Workshops
For the 2024 edition, 27 workshops are offered. They are divided into 6 sessions over 2 days.
Each workshop lasts 30 minutes.
| core facility | Title | Description | Speakers |
|---|---|---|---|
| EcogenO | DNBSEQ-G400 MGI sequencing, feedback on directional RNAseq | Transcriptomics studies by sequencing require a large number of sequences to obtain the finest and most exhaustive analysis possible. The EcogenO core facility is therefore equipped with a DNBSEQ-G400 sequencer from MGI. The first application developed and proposed is directional RNAseq. We carried out the first tests on RNA samples from plants and microorganisms. This feedback is an opportunity to compare the sequencing results with or without ribodepletion, and with manual or robotic preparation. You will also be given an overview of the sequencing capabilities on G400 and the applications currently being developed by EcogenO. | Sophie Michon-Coudouel, EcogenO |
| ViVeM center | Production and characterization of AAVr vectors: where are we? | Recombinant adeno-associated viruses (AAVs) are viral vectors of choice for in vivo gene therapy, with six products currently approved on the market. However, the process of manufacturing large quantities of AAV vectors remains a major challenge, particularly due to increasing clinical and commercial demands and the need to administer high doses systemically to achieve therapeutic efficacy. Our core facility (CPV) today ViVeM for Viral Vector Manufacturing center, “integrator in Biotherapies and Bioproduction, France 2030”, aims to meet these challenges from fundamental “vectorology” to pre-industrial manufacturing. Current AAV production and purification methods still produce a heterogeneous population of vectors, particularly with the presence of unwanted empty particles or intermediate particles filled with an incomplete DNA sequence. Determination of the ratio of full to empty capsids is a critical quality control requirement for rAAV production. Several analytical methods are currently used. Analytical Ultracentrifugation Sedimentation Velocity (AUC-SV) is considered the analytical technology par excellence for measuring the relative quantities of each particle subpopulation in the AAVr vector batch, in addition to particle aggregates, based on sedimentation coefficients of the different components. However, the AUC method has its limitations, including the sample volume required for analysis, the limit of detection, and the cost of the specific equipment required. Today, a wide range of other technologies for the evaluation of the full/empty AAVr ratio are used or evaluated, such as mass photometry, spectrophotometry, size exchange chromatography or capillary electrophoresis, but do all these methods allow a characterization as precise as the AUC? | Cécile Robin, ViVeM center |
| PLaTIMed and IRT b-com | Digital training in the operating room: 2 use cases with the INVOLVE project (In-Situ Volumetric Audio-Video Experience) and the OptimiX project (Radiation dose optimization for X-ray guided procedures). | The INVOLVE project, located at the intersection of media and health, makes a significant contribution to digital medical training. Using technologies such as virtual and augmented reality, its goal is to innovate in medical education. In the field of surgery, INVOLVE implements multi-point capture and 4D reconstruction techniques, thus facilitating the creation of photo-realistic immersive learning environments. This method allows trainees to become familiar with complex surgical scenarios and observe essential procedures in-depth. In addition to traditional training, this approach offers a practical and interactive experience, essential for acquiring specific skills in the operating room. The use of X-rays for medical purposes is associated with an inherent risk of exposure of patients, radiologists /interventional surgeons and medical personnel to harmful ionizing radiation. Studies have reported a considerable number of unnecessary exposures resulting from a lack of awareness, reduced concern for long-term exposure risks, and poor knowledge of the behavior of ionizing radiation. The overall objective of the OptimiX project is to improve the radiation protection of patients and clinical staff by (i) developing new approaches for rapid and accurate radiation simulation, (ii) proposing methods to optimize the configuration of a device x-ray imaging systems to minimize the dose delivered (iii) developing radiation awareness systems using augmented/virtual reality visualization to facilitate teaching, in an attractive and intuitive way, about the behavior to adopt against ionizing radiation. | Albert Murienne and Nicolas Ramin, IRT b-com and Guillaume Dardenne, PLaTIMed |
