MexT in a MexEF-oprN independent manner (Tian et al., 2009). To further establish the role of MexT in biofilm formation, preliminary flow-cell biofilm experiments have been performed. Analysis of the biofilm structure showed that biofilms of cells overexpressing MexT contain a higher microcolony-density with smaller average size as compared to control cells. These differences were independent of the MexEF-oprN efflux system. This project aims to dissect how MexT modulates biofilm formation. Several potential candidate genes have been identified using a transcriptome approach of cells overexpressing MexT, which will be subject to further evaluation (Tian et al., 2009). To further establish the role of MexT on virulence phenotypes, eukaryotic cell lines, as well as a ‘state of the art’ infection model that uses zebrafish embryos will be used. This study may identify potential targets for the modulation of biofilm formation. In the long term, these targets may provide new strategies to develop drugs that reduce the ability of Pseudomonas to form biofilms, thereby increasing the chance of successful antibiotic treatment therapies.

Keywords: infections,health sciences,chronic diseases
Molecular and functional characterization of sperm-expressed proteins with potential fusogenic roles during double fertilization in Arabidopsis thaliana (GAMETEFUSION)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Portugal
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-05-01
End date: 2014-04-30
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Sexual reproduction is a fundamental biological process common among eukaryotes. In angiosperms, fertilization although associated with pollination, is actually a fairly late phenomenon in the process of reproduction and involves a double fusion event between two male and two female gametes. In contrast to animal fertilization, the molecular mechanisms underlying this process in flowering plants are poorly understood and the molecular players unknown. With this project we intend to explore recent advances in the field, namely the availability of expression profiles of plant gametes to identify the molecular players which mediate sperm-egg cell/central cell fusion in Arabidopsis thaliana. We used bioinformatics approaches to identify plasma membrane proteins with expression in sperm cells and sharing structural similarities to known fusogenic peptides. The first candidates are two sperm-specific proteins which belong to the conserved family of tetraspanins. Functional analysis of the candidate proteins will be performed in knockout, amiRNA and overexpression transgenic lines. Interacting proteins in sperm cells and in the female partner cells will be identified using yeast-two hybrid system and validated by functional analysis. Candidate proteins will be assayed for specific functions during double fertilization, such as preferential gamete targeting, fusogenic properties, polyspermy block and fertilization barriers using manipulation of gene expression and proteomic approaches coupled to in vivo and in vitro assays. We also intend to develop an in vivo fluorescent based method to detect and track specific sperm-expressed mRNAs, in order to understand the importance of intercellular communication during double fertilization and initiation of embryogenesis. This project is addressing fundamental questions involving one of the most complex biological processes in nature and might provide novel tools for biotechnology applications and crop improvement.

Keywords: plant development,plant reproduction,plant genetics,genomics,arabidopsis,double fertilization,gamete fusion,fusogenic,sperm cell,egg cell,intercellular communication,tetraspanins.