
LI2D
Wikidata: Q61933161
5 Projects, page 1 of 1
assignment_turned_in ProjectFrom 2018Partners:CEA, Bactériologie-hygiène du CHRU de Lille, LI2DCEA,Bactériologie-hygiène du CHRU de Lille,LI2DFunder: French National Research Agency (ANR) Project Code: ANR-17-CE18-0023Funder Contribution: 435,004 EURThe early detection and diagnosis of infection by microbial pathogens is essential to establish an adapted therapy by identifying and characterizing the pathogens, ideally in the context of personalized medicine. A quicker detection without fastidious culturing steps of any virulent or opportunistic pathogen is of major interest for Public Health, and simultaneous identification of their antibiotic resistances will be a decisive breakthrough. Next-generation shotgun proteomics based on recent tandem mass spectrometers has the potential to identify any single or mixture of organisms in body tissues or body fluids and to describe their associated resistances. “Phylopeptidomics” consists in a new strategy to analyze peptide information for quick taxonomical identification: the proteins from a mixture of several organisms (pathogens & host) present in a given sample are analyzed by tandem mass spectrometry; the detected peptides are assigned to taxonomical data which are then deconvoluted to discriminate species and quantify them. Deconvolution of signals is based on specific organism signatures that have been calculated in terms of peptide sharing and patented by the consortium (patent n° EP2835751 A1). The software µorg.ID has been developed in-house in biopython to give the final answer within a few minutes for a 1h mass spectrometry measurement. This method has proved successful in identifying pathogens in complex biological matrices during several exercises organized by the Biotox-Piratox French national network. Recently, we have shown that enough shotgun peptidomic data can be recorded within 15 min by tandem mass spectrometry for allowing identification of a mixture of 24 different bacteria. We also obtained a quick overview of microbiota from feces within 60 min of mass spectrometry measurements. Our “without a priori” approach has been proved successful to identify bacteria and fungi from numerous samples. Even uncharacterized microorganisms can be classified in the most appropriate taxonomical groups. Moreover, the information obtained on the peptidome can be processed by bioinformatics to identify the bacterial resistances or toxins with appropriate database searches. Thus, phylopeptidomics represents a revolutionizing methodology for quick identification of any pathogen even present in mixtures and characterizing their antibiotic resistance arsenal and/or toxin production. The objectives of the phylopeptidomics project are to further develop the approach for obtaining a fast MS/MS identification of bacterial pathogens and antibiotic resistances of representative medical samples. The project should exemplify the different possible medical applications of this new concept. The project will focus on sample preparation to deal with common medical matrices (blood, stools, urine, respiratory tract samples and broncho-alveolar lavages) by Partners 1 & 2. For this, sample preparation protocols will be adapted for removing as much as possible host proteins and mass spectrometry incompatible substances when necessary. Numerous experimental datasets will be acquired by tandem mass spectrometry data for adjusting acquisition and interpretation parameters and establishing the range of use of this breakthrough methodology. Partner 1 will be in charge of interfacing generalist databases comprising antibiotic resistance-associated proteins and toxins with the µorg.ID software and defining specific scoring metrics and customer-oriented interface. It is reasonable to say that the whole result could be obtained in less than 3h including sample preparation by the end of the project. We propose to exemplify phylopeptidomics in a routine medical diagnostic laboratory to identify and quantify any bacterial pathogens (including microorganisms difficult to cultivate such as Mycobacteria) present in medical samples even as mixtures, and establish the list of antibiotic resistances and toxins they produce.
