Growth limiting conditions and denitrification govern extent and frequency of volume detachment of biofilms

This study aims at evaluating the mechanisms of biofilm detachment with regard of the physical properties of the biofilm. Biofilms were developed in Couette–Taylor reactor under controlled hydrodynamic conditions and under different environmental growth conditions. Five different conditions were tested and lead to the formation of two aerobic heterotrophic biofilms (aeHB1 and aeHB2), a mixed autotrophic and heterotrophic biofilm (MAHB) and two anoxic heterotrophic biofilms (anHB1 and anHB2). Biofilm detachment was evaluated by monitoring the size of the detached particles (using light-scattering) as well as the biofilm physical properties (using CCD camera and image analysis). Results indicate that volume erosion of large biofilm particles with size ranging from 50 to 500 lm dominated the biomass loss for all biofilms. Surface erosion of small particles with size lower than 20 lm dominates biofilm detachment in number. The extent of the volume detachment events was governed by the size of the biofilm surface heterogeneities (i.e., the absolute biofilm roughness) but never impacted more than 80% of the mean biofilm thickness due to the highly cohesive basal layer. Anoxic biofilms were smoother and thinner than aerobic biofilms and thus associated with the detachment of smaller particles. Our results contradict the simplifying assumption of surface detachment that is considered in many biofilm models and suggest that discrete volume events should be considered

Using the TEI as a pivot format for oral and multimodal language corpora

International audiencePresentation of the work of the GT2 team of the Consortium IRCOM.The goal of the project is to be able to convert classic oral transcription tools in the TEI format

Fibrillogenesis from nanosurfaces: multiphoton imaging and stereological analysis of collagen 3D self-assembly dynamics

International audienceThe assembly of proteins into fibrillar structures is an important process that concerns different biological contexts, including molecular medicine and functional biomaterials. Engineering of hybrid biomaterials can advantageously provide synergetic interactions of the biopolymers with an inorganic component to ensure specific supramolecular organization and dynamics. To this aim, we designed hybrid systems associating collagen and surface-functionalized silica particles and we built a new strategy to investigate fibrillogenesis processes in such multicomponents systems, working at the crossroads of chemistry, physics and mathematics. The self-assembly process was investigated by bimodal multiphoton imaging coupling second harmonic generation (SHG) and 2 photon excited fluorescence (2PEF). The in-depth spatial characterization of the system was further achieved using the three-dimensional analysis of the SHG/2PEF data via mathematical morphology processing. Quantitation of collagen distribution around particles offers strong evidence that the chemically induced confinement of the protein on the silica nanosurfaces has a key influence on the spatial extension of fibrillogenesis. This new approach is unique in the information it can provide on 3D dynamic hybrid systems and may be extended to other associations of fibrillar molecules with optically responsive nano-objects

Clément Hébert (a), Davy Carole (c), Franck Omnes (a), Etienne Gheeraert (a)

International audienceNanopores in insulating solid state membranes have recently emerged as potential candidates for sorting, probing and manipulating biopolymers, such as DNA, RNA and proteins in their native environment. Here a simple, fast and cost-effective etching technique to create nanopores in diamond membrane by self-assembled Ni nanoparticles is proposed. In this process, a diamond film is annealed with thin Ni layers at 800-850 degrees C in hydrogen atmosphere. Carbon from the diamond-metal interface is removed as methane by the help of Ni nanoparticles as catalyst and consequently, the nanoparticles enter the crystal volume. In order to optimize the etching process and understand the mechanism the annealed polycrystalline and nanocrystalline diamond films were analyzed by X-ray photoelectron spectroscopy (XPS), and the gas composition during the process was investigated by quadrupole mass spectrometer. With this technique, nanopores with lateral size in the range of 15-225 nm and as deep as about 550 nm in diamond membrane were produced without any need for lithography process. A model for etching diamond with Ni explaining the mechanism is discussed

