Tomographic Collection of Block-Based Sparse STEM Images: Practical Implementation and Impact on

The reduction of the electron dose in electron tomography of biological samples is of high significance to diminish radiation damages. Simulations have shown that sparse data collection can perform efficient electron dose reduction. Frameworks based on compressive-sensing or inpainting algorithms have been proposed to accurately reconstruct missing information in sparse data. The present work proposes a practical implementation to perform tomographic collection of block-based sparse images in scanning transmission electron microscopy. The method has been applied on sections of chemically-fixed and resin-embedded Trypanosoma brucei cells. There are 3D reconstructions obtained from various amounts of downsampling, which are compared and eventually the limits of electron dose reduction using this method are explored.

Alexandre Houy

DIVA

THE FIRST
HUMAN-IN-THE-LOOP
ANALYSIS PLATFORM

Via machine-aided interaction, results are extracted and decision are made at ease

A platform for 3D image visualization and handling in virtual reality environment

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For more information:  https://diva.pasteur.fr/  

 

Characterization of Pax3 and Sox10 transgenic Xenopus laevis embryos as tools to study neural crest

The neural crest is a multipotent population of cells that originates a variety of cell types. Many animal models are used to study neural crest induction, migration and differentiation, with amphibians and birds being the most widely used systems. A major technological advance to study neural crest development in mouse, chick and zebrafish has been the generation of transgenic animals in which neural crest specific enhancers/promoters drive the expression of either fluorescent proteins for use as lineage tracers, or modified genes for use in functional studies. Unfortunately, no such transgenic animals currently exist for the amphibians Xenopus laevis and tropicalis, key model systems for studying neural crest development. Here we describe the generation and characterization of two transgenic Xenopus laevis lines, Pax3-GFP and Sox10-GFP, in which GFP is expressed in the pre-migratory and migratory neural crest, respectively. We show that Pax3-GFP could be a powerful tool to study neural crest induction, whereas Sox10-GFP could be used in the study of neural crest migration in living embryos.

Avian models and the study of invariant asymmetry: how the chicken and the egg taught us to tell

While the external vertebrate body plan appears bilaterally symmetrical with respect to anterior-posterior and dorsal-ventral axes, the internal organs are arranged with a striking and invariant left-right asymmetry. This laterality is important for normal body function, as alterations manifest as numerous human birth defect syndromes. The left-right axis is set up very early during embryogenesis by an initial and still poorly understood break in bilateral symmetry, followed by a cascade of molecular events that was discovered 20 years ago in the chick embryo model. This gene regulatory network leads to activation of the pitx2 gene on the left side of the embryo which ultimately establishes asymmetric organogenesis of the heart, gut, brain, and other organs. In this review, we highlight the crucial contributions of the avian model to the discovery of the differential transcriptional cascades operating on the Left and Right sides, as well as to the physiological events operating upstream of asymmetric gene expression. The chick was not only instrumental in the discovery of mechanisms behind left-right patterning, but stands poised to facilitate inroads into the most fundamental aspects that link asymmetry to the rest of evolutionary developmental biology.

An atlas of Wnt activity during embryogenesis in Xenopus tropicalis.

Wnt proteins form a family of highly conserved secreted molecules that are critical mediators of cell-cell signaling during embryogenesis. Partial data on Wnt activity in different tissues and at different stages have been reported in frog embryos. Our objective here is to provide a coherent and detailed description of Wnt activity throughout embryo development. Using a transgenic Xenopus tropicalis line carrying a Wnt-responsive reporter sequence, we depict the spatial and temporal dynamics of canonical Wnt activity during embryogenesis. We provide a comprehensive series of in situ hybridization in whole-mount embryos and in cross-sections, from gastrula to tadpole stages, with special focus on neural tube, retina and neural crest cell development. This collection of patterns will thus constitute a valuable resource for developmental biologists to picture the dynamics of Wnt activity during development.