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For further information contact us at helpdesk@openaire.euassignment_turned_in ProjectFrom 2024Partners:CEA, ARYBALLE, Centre National de Référence Francisella tularensis, lnstitut de recherche interdisciplinaire de Grenoble, LI2DCEA,ARYBALLE,Centre National de Référence Francisella tularensis,lnstitut de recherche interdisciplinaire de Grenoble,LI2DFunder: French National Research Agency (ANR) Project Code: ANR-23-ASM2-0005Funder Contribution: 798,508 EURFrancisella tularensis is a highly infectious and virulent Gram-negative bacterium and a potential biological threat agent (category A of the Centers for Diseases Control, USA). This pathogen is responsible for a zoonosis, tularemia, a notifiable disease. Two subspecies are responsible for this disease: subsp. tularensis (type A) in North America, and subsp. holarctica (type B) in the northern hemisphere and southern Australia. Tularemia can manifest by regional infections (cutaneous, ocular, pharyngeal) with satellite lymphadenopathies which often evolve chronically and in 30% of cases towards suppuration requiring excision surgery. It can also manifest by systemic infections, in particular acute pneumonia whose spontaneous mortality for type A is close to 30%. Few antibiotics are active, and no effective vaccine is available. Humans become contaminated through the skin, conjunctival, oral, or respiratory route, through contact with infected animals, more rarely via arthropod vectors, contaminated food or water consumption, or contact with a contaminated hydrotelluric environment. The wild animal reservoir is extended and difficult to control. During the ANR ASTRID Tulamibe project, we showed that the aquatic reservoir is essential and the source of many human and animal infections. F. tularensis survives for a prolonged period in a natural aquatic environment, in particular through the formation of viable but non-cultivable bacteria (VBNC) which are more resistant in deleterious conditions. The monitoring and control of the environmental reservoir of F. tularensis appears to be an essential strategy in the prevention of human and animal infections, in civilian and military contexts. The ASMA TULADETECT project aims to develop a simple and reliable field tool allowing the detection, quantification, isolation, and culture of F. tularensis from environmental samples (water and aerosols). This tool will be developed from a system already marketed by the Aryballe company for the detection of volatile organic compounds. Preliminary results using this technology have shown the feasibility of the detection and semi-quantification of bacterial particles, and the possibility of isolating these bacteria from a complex sample containing other predominant bacterial species. The developed tool will use a chip with specific F. tularensis ligands for the detection and quantification of this species. We will also try to differentiate the two subspecies and identify the presence of VBNC. Finally, after isolation of F. tularensis from other microorganisms, we will try to cultivate this bacterium directly in the developed device. In case of difficulties, the isolated bacteria will be characterized and cultured in the laboratory using the bacteriological and molecular techniques already available. In a final step, we will test the possibility of extending the field tool developed to other pathogens, in particular to Legionella pneumophila, the agent of legionellosis. Indeed, many pathogens of civil or military interest have a hydrotelluric reservoir. Environmental monitoring of some of these microorganisms is a regulatory obligation. But no available tool meets the characteristics that we want to develop during this project. Given Aryballe's experience in technological innovations, the preliminary results available and the potential market for the strategy developed, we believe that this project has a strong chance of leading to the commercialization of an innovative field device.
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For further information contact us at helpdesk@openaire.euassignment_turned_in ProjectFrom 2017Partners:Génétique moléculaire, génomique et microbiologie, Architecture et Réactivité de lARN, CEA, ARN, LI2DGénétique moléculaire, génomique et microbiologie,Architecture et Réactivité de lARN,CEA,ARN,LI2DFunder: French National Research Agency (ANR) Project Code: ANR-17-CE07-0009Funder Contribution: 443,807 EURThe microbial biosphere represents the largest reservoir of catalysts for future industrial application. Yet it remains largely unexplored, with also the majority of genes identified in metagenomes still of unknown function. Using dehalogenation as a key major function with high-potential, versatile biocatalytic activity, dehalofluidX aims to address the major bottleneck faced by metagenomics today: the increasing recognition that genuinely novel biocatalysts with desired properties and unrelated sequences to already known enzymes, will only become accessible through novel approaches and pipelines. DehalofluidX is a tightly focussed 36-month innovative collaborative research project associating 3 partners from 3 research units in France, with complementary areas of expertise in microbial dehalogenation, microfluidics and omics technologies, and in particular microbial proteomics. The innovative concept of the high-throughput microfluidics-driven workflow is to use fluorescence quenching by halide ions in water-in-oil droplets to detect dehalogenation activity. This readout will be applicable to all halogenated compounds for which discovery of a novel dehalogenase catalyst is desirable. DehalofluidX does not require selective growth of dehalogenating organisms, and will target a much larger diversity of dehalogenating microbes and biocatalysts of the microbial biosphere than that accessed so far. DehalofluidX is organised in 3 successive well-defined, interconnected experimental tasks: (i) Droplet-based activity screening (validation of the microfluidics screening pipeline; isolating dehalogenating bacteria