| BIBS extension | Analysis of animal and human milk oligosaccharides by hydrophilic interaction liquid chromatography: an approach for exploring the diversity and impact of diet. | In order to study the impact of diet and genetics on the diversity and concentrations of milk oligosaccharides, the BIBS core facility of the BIA unit in Nantes has developed and implemented a simple and rapid method to identify and quantify these molecules. This method makes it possible to extract oligosaccharides from dairy matrices and their fermented derivatives, to stoichiometrically couple the oligosaccharides to a fluorophore and to analyze them by ultra-high performance liquid chromatography coupled to a mass spectrometer and a fluorescence detector. The method as well as its application to different milks makes it possible to reveal the similarities and divergences between human and animal milks. Furthermore, its use within the framework of various partnership projects (academic and private) and funded projects (Valorex, INRAE, SODIAAL dairy cooperative in particular) allows us to better understand the genetic and dietary impacts on the composition of milk oligosaccharides. and their abundance. | Sophie Le Gall, BIBS |
| MRic | RIM: New approach to high-resolution fluorescence imaging by random illumination. | The idea of RIM is to use the “speckles” of the full-field illumination laser to create a structured illumination pattern at the diffraction limit. By varying the pattern from one image to another using a diffracting element (in our case, an SLM), we are able to acquire a stack of images with a camera, which corresponds to cumulative homogeneous illumination. By solving the inverse problem, we are able to reconstruct a super-resolved image at the focal plane with unprecedented optical cross-section. Compared to conventional SIM, RIM is able to work deep within the sample because the speckle is insensitive to diffusion. The main application is the acquisition of super-resolved depth images with a very low amount of light and at high speed. This is a very good compromise between z-cut and super-resolution with full-field illumination particularly suited to thick live samples. | Nina Soler, MRic-Photonics, and Gilles Le Marchand, UMR 6290 IGDR |
| core facility | Title | Description | Speakers |
|---|---|---|---|
| protim | The revolution of DIA analysis in proteomics: to go further in the depth of proteome analysis | Until very recently the flagship method for analyzing complex proteomes by mass spectrometry was based on data-dependent acquisition (DDA) where fragment ions for MS/MS analysis are selected one by one at the time of acquisition. depending on the intensity of their signal. This has the disadvantage of not selecting certain low-intense ions and therefore losing information. In recent years, a new method of data independent acquisition (DIA) has been developed, allowing the acquisition of MS/MS data of all detected ions thanks to the simultaneous fragmentation of several ions in parallel over wide bands of isolation, generating very complex MS/MS spectra. This method is becoming more popular thanks in particular to the development of dedicated software using prediction algorithms based on artificial intelligence for the analysis of very complex spectra and thanks to the use in proteomics of the latest generation mass spectrometer with a mobility cell. ionic as an additional dimension of ion separation (4D-proteomics), combined with high sequencing speed without affecting resolution or sensitivity. During this workshop we will present this analysis method and we will illustrate its implementation on the Protim core facility through supported scientific projects. | Emmanuelle Com and Régis Lavigne, Protim |
| SynNanoVect | Non-viral transfer of nucleic acids vitro et in vivo : from the formulation of nanovectors to their use for gain or loss of function | The non-viral vectorization of nucleic acids has evolved considerably both by the nature of the transport agents (lipids and polycationic polymers), the diversity of the nucleic acids used (plasmid DNA, mRNA, siRNA, guide RNA and nucleases), their formulation particularly with the use of microfluidics, as well as adequate physicochemical characterization. Moreover, in vivo, different routes of administration are possible depending on the desired applications. On another side, the latest generation electroporation equipment offers tools and applications ranging from simple transfection for research purposes to gene correction ex vivo. The SynNanoVect core facility offers a workshop on non-viral DNA and RNA transfer technologies, mainly focusing on the formulation of nanovectors for their use. vitro and their administration in vivo as well as the latest developments in microfluidic technology and electroporation. | Pascal Loyer, Paul-Alain Jaffrès, Thierry Benvegnu, Brice Calvignac and Tristan Montier, SynNanoVect |
