Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Under the hood: Single-molecule studies of the DNA replication machinery (SINGLEREPLISOME)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Molecular and Structural Biology and Biochemistry
Countries involved: Netherlands
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-02-01
End date: 2016-01-31
Duration (months): 48.0
Total project cost (EUR): 2000000.0
EU funding (EUR): 2000000.0
Participants: 1
Project status: CLOSED

The study of biological processes at the single-molecule level has greatly influenced our view of the molecular mechanisms that define life. However, studies so far have mainly focused on individual, purified proteins in non-physiological environments. Since cellular processes are typically not mediated by single proteins, but rather by large complexes of dynamically interacting components, the development of the tools to study such large complexes with single-molecule sensitivity is an important direction. With our initial successes in developing the single-molecule tools to study DNA replication, we have begun to open the field of single-molecule biophysics to the study of large, multi-component complexes. Here we describe how we will develop new single-molecule approaches to study the physical interactions and molecular mechanisms that control the DNA replication machinery, both in simple model systems and in higher organisms. By measuring the elastic properties of DNA and simultaneously visualizing fluorescently labeled replication proteins acting on the same DNA we will be able to relate the physical structure and composition of the replication complex to its mechanism of action. We will also develop the tools to study the replication machinery in cellular extracts of higher organisms; an environment that is compatible with our nanomanipulation and fluorescence tools, but faithfully mimics the complex environment in which these processes normally take place. Our objective is to arrive at a complete molecular understanding of how DNA replication works. We will use the tools described in this proposal to address a number of poorly understood issues: What is the mechanism of coupling between DNA unwinding and synthesis? How are the two DNA polymerases coordinated? How does replication deal with roadblocks on the DNA? Our approach to obtain “molecular movies” of the replication process represents an entirely novel strategy to understand these issues.

Keywords: single-molecule studies,dna replication
Nationwide prospective study on community-acquired bacterial meningitis: from genetics to therapy (MENINGENE)

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: Netherlands
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-02-01
End date: 2017-01-31
Duration (months): 60.0
Total project cost (EUR): 1400000.0
EU funding (EUR): 1400000.0
Participants: 1
Project status: CLOSED

Meningitis is an inflammation of the membranes covering the brain and spinal cord (the meninges). Each year 35,000 European patients suffer from bacterial meningitis, resulting in 7000 deaths and leaving 7000 disabled. Streptococcus pneumoniae and Neisseria meningitidis are the most common causative bacteria of bacterial meningitis. These bacteria are common colonizers, but in some individuals, they are able to spread to the bloodstream, slip through the blood-brain barrier and cause meningitis, with devastating consequences. Genetics of host and pathogen are considered crucial in this host-pathogen interaction. Our objectives are to identify and characterize host genetic traits and bacterial virulence factors controlling occurrence and outcome of bacterial meningitis. In a nationwide prospective cohort study, using pathway and total exome sequencing, we will search for genetic variants in 2000 patients with community-acquired bacterial meningitis and 2000 controls. On the pathogen side, using whole genome sequencing, we will systematically search for new bacterial virulence factors in the 2000 causative bacteria. Subsequently, by analyzing clinical data, serum and cerebrospinal fluid, we will examine the potential impact and functionality of these host and pathogen factors. Next, we will validate and explore our findings in an animal model of meningitis and investigate whether treatment against these specific components can improve outcome. Finally, we will initiate an open-access European database on the genetics in bacterial meningitis. In addressing our objectives, I will combine my expertise in bacterial meningitis with groundbreaking, translational approaches using clinical data, human samples, next generation sequencing, in vitro techniques, and a mouse model. The results of this project will be translated into novel therapeutic strategies to advance patient care and will also be important for the development of disease prevention and vaccines.

