Publications

2019

• Quantitative Measures of Corneal Transparency, Derived from Objective Analysis of Stromal Light Backscattering with Full-Field Optical Coherence Tomography
  
  • Bocheux R.
  • Pernot P.
  • Borderie V.
  • Plamann K.
  • Irsch K.
  , 2019. (10.1364/ISA.2019.ITh2B.5)
  DOI : 10.1364/ISA.2019.ITh2B.5
• Probing living cells by terahertz attenuated total reflection: application to permeabilization dynamics
  
  • Gallot Guilhem
  • Zheng Xiujun
  • Grognot Marianne
  • Azan Antoine
  • Garcia-Sanchez Tomas
  • Descamps Lucie
  • Mir Lluis
  , 2019, 11075, pp.13. (10.1117/12.2526722)
  DOI : 10.1117/12.2526722
• Objective and quantitative analysis of corneal transparency with clinical spectral-domain optical coherence tomography
  
  • Bocheux R.
  • Rivière B.
  • Pernot P.
  • Georgeon C.
  • Borderie V.
  • Irsch K.
  • Plamann K.
  , 2019. (10.1117/12.2527085)
  DOI : 10.1117/12.2527085
• Dual-color 1.25-MHz sub-70-fs source at 1.3 and 1.7 mu m for multimodal 3-photon microscopy in water-transparency bands
  
  • Druon Frédéric
  • Guesmi Kkmaies
  • Abdeladim Lamiae
  • Berberian Tiphaine
  • Rigaud Philippe
  • Ferrer-Ortas Jùlia
  • Hanna Marc
  • Mahou Pierre
  • Livet Jean
  • Supatto Willy
  • Georges Patrick
  • Beaurepaire Emmanuel
  , 2019, pp.paper cf_2_1.
• Correlative multiphoton microscopy and infrared nanospectroscopy of label-free collagen
  
  • Mathurin Jérémie
  • Mosser Gervaise
  • Dazzi Alexandre
  • Deniset-Besseau Ariane
  • Schanne-Klein Marie-Claire
  • Latour Gael
  , 2019, 11076. (10.1117/12.2527101)
  DOI : 10.1117/12.2527101
• Publisher correction: Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy
  
  • Abdeladim Lamiae
  • Matho Katherine S
  • Clavreul Solène
  • Mahou Pierre
  • Sintes Jean-Marc
  • Solinas Xavier
  • Arganda-Carreras Ignacio
  • Turney Stephen G
  • Lichtman Jeff W
  • Chessel Anatole
  • Bemelmans Alexis-Pierre
  • Loulier Karine
  • Supatto Willy
  • Livet Jean
  • Beaurepaire Emmanuel
  Nature Communications, Nature Publishing Group, 2019, 10, pp.2160. Affiliation 4 incorrectly read 'University of the Basque Country (Ikerbasque), University of the Basque Country and Donostia International Physics Center, San Sebastian 20018, Spain.'Also, the affiliations of Ignacio Arganda-Carreras with 'IKERBASQUE, Basque Foundation for Science, Bilbao, 48013, Spain' and 'Donostia International Physics Center (DIPC), San Sebastian, 20018, Spain' were inadvertently omitted.Additionally, the third sentence of the first paragraph of the Results section entitled 'Multicontrast organ-scale imaging with ChroMS microscopy' incorrectly read 'For example, one can choose lambda1 = 850 and lambda2 = 110 nm for optimal two-photon excitation of blue and red chromophores.'. The correct version reads 'lambda2 = 1100 nm' instead of 'lambda2 = 110 nm'. These errors have now been corrected in the PDF and HTML versions of the Article. (10.1038/s41467-019-10225-w)
  DOI : 10.1038/s41467-019-10225-w
• Objective and quantitative analysis of corneal transparency with clinical spectral-domain optical coherence tomography
  
  • Bocheux Romain
  • Riviere Bathilde
  • Pernot Pascal
  • Georgeon Cristina
  • Borderie Vincent
  • Irsch Kristina
  • Plamann Karsten
  , 2019.
• Stratégies avancées d'imagerie multiphoton pour l'étude de processus périodiques rapides in vivo : des cils motiles au cœur battant
  
