Publications

2017

• An Overview of data science uses in bioimage informatics
  
  • Chessel Anatole
  Methods, Elsevier, 2017, 115, pp.110 - 118. (10.1016/j.ymeth.2016.12.014)
  DOI : 10.1016/j.ymeth.2016.12.014
• A novel microstructural interpretation for the biomechanics of mouse skin derived from multiscale characterization
  
  • Lynch Barbara
  • Bancelin Stéphane
  • Bonod-Bidaud Christelle
  • Gueusquin Jean-Baptiste
  • Ruggiero Florence
  • Schanne-Klein Marie-Claire
  • Allain Jean-Marc
  Acta Biomaterialia, Elsevier, 2017, 50, pp.302-311. Skin is a complex, multi-layered organ, with important functions in the protection of the body. The der-mis provides structural support to the epidermal barrier, and thus has attracted a large number of mechanical studies. As the dermis is made of a mixture of stiff fibres embedded in a soft non-fibrillar matrix, it is classically considered that its mechanical response is based on an initial alignment of the fibres, followed by the stretching of the aligned fibres. Using a recently developed setup combining mul-tiphoton microscopy with mechanical assay, we imaged the fibres network evolution during dermis stretching. These observations, combined with a wide set of mechanical tests, allowed us to challenge the classical microstructural interpretation of the mechanical properties of the dermis: we observed a continuous alignment of the collagen fibres along the stretching. All our results can be explained if each fibre contributes by a given stress to the global response. This plastic response is likely due to inner sliding inside each fibre. The non-linear mechanical response is due to structural effects of the fibres network in interaction with the surrounding non-linear matrix. This multiscale interpretation explains our results on genetically-modified mice with a simple alteration of the dermis microstructure. Statement of Significance: Soft tissues, as skin, tendon or aorta, are made of extra-cellular matrix, with very few cells embedded inside. The matrix is a mixture of water and biomolecules, which include the collagen fibre network. The role of the collagen is fundamental since the network is supposed to control the tissue mechanical properties and remodeling: the cells attach to the collagen fibres and feel the network deformations. This paper challenges the classical link between fibres organization and mechanical properties. To do so, it uses multiscale observations combined to a large set of mechanical loading. It thus appears that the behaviour at low stretches is mostly controlled by the network structural response, while, at large stretches, the fibre inner-sliding dominate. (10.1016/j.actbio.2016.12.051)
  DOI : 10.1016/j.actbio.2016.12.051
• Life-Long Neurogenic Activity of Individual Neural Stem Cells and Continuous Growth Establish an Outside-In Architecture in the Teleost Pallium
  
  • Furlan Giacomo
  • Cuccioli Valentina
  • Vuillemin Nelly
  • Dirian Lara
  • Muntasell Anna Janue
  • Coolen Marion
  • Dray Nicolas
  • Bedu Sébastien
  • Houart Corinne
  • Beaurepaire Emmanuel
  • Foucher Isabelle
  • Bally-Cuif Laure
  Current Biology, Elsevier, 2017, 27 (21), pp.3288-3301.e3. Spatiotemporal variations of neurogenesis are thought to account for the evolution of brain shape. In the dorsal telencephalon (pallium) of vertebrates, it remains unresolved which ancestral neurogenesis mode prefigures the highly divergent cytoarchitectures that are seen in extant species. To gain insight into this question, we developed genetic tools to generate here the first 4-dimensional (3D + birthdating time) map of pallium construction in the adult teleost zebrafish. Using a Tet-On-based genetic birthdating strategy, we identify a “sequential stacking” construction mode where neurons derived from the zebrafish pallial germinal zone arrange in outside-in, age-related layers from a central core generated during embryogenesis. We obtained no evidence for overt radial or tangential neuronal migrations. Cre-lox-mediated tracing, which included following Brainbow clones, further demonstrates that this process is sustained by the persistent neurogenic activity of individual pallial neural stem cells (NSCs) from embryo to adult. Together, these data demonstrate that the spatiotemporal control of NSC activity is an important driver of the macroarchitecture of the zebrafish adult pallium. This simple mode of pallium construction shares distinct traits with pallial genesis in mammals and non-mammalian amniotes such as birds or reptiles, suggesting that it may exemplify the basal layout from which vertebrate pallial architectures were elaborated. (10.1016/j.cub.2017.09.052)
  DOI : 10.1016/j.cub.2017.09.052
• Multiscale control and rapid scanning of time delays ranging from picosecond to millisecond
  
