Publications

2011

• Quantitative assessment of collagen i liquid crystal organizations: Role of ionic force and acidic solvent, and evidence of new phases
  
  • de Sa Peixoto Paulo
  • Deniset-Besseau Ariane
  • Schanne-Klein Marie-Claire
  • Mosser Gervaise
  Soft Matter, Royal Society of Chemistry, 2011, 7 (23), pp.11203. Collagen I is the major structural protein in mammals where it exhibits highly organized fibrillar distributions in connective tissues. In vitro, acidic solutions of collagen I display lyotropic liquid crystal organization. These concentrated organized liquid phases can be stabilized by a pH increase to generate in vitro fibrillar matrices with specific organization. The aim of this work is to understand the mechanisms responsible for liquid crystal chirality at acidic pH in order to guide the synthesis of collagen matrices reproducing the great diversity of organizations found in biological tissues. For this purpose, we quantitatively analyze collagen liquid crystal organization by use of multiphoton microscopy, combining fluorescence and second harmonic generation contrasts. The concentration of the isotropic to liquid crystal phase transition and the evolution of the half pitch of the helical phase with collagen concentration are reported in five physico-chemical conditions using hydrochloric and acetic acids at different pHs and ionic strengths. A new phase transition is observed in highly concentrated solutions ranging from 90 mg ml-1 to 300 mg ml-1 depending on the solvent. Our results bring new quantitative information on collagen chemical physics and further substantiate the on-going analysis of the driving parameters generating twists in liquid crystals. These findings could be advantageously exploited to develop new strategies and protocols for tissue engineering. This is crucial for fundamental studies of cell behavior in biomimetic three-dimensional environments and for medical and pharmaceutical applications. Cop. The Royal Society of Chemistry 2011. (10.1039/c1sm06076g)
  DOI : 10.1039/c1sm06076g
• Toward high-content/high-throughput imaging and analysis of embryonic morphogenesis
  
  • Truong Thai V.
  • Supatto Willy
  Genesis - The Journal of Genetics and Development, Wiley-Blackwell, 2011, 49 (7), pp.555. In vivo study of embryonic morphogenesis tremendously benefits from recent advances in live microscopy and computational analyses. Quantitative and automated investigation of morphogenetic processes opens the field to high-content and high-throughput strategies. Following experimental workflow currently developed in cell biology, we identify the key challenges for applying such strategies in developmental biology. We review the recent progress in embryo preparation and manipulation, live imaging, data registration, image segmentation, feature computation, and data mining dedicated to the study of embryonic morphogenesis. We discuss a selection of pioneering studies that tackled the current methodological bottlenecks and illustrated the investigation of morphogenetic processes in vivo using quantitative and automated imaging and analysis of hundreds or thousands of cells simultaneously, paving the way for high-content/high-throughput strategies and systems analysis of embryonic morphogenesis. Cop. 2011 Wiley-Liss, Inc. (10.1002/dvg.20760)
  DOI : 10.1002/dvg.20760
• 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
• 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
• 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.
• 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