Keywords: translational research,neurology,bacterial meningitis,disease prevention,therapy
Accelerated Atherosclerosis in Patients with Immune Mediated Disorders as a Model to Investigate the Link between Inflammation and Cardiovascular Disease: From Basic Mechanisms to Clinical Application (IM TARGETING CVD)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Physiology, Pathophysiology and Endocrinology
Countries involved: United Kingdom
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-04-01
End date: 2017-03-31
Duration (months): 60.0
Total project cost (EUR): 1499731.0
EU funding (EUR): 1499731.0
Participants: 1
Project status: CLOSED

Atherosclerosis is a chronic inflammatory disease of the arterial wall with (auto)immune component, initiated in response to modified (phospho)lipids. Despite important advances in our understanding of the inflammatory response in atherosclerosis, the critical pathways responsible for the breakdown of immune tolerance to lipoproteins and other self-antigens remain largely unknown. An important feature of ruptured/thrombosed atherosclerotic lesions is the accumulation of apoptotic, and secondary necrotic, lipid-laden macrophages and smooth muscle cells due to defective efferocytosis (clearance of apoptotic cells). This leads to the formation of a large ‘necrotic’ lipid core, associated with enhanced vascular inflammation. Interestingly, defective efferocytosis has been associated with the development of autoimmunity, and patients with systemic lupus erythematosus who show increased accumulation of apoptotic material are at very high risk of accelerated atherosclerosis and myocardial infarction. We hypothesize that accumulation of apoptotic/secondary necrotic cells due to defective efferocytosis, together with modified lipids, activate critical immuno-inflammatory pathways in macrophages and B cells, and break immune tolerance in atherosclerosis and post-myocardial infarction. This is consistent with the critical role played by defective efferocytosis and macrophage activation in atherosclerotic lesion progression, and with our recent unsuspected data showing a critical role for B cell activation in driving lesion development in several models of atherosclerosis. We also propose that interactions between macrophages and B cells are essential for the perpetuation of the pathogenic immuno-inflammatory response in cardiovascular disease. Finally, we will harness this knowledge for a better identification of patients at risk of cardiovascular complications, and will target these pathways to limit the progression and complications of cardiovascular disease.

Keywords: atherosclerosis,myocardial infarction,efferocytosis,inflammation,immunity
Gene x environment interactions in affective disorders - elucidating molecular mechanisms (GXE-MOLMECH)

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: Germany
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-03-01
End date: 2017-02-28
Duration (months): 60.0
Total project cost (EUR): 1254119.6
EU funding (EUR): 1254119.6
Participants: 1
Project status: CLOSED

Exposure to traumatic experiences as well as chronic stress has been shown to increase the risk for a number of psychiatric disorders including major depression and anxiety disorders by inducing longterm alterations in the reactivity of the stress hormone system. These effects can be moderated by genetic variants, one of them being functional polymorphisms in glucocorticoid receptor (GR) co-chaperone gene FKBP5. Preliminary studies in my laboratory suggest that this GxE interaction is mediated by allele-specific de-methylation of intronic glucocorticoid response elements (GREs) within FKBP5. The overarching aim of this grant is to identify the molecular mechanisms by which FKBP5 polymorphisms and early trauma interact to increase the risk for a number of depressive and anxiety disorders. In this application, I propose to extend these preliminary data by experiments in healthy controls and depressed patients, human lymphoblastiod cell lines as well as an animal model in outbred mice showing similar GxE interaction to address the molecular mechanism of these DNA-methylation changes as well as their cellular and system level consequences. Finally we will use expression quantitative trait locus analysis for GR stimulated gene expression to identify new loci relevant for GxE interactions in stress-related disorders. Overall, this proposal will follow up on one of the first putative molecular and systemic mechanisms identified for gene x environment interactions in affective disorders and will establish an animal model mimicking these specific interactions. The findings related to this proposal could be of major importance for understanding the biology of these disorders and to explore novel treatment options, including manipulations of epigenetic modifications.

Keywords: early trauma,fkbp5,stress hormone system,dna methylation
Molecular photoacoustic imaging of stem-cell driven tissue regeneration (MOPIT)

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: Germany
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-01-01
End date: 2016-12-31
Duration (months): 60.0
Total project cost (EUR): 1622736.0
EU funding (EUR): 1622736.0
Participants: 2
Project status: CLOSED