  • Pakula Guillaume
  , 2019. Les oscillateurs biologiques régissent le monde vivant à toutes les échelles. En biologie du développement, le cœur battant et les cils motiles en sont deux représentations dont les dimensions temporelles et spatiales sont analogues. Leur observation dynamique est un enjeu majeur pour permettre la compréhension de leur fonctionnement et des processus biologiques dans lesquels ils sont impliqués. Dans ce manuscrit, nous nous proposons de résoudre leur mouvement tridimensionnel in vivo chez un organisme-modèle de vertébré : le poisson-zèbre. Pour contourner les limites actuelles de vitesse d’imagerie, nous utiliserons la propriété de périodicité de ces oscillateurs biologiques, afin de développer des stratégies innovantes d'imagerie rapide en microscopie multiphoton.D’abord, le cil cellulaire est une extension cytoplasmique que l’on retrouve dans presque toutes les cellules eucaryotes dont le rôle est de générer un flux biologique lorsqu'il est motile. Au cours des dernières années, leurs dysfonctionnements ont été identifiés dans un nombre croissant de pathologies, regroupées sous le terme de ciliopathies. En particulier, ils sont présents en nombre dans l’organisateur gauche-droite du poisson-zèbre, la vésicule de Kupffer. Le flux directionnel qu’ils génèrent est responsable de la brisure de symétrie gauche-droite aux stades précoces, le dernier axe biologique à se spécifier chez les vertébrés. Dans ce manuscrit, nous détaillons une approche systématique d’analyse des cils cellulaires, exploitant les artefacts de balayage observés en microscopie multiphoton, issus du battement périodique de ceux-ci. Cette approche nous a notamment permis de découvrir une nouvelle forme d’asymétrie, ou de chiralité, apparaissant au sein de la vésicule de Kupffer.Par ailleurs, l’étude du cœur battant se heurte également à l’impossibilité de résoudre son mouvement rapide et en trois dimensions, par les techniques actuelles de microscopie. Dans ces travaux, nous proposons une méthode d’imagerie rapide à balayage point par point tirant profit de la propriété périodique du cœur, consistant en la synchronisation a posteriori de séquences de lignes balayées rapidement. Nous montrons que cette approche nous permet d’atteindre des résolutions temporelles sans précédent (de l’ordre de 1000 volumes par seconde), sans marquage, et sans compromettre d’autres paramètres d’acquisition (RSB, résolution spatiale, phototoxicité). En particulier, nous appliquons la méthode au suivi de la contraction des sarcomères cardiaques in vivo par génération de seconde harmonique (SHG), ainsi qu’à l’observation des valves cardiaques, les structures les plus dynamiques du cœur.
• Iron transitions during activation of allosteric heme proteins in cell signaling
  
  • Négrerie Michel
  Metallomics, Royal Society of Chemistry, 2019, 11, pp.868 - 893. Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals. (10.1039/c8mt00337h)
  DOI : 10.1039/c8mt00337h
• High-speed polarization-resolved third-harmonic microscopy
  
  • Morizet Joséphine
  • Ducourthial Guillaume
  • Supatto Willy
  • Boutillon Arthur
  • Legouis Renaud
  • Schanne-Klein Marie-Claire
  • Stringari Chiara
  • Beaurepaire Emmanuel
  Optica, Optical Society of America - OSA Publishing, 2019, 6 (3), pp.385-388. Polarization-resolved third-harmonic generation (P-THG) is a sensitive probe of material anisotropy and molecular ordering. Despite its promises, this property has little been used in biological tissues due to the lack of measurement schemes compatible with dynamic samples. We report here on the development of a fast P-THG microscope where excitation polarization is switched between line scans using an electro-optic modulator, providing temporal resolution in the 10 ms range for the polarimetric measurement. We demonstrate novel applications enabled by this approach, associated with Fourier-based analysis: probing molecular order in deforming lipid structures undergoing phase transition; revealing crystallinity of flowing particles in the zebrafish embryo’s inner ear; and detecting birefringence in vivo. These results establish that P-THG is ideally suited for probing lipid organization and mineralization in dynamic biological environments. (10.1364/OPTICA.6.000385)
  DOI : 10.1364/OPTICA.6.000385
• Targeting the transposable elements of the genome to enable large-scale genome editing and bio-containment technologies.
  
