Publications

2013

• Probing ordered lipid assemblies with polarized third-harmonic-generation microscopy
  
  • Zimmerley Maxwell
  • Mahou Pierre
  • Débarre Delphine
  • Schanne-Klein Marie-Claire
  • Beaurepaire Emmanuel
  Physical Review X, American Physical Society, 2013, 3 (1), pp.11002. Ordered lipid assemblies are responsible for important physiological functions including skin barrier and axon conductivity. However, techniques commonly used to probe molecular order such as X-ray scattering and nuclear magnetic resonance are not suited for in-situ tissue studies. Here, we identify and characterize a novel contrast mechanism in nonlinear optical microscopy which is sensitive to molecular ordering in multilamellar lipid vesicles (MLVs) and in samples obtained from human skin biopsy: polarized third-harmonic generation (P-THG). We develop a multiscale theoretical framework to calculate the anisotropic, nonlinear optical response of lipid arrays as a function of molecular order. This analysis reveals that conserved carbon-carbon bond and aliphatic tail directionality are the atomic- and molecular-scale sources of the observed P-THG response, respectively. Agreement between calculations and experiments on lipid droplets and MLVs validates the use of P-THG as a probe of lipid ordering. Finally, we show that P-THG can be used to map molecular ordering in the multilamellar, intercorneocyte lipid matrix of the stratum corneum of human skin. These results provide the foundation for the use of P-THG in probing molecular order and highlight a novel biomedical application of multiphoton microscopy in an optically accessible tissue relevant to monitoring lipid-related disorder. (10.1103/PhysRevX.3.011002)
  DOI : 10.1103/PhysRevX.3.011002
• Probing membrane protein interactions with their lipid raft environment using single-molecule tracking and Bayesian inference analysis.
  
  • Türkcan Silvan
  • Richly Maximilian U.
  • Alexandrou Antigoni
  • Masson Jean-Baptiste
  PLoS ONE, Public Library of Science, 2013, 8 (1), pp.e53073. The statistical properties of membrane protein random walks reveal information on the interactions between the proteins and their environments. These interactions can be included in an overdamped Langevin equation framework where they are injected in either or both the friction field and the potential field. Using a Bayesian inference scheme, both the friction and potential fields acting on the ε-toxin receptor in its lipid raft have been measured. Two types of events were used to probe these interactions. First, active events, the removal of cholesterol and sphingolipid molecules, were used to measure the time evolution of confining potentials and diffusion fields. Second, passive rare events, de-confinement of the receptors from one raft and transition to an adjacent one, were used to measure hopping energies. Lipid interactions with the ε-toxin receptor are found to be an essential source of confinement. ε-toxin receptor confinement is due to both the friction and potential field induced by cholesterol and sphingolipids. Finally, the statistics of hopping energies reveal sub-structures of potentials in the rafts, characterized by small hopping energies, and the difference of solubilization energy between the inner and outer raft area, characterized by higher hopping energies. (10.1371/journal.pone.0053073)
  DOI : 10.1371/journal.pone.0053073
• Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm
  