  • Solinas Xavier
  • Antonucci Laura
  • Bonvalet A.
  • Joffre Manuel
  Optics Express, Optical Society of America - OSA Publishing, 2017, 25 (15), pp.17811-17819. Femtosecond amplifiers seeded by two independent femtosecond oscillators normally produce amplified pulse pairs with a timing jitter equal to the oscillator period, which is typically around 12 ns for Titanium:Sapphire lasers. Combining Arbitrary-Detuning Asynchronous Optical Sampling (AD-ASOPS) with an appropriate selection of amplified pulses, we demonstrate that the time-delay distribution can be narrowed down to a 25-ps time window, allowing to produce spectral interference fringes for each amplified pulse pair. Subsequent AD-ASOPS determination of the actual time delay with subpicosecond accuracy allows to tailor the delay distribution with an electronic control all the way to the repetition period of the amplifiers. We thus demonstrate rapid scanning of the time delays up to nearly 1 ms with a sub-picosecond accuracy, which makes this method an ideal tool for multiscale pump-probe spectroscopy. (10.1364/oe.25.017811)
  DOI : 10.1364/oe.25.017811
• Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states
  
  • Kruglik Sergei
  • Yoo Byung-Kuk
  • Lambry Jean-Christophe
  • Martin Jean-Louis
  • Negrerie Michel
  Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2017, 19 (32), pp.21317-21334. Apart from its role in electron transfer, mitochondrial cytochrome c also plays a role in apoptosis and is subject to nitrosylation. The cleavage of the Fe–Met80 bond plays a role in several processes including the release of Cyt c from mitochondria or increase of its peroxidase activity. Nitrosylation of Cyt c precludes the reformation of the disrupted Fe–Met80 bond and was shown to occur during apoptosis. These physiological properties are associated with a conformational change of the heme center of Cyt c. Here, we demonstrate that NO binding induces pronounced heme conformational changes in the six-coordinate Cyt c–NO complex. Equilibrium and time-resolved Raman data reveal that the heme structural conformation depends both on the nature of the distal iron ligand (NO or Met80) and on the Fe2+ or Fe3+ heme redox state. Upon nitrosylation, the heme ruffling distortion is greatly enhanced for ferrous Cyt c. Contrastingly, the initial strong heme distortion in native ferric Cyt c almost disappears after NO binding. We measured the heme coordination dynamics in the picosecond to second time range and identified Met80 and NO rebinding phases using time-resolved Raman and absorption spectroscopies. Dissociation of NO instantly produces 5-coordinate heme with a domed structure which continues to rearrange within 15 ps, while the initial ruffling distortion disappears. The rates of Cyt c–NO complex formation measured by transient absorption are kon = 1.81 × 106 M−1 s−1 for ferric Cyt c and 83 M−1 s−1 for ferrous Cyt c. After NO dissociation and exit from the heme pocket, the rebinding of Met80 to the heme iron takes place 6 orders of magnitude more slowly (3–5 μs) than Met80 rebinding in the absence of NO (5 ps). Altogether, these data reveal the structural and dynamic properties of Cyt c in interaction with nitric oxide relevant for the molecular mechanism of apoptosis. (10.1039/C7CP02634J)
  DOI : 10.1039/C7CP02634J
• Stabilization of Collagen Fibrils by Gelatin Addition: A Study of Collagen/Gelatin Dense Phases
  
