Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Dissection of centromeric chromatin and components: A biosynthetic approach (BIOSYNCEN)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Genetics,Genomics,Bioinformatics and Systems Biology
Countries involved: United Kingdom,Germany
Call:  (ERC-2012-StG_20111109, 2012)
Start date: 2013-02-01
End date: 2019-01-31
Duration (months): 72.0
Total project cost (EUR): 1755959.99
EU funding (EUR): 1755959.99
Participants: 2
Project status: CLOSED

The centromere is one of the most important chromosomal elements. It is required for proper chromosome segregation in mitosis and meiosis and readily recognizable as the primary constriction of mitotic chromosomes. Proper centromere function is essential to ensure genome stability; therefore understanding centromere identity is directly relevant to cancer biology and gene therapy. How centromeres are established and maintained is however still an open question in the field. In most organisms this appears to be regulated by an epigenetic mechanism. The key candidate for such an epigenetic mark is CENH3 (CENP-A in mammals, CID in Drosophila), a centromere-specific histone H3 variant that is essential for centromere function and exclusively found in the nucleosomes of centromeric chromatin. Using a biosynthetic approach of force-targeting CENH3 in Drosophila to non-centromeric DNA, we were able to induce centromere function and demonstrate that CENH3 is sufficient to determine centromere identity. Here we propose to move this experimental setup across evolutionary boundaries into human cells to develop improved human artificial chromosomes (HACs). We will make further use of this unique setup to dissect the function of targeted CENH3 both in Drosophila and human cells. Contributing centromeric components and histone modifications of centromeric chromatin will be characterized in detail by mass spectroscopy in Drosophila. Finally we are proposing to develop a technique that allows high-resolution mapping of proteins on repetitive DNA to help further characterizing known and novel centromere components. This will be achieved by combining two independently established techniques: DNA methylation and DNA fiber combing. This ambitious proposal will significantly advance our understanding of how centromeres are determined and help the development of improved HACs for therapeutic applications in the future.

Keywords: centromere,kinetochore,chromatin,cenh3,cid,cenp-a,biosynthesis,epigenetics,histone modifications,human artificial chromosomes,gene therapy,microscopy,laci/laco system
DNA binding proteins for treatment of gain of function mutations (ALLELECHOKER)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Diagnostic tools, therapies and public health
Countries involved: Italy
Call:  (ERC-2012-StG_20111109, 2012)
Start date: 2013-02-01
End date: 2018-01-31
Duration (months): 60.0
Total project cost (EUR): 1354840.0
EU funding (EUR): 1354840.0
Participants: 1
Project status: CLOSED

Zinc finger (ZF) and transcription activator-like effector (TALE) based technologies are been allowing the tailored design of “artificial” DNA-binding proteins targeted to specific and unique DNA genomic sequences. Coupling DNA binding proteins to effectors domains enables the constitution of DNA binding factors for genomic directed transcriptional modulation or targeted genomic editing. We have demonstrated that pairing a ZF DNA binding protein to the transcriptional repressor Kruppel-associated box enables in vivo, the transcriptional repression of one of the most abundantly expressed gene in mammals, the human rhodopsin gene (RHO). We propose to generate RHO DNA binding silencers (“AlleleChoker”), which inactivate RHO either by transcriptional repression or targeted genome modification, irrespectively to wild-type or mutated alleles (mutational-independent approach), and combine RHO endogenous silencing to RHO replacement (silencing-replacement strategy). With this strategy in principle a single bimodal bio-therapeutic will enable the correction of any photoreceptor disease associated with RHO mutation. Adeno-associated viral (AAV) vector-based delivery will be used for photoreceptors gene transfer. Specifically our objectives are: 1) Construction of transcriptional repressors and nucleases for RHO silencing. Characterization and comparison of RHO silencing mediated by transcriptional repressors (ZFR/ TALER) or nucleases (ZFN/ TALEN) to generate genomic directed inactivation by non-homologous end-joining (NHEJ), and refer these results to RNA interference (RNAi) targeted to RHO; 2) RHO silencing in photoreceptors. to determine genome-wide DNA binding specificity of silencers, chromatin modifications and expression profile on human retinal explants; 3) Tuning silencing and replacement. To determine the impact of gene silencing-replacement strategy on disease progression in animal models of autosomal dominant retinitis pigmentosa (adRP) associated to RHO mutations

Keywords: adeno-associated,retina,eye
Mechanisms Underlying Treatment Responses in Psychosis (MUTRIPS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Neurosciences and neural disorders
Countries involved: United Kingdom
Call:  (ERC-2012-StG_20111109, 2012)
Start date: 2013-03-01
End date: 2018-11-30
Duration (months): 69.0
Total project cost (EUR): 1498902.0
EU funding (EUR): 1498902.0
Participants: 1
Project status: CLOSED