  • Nozawa Kayo
  • Ishitani Ryuichiro
  • Yoshihisa Tohru
  • Sato Mamoru
  • Arisaka Fumio
  • Kanamaru Shuji
  • Dohmae Naoshi
  • Mangroo Dev
  • Senger Bruno
  • Becker Hubert F.
  • Nureki Osamu
  Nucleic Acids Research, Oxford University Press, 2013, 41 (6), pp.3901-3914. In all eukaryotes, transcribed precursor tRNAs are maturated by processing and modification processes in nucleus and are transported to the cytoplasm. The cytoplasmic export protein (Cex1p) captures mature tRNAs from the nuclear export receptor (Los1p) on the cytoplasmic side of the nuclear pore complex, and it delivers them to eukaryotic elongation factor 1alpha. This conserved Cex1p function is essential for the quality control of mature tRNAs to ensure accurate translation. However, the structural basis of how Cex1p recognizes tRNAs and shuttles them to the translational apparatus remains unclear. Here, we solved the 2.2 A resolution crystal structure of Saccharomyces cerevisiae Cex1p with C-terminal 197 disordered residues truncated. Cex1p adopts an elongated architecture, consisting of N-terminal kinase-like and a C-terminal alpha-helical HEAT repeat domains. Structure-based biochemical analyses suggested that Cex1p binds tRNAs on its inner side, using the positively charged HEAT repeat surface and the C-terminal disordered region. The N-terminal kinase-like domain acts as a scaffold to interact with the Ran-exportin (Los1p.Gsp1p) machinery. These results provide the structural basis of Los1p.Gsp1p.Cex1p.tRNA complex formation, thus clarifying the dynamic mechanism of tRNA shuttling from exportin to the translational apparatus. (10.1093/nar/gkt010)
  DOI : 10.1093/nar/gkt010
• Achievement of cornea-like organizations in dense collagen I solutions: clues to the physico-chemistry of cornea morphogenesis
  
  • de Sa Peixoto Paulo
  • Deniset-Besseau Ariane
  • Schmutz Marc
  • Anglo Anny
  • Illoul Corinne
  • Schanne-Klein Marie-Claire
  • Mosser Gervaise
  Soft Matter, Royal Society of Chemistry, 2013, 9 (47), pp.11241-11248. Multiphoton and electron microscopic analyses show that acido-soluble collagen I prepared in 5 mM acetic acid (pH 3.5) at concentration above 45 mg mL−1 spontaneously generates liquid crystal phases mimicking plywood organization found in cornea tissues. Those organizations extend for several hundred micrometers. Transmission electron microscopy reveals the presence of small nanofibrils organized in a complex phase, coupling overall smectic and cholesteric organizations together with local order. Those nanofibrils could be the mesogen elements giving rise to this plywood organization. These data provide clues to physico-chemical events that may take place in cornea morphogenesis in vivo. This result is invaluable for bioengineering fields, as this liquid crystal organization paves the way for the generation of collagen based bio-mimetic cornea matrices. (10.1039/c3sm52097h)
  DOI : 10.1039/c3sm52097h
• Arbitrary-detuning asynchronous optical sampling pump-probe spectroscopy of bacterial reaction centers
  
  • Antonucci Laura
  • Bonvalet Adeline
  • Solinas Xavier
  • Jones Mickael R.
  • Vos Marten H.
  • Joffre Manuel
  Optics Letters, Optical Society of America - OSA Publishing, 2013, 38 (17), pp.3322-3324. A recently reported variant of asynchronous optical sampling compatible with arbitrary unstabilized laser repetition rates is applied to pump-probe spectroscopy. This makes possible the use of a 5.1 MHz chirped pulse oscillator as the pump laser, thus extending the available time window to almost 200 ns with a time resolution as good as about 320 fs. The method is illustrated with the measurement in a single experiment of the complete charge transfer dynamics of the reaction center from Rhodobacter sphaeroides. © 2013 Optical Society of America (10.1364/OL.38.003322)
  DOI : 10.1364/OL.38.003322
• Time-lapsed SHG imaging of collagen fibrillogenesis, correlation to electronic microscopy
  
  • Bancelin Stéphane
  • Aimé Carole
  • Machairas Vaïa
  • Decencière Etienne
  • Albert Claire
  • Mosser Gervaise
  • Coradin T.
  • Schanne-Klein Marie-Claire
  , 2013.
• Picosecond binding of the his ligand to four-coordinate heme in cytochrome c ': A one-way gate for releasing proximal NO
  