The neural border: Induction, specification and maturation of the territory that generates neural

The neural crest is induced at the edge between the neural plate and the nonneural ectoderm, in an area called the neural (plate) border, during gastrulation and neurulation. In recent years, many studies have explored how this domain is patterned, and how the neural crest is induced within this territory, that also participates to the prospective dorsal neural tube, the dorsalmost nonneural ectoderm, as well as placode derivatives in the anterior area. This review highlights the tissue interactions, the cell-cell signaling and the molecular mechanisms involved in this dynamic spatiotemporal patterning, resulting in the induction of the premigratory neural crest. Collectively, these studies allow building a complex neural border and early neural crest gene regulatory network, mostly composed by transcriptional regulations but also, more recently, including novel signaling interactions.

AKT signaling displays multifaceted functions in neural crest development.

AKT signaling is an essential intracellular pathway controlling cell homeostasis, cell proliferation and survival, as well as cell migration and differentiation in adults. Alterations impacting the AKT pathway are involved in many pathological conditions in human disease. Similarly, during development, multiple transmembrane molecules, such as FGF receptors, PDGF receptors or integrins, activate AKT to control embryonic cell proliferation, migration, differentiation, and also cell fate decisions. While many studies in mouse embryos have clearly implicated AKT signaling in the differentiation of several neural crest derivatives, information on AKT functions during the earliest steps of neural crest development had remained relatively scarce until recently. However, recent studies on known and novel regulators of AKT signaling demonstrate that this pathway plays critical roles throughout the development of neural crest progenitors. Non-mammalian models such as fish and frog embryos have been instrumental to our understanding of AKT functions in neural crest development, both in neural crest progenitors and in the neighboring tissues. This review combines current knowledge acquired from all these different vertebrate animal models to describe the various roles of AKT signaling related to neural crest development in vivo. We first describe the importance of AKT signaling in patterning the tissues involved in neural crest induction, namely the dorsal mesoderm and the ectoderm. We then focus on AKT signaling functions in neural crest migration and differentiation.

Réseau Européen ITN NEUCREST

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European NEUCREST ITN Network

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Nos vidéos

Vidéo 1: Oscillations spontanées de deux touffes ciliaires de l’oreille interne (saccule) de la grenouille taureau. Les touffes ciliaires sont vues de dessus à travers l’objectif d’un microscope optique. Le film est en temps réel.

Vidéo 2: La rigidité et la friction apparentes d’une touffe ciliaire sont modifiées par l’activation des canaux ioniques responsables de la transduction mécanoélectrique. Une force est appliquée à la touffe ciliaire en appliquant un mouvement à une fibre de verre flexible qui lui est accrochée. Un mouvement d’aller-retour triangulaire résulte en une relation force-position hystérétique qui traduit la dissipation d’énergie par la touffe ciliaire. Il y a un intervalle de positions près de l’origine où la pente de la relation force-position est plus faible et la hauteur du cycle d’hystérèse plus importante, ce qui correspond respectivement à une plus faible rigidité et à une plus haute friction de la touffe ciliaire. En réponse à une drogue (la gentamicine) qui bloque les canaux ioniques, les deux branches les plus longues du cycle deviennent linéaire et le cycle s’affine. Ces observations indiquent en retour que l’activation de ces canaux ioniques réduit la raideur apparente et augmente la friction apparente de la touffe ciliaire. Ces effets sont interprétés comme la conséquence du mécanisme de mécanosensibilité de la touffe ciliaire, qui résulte de l’activation mécanique directe de canaux ioniques par des liens élastiques dont la tension est modulée par le stimulus.

Our videos

Video 1: Spontaneaous hair-bundle oscillations. Two hair bundles from the inner ear (saccule) of the bullfrog are imaged from the top under the objective of an optical microscope. The movie is in real time.

