Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Algorithms and Tools for Mining Biological Sequence Data (ALMOND)

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: Israel
Call:  (FP7-PEOPLE-2011-IEF, 2011)
Start date: 2012-07-15
End date: 2014-07-14
Duration (months): 24.0
Total project cost (EUR): 250106.0
EU funding (EUR): 250106.0
Participants: 1
Project status: CLOSED

The goal of this proposal is to set up an interdisciplinary research training in the area of bioinformatics algorithms, that should lead to establishing a new level of expertise in certain techniques, methods and algorithms for handling the ever-increasing volume of biological sequence data (DNA, RNA, proteins). Bioinformatics is one of the flourishing research fields at the Computer Science Department of Ben-Gurion University in Israel, including four four faculty members and numerous growing collaborations with biological partners. In general, Ben-Gurion University is one of the most rapidly developing in Israel and provides a vibrant research atmosphere. Besides extending the range of competences to new research areas and increasing the actual expertise , this training will continue a recently started fruitful and promising collaboration between the applicant and the host institution, and should result in a series of high-level publications and new software tools available to the bioinformatics community. Moreover, the training is expected to lead to further collaborative projects involving the partners of the present proposal.

Keywords: bioinformatics,software development,algorithms,computational models,discrete mathematics,computational biology
Role of microRNAs in host responses to Crohn's disease-associated adherent-invasive Escherichia coli (MIRNA-AIEC)

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,France
Call:  (FP7-PEOPLE-2011-IIF, 2011)
Start date: 2012-08-01
End date: 2014-07-31
Duration (months): 24.0
Total project cost (EUR): 193594.8
EU funding (EUR): 193594.8
Participants: 2
Project status: CLOSED

Recent studies have shown dysregulation of microRNAs (miRNAs) in the mucosa of Crohn’s disease (CD) patients, suggesting a role for miRNAs as contributors to inflammatory bowel disease (IBD) susceptibility. The scientists from the host institution previously showed that ileal lesions in CD patients are colonized by pathogenic adherent-invasive Escherichia coli (AIEC), which are able to invade and to replicate within intestinal epithelial cells, and that functional autophagy is required to restrain AIEC replication. The overall hypothesis of this proposal is that miRNA pathway contributes to innate immune responses to AIEC colonization and/or inflammatory activities. The goal of our study is to determine the microRNAs dysregulated in host cells upon infection with AIEC, and the mechanism through which they contribute to responses of the host. In particular, three objectives will be addressed in this project: 1) To determine the potential role and mechanism by which miRNAs modulate the host responses of intestinal epithelial cells (IECs) to AIEC; 2) To investigate the regulation of CEACAM6, a host receptor for AIEC, by miRNAs in IECs during pathophysiological state, and in host responses to AIEC infection; and 3) To test the hypothesis that AIEC impair autophagy to replicate in host cells by modulating expression of host miRNAs. I propose to use IEC culture models of AIEC infection accompanied with bioinformatics tools to identify the miRNAs which are regulators of the key signaling pathways that modulate cross-talk between AIEC and host cells. The proposed studies in this project will shed light on the mechanism by which miRNAs are involved in host responses to AIEC infection, which could help to identify new biomarkers and potential therapeutic targets for IBD.

Keywords: adherent-invasive escherichia coli,crohn' disease,microrna.
Molecular mechanims of mRNA transport in neurons (NEURORNATRANSPORT)

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-2011-IEF, 2011)
Start date: 2012-07-01
End date: 2014-06-30
Duration (months): 24.0
Total project cost (EUR): 200371.8
EU funding (EUR): 200371.8
Participants: 1
Project status: CLOSED