  • Yoo Byung-Kuk
  • Lamarre Isabelle
  • Martin Jean-Louis
  • Andrew Colin R.
  • Negrerie Michel
  Journal of the American Chemical Society, American Chemical Society, 2013, 135 (8), pp.3248-3254. We provide a direct demonstration of a "kinetic trap" mechanism in the proximal 5-coordinate heme-nitrosyl complex (5c-NO) of cytochrome c' from Alcaligenes xylosoxidans (AXCP) in which picosecond rebinding of the endogenous His ligand following heme-NO dissociation acts as a one-way gate for the release of proximal NO into solution. This demonstration is based upon picosecond transient absorption changes following NO photodissociation of the proximal 5c-NO AXCP complex. We have determined the absolute transient absorption spectrum of 4-coordinate ferrous heme to which NO rebinds with a time constant tNO = 7 ps (kNO = 1.4 × 1011 s-1) and shown that rebinding of the proximal histidine to the 4-coordinate heme takes place with a time constant tHis = 100 ± 10 ps (kHis = 1010 s-1) after the release of NO from the proximal heme pocket. This rapid His reattachment acts as a one-way gate for releasing proximal NO by precluding direct proximal NO rebinding once it has left the proximal heme pocket and requiring NO rebinding from solution to proceed via the distal heme face. Cop. 2013 American Chemical Society. (10.1021/ja312140f)
  DOI : 10.1021/ja312140f
• SHG imaging and quantization of fibrosis
  
  • Schanne-Klein Marie-Claire
  , 2013, pp.349-372.
• Attenuated internal reflection terahertz imaging
  
  • Wojdyla Antoine
  • Gallot Guilhem
  Optics Letters, Optical Society of America - OSA Publishing, 2013, 38 (2), pp.112-114. We present a terahertz (THz) imaging technique based on attenuated internal reflection, which is ideally suited for the analysis of liquid and biological samples. Inserted in a THz time-domain system, and using a high-resistivity low loss silicon prism to couple the THz wave into the sample, the detection scheme is based on the relative differential spectral phase of two orthogonal polarizations. Biological sample imaging as well as subwavelength (?/16) longitudinal resolution are demonstrated. Cop. 2013 Optical Society of America.
• Parallel measurements of reaction kinetics using ultralow-volumes
  
  • Fradet Etienne
  • Abbyad Paul
  • Vos Marten H.
  • Baroud Charles N.
  Lab on a Chip, Royal Society of Chemistry, 2013, 13 (22), pp.4326-4330. We present a new platform for the production and manipulation of microfluidic droplets in view of measuring the evolution of a chemical reaction. Contrary to existing approaches, our device uses gradients of confinement to produce a single drop on demand and guide it to a pre-determined location. In this way, two nanoliter drops containing different reagents can be placed in contact and merged together, in order to trigger a chemical reaction. The reaction rate is extracted from an analysis of the observed reaction-diffusion front. We show that the results obtained using this platform are in excellent agreement with stopped-flow measurements, while decreasing the sample consumption 5000 fold. We also show how the device operation can be parallelized in order to react an initial sample with a range of compounds or concentrations, on a single integrated chip. This integrated chip thus further reduces sample consumption while reducing the time required for the experimental runs from hours to minutes. (10.1039/c3lc50768h)
  DOI : 10.1039/c3lc50768h
• THG microscopy of cells and tissues: contrast mechanisms and applications
  
  • Olivier Nicolas
  • Débarre Delphine
  • Beaurepaire Emmanuel
  , 2013, pp.51-80.
• Upregulation of Adhesion Molecules on Leukemia Targets Improves the Efficacy of Cytotoxic T Cells Transduced With Chimeric Anti-CD19 Receptor
  
  • Laurin David
  • Marin Virna
  • Biagi Ettore
  • Pizzitola Irene
  • Agostoni Valentina
  • Gallot Géraldine
  • Vié Henri
  • Christine Jacob Marie
  • Chaperot Laurence
  • Aspord Caroline
  • Plumas Joël
  Journal of Immunotherapy, Lippincott, Williams & Wilkins, 2013, 36 (3), pp.181-189. (10.1097/CJI.0b013e318288f8c1)
  DOI : 10.1097/CJI.0b013e318288f8c1
• Numerical simulation of polarization-resolved second harmonic microscopy in birefringent media
  
