A l’occasion de la MorningTech Photonique & Santé organisée par Photonics Bretagne et Biotech Santé Bretagne le 2 février 2021 de 9h30 à 12h00, Marc Tramier, coordinateur du Nœud Bretagne-Loire de France BioImaging présentera “les technologies photoniques des plateformes de Biogenouest au service de l’imagerie pré-clinique“.

Programme et inscriptions: https://www.biotech-sante-bretagne.fr/agenda/morningtech-photonique-sante/

Registration for France BioImaging Annual Meeting is now open!

France BioImaging is pleased to invite you to participate to France BioImaging 6th Annual Meeting.  For this edition, the meeting will be organized as a two-half days virtual meeting (from 9:00 AM to 1:00 PM) on February 4th & 5th, 2021.

This event, open to all members of the bioimaging community, aims to provide a platform to discuss pivotal subject matters in our field.

The 2021 program of the France BioImaging Annual meeting is built around two pillars:

  • February 4th: “Building and operating an integrated and open infrastructure for bioimaging
  • February 5th: “Latest and future developments in biological imaging

Registration is free but mandatory in order to receive the Zoom link: https://univ-nantes-fr.zoom.us/meeting/register/tJAof-itqjgjHNCQOGpsw4_2ERWm__3zUU0R

Preliminary Program 

We look forward to your participation!

Imaging of proteins, cells, and tissues is critical to understanding health and disease. On December 2nd, 2020, the Chan Zuckerberg Initiative (CZI) announced nearly $32 million in funding to support biomedical imaging researchers, technology development, and the BioImaging North America international network of bioimaging facilities and communities. CZI also opened a new Request for Applications (RFA) aimed at supporting technology development that will allow researchers to see the inner workings of cells, including proteins, at near-atomic resolution to better understand what causes disease and how to develop treatments.

Frontiers of Imaging: Visual Proteomics 

The Frontiers of Imaging initiative, part of CZI’s broader Imaging program, supports the development of disruptive imaging technologies that connect biological scales across organs, cells, and proteins, allowing researchers to directly visualize biological processes at the necessary resolution and context to obtain a mechanistic understanding of health and disease. As part of the Frontiers initiative, the new Visual Proteomics Imaging RFA supports technology development that will allow researchers to see the inner workings of cells, including proteins, at near-atomic resolution. CZI invites scientists to apply for this 2 1/2-year grant opportunity to support the development of hardware, software, and methods. Examples of research themes could include hardware and software development to enhance contrast and resolution for electron tomography, high-resolution correlated light and electron microscopy (CLEM), and FIB-SEM; sample preparation improvements for electron tomography; and development of software or new computational techniques and algorithms for identifying protein molecules inside cells and segmenting sub-cellular structures.

The Visual Proteomics Imaging RFA accept applications until February 17, 2021 at 5 p.m. Pacific Time.

For more information and application instructions, please visit CZI’s online grants management portal.

For administrative and programmatic inquiries, technical assistance, or other questions pertaining to this RFA, please contact: sciencegrants@chanzuckerberg.com.

Learn more about CZI’s Frontiers of Imaging effort.

Congratulations to Emmanuel Beaurepaire (CNRS Research Director from the Laboratory for Optics and Biosciences CNRS-INSERM-Polytechnique), PI of the ERC Synergy Grant project “HOPE”, and to Laurent Groc (CNRS Research Director ; Interdisciplinary Institute for Neuroscience), coordinator of the ERC Synergy Grant projectENSEMBLE“, Laurent Cognet (CNRS Research Director ; Laboratoire photonique numérique et nanosciences) and U. Valentin Nägerl (Professor at University of Bordeaux ; CNRS Research Director ; Interdisciplinary Institute for Neuroscience), both PIs of the ERC Synergy Grant projectENSEMBLE“.

These grants, each worth around 10 million euro over six years, are designed to enable groups of 2 to 4 scientists to tackle some of the world’s most challenging research problems, spanning several scientific disciplines.

The ERC Synergy Grant scheme is part of the EU’s research and innovation programme, Horizon 2020.

ERC Synergy Grant project “HOPE”

Reverse engineering the assembly of the hippocampal scaffold with novel optical and transgenic strategies” 

  • Emmanuel Beaurepaire, Directeur de recherche CNRS au Laboratoire d’optique et biosciences – LOB (CNRS/École polytechnique/INSERM),
  • Rosa Cossart, Directrice de recherche CNRS (Unité INSERM, Aix-Marseille Univ.)
  • Jean Livet, chercheur INSERM à l’Institut de la vision (CNRS, INSERM, Sorbonne Univ.)