Video 2: Hair-bundle compliance and friction from gating of mechanoelectrical transduction channels in the hair bundle. Force is applied to a hair bundle by moving the base of an attached flexible fiber. A back-and-forth triangular motion of the fiber results in a force-position relation that displays hysteresis as the result of energy dissipation. There is a range of positions where the slope of the relation is lower and the height of the cycle is larger, corresponding to lower  stiffness and higher friction of the hair bundle, respectively. Upon application of a channel blocker (the aminoglycoside gentamicin), the two long branches of the cycle become linear and the hysteretic cycle shrinks. These observations suggest in return that gating of the channels reduces the stiffness and increases the friction of the hair bundle. This effect is  interpreted as an inherent consequence of hair-bundle mechanosensitivity from direct mechanical activation of ion channels by force. See Bormuth et al (2014) PNAS 111:7185.

Controlling confinement and topology to study collective cell behaviors

Confinement and substrate topology strongly affect the behavior of cell populations and, in particular, their collective migration. In vitro experiments dealing with these aspects require strategies of surface patterning that remain effective over long times (typically several days) and ways to control the surface topology in three dimensions. Here, we describe protocols addressing these two aspects. High-resolution patterning of a robust cell-repellent coating is achieved by etching the coating through a photoresist mask patterned directly on the coated surface. Out-of-plane curvature can be controlled using glass wires or corrugated « wavy » surfaces.

Collective stresses drive competition between monolayers of normal and Ras-transformed cells

We study the competition for space between two cell lines that differ only in the expression of the Ras oncogene. The two cell populations are initially separated and set to migrate antagonistically towards an in-between stripe of free substrate. After contact, their interface moves towards the population of normal cells. We interpret the velocity and traction force data taken before and after contact thanks to a hydrodynamic description of collectively migrating cohesive cell sheets. The kinematics of cells, before and after contact, allows us to estimate the relative material parameters for both cell lines. As predicted by the model, the transformed cell population with larger collective stresses pushes the wild type cell population.

Nastassia Pricoupenko

Mathilde Lacroix

Thomas Vourc’h

Yasmina Fedala

05/2019-Actuellement :

Ingénieur de recherche :  Etude des propriétés du noyau par des outils d’imagerie et d’analyse d’images avancées.

 

 

2014-04/2019   

Postdoc : Développement et installation  d’un microscope  interférométrique pour l’étude des vésicules

 

  • (Institut Langevin « Ondes et Images », ESPCI CNRS (UMR7587) – INSERM (U979))
  • (I2BC , Institut de biologie intégrative de la cellule UMR9198 CNRS université Paris Sud)
  • (Micalis, Institut National de Recherche Agroalimentaire   UMR1319)
  • (Ecole Normale Supérieure, Département de biologie Ibens, CNRS UMR 8197-INSERM U 1024, Institut Langevin « Ondes et Images »,ESPCI CNRS (UMR7587) – INSERM (U979))

 

12/2011-11/2012

Postdoc : Detection de default surfacique par thermographie infrarouge

  • Laboratoire De Physique Et D’Etude Des Materiaux LPEM, ESPCI, Ecole Supérieure de Physique et Chimie Industrielle)                         

11/2010-12/2011

Postdoc : Etude de surface par Imagerie microscopique

 

  • Laboratoire de Physique de l’état condensé LPEC  MR 6087, CNRS)

03/2009-03/2010

Postdoc : Etude de surface par Imagerie microscopique, Microscopie à reflectance, Ellipsométrie, Electrochimie.