Second Harmonic Generation imaging of collagen fibrillogenesis

International audienceDevelopment of nonlinear optical microscopy has significantly improved three-dimensional (3D) imaging of biological tissues in recent years. In particular, collagen has been shown to exhibit endogenous Second Harmonic Generation (SHG) signals and SHG microscopy has proved to enable the visualization of collagen architecture in tissues with unequalled contrast and specificity [1, 2]. Type I collagen is a major structural protein in mammals and shows highly structured macromolecular organizations specific to each tissue. It is synthesized by cells as triple helices, which self-assemble outside the cells into fibrils that further form fibers, lamellae or other three-dimensional (3D) networks. This assembly mechanism depends critically on the collagen concentration, as well as on the temperature, pH and ionic strength of the solution in vitro. Thorough characterization of collagen fibrillogenesis is crucial to understand the biological mechanisms of tissue formation and tissue remodeling in response to a variety of pathologies. Booming of tissue engineering furthermore requires advanced in situ quantitative imaging techniques to verify whether the tissue substitutes display appropriate biomimetic 3D organization for cell culture scaffolds or functional implants. In this study, we continuously monitored the formation of collagen fibrils by time-lapse SHG microscopy [3]. Fibrillogenesis was triggered in a controlled way by increasing the pH in a dilute solution of collagen I. The fibril density was measured every 10 to 20 minutes as the number of voxels with significant SHG signal in 3D image stacks [1]. Our results showed reproducible dynamics of fibrillar collagen formation that could be changed by tuning the pH (see figure 1). We also monitored the growth of single fibrils and measured the length increase over time, which had never been reported before using an optical technique. We then correlated these SHG images to TEM images at nanometer-scale resolution by blocking the fibrillogenesis at early stages and drying the samples. It showed that SHG microscopy allows imaging of fibrils with a diameter down to 30-50 nm in our experimental conditions. We finally investigated surface-mediated fibrillogenesis by adding silica nanoparticles to the solution [4]. We used Two-Photon excited fluorescence (2PEF) microscopy to visualize the fluorescently-died nanoparticles and quantify the self-assembly of collagen around these nanoparticles. In conclusion, SHG microscopy enabled sensitive and well contrasted 3D visualization of collagen fibrillogenesis in a non invasive way. This work illustrates the potential of SHG microscopy for the rational design and characterization of collagen-based biomaterials. 0 200 400 600 800 0.0 0.5 1.0 1.5 2.0 2.5 Pixel fraction (%) Time (min) (d) (a) (c) (b) Fig 1. 3D reconstruction of SHG images of collagen fibrillogenesis (at pH=6.5) after a) 170 b) 410 and c) 730 minutes; d) Experimental kinetics of fibril density in the SHG images (black dots) with exponential fitting (red line). References [1] M

Etude exploratoire sur l'utilisation d'une base de données de corpus oraux d'interactions naturelles pour l'enseignement et l'apprentissage des pratiques sociales et langagières du français

International audienc

Uptake of fatty acids by the enterocyte: New insights gained from mathematical modeling

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A focus reduction neutralization assay for hepatitis C virus neutralizing antibodies

BACKGROUND/AIM: The role of humoral immunity in hepatitis C virus (HCV) infection is poorly understood. Nevertheless, there is increasing interest in characterizing the neutralizing antibodies in the serum of HCV-infected patients. Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses. Based on the recent development of a HCV cell culture system using the genotype 2 JFH-1-strain, we developed a focus reduction assay for HCV-neutralizing antibodies. METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted. The neutralizing anti-HCV antibodies titers of purified serum immunoglobulin samples from seventy-seven individuals were determined using a 50% focus reduction neutralization assay. Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. IgG antibodies were first purified from each serum in order to avoid the facilitating effect of HDL on HCV entry. RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18. The assay was compared with a commercial HCV ELISA and exhibited specificity and sensitivity values of 100% and 96.5%, respectively, and good reproducibility (with intra-assay and inter-assay coefficients of variation of 6.7% and 12.6%, respectively). The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples. The neutralizing antibodies titers were 2.13 log (1:134) for homologous samples from HCV genotype 2 infected patients harboring the same genotype as JFH-1 and 1.93 log (1:85) for heterologous samples from patients infected by genotypes other than type 2. These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system. CONCLUSION: This study presents a simple, specific and reproducible cell culture-based assay for determination of HCV-neutralizing antibodies in human sera. The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies

Morphological investigation of polylactide/microfibrillated cellulose composites

Optical microscopy and transmission electron microscopy have been used to investigate the morphology of polylactide (PLA)/microfibrillated cellulose (MFC) composites prepared by: compression molding of wet-comingled MFC and PLA latex or powder, twin-screw extrusion of the wet-comingled compounds, and solvent mixing of PLA with MFC or acetylated MFC. Compression molding of wet-comingled MFC and PLA latex or powder compounds resulted in a cellular MFC network, whereas solvent-cast films showed a more uniform dispersion of MFC fibers. Somewhat lower aggregate diameters observed in the acetylated MFC were assumed to be due to decreased MFC hydrophilicity and improved chemical affinity with the PLA matrix. The MFC networks in the commingled compounds were severely disrupted after twin-screw extrusion. This confirmed the limited deformability of the networks inferred from the extensive syneresis during the initial compression molding step, and accounted for substantial losses in stiffness reinforcement by the MFC after extrusio