RNA transport coupled to local translation presents an efficient means to regulate gene expression in time and space. Recent studies have indicated that this mode of post-transcriptional regulation is used in many different cell types and applied to hundreds to thousands of transcripts. mRNA transport is of particular importance in neurons, where it is involved in processes such as axon guidance and activity-induced synaptic plasticity. Loss of proteins involved in regulating RNA transport have been linked to hereditary mental retardation and dendritic targeting of certain mRNAs has been shown to be crucial for formation of long-term memories. However, which mRNAs are differentially localized in neurons and by what mechanism they are transported remains largely unknown. Here we propose to investigate this problem using the model organism Drosophila melanogaster, which offers significant experimental advantages, such as little genetic redundancy, powerful tools for loss- and gain-of-function studies and the possibility of visualize living neurons in their natural environment at high resolution. Furthermore, previous work has established that the overall mechanism of RNA transport is conserved from fly to humans. Thus, findings in the fly system are likely to have direct implications for our understanding of the human brain. We will adapt an established live cell imaging approach to identify mRNAs that are specifically enriched in neuronal processes. Identified transcripts will be characterized in further detail and used to search for RNA-binding proteins that specifically contact their localization elements. Candidate proteins will be tested for a role in mRNA transport using genetics coupled to high resolution imaging. Eventually, proteins regulating mRNA localization will be tested for a physiological role in the brain. Our work should reveal new insights into the cell biology of neurons and have broad implications for neuronal development, plasticity and disease.

Keywords: natural sciences,cell biology,mrna transport,drosophila,neurons,live cell imaging
New Insights on Micrometeorites (MICROMET)

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-2011-IIF, 2011)
Start date: 2013-04-15
End date: 2015-04-14
Duration (months): 24.0
Total project cost (EUR): 200371.8
EU funding (EUR): 200371.8
Participants: 1
Project status: CLOSED

Micrometeorites are extraterrestrial dust particles that reach the Earth’s surface. They largely originate from comets and asteroids, the small bodies of our solar system believed to contain primordial solar system materials in a range of states of preservation. The mineralogy of these materials provides a record of their formation environment (e.g. temperatures and materials available) and/or subsequent parent body processing they experienced since accretion (e.g. exposure to water or heat). Therefore, the study of micrometeorites can provide valuable information regarding conditions in the early solar system and evolution of the small solar system bodies from which they originate. Micrometeorites constitute more incoming mass of material and sample more parent bodies than the larger meteorites, yet much less research has been done on them as their small size has made analyzing and collecting them difficult until relatively recently. We propose to systematically characterize and compare new micrometeorites from the South Pole and a unique collection from Kwajalein with the aim of gaining new insights into the formation, evolution and current state of small solar system bodies. We will use state of the art facilities to prepare and analyze these particles in order to identify and interpret rare or unusual micrometeorites that represent previously unsampled parent bodies, understand atmospheric entry alteration and terrestrial weathering effects, and determine the sources (asteroid or comet) and flux of micrometeorite types with time. The proposed work will transfer the Fellow’s expertise in small sample preparation and analysis to the Natural History Museum and expand its repertoire of extraterrestrial material studies. This will reinforce Natural History Museum’s reputation as a world-class facility for the curation and study of extraterrestrial materials and strengthen research links between the UK and key NASA funded facilities in the USA.

Keywords: micrometeorites,comets,asteroids,solar system formation,small solar system body evolution
Pattern Formation in Microorganism Suspensions: Shear and Confinement (PFMS)

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-2011-IEF, 2011)
Start date: 2012-09-04
End date: 2014-09-03
Duration (months): 24.0
Total project cost (EUR): 209033.4
EU funding (EUR): 209033.4
Participants: 1
Project status: CLOSED

Microorganisms are present in almost every part of temperate aqueous environments, and they are heavily involved in pathoenic infection, digestion, reproduction and carbon dioxide capture and mixing in the oceans. Therefore, understanding their motility, collective dynamics and interaction with the environment is a key issue to overcome important challenges of our time such as collapse of ecological systems, global warming, and environmental pollution. The objective of this proposal is to contribute to our understanding of the behavior of swimming microorganisms, focusing particularly on their collective dynamics caused by interaction with surrounding hydrodynamic conditions, flow shear and confinement. Two state-of-the-art collective behaviors of microorganisms are considered: bioconvection and particle-stress-driven instability, and interaction of the collective dyanamics with shear flows and confinement will be analyzed using the-state-of-the-art linear and nonlinear stability theories, which are the candidate's particular expertise. A part of the theoretical prediction, particularly for particle-stress-driven instability, will also be verified by conducting a laboratory experiment. The work program in this proposal is designed to complete post doctoral training of the candidate, who has been trained within the European network. Interdisciplinary nature of the project will greatly improve the candidate's future mobility cutting across fluid mechanics, biophysics and applied mathematics. The results of this project is expected to provide a solid basis for understanding and predicting the collective dynamics of swimming microorganisms, and it will significantly contribute to the European excellence of environmental and energy science.