  • Portier François
  • Teulon Claire
  • Nowacka-Perrin Agnieszka
  • Guenneau Flavien
  • Schanne-Klein Marie-Claire
  • Mosser Gervaise
  Langmuir, American Chemical Society, 2017, 33 (45), pp.12916-12925. Collagen and its denatured form, gelatin, are biopolymers of fundamental interest in numerous fields ranging from living tissues to biomaterials, food, and cosmetics. This study aims at characterizing mixtures of those biopolymers at high concentrations (up to 100 mg·mL–1) at which collagen has mesogenic properties. We use a structural approach combining polarization-resolved multiphoton microscopy, polarized light microscopy, magnetic resonance imaging, and transmission electron microscopy to analyze gelatin and collagen/gelatin dense phases in their sol and gel states from the macroscopic to the microscopic scale. We first report the formation of a lyotropic crystal phase of gelatin A and show that gelatin must structure itself in particles to become mesogenic. We demonstrate that mixtures of collagen and gelatin phase segregate, preserving the setting of the pure collagen mesophase at a gelatin ratio of up to 20% and generating a biphasic fractal sample at all tested ratios. Moreover, differential scanning calorimetric analysis shows that each protein separates into two populations. Both populations of gelatins are stabilized by the presence of collagen, whereas only one population of collagen molecules is stabilized by the presence of gelatin, most probably those at the interface of the fibrillated microdomains and of the gelatin phase. Although further studies are needed to fully understand the involved mechanism, these new data should have a direct impact on the bioengineering of those two biopolymers. (10.1021/acs.langmuir.7b02142)
  DOI : 10.1021/acs.langmuir.7b02142
• Physical limits of flow sensing in the left-right organizer
  
  • Ferreira Rita R.
  • Vilfan Andrej
  • Julicher Frank
  • Supatto Willy
  • Vermot Julien
  eLife, eLife Sciences Publication, 2017, 25, pp.556 - 556. Fluid flows generated by motile cilia are guiding the establishment of the left-right asymmetry of the body in the vertebrate left-right organizer. Competing hypotheses have been proposed: the direction of flow is sensed either through mechanosensation, or via the detection of chemical signals transported in the flow. We investigated the physical limits of flow detection to clarify which mechanisms could be reliably used for symmetry breaking. We integrated parameters describing cilia distribution and orientation obtained in vivo in zebrafish into a multiscale physical study of flow generation and detection. Our results show that the number of immotile cilia is too small to ensure robust left and right determination by mechanosensing, given the large spatial variability of the flow. However, motile cilia could sense their own motion by a yet unknown mechanism. Finally, transport of chemical signals by the flow can provide a simple and reliable mechanism of asymmetry establishment. (10.7554/eLife.25078)
  DOI : 10.7554/eLife.25078
• Affine kinematics in planar fibrous connective tissues: an experimental investigation
  
  • Jayyosi Charles
  • Affagard Jean-Sébastien
  • Ducourthial Guillaume
  • Bonod-Bidaud Christelle
  • Lynch Barbara
  • Bancelin Stéphane
  • Ruggiero Florence
  • Schanne-Klein Marie-Claire
  • Allain Jean-Marc
  • Bruyère-Garnier Karine
  • Coret Michel
  Biomechanics and Modeling in Mechanobiology, Springer Verlag, 2017, pp.1–15. The affine transformation hypothesis is usually adopted in order to link the tissue scale with the fibers scale in structural constitutive models of fibrous tissues. Thanks to the recent advances in imaging techniques, such as multiphoton microscopy, the microstructural behavior and kinematics of fibrous tissues can now be monitored at different stretching within the same sample. Therefore, the validity of the affine hypothesis can be investigated. In this paper, the fiber reorientation predicted by the affine assumption is compared to experimental data obtained during mechanical tests on skin and liver capsule coupled with microstructural imaging using multiphoton microscopy. The values of local strains and the collagen fibers orientation measured at increasing loading levels are used to compute a theoretical estimation of the affine reorientation of collagen fibers. The experimentally measured reorientation of collagen fibers during loading could not be successfully reproduced with this simple affine model. It suggests that other phenomena occur in the stretching process of planar fibrous connective tissues, which should be included in structural constitutive modeling approaches. (10.1007/s10237-017-0899-1)
  DOI : 10.1007/s10237-017-0899-1
• Fast quantitative ROS detection based on dual-color single rare-earth nanoparticle imaging reveals signaling pathway kinetics in living cells
  
