Role of aIF5B in archaeal translation initiation.

In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.

Crystallization within Intermediate Amorphous Phases Determines the Polycrystallinity of Nanoparticles from Coprecipitation.

Intense research on nanocrystals synthesized in solution is motivated by their original physical properties, which are determined by their sizes and shapes on various scales. However, morphology control on the nanoscale is limited by our understanding of crystallization, which is challenged by the now well-established prevalence of noncrystalline intermediates. In particular, the impact of such intermediates on the final sizes and crystal quality remains unclear because the characterization of their evolution on the nanometer and millisecond scales with nonperturbative analyses has remained a challenge. Here we use in situ X-ray scattering to show that the nucleation and growth of YVO4:Eu nanocrystals is spatially restrained within amorphous, nanometer-scaled intermediates. The reactivity and size of these amorphous intermediates determine (i) the mono versus polycrystalline character of final crystals and (ii) the size of final crystals. This implies that designing amorphous intermediates themselves that form in <6 ms is one of the keys to controlled bottom-up syntheses of optimized nanoparticles.

Discriminative and quantitative analysis of norepinephrine and epinephrine by surface-enhanced Raman spectroscopy with gold nanoparticle suspensions.

Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical technique capable of increasing the Raman signal of an analyte using specific nanostructures. The close contact between those nanostructures, usually a suspension of nanoparticles, and the molecule of interest produces an important exaltation of the intensity of the Raman signal. Even if the exaltation leads to an improvement of Raman spectroscopy sensitivity, the complexity of the SERS signal and the numbers of parameters to be controlled allow the use of SERS for detection rather than quantification. The aim of this study was to develop a robust discriminative and quantitative analysis in accordance with pharmaceutical standards. In this present work, we develop a discriminative and quantitative analysis based on the previous optimized parameters obtained by the design of experiments fixed for norepinephrine (NOR) and extended to epinephrine (EPI) which are two neurotransmitters with very similar structures. Studying the short evolution of the Raman signal intensity over time coupled with chemometric tools allowed the identification of outliers and their removal from the data set. The discriminant analysis showed an excellent separation of EPI and NOR. The comparative analysis of the data showed the superiority of the multivariate analysis after logarithmic transformation. The quantitative analysis allowed the development of robust quantification models from several gold nanoparticle batches with limits of quantification of 32 µg/mL for NOR and below 20 µg/mL for EPI even though no Raman signal is observable for such concentrations. This study improves SERS analysis over ultrasensitive detection for discrimination and quantification using a handheld Raman spectrometer.

Nuclear Magnetic Resonance Spectroscopy: A Multifaceted Toolbox to Probe Structure, Dynamics, Interactions, and Real-Time In Situ Release Kinetics in Peptide-Liposome Formulations.

Liposomal formulations represent attractive biocompatible and tunable drug delivery systems for peptide drugs. Among the tools to analyze their physicochemical properties, nuclear magnetic resonance (NMR) spectroscopy, despite being an obligatory technique to characterize molecular structure and dynamics in chemistry as well as in structural biology, yet appears to be rather sparsely used to study drug-liposome formulations. In this work, we exploited several facets of liquid-state NMR spectroscopy to characterize liposomal delivery systems for the apelin-derived K14P peptide and K14P modified by Nα-fatty acylation. Various liposome compositions and preparation modes were analyzed. Using NMR, in combination with cryo-electron microscopy and dynamic light scattering, we determined structural, dynamic, and self-association properties of these peptides in solution and probed their interactions with liposomes. Using 31P and 1H NMR, we characterized membrane fluidity and thermotropic phase transitions in empty and loaded liposomes. Based on diffusion and 1H NMR experiments, we localized and quantified peptides with respect to the interior/exterior of liposomes and changes over time and upon thermal treatments. Finally, we assessed the release kinetics of several solutes and compared various formulations. Taken together, this work shows that NMR has the potential to assist the design of peptide/liposome systems and more generally drug delivery systems.

SERS characterization of aggregated and isolated bacteria deposited on silver-based substrates.

