Publications

2009

• Inferring maps of forces inside cell membrane microdomains
  
  • Masson J.-B.
  • Casanova Didier
  • Türkcan Silvan
  • Voisinne G.
  • Popoff Michel
  • Vergassola M.
  • Alexandrou Antigoni
  Physical Review Letters, American Physical Society, 2009, 102 (4), pp.48103. Mapping of the forces on biomolecules in cell membranes has spurred the development of effective labels, e.g., organic fluorophores and nanoparticles, to track trajectories of single biomolecules. Standard methods use particular statistics, namely the mean square displacement, to analyze the underlying dynamics. Here, we introduce general inference methods to fully exploit information in the experimental trajectories, providing sharp estimates of the forces and the diffusion coefficients in membrane microdomains. Rapid and reliable convergence of the inference scheme is demonstrated on trajectories generated numerically. The method is then applied to infer forces and potentials acting on the receptor of the toxin labeled by lanthanide-ion nanoparticles. Our scheme is applicable to any labeled biomolecule and results show its general relevance for membrane compartmentation. Cop. 2009 The American Physical Society. (10.1103/PhysRevLett.102.048103)
  DOI : 10.1103/PhysRevLett.102.048103
• Femtosecond spectroscopy from the perspective of a global multidimensional response function
  
  • Nuernberger Patrick
  • Lee Kevin F.
  • Joffre Manuel
  Accounts of Chemical Research, American Chemical Society, 2009, 42 (9), pp.1433-1441. At the microscopic level, multidimensional response functions, such as the nonlinear optical susceptibility or the time-ordered response function, are commonly used tools in nonlinear optical spectroscopy for determining the nonlinear polarization resulting from an arbitrary excitation. In this Account, we point out that the approach successfully developed for the nonlinear polarization can also be used in the case of a directly observable macroscopic quantity. This observable can be, for example, the electric field radiated in a nonlinear mixing experiment, the rate of fluorescence resulting from one- or two-photon absorption, or the rate of a photochemical reaction. For each of these physical processes, perturbation theory can be used to expand the measured quantity in a power series of the exciting field, and an appropriate global response function can be introduced for each order of perturbation. At order n, the multidimensional response function will depend on n variables (either time or frequency) and have the same general properties as the nonlinear susceptibility resulting, for example, from time invariance or causality. The global response function is introduced in this Account in close analogy with the nonlinear susceptibility or the time-ordered microscopic response. We discuss various applications of the global response function formalism. For example, it can be shown that in the weak field limit, a stationary signal induced in a time-invariant system is independent of the spectral phase of the exciting field. Although this result had been demonstrated previously, the global response function enables its derivation in a more general way because no specific microscopic model is needed. Multidimensional spectroscopy is obviously ideally suited to measure the global multidimensional response function. It is shown that the second (or third)-order response can be exactly measured with 2D (or 3D) spectroscopy by taking into account the exact shape of the exciting pulses. In the case of a 2D measurement of the third-order response, a particular projection of the complete 3D response function is actually measured. This projection can be related to a mixed time and frequency representation of the response function when the pulses are assumed to be infinitely short. We thus show that the global response function is a useful tool for deriving general results and that it should help in designing future experimental schemes for femtosecond spectroscopy. Cop. 2009 American Chemical Society. (10.1021/ar900001w)
  DOI : 10.1021/ar900001w
• Application of time-resolved circular dichroism to the study of conformational changes in photochemical and photobiological processes
  
  • Hache François
  Journal of Photochemistry and Photobiology A: Chemistry, Elsevier, 2009, 204 (2-3), pp.137-143. Circular dichroism is known to be a very sensitive probe of the molecular conformation and implementation of this technique in a pump-probe experiment is very appealing to access information on the dynamics of conformational changes occurring in photochemical or photobiological processes. In the past years, we have developed such techniques in various ways and applied them to several chemical or biological studies which are presented in this article. Applications concern spectroscopic studies of the excited state in ruthenium tris(bipyridyl) or tris(phenanthroline), dynamics of conformational changes in photoexcited binaphthol and study of the conformational changes occurring in photolyzed carboxy-myoglobin. Extension of these techniques towards biological issues such as protein folding is discussed. Cop. 2009 Elsevier B.V. All rights reserved. (10.1016/j.jphotochem.2009.03.012)
  DOI : 10.1016/j.jphotochem.2009.03.012
• Multimodal Multiphoton Imaging of Human Eye Tissues
  
