Kinetics of CrPV and HCV IRES-mediated eukaryotic translation using single-molecule fluorescence microscopy.

Protein synthesis is a complex multistep process involving many factors that need to interact in a coordinated manner to properly translate the messenger RNA. As translating ribosomes cannot be synchronized over many elongation cycles, single-molecule studies have been introduced to bring a deeper understanding of prokaryotic translation dynamics. Extending this approach to eukaryotic translation is very appealing, but initiation and specific labeling of the ribosomes are much more complicated. Here, we use a noncanonical translation initiation based on internal ribosome entry sites (IRES), and we monitor the passage of individual, unmodified mammalian ribosomes at specific fluorescent milestones along mRNA. We explore initiation by two types of IRES, the intergenic IRES of cricket paralysis virus (CrPV) and the hepatitis C (HCV) IRES, and show that they both strongly limit the rate of the first elongation steps compared to the following ones, suggesting that those first elongation cycles do not correspond to a canonical elongation. This new system opens the possibility of studying both IRES-mediated initiation and elongation kinetics of eukaryotic translation and will undoubtedly be a valuable tool to investigate the role of translation machinery modifications in human diseases.

Ferroelectric Texture of Individual Barium Titanate Nanocrystals.

Ferroelectric materials display exotic polarization textures at the nanoscale that could be used to improve the energetic efficiency of electronic components. The vast majority of studies were conducted in two dimensions on thin films that can be further nanostructured, but very few studies address the situation of individual isolated nanocrystals (NCs) synthesized in solution, while such structures could have other fields of applications. In this work, we experimentally and theoretically studied the polarization texture of ferroelectric barium titanate (BaTiO3, BTO) NCs attached to a conductive substrate and surrounded by air. We synthesized NCs of well-defined quasicubic shape and 160 nm average size that conserve the tetragonal structure of BTO at room temperature. We then investigated the inverse piezoelectric properties of such pristine individual NCs by vector piezoresponse force microscopy (PFM), taking particular care to suppress electrostatic artifacts. In all of the NCs studied, we could not detect any vertical PFM signal, and the maps of the lateral response all displayed larger displacement amplitude on the edges with deformations converging toward the center. Using field phase simulations dedicated to ferroelectric nanostructures, we were able to predict the equilibrium polarization texture. These simulations revealed that the NC core is composed of 180° up and down domains defining the polar axis that rotate by 90° in the two facets orthogonal to this axis, eventually lying within these planes forming a layer of about 10 nm thickness mainly composed of 180° domains along an edge. From this polarization distribution, we predicted the lateral PFM response, which was revealed to be in very good qualitative agreement with the experimental observations. This work positions PFM as a relevant tool to evaluate the potential of complex ferroelectric nanostructures to be used as sensors.

Calibrating optical tweezers with Bayesian inference.

We present a new method for calibrating an optical-tweezer setup that does not depend on input parameters and is less affected by systematic errors like drift of the setup. It is based on an inference approach that uses Bayesian probability to infer the diffusion coefficient and the potential felt by a bead trapped in an optical or magnetic trap. It exploits a much larger amount of the information stored in the recorded bead trajectory than standard calibration approaches. We demonstrate that this method outperforms the equipartition method and the power-spectrum method in input information required (bead radius and trajectory length) and in output accuracy.

Simultaneous optically sectioned fluorescence and optical coherence microscopy with full-field illumination.

Full-field optical coherence microscopy (FF-OCM) and optically sectioned fluorescence microscopy are two imaging techniques that are implemented here in a novel dual modality instrument. The two imaging modalities use a broad field illumination to acquire the entire field of view without raster scanning. Optical sectioning is achieved in both imaging modalities owing to the coherence gating property of light for FF-OCM, and a structured illumination setup for fluorescence microscopy. Complementary image data are provided by the dual modality instrument in the context of biological tissue screening. FF-OCM imaging modality shows the tissue microarchitecture, while fluorescence microscopy highlights specific tissue features with cellular-level resolution by using targeting contrast agents. Complementary tissue morphology and biochemical features could potentially improve the understanding of cellular functions and disease diagnosis.

Simultaneous calibration of optical tweezers spring constant and position detector response.

We demonstrate a fast and direct calibration method for systems using a single laser for optical tweezers and particle position detection. The method takes direct advantage of back-focal-plane interferometry measuring not an absolute but a differential position, i.e. the position of the trapped particle relative to the center of the optical tweezers. Therefore, a fast step-wise motion of the optical tweezers yields the impulse response of the trapped particle. Calibration parameters such as the detector's spatial and temporal response and the spring constant of the optical tweezers then follow readily from fitting the measured impulse response.

Statistical Tests for Force Inference in Heterogeneous Environments.

We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed drift includes a "spurious" force term when the diffusivity varies in space. We show how Bayesian inference can be leveraged to reliably infer forces by taking into account such spurious forces of unknown amplitude as well as experimental sources of error. The method is based on marginalizing the force posterior over all possible spurious force contributions. The approach is combined with a Bayes factor statistical test for the presence of forces. The performance of our method is investigated analytically, numerically and tested on experimental data sets. The main results are obtained in a closed form allowing for direct exploration of their properties and fast computation. The method is incorporated into TRamWAy, an open-source software platform for automated analysis of biomolecule trajectories.