Surface-enhanced Raman scattering (SERS), based on the enhancement of the Raman signal of molecules positioned within a few nanometres from a structured metal surface, is ideally suited to provide bacterial-specific molecular fingerprints which can be used for analytical purposes. However, for some complex structures such as bacteria, the generation of reproducible SERS spectra is still a challenging task. Among the various factors influencing the SERS variability (such as the nature of SERS-active substrate, Raman parameters and bacterial specificity), we demonstrate in this study that the environment of Gram-positive and Gram-negative bacteria deposited on ultra-thin silver films also impacts the origin of the SERS spectra. In the case of densely packed bacteria, the obtained SERS signatures were either characteristic of the secretion of adenosine triphosphate for Staphylococcus aureus (S. aureus) or the cell wall and the pili/flagella for Escherichia coli (E. coli), allowing for an easy discrimination between the various strains. In the case of isolated bacteria, SERS mapping together with principal component analysis revealed some variabilities of the spectra as a function of the bacteria environment and the bactericidal effect of the silver. However, the variability does not preclude the SERS signatures of various E. coli strains to be discriminated.

Toward a Chemical Control of Colloidal YVO4 Nanoparticles Microstructure.

Rare-earth-doped oxides are a class of compounds that have been largely studied in the context of the development of luminescent nanocrystals for various applications including fluorescent labels for bioimaging, MRI contrast agents, luminescent nanocomposite coatings, etc. Elaboration of colloidal suspensions is usually achieved through coprecipitation. Particles exhibit emission properties that are similar to the bulk counterparts, although altered by crystalline defects or surface quenching species. Focusing on YVO4:Eu, one of the first reported systems, the aim of this work is to revisit the elaboration of nanoparticles obtained through a simple aqueous coprecipitation route. The objective is more precisely to get a better understanding of the parameters affecting the particles' internal microstructure, a feature that is poorly controlled and characterized. We show that the hydroxyl concentration in the precursor solution has a drastic effect on the particles' microstructure. Moreover, discrepancies in the reported particle structure are shown to possibly arise from the carbonation of the strongly basic orthovanadate precursor. For this study, SAXS/WAXS is shown to be a powerful tool to characterize the multiscale structure of the particles. It could be shown that playing on the precursor composition, it may be varied between almost monocrystalline nanocrystals to particles exhibiting a hierarchical microstructure well described by a surface fractal model. This work provides a new methodology for the characterization of nanoparticles microstructure and opens new directions for its optimization in view of applications.

Secreted dengue virus nonstructural protein NS1 is an atypical barrel-shaped high-density lipoprotein.

Dengue virus (DENV) causes the major arboviral disease of the tropics, characterized in its severe forms by signs of hemorrhage and plasma leakage. DENV encodes a nonstructural glycoprotein, NS1, that associates with intracellular membranes and the cell surface. NS1 is eventually secreted as a soluble hexamer from DENV-infected cells and circulates in the bloodstream of infected patients. Extracellular NS1 has been shown to modulate the complement system and to enhance DENV infection, yet its structure and function remain essentially unknown. By combining cryoelectron microscopy analysis with a characterization of NS1 amphipathic properties, we show that the secreted NS1 hexamer forms a lipoprotein particle with an open-barrel protein shell and a prominent central channel rich in lipids. Biochemical and NMR analyses of the NS1 lipid cargo reveal the presence of triglycerides, bound at an equimolar ratio to the NS1 protomer, as well as cholesteryl esters and phospholipids, a composition evocative of the plasma lipoproteins involved in vascular homeostasis. This study suggests that DENV NS1, by mimicking or hijacking lipid metabolic pathways, contributes to endothelium dysfunction, a key feature of severe dengue disease.

Development of nanoparticles based on amphiphilic cyclodextrins for the delivery of active substances.