  • Castanon Velasco Oscar
  , 2019. Programmable and site-specific nucleases such as CRISPR-Cas9 have started a genome editing revolution, holding hopes to transform human health. Multiplexing or the ability to simultaneously introduce many distinct modifications in the genome will be required for basic and applied research. It will help to probe the physio-pathological functions of complex genetic circuits and to develop improved cell therapies or anti-viral treatments. By pushing the boundaries of genome engineering, we may reach a point where writing whole mammalian genomes will be possible. Such a feat may lead to the generation of virus-, cancer- or aging- free cell lines, universal donor cell therapies or may even open the way to de-extinction. In this doctoral research project, I outline the current state-of-the-art of multiplexed genome editing, the current limits and where such technologies could be headed in the future. We leveraged this knowledge as well as the abundant transposable elements present in our DNA to build an optimization pipeline and develop a new set of tools that enable large-scale genome editing. We achieved a high level of genome modifications up to three orders of magnitude greater than previously recorded, therefore paving the way to mammalian genome writing. In addition, through the observation of the cytotoxicity generated by multiple double-strand breaks within the genome, we developed a bio-safety switch that could potentially prevent the adverse effects of current and future cell therapies. Finally, I lay out the potential concerns and threats that such an advance in genome editing technology may be bringing and point out possible solutions to mitigate the risks.
• Combination of Traction Assays and Multiphoton Imaging to Quantify Skin Biomechanics
  
  • Bancelin Stéphane
  • Lynch Barbara
  • Bonod-Bidaud Christelle
  • Dokládal Petr
  • Ruggiero Florence
  • Allain Jean-Marc
  • Schanne-Klein Marie-Claire
  , 2019, 1944, pp.145-155. An important issue in tissue biomechanics is to decipher the relationship between the mechanical behavior at macroscopic scale and the organization of the collagen fiber network at microscopic scale. Here, we present a protocol to combine traction assays with multiphoton microscopy in ex vivo murine skin. This multiscale approach provides simultaneously the stress/stretch response of a skin biopsy and the collagen reorganization in the dermis by use of second harmonic generation (SHG) signals and appropriate image processing. (10.1007/978-1-4939-9095-5_11)
  DOI : 10.1007/978-1-4939-9095-5_11
• Tailoring the photophysical properties and excitonic radiative decay of soluble CdSe quantum dots by controlling the ratio of capping thiol ligand
  
  • Mrad Randa
  • Poggi Mélanie
  • Brahim Nassim Ben
  • Chaâbane Rafik Ben
  • Négrerie Michel
  Acta Materialia, Elsevier, 2019, 5, pp.100191. We report the physical and photophysical properties of CdSe quantum dots capped with three different thiol compounds (thioglycolic acid, 3-mercaptopropionic acid, mercaptosuccinic acid) synthesized through a hydrothermal protocol. We calculated the true molecular weight and molar absorption coefficient of QDs from their diameter (not from any empirical relation) which are in the range 3.5 – 5.9 nm. The aqueous synthesis method ensures the insertion of the sulfur atoms of thiol ligands in the crystal CdSe cubic lattice, producing hexagonal crystal unit defects at the surface of the QDs. The QDs steady-state emission spectra were analyzed in terms of Gaussian components, in correlation with the time-resolved emission. We have elaborated MSA-CdSe QDs capped with mercaptosuccinic acid using various stoichiometric Cd/MSA ratios during the aqueous synthesis. Modulating the Cd/MSA ratio directly affects the size and photophysics of the QDs, in particular the fluorescence emission spectrum and decay. We rationalized the effect on QDs size by a change of the CdSe formation rate during synthesis. Acting on the Cd/MSA ratio appears a mean of modulating the emission spectrum and understanding the photophysical processes involved with respect to the QD structure. (10.1016/j.mtla.2018.100191)
  DOI : 10.1016/j.mtla.2018.100191
• Synthesis and Structure–Activity Relationship Studies of Benzo[ b ][1,4]oxazin‐3(4 H )‐one Analogues as Inhibitors of Mycobacterial Thymidylate Synthase X
  