  • Gusachenko Ivan
  • Schanne-Klein Marie-Claire
  Physical Review A : Atomic, molecular, and optical physics [1990-2015], American Physical Society, 2013, 88 (5), pp.053811. Polarization-resolved second-harmonic microscopy has recently emerged as a valuable technique for in situ imaging of collagen structure in tissues. Nevertheless, collagen-rich tissues such as tendon, ligament, skin dermis, bone, cornea, or artery exhibit a heterogeneous and anisotropic architecture that results in complex optical properties. While experimental evidence of polarization distortions has been reported in various tissues, the physics of second-harmonic imaging within such tissues is not fully understood yet. In this work, we performed numerical simulations of polarization-resolved second-harmonic generation in a strongly focused regime within a birefringent tissue. We show that vectorial components due to strong focusing have a rather small effect on the measurement of the second-harmonic tensorial response, while birefringence and optical dispersion may affect these measurements dramatically. We show indeed that a difference in the focal field distribution for ordinary and extraordinary waves results in different phase-matching conditions, which strongly affects the relative efficacy of second-harmonic generation for different polarizations. These results are of great interest for extracting reliable quantitative parameters from second-harmonic images. ©2013 American Physical Society (10.1103/PhysRevA.88.053811)
  DOI : 10.1103/PhysRevA.88.053811
• Configurational fluctuations and flavin-substrate interactions in the flavoenzyme ThyX studied by time- and spectrally resolved fluorescence
  
  • Laptenok Sergey P.
  • Bouzhir-Sima Latifa
  • Myllykallio Hannu
  • Liebl Ursula
  • Vos Marten H.
  EPJ Web of Conferences, EDP Sciences, 2013, 41, pp.07011. Femtosecond-resolved fluorescence of bacterial thymidilate synthase using a Kerr-gate based setup identifies a close-by tyrosine involved in flavin fluorescence quenching, shows that the substrate dUMP acts as a strong quencher itself and highlights functional configurational flexibility. © Owned by the authors, published by EDP Sciences, 2013 (10.1051/epjconf/20134107011)
  DOI : 10.1051/epjconf/20134107011
• Primary processes in heme-based sensor proteins
  
  • Liebl Ursula
  • Lambry Jean-Christophe
  • Vos Marten H.
  Biochimica et Biophysica Acta Proteins and Proteomics, Elsevier, 2013, 1834 (9), pp.1684-1692. A wide and still rapidly increasing range of heme-based sensor proteins has been discovered over the last two decades. At the molecular level, these proteins function as bistable switches in which the catalytic activity of an enzymatic domain is altered mostly by binding or dissociation of small gaseous ligands (O2, NO or CO) to the heme in a sensor domain. The initial "signal" at the heme level is subsequently transmitted within the protein to the catalytic site, ultimately leading to adapted expression levels of specific proteins. Making use of the photolability of the heme-ligand bond that mimics thermal dissociation, early processes in this intra-protein signaling pathway can be followed using ultrafast optical spectroscopic techniques; they also occur on timescales accessible to molecular dynamics simulations. Experimental studies performed over the last decade on proteins including the sensors FixL (O2), CooA (CO) and soluble guanylate cyclase (NO) are reviewed with an emphasis on emerging general mechanisms. After heme-ligand bond breaking, the ligand can escape from the heme pocket and eventually from the protein, or rebind directly to the heme. Remarkably, in all sensor proteins the rebinding, specifically of the sensed ligand, is highly efficient. This "ligand trap" property possibly provides means to smoothen the effects of fast environmental fluctuations on the switching frequency. For 6-coordinate proteins, where exchange between an internal heme-bound residue and external gaseous ligands occurs, the study of early processes starting from the unliganded form indicates that mobility of the internal ligand may facilitate signal transfer. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. Cop. 2013 Elsevier B.V. All rights reserved. (10.1016/j.bbapap.2013.02.025)
  DOI : 10.1016/j.bbapap.2013.02.025