2005-2008       

Thèse de doctorat : Etude et conception d’une cavité Fabry Pérot à 4 miroirs de haute finesse

  • Laboratoire de l’accélérateur Linéaire (LAL)

Publications

 

  1. Eric Dugat-Bony, Julien Lossouarn, Marianne DePaepe, Anne-Sophie Sarthou, Yasmina Fedala, Marie-Agnès Petit, Stéphane Chaillou ; “ Viral metagenomic analysis of the cheese surface: a comparative study of rapid procedures for extracting virus-like particles”, doi: https://doi.org/10.1101/503599
  2. céline Roose-Amsaleg; Yasmina Fedala; Catherine Vénien-Bryan; Josette Garnier; Albert-Claude Boccara; Martine Boccara. « Utilization of interferometric light microscopy for the rapid analysis of virus abundance in river. » Elsevier Editorial System(tm) for Research in Microbiology, https://doi.org/10.1016/j.resmic.2017.02.004
  3. Boccara, Martine*, et Fedala, Yasmina*, et al. « Counting and differentiating aquatic biotic nanoparticles by full-field interferometry: from laboratory tests to Tara Oceans sample analysis. » Opt. Express 7, 3736-3746 (2016
  4. Fedala, Yasmina, et al. « Calibration procedures for quantitative multiple wavelengths reflectance microscopy. » Review of Scientific Instruments 87.1 (2016): 013702.
  5. Fedala, M. Streza, J.-P. Roger, G. Tessier, C. Boue. (2014). Open crack depth sizing by laser stimulated infrared lock-in thermography. J. Phys. D:Appl. Phys.47 (2014) 465501.
  6. Fedala, M. Streza, J.-P. Roger, G. Tessier, C. Boue. (2014). Infrared lock-in thermography crack localization on metallic surfaces for industrial diagnosis. Journal Of Nondestructive Evaluation , 33, no. 3 (2014): 335-341.
  7. Brisson, R. Cizeron and R. Chiche , E. Cormier , Y. Fedala , R. Flaminio , D. Jehanno , M. Lacroix , C. Michel , N. Pavloff , L. Pinard , V. Soskov , A. Variola , Y. Zaouter , F. Zomer. (2009). High finesse Fabry–Perot cavities in picosecond regime. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment , 608, S75 – S77.
  8. Sorin Munteanu, Jean Paul Roger, Yasmina Fedala, Fabien Amiot, Catherine Combellas, Gilles Tessierb and Frédéric Kanoufi . (2013). Mapping fluxes of radicals from the combination of electrochemical activation and optical microscopy. Faraday Discuss , 164, 241-258.
  9. Sorin Munteanu , Sarra Gam-Derouich , Cécile Flammier , Yasmina Fedala , Catherine Combellas , Fabien Amiot , and Frédéric Kanoufi . (2012). Scanning Electrochemical Microscopy Monitoring in Microcantilever Platforms. Chem , 84 (17), pp 7449–7455.
  10. Sawsan Mohamad, Olivier Noël, Jean-Luc Buraud, Guillaume Brotons, Yasmina Fedala, and Dominique Ausserré. (2012). Mechanism of Lipid Nanodrop Spreading in a Case of Asymmetric Wetting. Rev. Lett. , 109, 248108.
  11. Garraud, Y. Fedala, F. Kanoufi, G. Tessier, J. P. Roger, and F. Amiot. (2011). Multiple wavelength reflectance microscopy to study the multiphysical behavior of microelectromechanical systems. Optics Letters , 36 (4), 594-596.
  12. MUNTEANU Sorin, ROGER Jean Paul, FEDALA Yasmina, et al. (2013). Mapping fluxes of radical from combination electrochimical activation and optical microscopy. Faraday Discuss , 164, 241.
  13. Streza, Y. Fedala, J.-P. Roger, G. Tessier, C. Boue . (2013). Heat transfer modeling for surface crack depth evaluation. Meas. Sci. Technol , 24, 045602 .
  14. Streza , D. Dadarlat , Y. Fedala, et S. LONGUEMART. (2013). Depth estimation of surface cracks on metallic components by means of lock-in thermography. Rev Sci Instrum , 84(7):074902.
  15. Fabien Amiot, Yasmina Fedala, Cécile Flammier, Nicolas Garraud, Frédéric Kanoufi, Jean Paul Roger, Gilles Tessier. (2012). Surface Mechanics and Full-field Measurements for Micromechanical Sensors. IUTAM Symposium on Full-field Measurements and Identification in Solid Mechanics (pp. 7–14). Procedia IUTAM.
  16. Fabian Zomer, Yasmina Fedala, Nicolas Pavloff, Viktor Soskov, and Alessandro Variola. (2009). Polarization induced instabilities in external four-mirror Fabry–Perot cavities. Applied Optics , 48 (35), 6651-6661.