| Hyperion | 40 shades of metals to characterize the tissue microenvironment. | In recent years, multiplexed imaging technologies have developed considerably. Traditionally, immunohistochemical (IHC) markings performed on tissue sections (paraffin-embedded or frozen) are analyzed by a pathologist in a semi-quantitative manner. The disadvantage is that the number of parameters observable simultaneously remains limited. Hyperion™ (Standard BioTools) revolutionizes analyzes with currently a quantification of 40 parameters on the same tissue section [1]! The slides are marked with antibodies coupled to stable metal isotopes. These metal isotopes are detected by mass spectrometry, thus providing information on the intensity and spatial distribution of the markers. The system allows the analysis of tissue sections with a resolution of 1 μm2. Come and discover a range of projects carried out on our Brest core facility![1] Elaldi R, Hemon P, Petti L, Cosson E, Desrues B, Sudaka A, Poissonnet G, Van Obberghen-Schilling E, Pers JO, Braud VM, Anjuère F , Meghraoui-Kheddar A. High Dimensional Imaging Mass Cytometry Panel to Visualize the Tumor Immune Microenvironment Contexture. Front Immunol. 2021 Apr 16. | Patrice Hemon, Nadège Marec and Pierre Pochard, HYPERION |
| corsair | Metabolomics in the service of chemical ecology. | Chemical ecology aims to decipher the chemical interactions between living organisms, whether macro- or microscopic. This field of research is vast and affects various scientific communities working on numerous models of biotic interactions at different scales. Chemical ecology extends from fundamental research to various applications, such as the study of plant-insect interactions in agronomy and biomimetic solutions for biofilm control in the marine environment. Through targeted or non-targeted metabolic profiling, this workshop will illustrate the power and relevance of metabolomic analyzes for the characterization of chemo-diversity and the identification of chemical signatures involved in inter-organism mediation, in particular via the analytical tools available at the Corsair core facility. In this context, different examples from marine or terrestrial environments will be discussed. | Catherine Leblanc (Corsaire-MetaboMer), Olivier Grovel (Corsaire-ThalassOMICS) and Alain Bouchereau (Corsaire-P2M2) |
| Atlanpole Biotherapies | Funding for collaborative research (public/private). | The Atlanpole Biotherapies competitiveness cluster will present several calls for collaborative projects, involving companies and research structures, from different funding windows (Regions, France 2030, ANR, etc.). The center will also present its support for project development and labeling. | Benoît-Jules Youbicier-Simo, Atlanpole Biotherapies and Paul Bodin, ABF Décisions |
| core facility | Title | Description | Speakers |
|---|---|---|---|
| Impact | Development of bioinformatics tools around functional proteomics data for the inference of protein functions. | We have developed a set of bioinformatics tools using proteomics data or 3D structure to provide clues to the biological function of little-known proteins: For example, the PROZE tool identifies three-dimensional structure analogies to identify protein domains similar and infer potential biological functions. Another tool uses Node Embedding and a vector similarity and nearest neighbors algorithm to identify core proteins essential for the activity of our biological target from differential proteomics data. Let's see how the idea of these tools was born and go through the stages of development of these bioinformatics tools until their use to solve scientific problems. | Mike Maillasson, Impact |
| LGA | Preservation of organs for transplantation: development of innovative ex vivo preservation methods on large animal models. | In organ transplantation, the period between removal of the transplant from donors and its revascularization in the recipient is a particularly critical period because it is responsible for ischemia of the transplants. Within our laboratory and on the large animal laboratory (LGA) core facility, we seek to develop innovative preservation methods aimed at reducing transplant ischemia and ultimately improving their function. In this workshop, we will present the successive stages of development of preservation methods within a large mammal model. We will also explain how new methods of organ revascularization make it possible to replace the in vivo model and thus contribute to improving animal well-being. | Stéphanie Bernardet and Benoit Mesnard, LGA |
| APEX | A new light sheet microscope on APEX for 3D exploration of large samples. | The light sheet ultramicroscope recently installed on APEX presents three essential strengths for exploring the biodistribution of infectious or therapeutic agents or the three-dimensional microstructure of a tissue at the scale of the entire organ: (i) it is suitable for the exploration of large samples (e.g. whole mouse), (ii) it is compatible with all transparency techniques, in particular those which use organic solvents which are the most effective and (iii) it represents an open system which allows the observation of samples at different magnifications. This high-tech equipment complements all the tools available on the imaging core facilities of the Western France region and will contribute to strengthening the research activities carried out by the scientific community using Biogenouest core facilities. | Laurence Dubreil, APEX and UMR 703 PAnTher |