  • Aptel Florent
  • Olivier Nicolas
  • Deniset Ariane
  • Plamann Karsten
  • Denis P.
  • Legeais Jean-Marc
  • Schanne-Klein Marie-Claire
  • Beaurepaire Emmanuel
  Investigative Ophthalmology & Visual Science, Association for Research in Vision and Ophthalmology, 2009, 50, pp.E-Abstract 3693. Purpose:To evaluate three combined modalities of multiphoton microscopy, second-harmonic generation (SHG), third-harmonic generation (THG), and two-photon-excited fluorescence (2PEF) for imaging cornea and trabecular meshwork in human intact eye tissue. Methods:A tunable femtosecond laser chain ( = 700-1250 nm) comprising a titanium-sapphire laser oscillator and an optical parametric oscillator was used to produce 2PEF (380-620nm), SHG (/2=430 or 600nm) and THG (/3= 400nm). Eight corneoscleral discs from eye bank and seven fresh corneal buttons obtained after penetrating keratoplasty were examined with water-immersion objectives. Forward and backward signals were detected and compared. Results:The three imaging modalities provide complementary information on intact tissue over the entire thickness of the cornea. THG imaging reveals the tissue morphology, including the epithelium structure with sub-cellular resolution. Polarization-resolved THG microscopy reveals stromal birefringent domains. In phenol-stained corneas, THG also reveals the keratocytes network. SHG imaging probes the distribution of stromal collagen lamellas organization. 2PEF imaging reveals the elastic component of the extra-cellular matrix and the distribution of fluorescent organelles (i.e. mitochondria) in stromal and epithelial cells. The trabeculum images show the three-dimensional organisation of the trabecular lamellas. Emission is predominantly forward directed for THG and SHG but in some cases, images can be recorded in the epi-direction. Conclusions:The combined imaging modalities of SHG, THG, and 2PEF microscopy are effective methods to evaluate cornea and trabecular meshwork microstructures in situ. This imaging approach should prove particularly appropriate for assessing corneal and glaucoma physiopathology, and might be amenable to in vivo diagnostics.
• Unobtrusive interferometer tracking by path length oscillation for multidimensional spectroscopy
  
  • Lee Kevin F.
  • Bonvalet Adeline
  • Nuernberger Patrick
  • Joffre Manuel
  Optics Express, Optical Society of America - OSA Publishing, 2009, 17 (15), pp.12379-12384. We track the path difference between interferometer arms with few-nanometer accuracy without adding optics to the beam path. We measure the interference of a helium-neon beam that copropagates through the interferometer with midinfrared pulses used for multidimensional spectroscopy. This can indicate motion, but not direction. By oscillating the path length of one arm with a mirror on a piezoelectric stack and monitoring the oscillations of the recombined helium-neon beam, the direction can be calculated, and the path delay can be continuously tracked. © 2009 Optical Society of America. (10.1364/OE.17.012379)
  DOI : 10.1364/OE.17.012379
• Apports récents des techniques de quantification de la fibrose pour l'examen anatomopathologique en transplantation rénale
  
  • Servais A.
  • Meas-Yedid V.
  • Morelon E.
  • Strupler Mathias
  • Schanne-Klein Marie-Claire
  • Legendre C.
  • Olivo-Marin J.-C.
  • Thervet É.
  Médecine/Sciences, EDP Sciences, 2009, 25 (11), pp.945-950. La néphropathie chronique d'allogreffe constitue la cause principale de perte des greffons rénaux à long terme. Elle peut être détectée précocement par des biopsies de dépistage effectuées de manière systématique. La classification usuelle, semi-quantitative, souffre d'une mauvaise reproductibilité. Diverses méthodes morphométriques ont donc été développées pour quantifier la fibrose interstitielle qui caractérise cette néphropathie. Certaines utilisent la coloration spécifique par le rouge Sirius. L'analyse d'image couleur par segmentation permet une quantification automatique, rapide et robuste de la fibrose interstitielle. Elle utilise une segmentation couleur associée à une analyse de couleur, de localisation spatiale et de forme sur des biopsies colorées au trichrome de Masson. À l'avenir, l'étude des collagènes fibrillaires par la génération de second harmonique pourrait permettre une approche spécifique des composants de la fibrose. (10.1051/medsci/20092511945)
  DOI : 10.1051/medsci/20092511945
• Suppression of perturbed free-induction decay and noise in experimental ultrafast pump-probe data
  