 

  1. Variola and J.P. Brasile and C. Bruni and R. Chehab and R. Chiche and R. Cizeron and F.
    1. Couchot and Y. Fedala and J. Haissinski and M. Jacquet and D. Jehanno and M. Lacroix and P. Lepercq and B. Mouton and R. Roux and V. Soskov and A. Vivoli and F. Zom. (2009). The LALCompton program. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment , 608, S83 – S86.
  2. Bruni, C., Fedala, Y., Haissinski, J., Lacroix, M., Mouton, B., Roux,R., Variola, A., Wormser, G., Zomer, F., Brunelle, P., Couprie, M.E., Denard, J. C., Guillotin, N., Lebasque, P., Loulergue, A., Marchand, P., Marteau, F., Nagaoka, R., Bressi, E., & Gladkikh, P. »The ThomX X-Ray Source and its possible extension to 1-10 MeV for ELI Nuclear Physics Applications ». AIP Conference Proceedings, 1228: 68-70. (2010).
  3. SuperB Collaboration; SuperB: A High-Luminosity Asymmetric e+e- Super Flavour Factory. Conceptual Design Report; arXiv:0709.0451v2

Active cargo positioning in antiparallel transport networks.

Cytoskeletal filaments assemble into dense parallel, antiparallel, or disordered networks, providing a complex environment for active cargo transport and positioning by molecular motors. The interplay between the network architecture and intrinsic motor properties clearly affects transport properties but remains poorly understood. Here, by using surface micropatterns of actin polymerization, we investigate stochastic transport properties of colloidal beads in antiparallel networks of overlapping actin filaments. We found that 200-nm beads coated with myosin Va motors displayed directed movements toward positions where the net polarity of the actin network vanished, accumulating there. The bead distribution was dictated by the spatial profiles of local bead velocity and diffusion coefficient, indicating that a diffusion-drift process was at work. Remarkably, beads coated with heavy-mero-myosin II motors showed a similar behavior. However, although velocity gradients were steeper with myosin II, the much larger bead diffusion observed with this motor resulted in less precise positioning. Our observations are well described by a 3-state model, in which active beads locally sense the net polarity of the network by frequently detaching from and reattaching to the filaments. A stochastic sequence of processive runs and diffusive searches results in a biased random walk. The precision of bead positioning is set by the gradient of net actin polarity in the network and by the run length of the cargo in an attached state. Our results unveiled physical rules for cargo transport and positioning in networks of mixed polarity.

Stiffness and tension gradients of the hair cell’s tip-link complex in the mammalian cochlea.

Sound analysis by the cochlea relies on frequency tuning of mechanosensory hair cells along a tonotopic axis. To clarify the underlying biophysical mechanism, we have investigated the micromechanical properties of the hair cell’s mechanoreceptive hair bundle within the apical half of the rat cochlea. We studied both inner and outer hair cells, which send nervous signals to the brain and amplify cochlear vibrations, respectively. We find that tonotopy is associated with gradients of stiffness and resting mechanical tension, with steeper gradients for outer hair cells, emphasizing the division of labor between the two hair-cell types. We demonstrate that tension in the tip links that convey force to the mechano-electrical transduction channels increases at reduced Ca. Finally, we reveal gradients in stiffness and tension at the level of a single tip link. We conclude that mechanical gradients of the tip-link complex may help specify the characteristic frequency of the hair cell.