| LIPIDOCEAN, LEMAR, BEEP-LEP and Polaris | Isotopic analysis of marine lipids: applications from ecology to industry. | The lipid composition of marine organisms is regulated by biological mechanisms in response to biotic and abiotic factors. Indeed, the molecular and isotopic signatures of the lipids of marine organisms have certain specificities linked to the type of organism studied and can be modified in response to environmental disturbances such as thermal or trophic stress. Within the LIPIDOCEAN core facility at LEMAR, the use of GC-MS and GC-IRMS allows the fine analysis of marine lipids (fatty acids, steroids, etc.) at molecular and atomic scales. The structural and functional analysis of lipids by classic chromatography methods is thus combined with spectrometric analyzes of isotope ratios on specific compounds (CSIA). This innovative approach makes it possible to answer questions and needs ranging from fundamental research to industrial R&D: – for the study of the trophic ecophysiology of organisms within or at the interface of ecosystems. – for the traceability of seafood products (including industrial oils), an economic sector increasingly exposed to fraud. – for applications in metabolomics and fluxomics via the biosynthetic production of polyunsaturated fatty acids uniformly labeled in 13C. | Manon Buscaglia, LEMAR; Loïc Harrault, CNRS-Polaris; Margaux Mathieu-Resuge, Ifremer – BEEP – LEP |
| Atlanpole Biotherapies | Feedback from collaborative projects. | Companies and researchers from the region will present two collaborative projects in which they participated through the context, objectives and results of the project but also the support by a competitiveness cluster and the success factors. | Benoît-Jules Youbicier-Simo, Atlanpole Biotherapies |
| core facility | Title | Description | Speakers |
|---|---|---|---|
| P2R | Current standards for protein quality control. | The use of poorly or poorly characterized recombinant proteins can lead research work to problems of reproducibility, or even to erroneous conclusions. This may be due to the presence in the sample of aggregates and/or proteins with a non-native conformation. At the initiative of the P4EU and Arbre Mobieu networks, international recommendations for best practices in protein quality control were defined in 2021. During this presentation, we will discuss these recommendations and associated biophysical techniques, several of which are accessible on the P2R core facility or are currently being implemented there. | Frédéric Pecorari, P2R |
| ImPACcell and IGDR | The dog, man's best ally: development of canine tumor cell lines as drug testing models in comparative oncology. | The canine species includes more than 400 breeds resulting from artificial selection imposed by humans for more than 10 years. Thus, in addition to the fixation of numerous phenotypes in each race, genetic diseases with racial predispositions such as cancers are numerous. The Dog Genetics team, led by Catherine André, from UMR 000 IGDR in Rennes, works on canine cancers as genetic and therapeutic models of homologous cancers in humans. After developing tumor lines from canine tumor tissues (e.g. melanomas, sarcomas), we characterized them genetically, performed drug response tests (in vitro IC6290 tests on the ImPACcell core facility) and verified their tumorigenicity in immunodeficient mice (in collaboration with Biotrial as part of Oncotrial). The results of all of these tests allow us to identify relevant tumor lines with characteristics homologous to human cancers which can be used for the development of new drugs. To date, a panel of around twenty canine tumor lines has been established, constituting a relevant tool for carrying out oncology studies with dual benefits for humans and dogs. | Caroline Confais, UMR 6290 IGDR |
| MicroPICell | Innovative imaging of organoids enables new analyses. | Thanks to their ability to reproduce selected features of organs, organoids offer a wealth of information to study diseases and test new drugs precisely and ethically. Imaging plays a vital role in the study of these organoids, allowing researchers to visualize their structure and inner workings. Advanced imaging techniques, such as confocal or light sheet microscopy, or histology approaches on serial sections, make it possible to obtain detailed images of organoids in 3 dimensions, thus opening new perspectives for research. medical and regenerative medicine. Associated with new methods such as transparency, we study cerebroids, cardioids or other organoids differentiated from induced pluripotent stem cells. | Aurélie Doméné, Anne Gaignerie and Philippe Labrot, MicroPICell |