I propose to develop a new generation of molecular photoacoustic imaging technologies and methods capable of detecting single deep tissue cells in preclinical studies of tissue regeneration. In order to achieve this goal, an interdisciplinary research programme involving physicists, engineers and life scientists is required to address the following objectives: 1) the development of novel photoacoustic imaging technology that provides high sensitivity and acquisition speed, 2) the development of the theoretical framework and experimental methods for quantitative imaging, 3) the development of novel genetically expressed reporters, and 4) the preclinical application in small animal models of tissue regeneration. This will result in a preclinical imaging modality has the potential to combine single cell sensitivity and microscale spatial resolution in deep (centimetre range) tissue regions with molecular, physiological, and anatomical imaging capabilities. The instrumentation and methodologies developed in this project will be applied to noninvasive, longitudinal, and quantitative studies of stem cell driven tissue regeneration, such as angiogenesis in bone fractures and muscle trauma. It will allow the detection and tracking of single stem cells and the probing of stem cell function. This will provide unprecedented opportunities for correlating cellular localization, migration, and function and with anatomical changes - knowledge that can be exploited to develop novel drugs and cell-based clinical therapies. Crucially, the technologies and methodologies developed in this project will be directly applicable to a wide range of other fields of the life sciences, such as cancer research and neurology.

Keywords: photoacoustic imaging,spectroscopy,molecular imaging,stem and progenitor cells,genetic contrast agents
Functional Metagenomics – Harnessing the Biotechnological Potential of Completely Novel Protein Families (FUME)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Applied life sciences and biotechnology
Countries involved: Germany
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2011-10-01
End date: 2016-11-30
Duration (months): 62.0
Total project cost (EUR): 1499441.6
EU funding (EUR): 1499441.6
Participants: 1
Project status: CLOSED

Today the vast amount of newly published genomic data is generated by metagenomic projects. The annotation of these sequences of organisms, whose existence was not even known before their DNA was extracted from environmental samples, has led to the identification of thousands of new protein families with no detectable homology to any proteins in sequenced and cultivable organisms. While these protein families now make up a major part of the protein universe, we do not know anything about their functions or biocatalytic activity. In this grant application, we propose to lay the groundwork for studying the function of this vast set of proteins and exploit their biocatalytic potential. However, many of the techniques traditionally used to elucidate protein function, such as genetics and “omics”-technologies are not applicable, because the organisms in which these proteins exist are as of yet unknown. Therefore we plan to: 1. Computationally analyze the newly discovered protein families to identify one paradigmatic member of every novel family. 2. Create an expression-plasmid library of those paradigmatic representatives by de novo gene-synthesis. 3. Use this library, combined with the power of Escherichia coli genetics, for specific complementation studies and biochemical assays to assign functions to novel protein families. This combination of synthetic biology and metagenomics will provide the starting point for a novel systematic approach to harness the biocatalytic potential and to understand the function of an unknown sector of biology that has only very recently been discovered.

Keywords: metagenomics thiol-disulfide-oxidoreductases
Synthetic regulatory circuits for programmable control of cell physiology (CELLCONTROL)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Applied life sciences and biotechnology
Countries involved: Switzerland
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2011-10-01
End date: 2017-09-30
Duration (months): 72.0
Total project cost (EUR): 1479008.7
EU funding (EUR): 1479008.7
Participants: 1
Project status: CLOSED

The newly emerging discipline of Synthetic Biology holds the promise of radically changing the way we probe, control and augment living matter from single cells to entire organisms, and revolutionize basic biological research, biotechnology, and medicine. However, practical work toward these important goals is still in its infancy, in part because concrete approaches to achieve rational control of cell physiology are currently lacking. In order to advance this vision, here we propose a detailed strategy toward engineered regulatory circuits that read out complex cellular states based on multiple biological signals, and convert this information into a desired action based on pre-programmed signal integration. If successful, our strategy will enable unprecedented level of rational intervention with the cell. Specifically, we suggest to read out cellular information as relayed by expression and activity of cell’s transcription factors, proteins that control gene expression and serve as major regulators of cell fate and cell response to transient stimuli. The readout will be accomplished with the help of specially-designed sensor promoters that will in turn drive the expression of engineered microRNA molecules. Those molecules in turn will converge on a small number of response elements in engineered downstream transcripts, implementing highly-flexible and programmable logic integration of the original transcription factor signals (Rinaudo et al, Nature Biotechnology, 2007 and Leisner et al, Nature Nanotechnology, 2010). We propose a stepwise bottom-up construction strategy whereby we first design, test and optimize sensor promoters for individual TFs, next we integrate them into large networks, and finally we show how to utilize these networks as prototype selective anti-cancer therapies. To validate our approaches, we will use human cancer cell lines as a model system.