At the heart of our brain, a structure plays a key role in memory, and more particularly in the acquisition and maintenance of our memories: the hippocampus. Classically considered as a “cognitive GPS” for space and time, it is also the seat of our episodic memory.

Over the last decade, the neural circuits of the hippocampus have been better described, in particular by the team of Rosa Cossart, director of the Institut de neurobiologie de la méditerranée (Inmed), but the nature, origin and remodeling of these circuits during development and pathologies remain to be understood.

On the other hand, genetic engineering techniques for staining neurons, developed by Jean Livet, Inserm research director at the Institut de la vision, coupled with multi-photon microscopy developed by the team of Emmanuel Beaurepaire, CNRS research director at the Laboratoire d’optique et biosciences – LOB (illustration below / read the 2019 press release in French), have demonstrated their ability to accurately map the complex architecture of neuronal circuits and their evolution during development.

By combining these exceptional multidisciplinary advances, HOPE aims to answer three interdependent questions:

  • Is the architecture of the adult seahorse carried by specific circuits?
  • Are the circuits of the hippocampus pre-wired or shaped by experience?
  • How does this structure reorganize itself in pathological conditions?

HOPE aims to shed new light on the function of the hippocampus and the role of its neuronal circuits through the design of a new, non-invasive and universal method to monitor the growth and construction of brain circuits located deep in the brain, from their neurogenesis to adulthood, under normal and pathological conditions.

Developed by the LOB team, ChroMS is a new microscopy technique combining color, 3D and high resolution, introducing a real revolution in vertebrate brain imaging. © Lamiae ABDELADIM / LOB / Institut de la Vision / CNRS Photothèque

Taken from CNRS Press release: https://www.iledefrance-gif.cnrs.fr/fr/cnrsinfo/erc-synergy-grant-2020-3-projets-impliquant-le-cnrs-sur-le-territoire-paris-saclay

ERC Synergy Grant project “ENSEMBLE”

“Structure and functions of the brain extracellular space

  • Laurent Groc (Research Director CNRS ; Interdisciplinary Institute for Neuroscience), 
  • Erwan Bézard (Research Director INSERM; Institute of Neurodegenerative Disorders), 
  • Laurent Cognet (Research Director CNRS ; Laboratoire photonique numérique et nanosciences)
  • U. Valentin Nägerl (Professor at University of Bordeaux ; Research Director CNRS ; Interdisciplinary Institute for Neuroscience)

The ENSEMBLE project aims at underpinning the molecular mechanisms of physiological and pathological brain function. This ambitious and innovative endeavor is based on our ability to develop new approaches in high-resolution microscopy at the service of a new conceptual framework in brain cell communication.

Brain, high resolution iimage. Credit: U.V. Nägerl
Credit: U.V. Nägerl

This project has roots in the international leadership of the Bordeaux community in the fields of microscopy, nanophotonics, fundamental and translational neuroscience. The opportunity that is offered to these 4 investigators to break a frontier knowledge was permitted by the continuous support of local institutional actors. The installation of Prof. Valentin Nägerl’s laboratory in 2009 with a “Chaire Accueil” from the Regional Council of Aquitaine, the support of LabEx BRAIN, the Laphia Cluster and the IdEx of the University of Bordeaux provided the ground to build elementary blocks necessary for the challenging adventure of the ERC Synergy project (10 million euros, 6 years).

Taken from Bordeaux Neurocampus Press release: https://www.bordeaux-neurocampus.fr/en/erc-synergy-award-2020-for-groc-bezard-nagerl-and-cognet/

We are very pleased to announce that FBI Bretagne-Loire Node application to become a Euro BioImaging facility has been evaluated as highly recommended by the EuBI Scientific Advisory Board (SAB) and ratified by the EuBI Board on November 30th, 2020.

The Bretagne Loire Node became a node of the national infrastructure France BioImaging in November 2019 and applied to become a EuBI facility during the last EuBI Call for Nodes (June 2020).

The Bretagne Loire Node brings together four cellular imaging and histology facilities, two in Rennes (MRic and H2P2) and two in Nantes (MicroPIcell and APEX). These facilities have complementary expertise for live imaging and pathological anatomy. The added value of the Bretagne Loire Node is to be able to offer a continuum between biological imaging and medical imaging, through the development of a new line of services as well as methodological and technological transfer to users of microscopy technologies for preclinical studies.