Although amphiphilic cyclodextrin derivatives (ACDs) serve as valuable building blocks for nanomedicine formulations, their widespread production still encounters various challenges, limiting large-scale manufacturing. This work focuses on a robust alternative pathway using mineral base catalysis to transesterify ß-cyclodextrin with long-chain vinyl esters, yielding ACD with modular and controlled hydrocarbon chain grafting. ACDs with a wide range of degrees of substitution (DS) were reliably synthesized, as indicated by extensive physicochemical characterization, including MALDI-TOF mass spectrometry. The influence of various factors, including the type of catalyst and the length of the hydrocarbon moiety of the vinyl ester, was studied in detail. ACDs were assessed for their ability to form colloidal suspensions by nanoprecipitation, with or without PEGylated phospholipid. Small-angle X-ray scattering and cryo-electron microscopy revealed the formation of nanoparticles with distinct ultrastructures depending on the DS: an onion-like structure for low and very high DS, and reversed hexagonal organization for DS between 4.5 and 6.1. We confirmed the furtivity of the PEGylated versions of the nanoparticles through complement activation experiments and that they were well tolerated in-vivo on a zebrafish larvae model after intravenous injection. Furthermore, a biodistribution experiment showed that the nanoparticles left the bloodstream within 10 h after injection and were phagocytosed by macrophages.

Optical and topological characterization of gold nanoparticle dimers linked by a single DNA double strand.

We demonstrate that symmetric or asymmetric gold nanoparticle dimers with substantial scattering cross sections and plasmon coupling can be produced with a perfectly controlled chemical environment and a high purity using a single DNA linker as short as 7 nm. A statistical analysis of the optical properties and morphology of single dimers is performed using darkfield and cryo-electron microscopies. These results, correlated to Mie theory calculations, indicate that the particle dimers are stretched in water by electrostatic interactions.

Grid batch-dependent tuning of glow discharge parameters.

Sample preparation on cryo-EM grids can give various results, from very thin ice and homogeneous particle distribution (ideal case) to unwanted behavior such as particles around the "holes" or complexes that do not entirely correspond to the one in solution (real life). We recently run into such a case and finally found out that variations in the 3D reconstructions were systematically correlated with the grid batches that were used. We report the use of several techniques to investigate the grids' characteristics, namely TEM, SEM, Auger spectroscopy and Infrared Interferometry. This allowed us to diagnose the origin of grid preparation problems and to adjust glow discharge parameters. The methods used for each approach are described and the results obtained on a common specific case are reported.

New Insights into the Reactivity of Detonation Nanodiamonds during the First Stages of Graphitization.

The present study aims to compare the early stages of graphitization of the same DND source for two annealing atmospheres (primary vacuum, argon at atmospheric pressure) in an identical set-up. DND samples are finely characterized by a combination of complementary techniques (FTIR, Raman, XPS, HR-TEM) to highlight the induced modifications for temperature up to 1100 °C. The annealing atmosphere has a significant impact on the graphitization kinetics with a higher fraction of sp2-C formed under vacuum compared to argon for the same temperature. Whatever the annealing atmosphere, carbon hydrogen bonds are created at the DND surface during annealing according to FTIR. A "nano effect", specific to the <10 nm size of DND, exalts the extreme surface chemistry in XPS analysis. According to HR-TEM images, the graphitization is limited to the first outer shell even for DND annealed at 1100 °C under vacuum.

Monazite LaPO4:Eu3+ nanorods as strongly polarized nano-emitters.

Orientation analyses of macromolecules or artificial particles are vital for both fundamental research and practical bio-applications. An accurate approach is monitoring the polarization spectroscopy of lanthanide-doped nanocrystalline materials. However, nanomaterials are often far from ideal for the colloidal and polarization luminescence properties. In the present study, we synthesize well-dispersed LaPO4:Eu3+ nanomaterials in an anisotropic rod shape. Microwave heating with excess addition of phosphate precursor invokes a rapid phase transition of rhabdophane into monazite. The colloidal stability of the nanorod suspension is outstanding, demonstrated by showing liquid crystalline behaviors. The monazite nanorods are also superior in luminescence efficiency with limited defects. The emission spectrum of Eu3+ consists of well-defined lines with prominent polarization dependencies for both the forced electric dipole transitions and the magnetic dipole transitions. All the results demonstrate that the synthesized monazite nanorods can serve as an accurate probe in orientation analyses and potential applications, such as in microfluidics and biological detections.

Measuring 3D orientation of nanocrystals via polarized luminescence of rare-earth dopants.