  • Modranka Jakub
  • Li Jiahong
  • Parchina Anastasia
  • Vanmeert Michiel
  • Dumbre Shrinivas
  • Salman Mayla
  • Myllykallio Hannu
  • Becker Hubert
  • Vanhoutte Roeland
  • Margamuljana Lia
  • Nguyen Hoai Viet
  • Abu el‐asrar Rania
  • Rozenski Jef
  • Herdewijn Piet
  • De jonghe Steven
  • Lescrinier Eveline
  ChemMedChem, Wiley-VCH Verlag, 2019, 14 (6), pp.645-662. (10.1002/cmdc.201800739)
  DOI : 10.1002/cmdc.201800739
• Frequency-Domain Two-Dimensional Infrared Spectroscopy using an Acousto-Optic Programmable Dispersive Filter
  
  • Alberto de La Paz José
  • Bonvalet Adeline
  • Joffre Manuel
  Optics Express, Optical Society of America - OSA Publishing, 2019, 27 (4), pp.4140-4146. We report on multidimensional spectroscopy in the mid-infrared performed using a calomel-based acousto-optic programmable dispersive filter. Although the associated spectral resolution is currently not as good as what has been previously reported using time-domain interferometers or other pulse-shaping technologies, the extreme compactness of the calomel crystal allows a straightforward implementation in a pre-existing pump-probe setup. Furthermore, the frequency-domain approach allows easy measurement of 2D slices of the multidimensional spectrum associated with a given pump frequency. We demonstrate our method with the measurement of the mid-infrared spectrum of carboxy-hemoglobin in three spectro-temporal dimensions. (10.1364/OE.27.004140)
  DOI : 10.1364/OE.27.004140
• Device for managing pulses in pump-probe spectroscopy
  
  • Antonucci Laura
  • Bonvalet Adeline
  • Joffre Manuel
  • Solinas Xavier
  , 2019.
• Third harmonic generation imaging and analysis of the effect of low gravity on the lacuno-canalicular network of mouse bone
  
  • Genthial Rachel
  • Gerbaix Maude
  • Farlay Delphine
  • Vico Laurence
  • Beaurepaire Emmanuel
  • Débarre Delphine
  • Gourrier Aurélien
  PLoS ONE, Public Library of Science, 2019, 14 (1), pp.e0209079. The lacuno-canalicular network (LCN) hosting the osteocytes in bone tissue represents a biological signature of the mechanotransduction activity in response to external biomechanical loading. Using third-harmonic generation (THG) microscopy with sub-micrometer resolution, we investigate the impact of microgravity on the 3D LCN structure in mice following space flight. A specific analytical procedure to extract the LCN characteristics from THG images is described for ex vivo studies of bone sections. The analysis conducted in different anatomical quadrants of femoral cortical bone didn't reveal any statistical differences between the control, habitat control and flight groups, suggesting that the LCN connectivity is not affected by one month space flight. However, significant variations are systematically observed within each sample. We show that our current lack of understanding of the extent of the LCN heterogeneity at the organ level hinders the interpretation of such investigations based on a limited number of samples and we discuss the implications for future biomedical studies. (10.1371/journal.pone.0209079)
  DOI : 10.1371/journal.pone.0209079
• Monitoring dynamic collagen reorganization during skin stretching with fast polarization‐resolved second harmonic generation imaging
  