Psychotic symptoms (hallucinations and delusions) have been associated with a striatal hyperdopaminergic state. Less explored, but also implicated are functional abnormalities in cognitive control, particularly in the prefrontal cortex; and a functional and structural disconnectivity between this and other areas of the brain. Such a disconnectivity would explain the lack of coherent response to conventional treatment: antipsychotic drugs do not benefit between 20 and 45 per cent of people with schizophrenia. The aim of this project is twofold: firstly, to explore the neural mechanisms underling cognitive control and the level at which cognitive control dysfunction operates in treatment refractory psychosis. The second is to test the hypothesis that cognitive dysfunction in patients who have treatment-resistant psychosis is associated with a specific neural signature – and discover whether that neural signature can be used as a biomarker of treatment resistance. Such a biomarker would help personalise treatment decisions and make treatment regimes more effective. It would also aid the development of novel treatments (other complementary work is investigating medication that enhances frontal cortical function as well as non-invasive brain stimulation techniques such as transcranial direct cortical stimulation). The project involves two linked brain imaging studies. The first will establish the indicative biomarker using both structural and functional MRI scanning and tasks to assess cognitive control at different levels of complexity. The second study will establish the validity of the biomarker by following a cohort of first episode psychosis patients for two years to discover whether their actual outcome corresponds with the outcome predicted by the neural signature shown in MRI scans.

Keywords: imaging biomarker treatment response schizophrenia
The role of CpG island RNAs and Polycomb-RNA interactions in developmental gene regulation (CHROMATINRNA)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Genetics,Genomics,Bioinformatics and Systems Biology
Countries involved: United Kingdom
Call:  (ERC-2012-StG_20111109, 2012)
Start date: 2013-09-01
End date: 2019-04-30
Duration (months): 68.0
Total project cost (EUR): 1499094.0
EU funding (EUR): 1499094.0
Participants: 1
Project status: CLOSED

A great challenge in developmental biology research has been to understand how cell type specific expression programs are orchestrated through regulated access to chromatin. The interaction between non-coding RNAs and chromatin regulators is emerging as an exciting new research area with the potential to explain how chromatin modifications are targeted. Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain developmental regulator genes specific for other cell types in a repressed state and is essential for embryogenesis across Metazoa. We have recently determined that CpG islands targeted by PRC2 generate a class of short non-coding RNAs. The RNAs are produced independently from mRNA, indicative of hitherto uncharacterised transcriptional processes. Furthermore, we have found that the PRC2 subunit Suz12 is an RNA binding protein and directly interacts with these short RNAs and with other RNAs in cells. The role of ncRNA in targeting PRC2 to CpG islands and the importance of PRC2 RNA binding activity for development remains to be understood. Our aims are to: 1. Determine the functional properties of CpG-island RNAs by A. identifying their conserved features, B. determining their role in polycomb targeting of CpG islands and C. investigating whether such a role relates to the antagonism of polycomb targeting by DNA methylation. 2. Establish the biological role for Suz12 RNA binding activity by A. determining the structural determinants for Suz12 binding in vitro, B. verifying these features play a role in PRC2 RNA binding in cells and C. determining the role for PRC2-RNA interactions for polycomb function and development. This work promises to characterise a potentially fundamental aspect of cell biology and will open a number of avenues for understanding the function of ncRNAs, the RNA binding activity of chromatin regulators, how transcription and chromatin structure are regulated, and how cell state is maintained and reshaped during development.

Keywords: chromatin,non-coding rna,transcription,cell identity,structure-function relationships
Brain reading of contextual feedback and predictions (BRAINREADFBPREDCODE)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Neurosciences and neural disorders
Countries involved: United Kingdom
Call:  (ERC-2012-StG_20111109, 2012)
Start date: 2012-12-01
End date: 2017-11-30
Duration (months): 60.0
Total project cost (EUR): 1494713.8
EU funding (EUR): 1494713.8
Participants: 1
Project status: CLOSED