  • Nuernberger Patrick
  • Lee Kevin F.
  • Bonvalet Adeline
  • Polack Thomas
  • Vos Marten H.
  • Alexandrou Antigoni
  • Joffre Manuel
  Optics Letters, Optical Society of America - OSA Publishing, 2009, 34 (20), pp.3226-3228. We apply a Fourier filtering technique for the global removal of coherent contributions, like perturbed freeinduction decay, and noise, to experimental pump-probe spectra. A further filtering scheme gains access to spectra otherwise only recordable by scanning the probe's center frequency with adjustable spectral resolution. These methods cleanse pump-probe data and allow improved visualization and simpler analysis of the contained dynamics. We demonstrate these filters using visible pump/mid-infrared probe spectroscopy of ligand dissociation in carboxyhemoglobin. Cop. 2009 Optical Society of America. (10.1364/OL.34.003226)
  DOI : 10.1364/OL.34.003226
• Heme ligand binding properties and intradimer interactions in the full-length sensor protein Dos from Escherichia coli and its isolated heme domain
  
  • Lechauve C.
  • Bouzhir-Sima Latifa
  • Yamashita Taku
  • Marden M.C.
  • Vos Marten H.
  • Liebl Ursula
  • Kiger L.
  Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2009, 284 (52), pp.36146. Dos from Escherichia coli is a bacterial gas sensor protein comprising a heme-containing gas sensor domain and a phosphodiesterase catalytic domain. Using a combination of static light scattering and gel filtration experiments, we established that, as are many other sensor proteins, the full-length protein is dimeric. The full-length dimer (association constant <10 nm) is more stable than the dimeric heme domain (association constant ∼1 μm), and the dimer interface presumably includes both sensor and catalytic domains. Ultrafast spectroscopic studies showed little influence of the catalytic domain on kinetic processes in the direct vicinity of the heme. By contrast, the properties of ligand (CO and O2) binding to the heme in the sensor domain, occurring on a microsecond to second time scale, were found to be influenced by (i) the presence of the catalytic domain, (ii) the dimerization state, and in dimers, (iii) the ligation state of the other subunit. These results imply allosteric interactions within dimers. Steady-state titrations demonstrated marked cooperativity in oxygen binding to both the full-length protein and the isolated heme domain, a feature not reported to date for any dimeric sensor protein. Analysis of a variety of time-resolved experiments showed that Met-95 plays a major role in the intradimer interactions. The intrinsic binding and dissociation rates of Met-95 to the heme were modulated ∼10-fold by intradimer and sensor-catalytic domain interactions. Dimerization effects were also observed for cyanide binding to the ferric heme domains, suggesting a similar role for Met-95 in ferric proteins. (10.1074/jbc.M109.066811)
  DOI : 10.1074/jbc.M109.066811
• Removing cross-phase modulation from midinfrared chirped-pulse upconversion spectra
  
  • Lee Kevin F.
  • Nuernberger Patrick
  • Bonvalet Adeline
  • Joffre Manuel
  Optics Express, Optical Society of America - OSA Publishing, 2009, 17 (21), pp.18738-18744. We observe that narrow spectral features in mid-infrared spectra obtained by chirped-pulse up-conversion are strongly distorted by crossphase modulation between the mid-infrared field and the chirped pulse. We discuss the consequences of this effect on spectral resolution, and introduce a correction method that recovers masked lines. This simple correction can be applied either when the upconverted field is fully characterized, such as in multidimensional spectroscopy, or when causality can be used, such as in absorption spectroscopy, which we demonstrate experimentally. Cop.2009 Optical Society of America. (10.1364/OE.17.018738)
  DOI : 10.1364/OE.17.018738
• Femto-second ultrashort laser wakefield electron bunch-duration measurements: a prism-based dispersion visible-to-IR spectrometer
  
  • Lim J.
  • Faure Jérôme
  • Gallot Guilhem
  • Lundh O.
  • Rechatin C.
  • Malka Victor
  , 2009, pp.735919. (10.1117/12.829134)
  DOI : 10.1117/12.829134
• Extended fano model of extraordinary electromagnetic transmission through subwavelength hole arrays in the terahertz domain
  
  • Masson Jean-Baptiste
  • Podzorov Alexander
  • Gallot Guilhem
  Optics Express, Optical Society of America - OSA Publishing, 2009, 17 (17), pp.15280-15291. We developed an extended Fano model describing the Extraordinary Electromagnetic Transmission (EET) through arrays of subwavelength apertures, based on terahertz transmission measurements of arrays of various hole size and shapes. Considering a frequency-dependent coupling between resonant and non-resonant pathways, this model gives access to a simple analytical description of EET, provides good agreement with experimental data, and offers new parameters describing the influence of the hole size and shape on the transmitted signal. Cop. 2009 Optical Society of America. (10.1364/OE.17.015280)
  DOI : 10.1364/OE.17.015280