  • Ducourthial Guillaume
  • Affagard Jean‐sébastien
  • Schmeltz Margaux
  • Solinas Xavier
  • Lopez‐poncelas Maeva
  • Bonod‐bidaud Christelle
  • Rubio‐amador Ruth
  • Ruggiero Florence
  • Allain Jean-Marc
  • Beaurepaire Emmanuel
  • Schanne-Klein Marie-Claire
  Journal of Biophotonics, Wiley, 2019, 12 (5), pp.e201800336. The mechanical properties of biological tissues are strongly correlated to the specific distribution of their collagen fibers. Monitoring the dynamic reorganization of the collagen network during mechanical stretching is however a technical challenge because it requires mapping orientation of collagen fibers in a thick and deforming sample. In this work, a fast polarization-resolved SHG microscope is implemented to map collagen orientation during mechanical assays. This system is based on line-to-line switching of polarization using an electro-optical modulator and works in epidetection geometry. After proper calibration, it successfully highlights the collagen dynamic alignment along the traction direction in ex vivo murine skin dermis. This microstructure reorganization is quantified by the entropy of the collagen orientation distribution as a function of the stretch ratio. It exhibits a linear behavior, whose slope is measured with a good accuracy. This approach can be generalized to probe a variety of dynamic processes in thick tissues. (10.1002/jbio.201800336)
  DOI : 10.1002/jbio.201800336
• Multiscale characterization of skin mechanics through in situ imaging
  
  • Allain Jean-Marc
  • Lynch Barbara
  • Schanne-Klein Marie-Claire
  , 2019, 22, pp.265-280. The complex mechanical properties of skin have been studied intensively over the past decades. They are intrinsically linked to the structure of the skin at several length scales, from the macroscopic layers (epidermis, dermis and hypodermis) down to the microstructural organization at the molecular level. Understanding the link between this microscopic organization and the mechanical properties is of significant interest in the cosmetic and medical fields. Nevertheless, it only recently became possible to directly visualize the skin’s microstructure during mechanical assays, carried out on the whole tissue or on isolated layers. These recent observations have provided novel information on the role of structural components of the skin in its mechanical properties, mainly the collagen fibers in the dermis, while the contribution of others, such as elastin fibers, remains elusive. In this chapter we present current methods used to observe skin’s microstructure during a mechanical assay, along with their strengths and limitations, and we review the unique information they provide on the link between structure and function of the skin. (10.1007/978-3-030-13279-8_8)
  DOI : 10.1007/978-3-030-13279-8_8
• Generalized time delay, velocity, and absorption in dispersive and absorbing media
  
  • Gallot Guilhem
  Physical Review A, American Physical Society, 2019, 99 (1). (10.1103/PhysRevA.99.013829)
  DOI : 10.1103/PhysRevA.99.013829
• Ces manuscrits que l’on croyait perdus – La renaissance des manuscrits de Chartres
  
  • Robinet Laurianne
  • Pottier Fabien
  • Schmeltz Margaux
  • Heu-Thao Sylvie
  • Poirel Dominique
  • Rabel Claudia
  • Schanne-Klein Marie-Claire
  • Latour Gaël
  • Michelin Anne
  Support Tracé, Association pour la Recherche Scientifique sur les Arts Graphiques (ARSAG), 2019, 18, pp.12-21.
• Differences between foetal and adult meniscus and cartilage revealed by Polarization Second Harmonic Generation Microscopy
  
  • Pinsard Maxime
  • Richard Hélène
  • Dubuc Julia
  • Laverty Sheila
  • Schanne-Klein Marie-Claire
  • Legare Francois
  , 2019, pp.1-1. (10.1109/PN.2019.8819544)
  DOI : 10.1109/PN.2019.8819544
• Size-Exclusion Mechanism Driving Host-Guest Interactions between Octahedral Rhenium Clusters and Cyclodextrins
  