We are currently witnessing a paradigm shift in our understanding of human brain function, moving towards a clearer description of cortical processing. Sensory systems are no longer considered as 'passively recording' but rather as dynamically anticipating and adapting to the rapidly changing environment. These new ideas are encompassed in the predictive coding framework, and indeed in a unifying theory of the brain (Friston, 2010). In terms of brain computation, a predictive model is created in higher cortical areas and communicated to lower sensory areas through feedback connections. Based on my pioneering research I propose experiments that are capable of ‘brain-reading’ cortical feedback– which would contribute invaluable data to theoretical frameworks. The proposed research project will advance our understanding of ongoing brain activity, contextual processing, and cortical feedback - contributing to what is known about general cortical functions. By providing new insights as to the information content of cortical feedback, the proposal will fill one of the most important gaps in today’s knowledge about brain function. Friston’s unifying theory of the brain (Friston, 2010) and contemporary models of the predictive-coding framework (Hawkins and Blakeslee, 2004;Mumford, 1992;Rao and Ballard, 1999) assign feedback processing an essential role in cortical processing. Compared to feedforward information processing, our knowledge about feedback processing is in its infancy. The proposal introduces parametric and explorative brain reading designs to investigate this feedback processing. The chief goal of my proposal will be precision measures of cortical feedback, and a more ambitious objective is to read mental images and inner thoughts.

Keywords: predictive coding
Global and Local food chain Assessment: a MUltidimensional performance-based approach (GLAMUR)

Framework: FP7 — Cooperation
Programme: Food, Agriculture and Fisheries, and Biotechnology
Destination: Fork to farm: Food (including seafood), health and well being
Action type: Collaborative project
Countries involved: Netherlands,Italy,United Kingdom,France,Belgium,Switzerland,Netherlands,Spain,United Kingdom,United Kingdom,Latvia,Denmark,Serbia
Call:  (FP7-KBBE-2012-6-singlestage, 2012)
Start date: 2013-02-01
End date: 2016-01-31
Duration (months): 36.0
Total project cost (EUR): 3696100.35
EU funding (EUR): 2932328.0
Participants: 15
Project status: CLOSED

General objective of the project is to integrate advancement in scientific knowledge about the impact of food chains with application of knowledge to practice to increase food chains sustainability through public policies and private strategies. This general objective will be pursued through the following specific objectives: • To develop and validate a ‘performance criteria matrix’ for assessment and comparison of food chains operating at a range of geographical scales through analysis of how food chain impacts are communicated in different spheres of society. • To build a database of quantifiable indicators of impact and a set of 20 case studies aimed at understanding how impacts are generated within specific food chains. • To advance knowledge on methodological problems and trade-offs arising when measuring and comparing the impact of food chains within and between sectors. • To assess how performance is perceived by stakeholders in different national contexts through participatory assessment and multicriteria analysis of the different typologies of food chains. • To assess the actual and potential role of public and private policies addressing food chains and to turn assessment into policy recommendations. • To build a network that turns the advancement of scientific knowledge into decision making tools for domestic and public consumers, producers, citizens, scientists, policy makers, civil society organizations. The project will be developed around the following assumptions: • Costs and benefits analysis needs methodological update: for this reason the broader concept of performance is used • The performance of food chains has multiple dimensions (economic, social, environmental, health, ethical) • To turn knowledge into practice a demand-driven approach is necessary, focusing on how food choice affects the five dimensions of impact The complexity of impacts of food chains requires plurality of methods and transdisciplinarity

Keywords: local food supply chains,global food supply chains,eu policies,sustainability,real costs of food,performance,multicriteria,access to food.
LInking farmland Biodiversity to Ecosystem seRvices for effective ecofunctional intensificATION (LIBERATION)

Framework: FP7 — Cooperation
Programme: Food, Agriculture and Fisheries, and Biotechnology
Destination: Sustainable production and management of biological resources from land, forest, and aquatic environment
Action type: Collaborative project
Countries involved: Netherlands,Netherlands,United Kingdom,Sweden,Sweden,Germany,Germany,Hungary,Italy,Poland,Italy
Call:  (FP7-KBBE-2012-6-singlestage, 2012)
Start date: 2013-02-01
End date: 2017-01-31
Duration (months): 48.0
Total project cost (EUR): 3808561.3
EU funding (EUR): 2997630.0
Participants: 12
Project status: CLOSED

The next few decades will witness a rapidly increasing demand for agricultural products. This growing demand needs to be met largely through intensification (produce more from the same land surface) because there is little scope for an increase in agricultural area. Eco-functional intensification has been proposed as a promising solution. Eco-functional intensification is the optimization of all provisioning, regulating and supporting ecosystem services in the agricultural production process. LIBERATION aims to provide the evidence base for eco-functional intensification and demonstrate the concept in seven representative agricultural landscape types in Europe. Using existing datasets from past and on-going European-scale studies we will first identify general relationships between the configuration of semi-natural habitats, on-farm management and biodiversity in a range of European landscapes and farming systems. Using a modelling approach we will link biodiversity to ecosystem services, by determining relationships between biodiversity, the delivery of multiple ecosystem services and agronomic yield. A novel aspect is that LIBERATION considers above- and below-ground ecosystem services simultaneously and analyses synergies and trade-offs between different ecosystem services. Using this modelling approach we will analyse which on-farm management practices and spatial configuration of semi-natural habitats optimizes yield and which optimizes farm income. We will synthesise management and policy recommendations. We will raise awareness and promote uptake of eco-functional intensification by disseminating project results to the widest possible range of stakeholders, amongst others by means of demonstration projects. This way we hope to liberate the forces of nature to the benefit of agricultural production.
A whole-systems approach to optimising feed efficiency and reducing the ecological footprint of monogastrics (ECO-FCE)