Keywords: biophysics,fluid dynamics,biomathematics,ecology
Computational Design of Highly Active Biocatalysts of Interest in the Chemical Industry (COMPBIOCATDESIGN)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Outgoing Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Spain
Call:  (FP7-PEOPLE-2011-IOF, 2011)
Start date: 2013-03-01
End date: 2016-08-31
Duration (months): 36.0
Total project cost (EUR): 256206.0
EU funding (EUR): 256206.0
Participants: 1
Project status: CLOSED

Developing new enzymes for catalyzing non natural reactions is a grand challenge for obtaining more efficient synthetic strategies for chemical industry as well as building complex molecules under enantioselective control with potential applications in medicine. Given the high specificity of natural enzymes for their substrates, new techniques are necessary for redesigning natural enzymes to perform novel reactions. Recently the group led by Prof. David Baker at University of Washington in Seattle (outgoing host) has made a breakthrough in the development of Computational Enzyme Design strategies to create new enzymes able to catalyze retro-aldol, Kemp elimination and Diels-Alder reactions. The methodology they have developed has proved to be a powerful tool for obtaining new activities with rate-enhancements up to 104 that allow further optimization with directed evolution techniques. The catalytic efficiency of designed enzymes, however, is much lower than that of natural enzymes and significant improvements are required to extend the applicability of these methods to any desired reaction. The first goal of the current project is to improve the current computational enzyme design methodology with a description of protein dynamics in order to achieve catalytic efficiencies closer to that of natural enzymes. As a second goal, we aim to use the improved Enzyme Design methodology to improve the activity of past designs and create new enzyme catalysts for the Bayliss-Hillman reaction. This is a carbon-carbon bond formation reaction that creates a new chiral center that allows to increase the complexity of molecules with potential applications in biomedicine. To complement the design process, QM/MM calculations will be performed to evaluate the reactivity of different designs and give insight into possible ways of improving the activity.

Keywords: enzimology,computational chemistry,carbon chemistry,industrial chemistry,environmental chemistry,pharmaceutical chemistry
A coupled ice sheet - ocean model for calibrated prediction of the future contribution to sea level change from the Pine Island Glacier, Antarctica (CRAG)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Outgoing Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Switzerland
Call:  (FP7-PEOPLE-2011-IOF, 2011)
Start date: 2013-07-01
End date: 2016-06-30
Duration (months): 36.0
Total project cost (EUR): 381525.1
EU funding (EUR): 381525.1
Participants: 1
Project status: CLOSED

The potential of marine ice sheets to undergo rapid irreversible retreat has been considered in the glaciological community since the 1970s. One of the world’s major marine ice sheets, the West Antarctic Ice Sheet (WAIS), contains enough ice to raise global mean sea level by approximately 5m. However, of immediate relevance to policy makers, the likely rate of WAIS contribution to sea level change on century timescales is not known. This project will couple a state of the art ice sheet model and ocean circulation model. Ice sheet models are only now reaching sufficient maturity to be applied to predictive studies of marine ice sheet behaviour, partly due to the candidate’s recent advances in modelling the grounding line (the line dividing ice grounded on bedrock from the floating part of the ice sheet). Ocean models incorporating ice shelf cavity processes are also emerging, and the candidate’s collaborators at the outgoing host are leading development in this area. Ice sheet – ocean model coupling is essential in predictive studies due to the feedback between evolving ice shelf cavity geometry/grounding line location and ice shelf cavity circulation via sub ice shelf melt rates. The model will be applied to the Pine Island Glacier (PIG), an important outlet glacier draining a portion of the WAIS, which has been studied extensively and is currently thinning at an increasing rate. The project will use new coupled model and Bayesian calibration techniques to ascertain whether the PIG has crossed a threshold for irreversible retreat and provide a probabilistic quantification of the PIG contribution to sea level change over the next two centuries. The project is novel in the ice sheet - ocean coupling (this will be the first 3D ocean circulation model fully coupled to an evolving ice sheet model) and in the use of Bayesian calibration to provide a probabilistic prediction, an approach rarely used in glaciology.