  • Ivanov Anton A
  • Falaise Clement
  • Laouer Kevin
  • Hache François
  • Changenet Pascale
  • Mironov Yuri V
  • Landy David
  • Molard Yann
  • Cordier Stéphane
  • Shestopalov Michael A
  • Haouas Mohamed
  • Cadot Emmanuel
  Inorganic Chemistry, American Chemical Society, 2019, 58 (19), pp.13184-13194. In aqueous solution, cyclodextrins (CDs) are able to bind strongly either hydrophobic species or also hydrophilic molecules such as octahedral hexametallic cluster. Systematic investigation of the reactivity between native CDs (α- or β-CD) and water-soluble rhenium clusters [ReQ(CN)] with Q = S, Se, and Te were performed, leading to six new crystal structures revealing different types of supramolecular arrangements. Encapsulation of [ReQ(CN)] (Q = S, Se, or Te) within two β-CDs is observed regardless of the cluster size. Interestingly, different assembling scenarios are pointed out depending on the host-guest matching featured by no, partial, or deep inclusion complexes that involved either primary or secondary rim of the CD tori. In the specific case of α-CD, only the smaller cluster [ReS(CN)] is able to form inclusion complex with the tori host. Solution investigations, using a set of complementary techniques including isothermal titration calorimetry, multinuclear NMR methods, cyclic voltammetry, and electrospray ionization mass spectrometry, corroborate nicely conclusions of the solid-state studies. It appears clearly that size-matching supported by solvent effects play key roles in the stability of the host-guest complexes. At last, circular dichroism studies underline that the chirality induction from cyclodextrins to the rhenium cluster depends strongly on the strength of host-guest interactions. (10.1021/acs.inorgchem.9b02048)
  DOI : 10.1021/acs.inorgchem.9b02048
• Removing artifacts in Second Harmonic Generation imaging by interferometry
  
  • Pinsard Maxime
  • Schmeltz Margaux
  • Kolk Jarno
  • Patten Kessen
  • Ramunno Lora
  • Schanne-Klein Marie-Claire
  • Legare Francois
  , 2019, pp.1-1. (10.1109/PN.2019.8819578)
  DOI : 10.1109/PN.2019.8819578
• An actin-based viscoplastic lock ensures progressive body-axis elongation
  
  • Lardennois Alicia
  • Ferraro Teresa
  • Llense Flora
  • Labouesse Michel
  • Pásti Gabriella
  • Pontabry Julien
  • Rodriguez David
  • Kim Samantha
  • Gally Christelle
  • Mahou Pierre
  • Beaurepaire Emmanuel
  • Ono Shoichiro
  Nature, Nature Publishing Group, 2019, 573 (7773), pp.266-270. Body-axis elongation constitutes a key step in animal development, laying out the final form of the entire animal. It relies on the interplay between intrinsic forces generated by molecular motors1,2,3, extrinsic forces exerted by adjacent cells4,5,6,7 and mechanical resistance forces due to tissue elasticity or friction8,9,10. Understanding how mechanical forces influence morphogenesis at the cellular and molecular level remains a challenge1. Recent work has outlined how small incremental steps power cell-autonomous epithelial shape changes1,2,3, which suggests the existence of specific mechanisms that stabilize cell shapes and counteract cell elasticity. Beyond the twofold stage, embryonic elongation in Caenorhabditis elegans is dependent on both muscle activity7 and the epidermis; the tension generated by muscle activity triggers a mechanotransduction pathway in the epidermis that promotes axis elongation7. Here we identify a network that stabilizes cell shapes in C. elegans embryos at a stage that involves non-autonomous mechanical interactions between epithelia and contractile cells. We searched for factors genetically or molecularly interacting with the p21-activating kinase homologue PAK-1 and acting in this pathway, thereby identifying the α-spectrin SPC-1. Combined absence of PAK-1 and SPC-1 induced complete axis retraction, owing to defective epidermal actin stress fibre. Modelling predicts that a mechanical viscoplastic deformation process can account for embryo shape stabilization. Molecular analysis suggests that the cellular basis for viscoplasticity originates from progressive shortening of epidermal microfilaments that are induced by muscle contractions relayed by actin-severing proteins and from formin homology 2 domain-containing protein 1 (FHOD-1) formin bundling. Our work thus identifies an essential molecular lock acting in a developmental ratchet-like process. (10.1038/s41586-019-1509-4)
  DOI : 10.1038/s41586-019-1509-4