| GO-EV unifying project | Characterization of extracellular vesicles in the Great West. | Extracellular vesicles (EVs) are nanoparticles delimited by a lipid bilayer and naturally produced by cells. These EVs are now proposed as alternative biotherapies or innovative biomarkers. The importance of their cargo in cellular communication and regenerative medicine make them promising players in the fields of health. During the workshop, EV extraction and characterization techniques explored in the Grand-Ouest network will be presented. GO-EV is a multi-site and disciplinary network bringing together academic laboratories, core facilities and clinical services. | Laëtitia Guével, GO-EV network, with the participation of the APEX, Cytocell, IMPACT, MicroPICell, Mass Spectrometry (Lipidomics) core facilities |
| core facility | Title | Description | Speakers |
|---|---|---|---|
| CrystalO | Protein crystallography in the AlphaFold era | Since its publication (*) and availability in 2020, Alphafold2 (AF2) is able to revolutionize the way we do and use structural biology. The workshop offered by the CristalO core facility will present in a short introduction the history leading to the creation of AF2, to then illustrate with some concrete examples how this program is introduced to solve crystallographic structures, and how to use/interpret the structural models produced. by AF2 if a 3D structure is not envisaged. The workshop will also present an opening towards examples of actions that are done using AF2 and/or RoseTTAFold on a large scale. (*) Senior AW, et al. Nature. 2020, 577(7792):706-710. doi:10.1038/s41586-019-1923-7. | Mirjam Czjzek, CristalO |
| Biodimar | Marine biotechnologies and marine bioprospecting: development of custom protocols. | During this workshop, we will present the latest developments carried out on the Biodimar core facility and the opportunities for developing custom bioprospecting protocols in order to valorize marine biomasses by biorefinery principle and towards various markets. | Claire Hellio and Marilyne Fauchon, Biodimar |
| CHEM-Symbiosis | Study of molecular standards for the identification of non-intentionally added substances (NIAS) | The development of new polymers currently presents an interesting alternative following the regulations on the use of Bisphenol A for materials in contact with foodstuffs. However, the interest in identifying the presence of non-intentionally added substances (NIAS) appears to be major in order to respond to the concerns of consumers and manufacturers. These NIAS, of unknown structures, can appear during the formation of polymers, during the coating process or even after long-term degradation. After LC/HRMS characterization of NIAS from polymers by our collaborators, the CHEM-Symbiose core facility attempted to respond to their request for the synthesis of analytical standards in order to validate the structural identification hypotheses and also be able to quantify them. | David Rupérez Cebolla, Arnaud Tessier and Matthieu Rivière, CHEM-Symbiose |
| Merimage and LBI2M | The mTOR signaling pathway regulates a translational network stimulating lysosome biogenesis in the early sea urchin embryo. | In metazoans, fertilization triggers a mechanism called the egg-embryo transition, a developmental process during which the molecular landscape of the egg is completely remodeled to create a totipotent cell capable of generating a new individual. In sea urchins, fertilization immediately triggers protein translation, which is essential for cell cycle resumption and embryonic development. Although activation of protein synthesis has been shown to be under the control of the mTOR pathway, little is known regarding the specific contributions of mTOR translation and signaling to the regulation of biological processes participating in protein synthesis. egg-embryo transition. Using lysosomotropic markers, we showed that fertilization induces the formation of a large number of acidic organelles. Our results reveal that these organelles correspond to lysosomes and that the translation of messenger RNAs as well as mTOR activity are essential for their formation and maintenance. Furthermore, our translatomics data indicate that many messenger RNAs encoding lysosomal components are actively recruited to polysomes in response to fertilization in an mTOR-dependent manner. Our findings thus reveal that mTOR activity could orchestrate a translational network controlling lysosome biogenesis. | Sonia Dufour, UMR 8227 “Laboratory of Integrative Biology of Marine Models” (LBI2M) |
| core facility | Title | Description | Speakers |
|---|---|---|---|
| KISSf and SeaBeLife Biotech | Kinases and human pathologies: focus on the inhibition of the RIPK1 target | The 1970s saw the emergence of the concept of programmed cell death with the description of apoptosis. We know today that this was only part of a complex puzzle including death by regulated necrosis which is significantly involved in various human pathologies including neurodegenerative disorders and liver and kidney failure linked to inflammation. In 2013, Roscoff's "KISSf" kinase inhibitor study core facility and IRSET in Rennes undertook a vast screening campaign which led to the filing of three international patents now exploited by the start-up SeaBeLife Biotech to prolong tissue life by chemically preventing its regulated death. During this workshop, the use of a phenotypic screening technique for the detection of inhibitors of a kinase of therapeutic interest will be presented. | Claire Delehouzé, SeaBeLife Biotech, and Stéphane Bach, KISSf |