Keywords: glaciology,physical oceanography,marine ice sheet instability,ice sheet modelling,antarctica,sea level change,software development,bayesian inference
Synthesis and evaluation of new macrocyclic compounds based on jatrophane scaffold (MDR MODULATOR)

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: Ireland
Call:  (FP7-PEOPLE-2011-IEF, 2011)
Start date: 2012-04-01
End date: 2014-03-31
Duration (months): 24.0
Total project cost (EUR): 191938.2
EU funding (EUR): 191938.2
Participants: 1
Project status: CLOSED

Abstract Jatrophane are natural compounds isolated from Euphorbia (Euphorbiaceae, spurge family). More than 150 jathrophane have been isolated so far. The general structure is an highly functionalized trans-bicyclo[10.3.0]pentadecane skeleton. Jatrophanes possess a variety of different biological activities such as inhibitory activity on the mammalian mitochondrial respiratory chain, cell cleavage arrest, cytotoxicity against various human cancer cell lines, antiviral activity, antiplasmodial activity, microtubule interaction and cytotoxicity against human cancer cell lines. Most notably, they are inhibitors of the P-glycoprotein (Pgp), a membrane protein whose major function is the active transport of amphiphatic xenotoxins out of the cytoplasm. The over expression of the multi-drug resistance protein 1 (MDR1) gene (which encode for Pgp) contributes to the resistance of cancer cells against a large spectrum of anticancer drugs. Only natural occurring jatrophane have been investigated as modulator of multidrug resistance so far. Despite the large number of jatrophane isolated and the promising biological properties, the preparation this class of compounds can be regarded as a synthetic and biological challenge. The fellow has already an excellent background in synthetic chemistry. This project will allow him to increase his experience and knowledge in natural products chemistry, carbohydrate chemistry, development of bioactive compounds as well as enhance his synthetic experience. He proposes to join NUI Galway which is strategically developing strength in Biomedical Research, Cancer and Glycoscience, thus helping an objective 1 region of Europe to develop its research programme. NUI GAlway will also offer a series of transferrable skills and personal development courses to Dr. Lo Re. Both the scientific and personal training will contribute to the maturing of Dr. Lo Re to becoming an independent researcher.

Keywords: health sciences,p-glycoprotein,multidrug-resistance,cancer,jathropane,ring-closing-methathesis,evolutionary-scaffold
Unlocking Historical and Molecular Archives (PALIMPSEST)

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-2011-IEF, 2011)
Start date: 2012-05-01
End date: 2014-04-30
Duration (months): 24.0
Total project cost (EUR): 200371.8
EU funding (EUR): 200371.8
Participants: 1
Project status: CLOSED

Europe’s rich historical record has been plundered for information about climate and weather in the past. From instrumental data, to correspondence and even paintings, climate historians have tried to link direct human record with molecular records from trees, lakes, caves and oceans. My fellowship seeks to explore a new avenue, the rich collections of parchment held in archives across Europe. The corpus of handwritten parchment represents one of the major cultural assets of European heritage. Research has tended to focus on the written texts, but we propose an overarching investigation that attempts to explore the potential of parchment records to be annual records of molecular change. Parchment is comprised predominately of collagen, a protein that is easy to isolate and purify. Skin collagen turns over once a year, thus the collagen in parchment represent a molecular signal from a year of skin production. In this project we will focus on the potential of the Archbishops’ Registers held in the Borthwick Archive in York. The series of York archiepiscopal registers begins in 1225 and continues, with only brief gaps, until 1972 when the practice of keeping registers was discontinued; 700 years of near continuous record keeping. This project aims to achieve an optimized microsampling technique in order to obtain the most amount of information with the smallest possible sample size of parchment. With the use of protein mass spectrometry we will determine the species used to make the parchment and assess its state of preservation. The use of stable isotope analysis will allow the dating of the parchment as well as possible associations to climatic conditions at the time the parchment was created. The research will also aid historians working on the provenance of manuscripts and the identity of scribes and authors; on peripatetic households; on the nature of medieval and early modern record keeping and the development of ecclesiastical and secular bureaucracies.

Keywords: archaeology,medieval history,analytical chemistry,biochemical technology,dating techniques