These facilities will now be open to Euro-BioImaging users as part of the French BioImaging Node of Euro-BioImaging.

As part of the Euro-BioImaging research infrastructure, the services provided by these facilities will be open to all scientists, regardless of their discipline or affiliation.

Euro BioImaging press release

The PICsL-FBI microscopy core facility is located on two sites: Centre d’Immunologie de Marseille Luminy (CIML) and Institut de Biologie du Développement de Marseille (IBDM).The PICsL-FBI facility of the CIML called ImagImm (Imaging Immunity) via its microscopy resources – from the molecule to whole organisms – is dedicated to help its users deciphering cellular mechanisms in the fields of immunology.

Major research implications of the ImagImm facility:

  • Technology transfer: spot variation Fluorescence Correlation Spectroscopy (svFCS)

In collaboration with Tomasz Trombik (Faculty of Biotechnology, University of Wroclaw – Wroclaw, Poland), Sophie Brustlein (Institut de Convergences Centuri, AMU,CNRS – Marseille, France) and Nicolas Bertaux (Institut Fresnel, AMU, Centrale Marseille, CNRS – Marseille, France), Sébastien Mailfert and Didier Marguet published the procedure for implementing spot variation Fluorescence Correlation Spectroscopy (svFCS) measurements using a classical fluorescence microscope that has been customized1. This publication is following the technology transfer made in 2018: the svFCS developed by Didier Marguet’s lab was duplicated by Sébastien Mailfert and Sophie Brustlein and built from scratch in 7 days on site, in Poland.

Dynamic biological processes in living cells, including those associated with plasma membrane organization, occur on various spatial and temporal scales, ranging from nanometers to micrometers and microseconds to minutes, respectively. Such a broad range of biological processes challenges conventional microscopy approaches. The published protocol includes a specific performance check of the svFCS setup and the guidelines for molecular diffusion measurements by svFCS on the plasma membrane of living cells under physiological conditions. Additionally, a procedure for disrupting plasma membrane raft nanodomains by cholesterol oxidase treatment is provided and how these changes in the lateral organization of the plasma membrane might be revealed by svFCS analysis. This fluorescence-based method can provide unprecedented details on the lateral organization of the plasma membrane with the appropriate spatial and temporal resolution.

Figure 1: Schematic view of excitation and emission optical paths of the svFCS setup and pictures of the setup. The svFCS setup contains four modules: (1) the output of a fibered 488 nm laser is collimated, (2) a combination of a half-wave plate and polarizing beamsplitter sets the optical power, (3) the laser beam focused on the sample after traveling through a tube-lens free motorized microscope, and (4) the fluorescence is detected through a confocal-like detection path onto an avalanche photodiode coupled to a single photon counting module, which delivers a signal to a hardware correlator. Simplicity gives the system its sensitivity, robustness, and ease of use.
  • SAPHIR : a Shiny application to analyze tissue section images

In collaboration with Hugues Lelouard (CIML, Inserm, CNRS, AMU) and Elodie Germani, Mathieu Fallet published a powerful method for both basic and medical research to study cell populations in tissues using immunofluorescence. Image acquisitions performed by confocal microscopy notably allow excellent lateral resolution and more than 10 parameter measurement when using spectral or multiplexed imaging. Analysis of such complex images can be very challenging and easily lead to bias and misinterpretation. They developed the Shiny Analytical Plot of Histological Images Results (SAPHIR), an R shiny application for histo-cytometry using scatterplot representation of data extracted by segmentation. It offers many features, such as filtering of spurious data points, selection of cell subsets on scatterplot, visualization of scatterplot selections back into the image, statistics of selected data and data annotation. This application allows to quickly characterize labeled cells, from their phenotype to their number and location in the tissue, as well as their interaction with other cells.

Figure 2: Flow chart of tissue image analysis from image acquisition and segmentation (left side) to extract data analysis with SAPHIR (right side)
  • Wound healing in C. elegans

In collaboration with Nathalie Pujol and Jonathan Ewbank (CIML, Inserm, CNRS, AMU), Mathieu Fallet and Sébastien Mailfert participated in the project on the immune response by showing that wounding provokes a reorganization of plasma membrane subdomains3.  The skin protects animals from infection and physical damage. In Caenorhabditis elegans, wounding the epidermis triggers an immune reaction and a repair response, but it is not clear how these are coordinated. Previous work implicated the microtubule cytoskeleton in the maintenance of epidermal integrity (Chuang et al., 2016). Taffoni et al. show the reorganization of the plasma membrane subdomains by a simple wounding system. This is followed by recruitment of the microtubule plus end-binding protein EB1/EBP-2 around the wound and actin ring formation, dependent on ARP2/3 branched actin polymerization. They show that microtubule dynamics are required for the recruitment and closure of the actin ring, and for the trafficking of the key signaling protein SLC6/SNF-12 toward the injury site. Without SNF-12 recruitment, there is an abrogation of the immune response. These results suggest that microtubule dynamics coordinate the cytoskeletal changes required for wound repair and the concomitant activation of innate immunity.