Keywords: rna interference,smart anti-cancer therapies
Structural studies of Nucleotide Excision Repair complexes (NERCOMP)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Molecular and Structural Biology and Biochemistry
Countries involved: Poland
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-01-01
End date: 2017-12-31
Duration (months): 72.0
Total project cost (EUR): 1498000.0
EU funding (EUR): 1498000.0
Participants: 1
Project status: CLOSED

DNA damage caused by chemical and physical factors can lead to detrimental effects to the cell and must be corrected. One of the primary pathways to achieve this repair is nucleotide excision repair (NER). In NER, the DNA damage is first located, a stretch of bases harboring the lesion is removed, and the gap is filled by a DNA polymerase. The unique feature of NER is its ability to correct a wide spectrum of DNA modifications of different sizes and chemical structures. The aim of the project is to structurally and biochemically characterize protein complexes involved in NER pathways in bacteria and eukaryotes. In bacterial NER, a complex of UvrA and UvrB proteins locates the damage and verifies its presence. In the first part of the project we plan to determine the crystal and small-angle X-ray scattering (SAXS) structures of a UvrA-UvrB-DNA complex to elucidate the details of the mechanism of the first steps of bacterial NER. In eukaryotic NER, the 3′ incision is executed by XPG/Rad2 protein. Currently, no structural information is available for this protein. In the second part of the project, we plan to solve the crystal structures of XPG/Rad2 nuclease in apo form and in complex with the DNA substrate to elucidate the mechanism of the 3′ cut. We also plan to determine the structure of XPG/Rad2 in complex with the XPG/Rad2-binding domain from the p62 component of TFIIH, which will be an important building block for the determination of the architecture of the eukaryotic NER pre-incision complex. The third part of the project will elucidate the structure and mechanism of the Rad16-Rad7 yeast NER complex. It is implicated in numerous stages of NER, from damage detection to ubiquitination of other NER components. We plan to solve the crystal structures of the Rad16-Rad7 alone and in complexes with DNA or partner protein Abf1 to elucidate the mechanisms of various activities of Rad16-Rad7 and help design experiments that could test the in vivo function of this complex.

Keywords: dna damage,dna repair,nucleotide excision repair
DNA traffic during bacterial cell division (DNATRAFFIC)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Molecular and Structural Biology and Biochemistry
Countries involved: France
Call:  (ERC-2011-StG_20101109, 2011)
Start date: 2012-02-01
End date: 2017-01-31
Duration (months): 60.0
Total project cost (EUR): 1565938.0
EU funding (EUR): 1565938.0
Participants: 1
Project status: CLOSED

The molecular mechanisms that serve to couple DNA replication, chromosome segregation and cell division are largely unknown in bacteria. This led a considerable interest to the study of Escherichia coli FtsK, an essential cell division protein that assembles into DNA-pumps to transfer chromosomal DNA between the two daughter cell compartments during septation. Indeed, our recent work suggests that FtsK might regulate the late stages of septation to ensure DNA is fully cleared from the septum before it is allowed to close. This would be the first example of a cell cycle checkpoint in bacteria. FtsK-mediated DNA transfer is required in 15% of the cells at each generation in E. coli, in which it serves to promote the resolution of topological problems arising from the circularity of the chromosome by Xer recombination. However, the FtsK checkpoint could be a more general feature of the bacterial cell cycle since FtsK is highly conserved among eubacteria, including species that do not possess a Xer system. Indeed, preliminary results from the lab indicate that DNA transfer by FtsK is required independently of Xer recombination in Vibrio cholerae. To confirm the existence and the generality of the FtsK checkpoint in bacteria, we will determine the different situations that lead to a requirement for FtsK-mediated DNA transfer by studying chromosome segregation and cell division in V. cholerae. In parallel, we will apply new fluorescent microscopy tools to follow the progression of cell division and chromosome segregation in single live bacterial cells. PALM will notably serve to probe the structure of the FtsK DNA-pumps at a high spatial resolution, FRET will be used to determine their timing of assembly and their interactions with the other cell division proteins, and TIRF will serve to follow in real time their activity with respect to the progression of chromosome dimer resolution, chromosome segregation, and septum closure.

Keywords: chromosome dimer resolution,cell division,chromosome segregation,cellular biology of prokaryotes,dna translocation