Orientation of nanoscale objects can be measured by examining the polarized emission of optical probes. To retrieve a three-dimensional (3D) orientation, it has been essential to observe the probe (a dipole) along multiple viewing angles and scan with a rotating analyzer. However, this method requires a sophisticated optical setup and is subject to various external sources of error. Here, we present a fundamentally different approach employing coupled multiple emission dipoles that are inherent in lanthanide-doped phosphors. Simultaneous observation of different dipoles and comparison of their relative intensities allow to determine the 3D orientation from a single viewing angle. Moreover, the distinct natures of electric and magnetic dipoles originating in lanthanide luminescence enable an instant orientation analysis with a single-shot emission spectrum. We demonstrate a straightforward orientation analysis of Eu3+-doped NaYF4 nanocrystals using a conventional fluorescence microscope. Direct imaging of the rod-shaped nanocrystals proved the high accuracy of the measurement. This methodology would provide insights into the mechanical behaviors of various nano- and biomolecular systems.

Evidence of double-walled Al-Ge imogolite-like nanotubes. a cryo-TEM and SAXS investigation.

It has been recently discovered that the synthesis of Al-Ge imogolite-like nanotubes is possible at high concentration. Despite this initial success, the structure of these Al-Ge imogolite-like nanotubes remains not completely understood. Using high resolution cryo-TEM and Small Angle X-ray Scattering, we unravel their mesoscale structure in two contrasted situations. On the one hand, Al-Ge imogolite nanotubes synthesized at 0.25 M are double-walled nanotubes of 4.0 +/- 0.1 nm with an inner tube of 2.4 +/- 0.1 nm. Moreover, SAXS data also suggest that the two concentric tubes have an equal length and identical wall structure. On the other hand, at higher concentration (0.5M), both SAXS and cryo-TEM data confirm the formation of single-walled nanotubes of 3.5 +/- 0.15 nm. Infrared spectroscopy confirms the imogolite structure of the tubes. This is the first evidence of any double-walled imogolite or imogolite-like nanotubes likely to renew interest in these materials and associated potential applications.

Elaboration of Superparamagnetic and Bioactive Multicore-Shell Nanoparticles (γ-Fe2O3@SiO2-CaO): A Promising Material for Bone Cancer Treatment.

The past few decades have seen the development of new bone cancer therapies, triggered by the discovery of new biomaterials. When the tumoral area is small and accessible, the common clinical treatment implies the tumor mass removal followed by bone reconstruction or consolidation with a bioceramic or a metallic scaffold. Even though the treatment also involves chemotherapy or radiotherapy, resurgence of cancer cells remains possible. We have thus designed a new kind of heterostructured nanobiomaterial, composed of SiO2-CaO bioactive glass as the shell and superparamagnetic γ-Fe2O3 iron oxide as the core in order to combine the benefits of bone repair thanks to the glass bioactivity and cancer cell destruction through magnetic hyperthermia. These multifunctional core-shell nanoparticles (NPs) have been obtained using a two-stage procedure, involving the coprecipitation of 11 nm sized iron oxide NPs followed by their encapsulation inside a bioactive glass shell by sol-gel chemistry. The as-produced spherical multicore-shell NPs show a narrow size distribution of 73 ± 7 nm. Magnetothermal loss measurements by calorimetry under an alternating magnetic field and in vitro bioactivity assessment performed in simulated body fluid showed that these heterostructures exhibit a good heating capacity and a fast mineralization process (hydroxyapatite forming ability). In addition, their in vitro cytocompatibility, evaluated in the presence of human mesenchymal stem cells during 3 and 7 days, has been demonstrated. These first findings suggest that γ-Fe2O3@SiO2-CaO heterostructures are a promising biomaterial to fill bone defects resulting from bone tumor resection, as they have the ability to both repair bone tissue and act as thermoseeds for cancer therapy.

Rapid and sensitive identification of uropathogenic Escherichia coli using a surface-enhanced-Raman-scattering-based biochip.