Figure 3: Time line of events

References:

  1. Mailfert, S., Wojtowicz, K., Brustlein, S., Blaszczak, E., Bertaux, N., Łukaszewicz, M., Marguet, D., Trombik, T. Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells, JoVE, 165, 1-19 (2020).
  2. Germani, E., Lelouard, H., Fallet, M. SAPHIR: a Shiny application to analyze tissue section images, F1000Research, Faculty of 1000, 9, 1276-1285 (2020).
  3. Taffoni, C., Omi, S., Huber, C., Mailfert, S., Fallet, M., Rupprecht, J-F,. Ewbank, J., Pujol., N. Microtubule plus-end dynamics link wound repair to the innate immune response, eLIFE, 9, e45047 (2020)

Congratulations to Patrick LEMAIRE, CNRS Research Director from the
Centre de recherche en biologie cellulaire de Montpellier (CRBM) – CNRS / Université de Montpellier, member of France BioImaging Montpellier Node, who has been awarded the Mottart prize.

With his team members, Patrick Lemaire is studying the embryonic development of a small marine invertebrate, the sea squirt Phallusia mammillata, chosen for the simplicity and transparency of its embryos. His latest work has combined microscopy, image analysis and mathematical modeling approaches to describe, cell by cell, the embryogenesis of this animal and to analyze the role of communication between cells.

To learn more about the study: https://france-bioimaging.org/announcement/news-from-nodes/montpellier-node-participated-on-a-study-of-the-dynamics-of-cell-movement-during-embryonic-development/

COMULIS is an EU-funded COST Action that aims at fueling urgently needed collaborations in the field of correlated multimodal imaging (CMI), promoting and disseminating its benefits through showcase pipelines, and paving the way for its technological advancement and implementation as a versatile tool in biological and preclinical research. CMI combines two or more modalities to gather holistic information about the same specimen. It creates a composite view of the sample with multidimensional information about its macro, meso- and microscopic structure, dynamics, function and chemical composition. Since no single technique can reveal all these details, CMI is the only way to understand biomedical processes mechanistically.

In order to encourage correlated multi-modal imaging projects, COMULIS Short Term Scientific Missions (STSMs) provides travel grants to individuals wishing to explore new imaging techniques. The grants are presented in the form of a lump sum of up to 3,500 Euros (depending on the duration of the mission), to cover travel and subsistence. COMULIS COST accepts applications on a continuous basis from Early Career Investigators and Experienced Imaging Scientists who would like to travel internationally to collaborate with a Host facility on a Correlated Multi-modal imaging project. There is a rapid review process and around 10 grants are awarded every year.

In addition, COMULIS STSM can provide funding for core facility staff to learn a new imaging  technique or work with new software tools to bring the expertise back to their own facility.

Applications can be submitted any time & will be reviewed at the end of each month.

More info and application procedure: https://www.comulis.eu/stsm-open-call

The image depicts a spheroid of human stem cells (green) and its actin cytoskeleton (purple), produced by Philippe Cohen during its PhD at Treefrog. This nice picture serves as an illustration for an article covering the use of stem cells for regenerative medicine.
Acquisition was made by Philippe Cohen on a scanning confocal microscope and 3D rendering was done by Jérémie Teillon using Agave software.
Agave is a free 3D visualization software, using light path-trace light rendering.
 

The Bordeaux Imaging Center team offers training and support on 3D commercial softwares such as Imaris and Arivis as well as other freeware such as Agave. Don’t hesitate to contact them (bic@u-bordeaux.fr) if you are interested  in 3D rendering and visualization of your microscopy data!

Agave software:
https://www.allencell.org/software-and-code.html
https://www.allencell.org/pathtrace-rendering.html
Article (in French):
https://www.science-et-vie.com/corps-et-sante/regenerer-le-cerveau-des-cellules-souches-retablissent-les-liaisons-neuronales-p-58266#dossier-58457

During embryonic development, cells take on increasingly precise roles in the body as they divide. Be they skin cells, muscle cells or neurons, the different cell types that make up the embryo emerge gradually from a very fine orchestration of their positions and identities, coordinated by the signals they exchange with each other. Like us, the cells need to “talk” to each other to make decisions.