  • Abdesselem M.
  • Ramodiharilafy R.
  • Devys L.
  • Gacoin T.
  • Alexandrou A.
  • Bouzigues C. I.
  Nanoscale, Royal Society of Chemistry, 2017, 9 (2), pp.656 - 665. Reactive oxygen species (ROS), and notably hydrogen peroxide H2O2, are cellular second messengers that are known to control a variety of signaling processes. They can finely regulate the dynamics of signal transduction, cell response and ultimately tissue function. However, there are very few local, quantitative and time-resolved descriptions of their cellular organization at the scale of molecular reactions, due to the lack of efficient sensors. We thus developed a novel nanoprobe-based ROS detection system using the simultaneous imaging of single lanthanide nanoparticles (YAG:Ce and chemically reduced Gd0.6Eu0.4VO4). We reveal that both particle luminescence signals are controlled by their H2O2 local environment. By simultaneously tracking their luminescence, we devised a new approach providing a quantitative (0.5 μM accuracy in the 1–10 μM range) H2O2 measurement with a 500 ms time resolution, surpassing all existing methods by two orders of magnitude, and revealing previously inaccessible molecular events controlling ROS concentration. We used this nanoprobe in living cells to track fast signaling pathways, by measuring the dynamics of H2O2 intracellular concentrations, induced by endothelin-1 (ET-1) stimulation. We thus revealed the mechanisms controlling ROS production, notably the activity modulation of the ROS-producing enzyme NADPH oxidase by fast (<10 s) EGFR transactivation, and measured quantitatively their kinetic parameters through a minimal analytical model. Altogether, these results illustrate how lanthanide nanoparticle-based sensors are a powerful tool to dynamically probe molecular mechanisms shaping the oxidative cell response. (10.1039/C6NR07413H)
  DOI : 10.1039/C6NR07413H
• Polarization-resolved Second Harmonic Imaging of collagen organization in connective tissues - Application to biomechanics
  
  • Teulon Claire
  • Latour Gaël
  • Gusachenko Ivan
  • Ducourthial Guillaume
  • Bancelin Stéphane
  • Bonod-Bidaud Christelle
  • Ruggiero Florence
  • Affagard Jean-Sébastien
  • Lynch Barbara
  • Benoit Aurélie
  • Allain Jean-Marc
  • Schanne-Klein Marie-Claire
  , 2017, pp.NW3C.2. Polarization-resolved SHG microscopy enables measurements of the main orientation and the angular dispersion of collagen fibrils within the focal volume. Results are presented in cornea, tendon and skin, eventually as function of mechanical stress. (10.1364/NTM.2017.NW3C.2)
  DOI : 10.1364/NTM.2017.NW3C.2
• Stromal striae: a new insight into corneal physiology and mechanics
  
  • Grieve Kate
  • Ghoubay Djida
  • Georgeon Cristina
  • Latour Gaël
  • Nahas Amir
  • Plamann Karsten
  • Crotti Caroline
  • Bocheux Romain
  • Borderie Marie
  • Nguyen Thu-Mai
  • Andreiuolo Felipe
  • Schanne-Klein Marie-Claire
  • Borderie Vincent M.
  Scientific Reports, Nature Publishing Group, 2017, 7, pp.13584. We uncover the significance of a previously unappreciated structural feature in corneal stroma, important to its biomechanics. Vogt striae are a known clinical indicator of keratoconus, and consist of dark, vertical lines crossing the corneal depth. However we detected stromal striae in most corneas, not only keratoconus. We observed striae with multiple imaging modalities in 82% of 118 human corneas, with pathology-specific differences. Striae generally depart from anchor points at Descemet’s membrane in the posterior stroma obliquely in a V-shape, whereas in keratoconus, striae depart vertically from posterior toward anterior stroma. Optical coherence tomography shear wave elastography showed discontinuity of rigidity, and second harmonic generation and scanning electron microscopies showed undulation of lamellae at striae locations. Striae visibility decreased beyond physiological pressure and increased beyond physiological hydration. Immunohistology revealed striae to predominantly contain collagen VI, lumican and keratocan. The role of these regions of collagen VI linking sets of lamellae may be to absorb increases in intraocular pressure and external shocks. (10.1038/s41598-017-13194-6)
  DOI : 10.1038/s41598-017-13194-6
• Microscopie de fluorescence et pince optique pour étudier la dynamique de mécanismes cellulaires
  