Framework: FP7 — Cooperation
Programme: Food, Agriculture and Fisheries, and Biotechnology
Destination: Sustainable production and management of biological resources from land, forest, and aquatic environment
Action type: Collaborative project
Countries involved: United Kingdom,Ireland,Spain,Poland,Austria,Switzerland,Denmark,Germany,Austria,Poland,Poland,United Kingdom,Austria,United Kingdom
Call:  (FP7-KBBE-2012-6-singlestage, 2012)
Start date: 2013-02-01
End date: 2017-01-31
Duration (months): 48.0
Total project cost (EUR): 7852656.6
EU funding (EUR): 5999814.0
Participants: 18
Project status: CLOSED

ECO-FCE’s objective is to firstly understand the interactions within the monogastric biological system which create diversity, optimise feed use efficiency and reduce greenhouse gas emissions, nitrogen and phosphorus excretion, whilst not adversely affecting animal health, welfare or product quality. Secondly, ECO-FCE will develop industry-ready tools which will facilitate the selection of breeding stock and nutritional strategies for improved gut health and functionality and host performance. ECO-FCE will achieve these objectives through five scientific work packages. Work package 1 involves a systematic literature review which will collate information in the open and grey literature on the effect of nutrition, gut characteristics and host genetics on feed use efficiency, nutrient utilization, greenhouse gas emissions, nitrogen and phosphorus excretion in pigs and poultry. Work package 2 will focus on the effect of nutrition. Aspects including how and when feed is offered and diet ingredients (raw materials and feed additives) will be investigated. Particular focus will be on nutritional strategies to reduce N and P excretion and to accurately determine and reduce GHG emissions. The effect of environment pre birth and nutrition post birth in pigs will also be investigated. Data and samples from WP 2 will then be used in WPs 3 and 4. Initial work in work packages 3 and 4 will specifically focus on common gut and host genetic factors which promote good or poor FCE. Other work in WP 3 will then investigate the feasibility of inoculating pigs and poultry with this ‘good’ gut microflora. WP 4 will focus on host genomics and will specifically attempt to relate genomic variation to variation in FCE. Further work in this work package will apply 'omics' techniques and will aim to derive biomarkers as tools to improve monogastric FCE. In WP 5 novel, industry-ready tools in the form of models will be developed and tested using data collated throughout the project.

Keywords: monogastrics feed efficiency systems biology nutrition omics ecological footprint
Sustainable Coating for Food Packaging based on Starch and Seaweed Extracts (PLANTPACK)

Framework: FP7 — Capacities
Programme: Research for the benefit of SMEs
Destination: Research for SMEs
Action type: Research for the benefit of specific groups
Countries involved: Spain,United Kingdom,Türkiye,Poland,Spain,United Kingdom
Call:  (FP7-SME-2012, 2012)
Start date: 2012-11-01
End date: 2014-10-31
Duration (months): 24.0
Total project cost (EUR): 1258826.33
EU funding (EUR): 954997.9
Participants: 8
Project status: CLOSED

Food packaging coatings (on paper wraps, cartons and cardboard) are essential to providing a physical barrier to protect food products in the packaging container during storage and transportation. Current packaging coatings are based on petrochemical derived waxes and polymers. However, with increasing petroleum costs and recent instability and volatility in some oil producing countries, the food packaging sector is searching for an alternative reliable and sustainable coating product. This would also promote the recycling characteristics of spent paper food packaging (currently this is difficult, as petroleum based coatings commonly used for this purpose reduce the compostability of paper. Our proposed research project, PlantPack, will aim to develop a sustainable, eco-friendly food packaging coating product made from seaweed extracts and starch, which will be applied to paper and cardboard in the form of a spray. This new coating will replace the current petroleum derived coating products, and thus improve the sustainability and biodegradability characteristics of both coatings and the final food packaging developed.

Keywords: packaging,paper,seaweed,starch,coating,biodegradable,recyclable,food,waste