| MRic | From a rare dynamic event to its ultrastructure: the possibilities of HPM live µ from CryoCapCell, | Newly arrived on the MRic-TEM core facility, the HPM live µ, CryoCapCell's high pressure freezer, allows the vitrification of thick samples for different imaging techniques in electron microscopy (TEM, Cryo-TEM, SEM, Cryo-SEM, CLEM…). Our HPM live µ is coupled to a Zeiss LSM 900 confocal fluorescence microscope, allowing rapid wide-field imaging with the possibility of deconvolution or more resolution in LSM+ confocal mode. This association makes it possible to follow a biological molecule, in a sample, using fluorescence. As soon as a rare event of interest is detected, the sample is quickly (1,30 sec) transferred to the high pressure freezer allowing the phenomenon to be captured with the aim of observing it on the ultrastructural scale. In this workshop, we will go through the possibilities available on this system, | Aurélien Dupont, MRic-TEM |
| ABiMS, GenOuest and SeBiMER | BYTE-SEA: the digital infrastructure serving the ATLASEA PEPR for sequencing the genomes of marine organisms. Contribution from the Breton core facilities of the Bioinformatics axis of Biogenouest. | In the field of marine science, exploring diversity represents a major challenge, as only about 10% of marine species are known and only around XNUMX high-quality genomes of marine organisms have been made available to the scientific community. . The ATLASEa (PEPR Exploratory) program aims to decipher and exploit the colossal mine of information from marine species on the French coast. Four thousand five hundred marine species, with high coverage of mainland species but also including species from overseas territories, will be sampled by the Targeted Project (PC1) DIVE-SEA. The samples will be entrusted to the SEQ-SEA Targeted Project (PC2) teams to produce genome assemblies associated with high-quality structural annotations. The targeted project (PC3) BYTE-SEA will aim to centralize all the genomics data produced by the ATLASEa project in a single portal and to integrate the genomes of related organisms sequenced by other consortia. It will ensure the interoperability and security of data, and facilitate their dissemination and use in accordance with the FAIR and Open Science principles. The developed environment will thus allow access to genome sequencing data from marine organisms. The data made available will include information on genomic sequence, genes, coding and non-coding regions. The portal will also offer tools for sequence searching, genome analysis, genome comparison and data visualization. It will make it possible to monitor the progress of the project and will provide a management tool for members of the consortium and monitoring for the community. | Anthony Bretaudeau, GenOuest; Erwan Corre and Gildas Le Corguillé, ABiMS and Patrick Durand, SeBiMER |
| OuestOÏD unifying project | Overview of expertise related to organoids in the Great West. | OuestOÏD is the first scientific network dedicated to organoids and 3D cellular models in the great West. Initiated a year ago by a unifying project Biogenouest, and supported by the Bretagne and Pays de la Loire regions, OuestOÏD brings together researchers and technological core facilities who use the organoid model to advance knowledge in different fields such as biology development, physio-pathology, the development and evaluation of new therapies, personalized medicine, or even regenerative medicine. Organoids indeed make it possible to reproduce certain physiological functions vitro. They are made up of stem cells which differentiate and organize themselves in 3 dimensions, thus promoting cellular interactions. The development of these models is currently booming. Federating skills around these models makes it possible to promote homogeneous, robust, responsible practices that meet quality requirements. This is the role of the OuestOÏD network, through connecting different scientific stakeholders, disseminating knowledge and expertise through meetings and seminars, and promoting training and collaboration between network stakeholders. During this workshop, we will first present to you the tools developed for the network, in particular the directory of expertise, available online for the entire scientific community. We will then explore the network: its actors, the models and types of organoids produced, the species represented, as well as the different services available on the network to produce or characterize organoids, and the applications of these models. We will end by putting the activities of the OuestOÏD network into perspective with local or national initiatives in areas related to organoids. | Bénédicte Martin, OuestOÏD network |