  • Westbrook Nathalie
  • Barbier Nathalie
  • Bugaud Olivier
  • Namy Olivier
  • Gillant Flavie
  • Moreau Julien
  • Richly Maximilian U.
  • Alexandrou Antigoni
  • Perronet Karen
  , 2017.
• Ultrafast photochemistry of the bc 1 complex
  
  • Vos Marten H.
  • Reeder Brandon J.
  • Daldal Fevzi
  • Liebl Ursula
  Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2017, 19 (9), pp.6807-6813. We present a full investigation of ultrafast light-induced events in the membraneous cytochrome bc1 complex by transient absorption spectroscopy. This energy-transducing complex harbors four redox-active components per monomer: heme c1, two 6-coordinate b-hemes and a [2Fe-2S] cluster. Using excitation of these components in different ratios under various excitation conditions, probing in the full visible range and under three well-defined redox conditions, we demonstrate that for all ferrous hemes of the complex photodissociation of axial ligands takes place and that they rebind in 5-7 ps, as in other 6-coordinate heme proteins, including cytoglobin, which is included as a reference in this study. By contrast, the signals are not consistent with photooxidation of the b hemes. This conclusion contrasts with a recent assessment based on a more limited data set. The binding kinetics of internal and external ligands are indicative of a rigid heme environment, consistent with the electron transfer function. We also report, for the first time, photoactivity of the very weakly absorbing iron-sulfur center. This yields the unexpected perspective of studying photochemistry, initiated by excitation of iron-sulfur clusters, in a range of protein complexes. (10.1039/C7CP00193B)
  DOI : 10.1039/C7CP00193B
• Ultra-wide range field-dependent measurements of the relaxivity of Gd1−xEuxVO4 nanoparticle contrast agents using a mechanical sample-shuttling relaxometer
  
  • Chou Ching-Yu
  • Abdesselem Mouna
  • Bouzigues Cedric
  • Chu Minglee
  • Guiga Angelo
  • Huang Tai-Huang
  • Ferrage Fabien
  • Gacoin Thierry
  • Alexandrou Antigoni
  • Sakellariou Dimitris
  Scientific Reports, Nature Publishing Group, 2017, 7, pp.44770. The current trend for Magnetic Resonance Imaging points towards higher magnetic fields. Even though sensitivity and resolution are increased in stronger fields, T1 contrast is often reduced, and this represents a challenge for contrast agent design. Field-dependent measurements of relaxivity are thus important to characterize contrast agents. At present, the field-dependent curves of relaxivity are usually carried out in the field range of 0 T to 2 T, using fast field cycling relaxometers. Here, we employ a high-speed sample shuttling device to switch the magnetic fields experienced by the nuclei between virtually zero field, and the center of any commercial spectrometer. We apply this approach on rare-earth (mixed Gadolinium-Europium) vanadate nanoparticles, and obtain the dispersion curves from very low magnetic field up to 11.7 T. In contrast to the relaxivity profiles of Gd chelates, commonly used for clinical applications, which display a plateau and then a decrease for increasing magnetic fields, these nanoparticles provide maximum contrast enhancement for magnetic fields around 1–1.5 T. These field-dependent curves are fitted using the so-called Magnetic Particle (MP) model and the extracted parameters discussed as a function of particle size and composition. We finally comment on the new possibilities offered by this approach. (10.1038/srep44770)
  DOI : 10.1038/srep44770
• Correction: Ultrafast photochemistry of the bc 1 complex
  
  • Vos Marten H.
  • Reeder Brandon J.
  • Daldal Fevzi
  • Liebl Ursula
  Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2017, 19 (13), pp.9320 - 9320. (10.1039/C7CP90057K)
  DOI : 10.1039/C7CP90057K
• Microscopie de fluorescence et pince optique : dispositifs optiques pour l’étude de processus biologiques à l’échelle d’un système unique
  
  • Barbier Nathalie
  • Fiszman Nicolas
  • Bugaud Olivier
  • Chommy Hélène
  • Namy Olivier
  • Gillant Flavie
  • Moreau Julien
  • Richly Maximilian U.
  • Alexandrou Antigoni
  • Westbrook Nathalie
  • Perronet Karen
  , 2017.