Publications

2011

• Biological applications of rare-earth based nanoparticles
  
  • Bouzigues Cédric
  • Gacoin T.
  • Alexandrou Antigoni
  ACS Nano, American Chemical Society, 2011, 5 (11), pp.8488. Biomedicine and cell and molecular biology require powerful imaging techniques of the single molecule scale to the whole organism, either for fundamental science or diagnosis. These applications are however often limited by the optical properties of the available probes. Moreover, in cell biology, the measurement of the cell response with spatial and temporal resolution is a central instrumental problem. This has been one of the main motivations for the development of new probes and imaging techniques either for biomolecule labeling or detection of an intracellular signaling species. The weak photostability of genetically encoded probes or organic dyes has motivated the interest for different types of nanoparticles for imaging such as quantum dots, nanodiamonds, dye-doped silica particles, or metallic nanoparticles. One of the most active fields of research in the past decade has thus been the development of rare-earth based nanoparticles, whose optical properties and low cytotoxicity are promising for biological applications. Attractive properties of rare-earth based nanoparticles include high photostability, absence of blinking, extremely narrow emission lines, large Stokes shifts, long lifetimes that can be exploited for retarded detection schemes, and facile functionalization strategies. The use of specific ions in their compositions can be moreover exploited for oxidant detection or for implementing potent contrast agents for magnetic resonance imaging. In this review, we present these different applications of rare-earth nanoparticles for biomolecule detection and imaging in vitro, in living cells or in small animals. We highlight how chemical composition tuning and surface functionalization lead to specific properties, which can be used for different imaging modalities. We discuss their performances for imaging in comparison with other probes and to what extent they could constitute a central tool in the future of molecular and cell biology. Cop. 2011 American Chemical Society. (10.1021/nn202378b)
  DOI : 10.1021/nn202378b
• Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging
  
  • Luengo-Oroz Miguel Angel
  • Savy Thierry
  • Rubio-Guivernau José L.
  • Duloquin Louise
  • Faure Emmanuel
  • Olivier Nicolas
  • Ledesma-Carbayo María Jesús
  • Debarre Delphine
  • Bourgine Paul
  • Beaurepaire Emmanuel
  • Peyriéras Nadine
  , 2011, pp.1561-1564. The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and μm spatial resolution. (10.1109/ISBI.2011.5872699)
  DOI : 10.1109/ISBI.2011.5872699
• Dynamics of NO interacting with soluble guanylate cyclase from 1 ps to 0.1 s and induced structural transitions
  
  • Yoo Byung-Kuk
  • Lamarre Isabelle
  • Martin Jean-Louis
  • Rappaport Fabrice
  • Negrerie Michel
  BMC Pharmacology, BioMed Central, 2011, 11 (Suppl 1), pp.P77.
• Vibrational Motions Associated with Primary Processes in Bacteriorhodopsin Studied by Coherent Infrared Emission Spectroscopy
  
  • Groma Geza I.
  • Colonna Anne
  • Martin Jean-Louis
  • Vos Marten H.
  Biophysical Journal, Biophysical Society, 2011, 100 (6), pp.1578. The primary energetic processes driving the functional proton pump of bacteriorhodopsin take place in the form of complex molecular dynamic events after excitation of the retinal chromophore into the Franck-Condon state. These early events include a strong electronic polarization, skeletal stretching, and all-trans-to-13-cis isomerization upon formation of the J intermediate. The effectiveness of the photoreaction is ensured by a conical intersection between the electronic excited and ground states, providing highly nonadiabatic coupling to nuclear motions. Here, we study real-time vibrational coherences associated with these motions by analyzing light-induced infrared emission from oriented purple membranes in the 750-1400 cm(-1) region. The experimental technique applied is based on second-order femtosecond difference frequency generation on macroscopically ordered samples that also yield information on phase and direction of the underlying motions. Concerted use of several analysis methods resulted in the isolation and characterization of seven different vibrational modes assigned as C-C stretches, out-of-plane methyl rocks, and hydrogen out-of-plane wags, whereas no in-plane H rock was found. Based on their lifetimes and several other criteria, we deduce that the majority of the observed modes take place on the potential energy surface of the excited electronic state. In particular, the direction sensitivity provides experimental evidence for large intermediate distortions of the retinal plane during the excited-state isomerization process. (10.1016/j.bpj.2011.02.011)
  DOI : 10.1016/j.bpj.2011.02.011
• Combining rails and anchors with laser forcing for selective manipulation within 2D droplet arrays.
  