from environmental samples); (ii) Processing of cells with dehalogenase activity (processing of cultivable, poorly cultivable or non-cultivable cells with dehalogenase activity; phylogenetic and proteomic characterization, PCR screening for known dehalogenases); and (iii) Characterisation of novel catalysts (identification of genomic regions encoding dehalogenase activity; enzymatic characterisation of newly identified dehalogenases). Through its goal of discovering novel enzymes from the environmental microbiome for subsequent application and/or optimisation by biotech companies, dehalofluidX perfectly fits axis 3 of ANR Défi 3, as it may yield both new basic knowledge and technological know-how indispensable for the discovery of new biocatalysts. DehalofluidX also fits well with the National Strategy of Research ("green factory", Orientation 12 of the SNR), and has a direct link with the “Investments for the Future” program through partner DBR, member of LabEx NetRNA. The project PI has access to both pristine and contaminated environments as a source of new dehalogenating microbes and enzymes. Strong consortium expertise in all aspects of the proposed work strongly reduces potential challenges to success. Key requirements of droplet-based microfluidic high-throughput screening (droplet stability, maintenance of phenotype-genotype linkage, and signal sensitivity) have already been validated in preliminary experiments of halide-dependent fluorescence quenching in the presence of halogenated substrates. A thorough risk assessment was also performed on all stages of the dehalofluidX workflow, and potential issues and experimental fall-back solutions were identified and described. DehalofluidX will have major scientific impact, through delivery of novel biocatalysts for sustainable production of chemicals and bioremediation, and proof-of-concept of a novel activity-driven microfluidics high-throughput screening pipeline, expected to become generally applicable to other types of catalysts and R&D topics in the future. Technological impact will also be significant due to the novelty of the proposed activity-based approach for enzyme discovery. From an economic viewpoint, newly identified catalysts will be patented and licensed, as handled by SATT Conectus, the technology transfer instrument at Université de Strasbourg.
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For further information contact us at helpdesk@openaire.euassignment_turned_in ProjectFrom 2016Partners:Laboratoire dInnovations technologiques pour la Détection et le Diagnostic, LETI, LI2D, Centre National de la Recherche Scientifique/LAAS, Commissariat à lEnergie atomique et aux énergies alternatives +1 partnersLaboratoire dInnovations technologiques pour la Détection et le Diagnostic,LETI,LI2D,Centre National de la Recherche Scientifique/LAAS,Commissariat à lEnergie atomique et aux énergies alternatives,CEAFunder: French National Research Agency (ANR) Project Code: ANR-16-ASTR-0020Funder Contribution: 298,212 EURSeveral diseases spread between persons via the interaction of our bare hands with the outside world. Indeed, a large number of pathogens can survive on inert objects and surfaces and be later transferred onto a person hand who will then auto-contaminate herself. High morbidity or high mortality disease transmission through the contact of our hand with contaminated fomites is responsible each year of a large amount of hospitalizations, with a high associated societal and economical cost. At the present time, owing to a lack of appropriate technology, it is impossible to track down the path of a pathogen being deposited onto a fomite and transferred onto our hands with portable, automated equipment. Indeed, portable miniaturized biological sensors available are only able to detect pathogen at relatively high concentrations. Typically, the measurable pathogen concentrations of current portable equipment correspond to the concentration levels one would find inside the body fluids of an already sick person. So there is currently no fast and portable method to detect pathogen presence on field before they have contaminated and multiplied into a person, which limits disease and biological risk surveillance to “detect-to-treat” approaches. This proposal aims at demonstrating the proof-of-concept of an innovative biological detection and identification technology that would allow the sensing of few pathogen units inside of middle-size liquid volume (typically the volume needed to rinse one’s hands). The short term goal is to combine a pathogen pre-concentrator system with an array of MEMS liquid biological sensors to demonstrate sensing of low viral particles concentrations within a short response time. Neither of these approaches has ever been implemented before to the consortium’s best knowledge. As a matter of fact, the challenge is significant to provide a MEMS sensor that at the same time exhibits good mass sensitivity, a large capture area and that has been properly functionalized with high specificity antibodies to avoid at maximum the occurrence of false-positives. Challenges are also numerous to implement a fluidic tool enabling pre-concentration of viral particles at low concentrations within large volumes and record timing. To overcome these challenges with success, a strong consortium has been built between LETI, LI2D and LASS. This team has combined expertise in micro/nano fluidic systems, MEMS/NEMS based biological sensors, biological functionalization protocols and in design and production of highly sensitive and specific monoclonal antibodies towards specific pathogen viral strains. The long term goal of the proposed research is to provide an upper TRL technological unit enabling fast, ultra-sensitive and fully reliable detection method for pathogens. Such a key enabling technology could be applied, as an example to detect pathogen sampled directly from persons’ hands. Being able to detect pathogen on the hand of a still uncontaminated person would unlock many potential applications and will open a new paradigm in epidemiological surveillance.