Screaming or whispering: the embryonic cell dilemma

In vertebrate embryos, cells have a very dynamic behaviour. They move around, exchange their neighbours or migrate over long distances. The signals they exchange therefore need to have a long range, which could be characterized as “shouting”. The study of the embryonic development of a sea squirt, a small marine animal with optically transparent embryos, has enabled scientists from several teams at CNRS and INRIA in France, in collaboration with a team from the European Molecular Biology Laboratory (EMBL, Germany), to capture and describe in detail a more discreet mode of cell communication.

The scientists recorded the development of live embryos every two minutes with a new-generation « light-sheet » microscope. They then created software to automatically detect each cell and analyze its position, shape and neighbours up to an advanced stage of development. This work revealed an unusually reproducible mode of development, in which the same cell can be found in the same position across all embryos and where cells move very little in relation to each other. The authors of the study then annotated the films thus made with information on the cell type and the molecular signals emitted by each cell. Using mathematical modelling to integrate the quantitative description of the embryonic geometry with these annotations, their work suggest that cells communicate with very short-range signals. Moreover, the interpretation of these signals is modulated by the area of the contacts between cells. Unlike vertebrates, the cells of ascidian embryos thus have a static and fixed behaviour and the range of their “whispered” signals is very small.

Top: embryonic development of an ascidian from egg to tadpole. The part framed in white is the part of embryogenesis that we have imaged and then segmented (below, segmented cells coloured according to their cell fate). The lower part of the figure illustrates that the light green cells “whisper” instructions to their immediate neighbours by short-range signals.

This study indicates that the dynamics of cell movement varies greatly between animals and that these different modalities could be strongly related to the range of signals that the cells exchange with each other. By extending the repertoire of cellular communication mechanisms, this work opens new perspectives on the understanding of self-organization strategies of living forms.

Article: L. Guignard*, U.-M. Fiuza*, B. Leggio, J. Laussu, E. Faure, G. Michelin, K. Biasuz, L. Hufnagel, G. Malandain, C. Godin#, P. Lemaire# (2020) Contact-area dependent cell communications and the morphological invariance of ascidian embryogenesis (Science, July 10 2020 issue, https://science.sciencemag.org/content/369/6500/eaar5663)

2 recent publications using the laser irradiation and photoablation systems available on the MRic facility from the Bretagne-Loire Node are presented here:

  • Esmangart de Bournonville and Le Borgne (IGDR) characterized the assembly and interactions of tricellular junction components in Drosophila epithelial cytokinesis using laser ablation on a SP5 confocal. Their article entitled “Interplay between Anakonda, Gliotactin, and M6 for Tricellular Junction Assembly and Anchoring of Septate Junctions in Drosophila Epithelium” was published last august in Current Biology (https://doi.org/10.1016/j.cub.2020.07.090).
  • Rebecca Smith, post-doc in Sébastien Huet’s team (IGDR) in collaboration with Szilvia Juhász from Gyula Timinszky’s team (Szeged, Hungary) used laser irradiation to study chromatin remodeling following DNA damage. Their paper entitled “The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment” has just been accepted in Science Advances.

During this year 2020, the MicroPICell facility from the Bretagne Loire Node acquired several imaging systems, some of which offer access to new technologies on the Nantes health research site:

  • a complete Zeiss Lighsheet 7 light sheet microscope associated to an X-Clarity clearing system and an Arivis Vision 4D Offline station,
  • a motorized Nanolive holotomographic microscope,
  • a high-end Nikon confocal microscope (resonant, spectral, FLIM, large field of view),
  • an Akoya CODEX system of multiplex fluorescent tissue labeling.
Holography offers a unique means to measure cells in their native environment: label-free, non-invasive, manipulation-free, and interference-free.

Moreover, the MicroPICell facility, in collaboration with the training organization of the CNRS, is organizing in March 2021 a training on histology: from sample preparation to markers validation by image analysis. This training (lectures, workshops) will take place over 4 days between 03/22/2021 and 04/24/2021.

Link: https://cnrsformation.cnrs.fr/stage-21290-Histologie–de-la-preparation-dechantillons-a-la-validation-des-marquages-par-analyse-dimage.html?stage=21290&axe=138