Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.

The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.

Utilization of interferometric light microscopy for the rapid analysis of virus abundance in a river.

There is a constant need for direct counting of biotic nanoparticles such as viruses to unravel river functioning. We used, for the first time in freshwater, a new method based on interferometry differentiating viruses from other particles such as membrane vesicles. In the French Marne River, viruses represented between 42 and 72% of the particles. A spring monitoring in 2014 revealed their increase (2.1 × 107 to 2.1 × 108 mL-1) linked to an increase in algal biomass and diversity of bacterial plankton. Predicted virus size distributions were in agreement with transmission electron microscopy analysis suggesting a dominance of large viruses (≥60 nm).

Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans.

There is a huge abundance of viruses and membrane vesicles in seawater. We describe a new full-field, incoherently illuminated, shot-noise limited, common-path interferometric detection method that we couple with the analysis of Brownian motion to detect, quantify, and differentiate biotic nanoparticles. We validated the method with calibrated nanoparticles and homogeneous DNA or RNA viruses. The smallest virus size that we characterized with a suitable signal-to-noise ratio was around 30 nm in diameter. Analysis of Brownian motions revealed anisotropic trajectories for myoviruses.We further applied the method for vesicles detection and for analysis of coastal and oligotrophic samples from Tara Oceans circumnavigation.

Calibration procedures for quantitative multiple wavelengths reflectance microscopy.

In order to characterize surface chemo-mechanical phenomena driving micro-electro-mechanical systems (MEMSs) behavior, it has been previously proposed to use reflected intensity fields obtained from a standard microscope for different illumination wavelengths. Wavelength-dependent and -independent reflectivity fields are obtained from these images, provided the relative reflectance sensitivities ratio can be identified. This contribution focuses on the necessary calibration procedures and mathematical methods allowing for a quantitative conversion from a mechanically induced reflectivity field to a surface rotation field, therefore paving the way for a quantitative mechanical analysis of MEMS under chemical loading.

Mapping fluxes of radicals from the combination of electrochemical activation and optical microscopy.

The coating of gold (Au) electrode surfaces with nitrophenyl (NP) layers is studied by combination of electrochemical actuation and optical detection. The electrochemical actuation of the reduction of the nitrobenzenediazonium (NBD) precursor is used to generate NP radicals and therefore initiate the electrografting. The electrografting process is followed in situ and in real time by light reflectivity microscopy imaging, allowing for spatio-temporal imaging with sub-micrometer lateral resolution and sub-nanometer thickness sensitivity of the local growth of a transparent organic coating onto a reflecting Au electrode. The interest of the electrochemical actuation resides in its ability to finely control the grafting rate of the NP layer through the electrode potential. Coupling the electrochemical actuation with microscopic imaging of the electrode surface allows quantitative estimates of the local grafting rates and subsequently a real time and in situ mapping of the reacting fluxes of NP radicals on the surface. Over the 2 orders of magnitude range of grafting rates (from 0.04 to 4 nm s(-1)), it is demonstrated that the edge of Au electrodes are grafted -1.3 times more quickly than their centre, illustrating the manifestation of edge-effects on flux distribution at an electrode. A model is proposed to explain the observed edge-effect, it relies on the short lifetime of the intermediate NP radical species.

Scanning electrochemical microscopy monitoring in microcantilever platforms.

The deflection of cantilever systems may be performed by an indirect electrochemical method that consists of measuring the local cantilever activity and deflection in a feedback generation-collection configuration of the SECM. This is illustrated during the electrochemically assisted adsorption of Br onto a gold-coated cantilever, either in its pristine state or previously coated with a thin organic barrier. It is further extended to the adsorption of an antibody in a heterogeneous immunoassay at an allergen-coated microcantilever platform. In both reactions, the cantilever deflection is qualitatively detected from the SECM tip current measurement and a quantitative estimate is obtained through modeling. This electroanalytical strategy provides an alternative approach to standard optical detection. It can overcome some limitations of the optical method by allowing electrochemical characterization of nonconductive cantilevers and appropriate use for closed systems.

Mechanism of lipid nanodrop spreading in a case of asymmetric wetting.

Using the surface enhanced ellipsometric contrast microscopy, we follow the last stage of the spreading of egg phosphatidylcholine nanodroplets on a hydrophilic substrate in a humid atmosphere, focusing on the vanishing trilayer in terraced droplets reduced to coexisting monolayer and trilayer. We find that the line interface between them exhibits two coexisting states, one mobile and one fixed. From there, it is possible to elucidate the internal structure and the spreading mechanism of the stratified liquid in a case of asymmetric wetting, i.e., where the lipid film is made of an odd number of leaflets.

Polarization induced instabilities in external four-mirror Fabry-Perot cavities.

Various four-mirror optical resonators are studied from the perspective of realizing passive stacking cavities. A comparative study of the mechanical stability is provided. The polarization properties of the cavity eigenmodes are described, and it is shown that the effect of mirror misalignments (or motions) induces polarization and stacking power instabilities. These instabilities increase with the finesse of the Fabry-Perot cavity. A tetrahedral configuration of the four mirrors is found to minimize the consequences of the mirrors' motion and misalignment by reducing the instability parameter by at least 2 orders of magnitude.