  • Fradet Etienne
  • Mcdougall Craig
  • Abbyad Paul
  • Dangla Rémi
  • Mcgloin David
  • Baroud Charles N.
  Lab on a Chip, Royal Society of Chemistry, 2011, 11 (24), pp.4228-4234. We demonstrate the combination of a rails and anchors microfluidic system with laser forcing to enable the creation of highly controllable 2D droplet arrays. Water droplets residing in an oil phase can be pinned to anchor holes made in the base of a microfluidic channel, enabling the creation of arrays by the appropriate patterning of such holes. The introduction of laser forcing, via laser induced thermocapillary forces to anchored droplets, enables the selective extraction of particular droplets from an array. We also demonstrate that such anchor arrays can be filled with multiple, in our case two, droplets each and that if such droplets have different chemical contents, the application of a laser at their interface triggers their merging and a chemical reaction to take place. Finally by adding guiding rails within the microfluidic structure we can selectively fill large scale arrays with monodisperse droplets with significant control over their contents. In this way we make a droplet array filled with 96 droplets containing different concentrations of fluorescent microparticles. (10.1039/C1LC20541B)
  DOI : 10.1039/C1LC20541B
• Strong Ligand-Protein Interactions Revealed by Ultrafast Infrared Spectroscopy of CO in the Heme Pocket of the Oxygen Sensor FixL
  
  • Nuernberger Patrick
  • Lee Kevin F.
  • Bonvalet Adeline
  • Bouzhir-Sima Latifa
  • Lambry Jean-Christophe
  • Liebl Ursula
  • Joffre Manuel
  • Vos Marten H.
  Journal of the American Chemical Society, American Chemical Society, 2011, 133 (43), pp.17110. In heme-based sensor proteins, ligand binding to heme in a sensor domain induces conformational changes that eventually lead to changes in enzymatic activity of an associated catalytic domain. The bacterial oxygen sensor FixL is the best-studied example of these proteins and displays marked differences in dynamic behavior with respect to model globin proteins. We report a mid-IR study of the configuration and ultrafast dynamics of CO in the distal heme pocket site of the sensor PAS domain FixLH, employing a recently developed method that provides a unique combination of high spectral resolution and range and high sensitivity. Anisotropy measurements indicate that CO rotates toward the heme plane upon dissociation, as is the case in globins. Remarkably, CO bound to the heme iron is tilted by similar to 30 degrees with respect to the heme normal, which contrasts to the situation in myoglobin and in present FixLH-CO X-ray crystal structure models. This implies protein-environment-induced strain on the ligand, which is possibly at the origin of a very rapid docking-site population in a single conformation. Our observations likely explain the unusually low affinity of FixL for CO that is at the origin of the weak ligand discrimination between CO and O(2). Moreover, we observe orders of magnitude faster vibrational relaxation of dissociated CO in FixL than in globins, implying strong interactions of the ligand with the distal heme pocket environment. Finally, in the R220H FixLH mutant protein, where CO is H-bonded to a distal histidine, we demonstrate that the H-bond is maintained during photolysis. Comparison with extensively studied globin proteins unveils a surprisingly rich variety in both structural and dynamic properties of the interaction of a diatomic ligand with the ubiquitous b-type heme-proximal histidine system in different distal pockets. (10.1021/ja204549n)
  DOI : 10.1021/ja204549n
• From Cilia Hydrodynamics to Zebrafish Embryonic Development
  
  • Supatto Willy
  • Vermot Julien
  , 2011, pp.vol. 95, 33-66. Embryonic development involves the cellular integration of chemical and physical stimuli. A key physical input is the mechanical stress generated during embryonic morphogenesis. This process necessitates tensile forces at the tissue scale such as during axis elongation and budding, as well as at the cellular scale when cells migrate and contract. Furthermore, cells can generate forces using motile cilia to produce flow. Cilia-driven flows are critical throughout embryonic development but little is known about the diversity of the forces they exert and the role of the mechanical stresses they generate. In this chapter, through an examination of zebrafish development, we highlight what is known about the role of hydrodynamics mediated by beating cilia and examine the physical features of flow fields from the modeling and experimental perspectives. We review imaging strategies to visualize and quantify beating cilia and the flow they generate in vivo. Finally, we describe the function of hydrodynamics during left-right embryonic patterning and inner ear development. Ideally, continued progress in these areas will help to address a key conceptual problem in developmental biology, which is to understand the interplay between environmental constraints and genetic control during morphogenesis (10.1016/B978-0-12-385065-2.00002-5)
  DOI : 10.1016/B978-0-12-385065-2.00002-5
• Measurement of circular dichroism dynamics in a nanosecond temperature-jump experiment
  
  • Khuc Mai-Thu
  • Mendonça Lucille
  • Sharma S.
  • Volk M.
  • Solinas Xavier
  • Hache François
  Review of Scientific Instruments, American Institute of Physics, 2011, 82 (5). The use of a fast temperature jump (T-jump) is a very powerful experiment aiming at studying protein denaturation dynamics. However, probing the secondary structure is a difficult challenge and rarely yields quantitative values. We present the technical implementation of far-UV circular dichroism in a nanosecond T-jump experiment and show that this experiment allows us to follow quantitatively the change in the helical fraction of a poly(glutamic acid) peptide during its thermal denaturation with 12 ns time resolution. Cop. 2011 American Institute of Physics. (10.1063/1.3592331)
  DOI : 10.1063/1.3592331