Rapid, selective and sensitive sensing of bacteria remains challenging. We report on a highly sensitive and reproducible surface-enhanced Raman spectroscopy (SERS)-based sensing approach for the detection of uropathogenic Escherichia coli (E. coli) bacteria in urine. The assay is based on the specific capture of the bacteria followed by interaction with cetyltrimethylammonium bromide (CTAB)-stabilised gold nanorods (Au NRS) as SERS markers. High sensitivity up to 10 CFU mL-1 is achieved by optimizing the capture interface based on hydrogenated amorphous silicon a-Si:H thin films. The integration of CH3O-PEG750 onto a-Si:H gives the sensing interface an efficient anti-fouling character, while covalent linkage of antibodies directed against the major type-1 fimbrial pilin FimA of the human pathogen E. coli results in the specific trapping of fimbriated E. coli onto the SERS substrate and their spectral fingerprint identification.

NaYF4 Microstructure, beyond Their Well-Shaped Morphology.

Lanthanide-doped nanoparticles are widely investigated for their optical properties. However, the sensitivity of the lanthanide ions' luminescence to the local symmetry, useful when investigating structural environments, becomes a drawback for optimized properties in the case of poorly controlled crystallinity. In this paper, we focus on ß -NaYF4 nanorods in order to provide a detailed description of their chemical composition and microstructure. The combination of detailed XRD analysis and TEM observations show that strong variation may be observed from particles from a same batch of synthesis, but also when considering small variations of synthesis conditions. Moreover, also the nanorods observed by SEM exhibit a very nice faceted shape, they are far from being monocrystalline and present significant local deviation of crystalline symmetry and orientation. All these structural considerations, sensitively probed by polarized emission analysis, are crucial to analyze for the development of optimal systems toward the targeted applications.

Strain engineering of photo-induced phase transformations in Prussian blue analogue heterostructures.

Heterostructures based on Prussian blue analogues (PBA) combining photo- and magneto-striction have shown a large potential for the development of light-induced magnetization switching. However, studies of the microscopic parameters that control the transfer of the mechanical stresses across the interface and their propagation in the magnetic material are still too scarce to efficiently improve the elastic coupling. Here, this coupling strength is tentatively controlled by strain engineering in heteroepitaxial PBA core-shell heterostructures involving the same Rb0.5Co[Fe(CN)6]0.8·zH2O photostrictive core and isostructural shells of similar thickness and variable mismatch with the core lattice. The shell deformation and the optical electron transfer at the origin of photostriction are monitored by combined in situ and real time synchrotron X-ray powder diffraction and X-ray absorption spectroscopy under visible light irradiation. These experiments show that rather large strains, up to +0.9%, are developed within the shell in response to the tensile stresses associated with the expansion of the core lattice upon illumination. The shell behavior is, however, complex, with contributions in dilatation, in compression or unchanged. We show that a tailored photo-response in terms of strain amplitude and kinetics with potential applications for a magnetic manipulation using light requires a trade-off between the quality of the interface (which needs a small lattice mismatch i.e. a small a-cubic parameter for the shell) and the shell rigidity (decreased for a large a-parameter). A shell with a high compressibility that is further increased by the presence of misfit dislocations will show a decrease in its mechanical retroaction on the photo-switching properties of the core particles.

Lanthanoid-Doped Phosphate/Vanadate Mixed Hollow Particles as Ratiometric Luminescent Sensors.

Rare earth (RE) phosphates and vanadates are structurally similar compositions that display distinct but complementary luminescent properties. The properties of these phosphors can be combined in REPO4-REVO4 heterostructures during the development of new sensing technologies for biological applications. This work presents the synthesis of hollow RE phosphate/vanadate colloidal particles and evaluates their applicability as luminescent markers. Hydrothermal treatments of RE hydroxycarbonate particles in the presence of the PO43- and VO43- precursors afforded the final REPO4-REVO4 solids in a two-step template synthesis. We converted precursor hydroxycarbonate particles into the final heterostructures and characterized their structure and morphology. According to our detailed study into the spectroscopic properties of Eu3+-doped particles and their luminescence response to several species, the presence of the phosphate and vanadate phases in a single particle provided different chemical environments and enabled the design of a ratiometric approach to detect H2O2. These results open new perspectives for the development of new intracellular luminescent markers.