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For further information contact us at helpdesk@openaire.euassignment_turned_in ProjectFrom 2020Partners:CEA, Laboratoire Interdisciplinaire des Environnements Continentaux, IPMC, IAM, LI2D +1 partnersCEA,Laboratoire Interdisciplinaire des Environnements Continentaux,IPMC,IAM,LI2D,INSBFunder: French National Research Agency (ANR) Project Code: ANR-19-CE34-0009Funder Contribution: 592,190 EURFrance, as well as many countries over the world, has large polluted industrial sites contaminated by polycyclic aromatic hydrocarbons (PAH). Among remediation strategies, phytoremediation is considered as one of the most promising approach. The PAH biodegradation enhancement in the plant rhizosphere has been largely studied in the past. However, the direct enhancement of the PAH loss through plant uptake and in planta degradation was very little explored. Although PAH parent compounds are apparently detected at low concentration, various transformation and conjugation process generating PAH metabolites and derivatives have been proposed but never explored in complex plant system. Research effort is required to better understand the dynamic and fate of PAH in soils under plant influence and recently developed metabolomics tool could help identifying PAH-derivatives in plants. Plants are naturally colonized with a wide variety of microorganisms. While the role of the rhizosphere microbiome in PAH dissipation have been largely investigated, our knowledge regarding the endosphere microbiome remains limited. Bacterial and fungal endophytes are well known for their plant growth promotion (PGP) properties, and some of them are capable of degrading PAH, but the microbial PAH-degradation pathways and the physiological interactions with the plant have never been explored in planta. Although, positive biotic interactions between bacteria and fungi are well known, studies rarely focus on both at the same time. Consequently, the joint response of the plant and its endophytes to the PAH pollution need to be studied benefiting of the development of OMICs tools giving information on the cellular response at the genomic, transcriptomic, proteomic and metabolomics levels. In this context, the EndOMiX project will characterize the interactions between bacterial and fungal root endophytes and plants in the context of PAH-contaminated soils to unravel the fundamental molecular processes set up and thus make the most of phytoremediation. The 1st objective is to assess the impact of a PAH contamination gradient on the response of the plant and its microbiome, using combination of enzymatic and molecular omics tools. Data will help understanding how the pollution rate structures the diversity of microbial communities and modulates the metabolic activity of the plant and endophytes. As the fate of PAH in plants is still poorly understood, our 2nd objective is to identify, track, and localize the PAH parent compound and derivatives, in the rhizospheric soil, plant tissues and associated microbial biomass using 13C-labelled PAH and combining metabolomic tools and DNA-stable isotope probing to identify the microorganisms benefiting from this carbon source. The results will make it possible to propose scenarios concerning the fate of PAHs in soil-plant systems. The 3rd objective is to isolate bacterial and fungal endophytes under PAH stress and determine their functional traits (i.e. PGP and degradation of PAH). This part will provide a large bank of bacterial and fungal strains usable in phytoremediation. The last objective is to decipher, in simplified and controlled conditions, the role of the 3 partners (bacterium, fungus and plant) and the underlying functional mechanisms to reveal who is doing what, how and where, through the tracking of 13C-PAH. We will then fully understand the metabolic functioning of our system and reconstruct the major steps of PAH transformation in plants.
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