Sylvie Morin

Global Organization of a Positive-strand RNA Virus Genome

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2′-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

In situ STM study of electrodeposition and anodic dissolution of Ni on Ag(111)

A study of the electrodeposition and electrochemical dissolution of ultrathin Ni films on Ag(111) electrodes in Watts electrolyte by in situ scanning tunneling microscopy (STM), electrochemical quartz microbalance (EQCM), and cyclic voltammetry (CV) is presented. Ni deposition starts at potentials negative of − 0.72 V s. SCE (i.e., overpotentials η160 mV), where an incommensurate, (111)-oriented film with an in-plane lattice rotation of 0.5° relative to the Ag substrate lattice is formed. The lateral nearest neighbor spacing is as in bulk Ni (2.49 A) for a film thickness 3 ML and expanded for monolayer (2.54 A) and bilayer (2.52 A) films. Depending on the deposition potential, three growth regimes, resulting in different deposit morphologies, are observed: At low overpotentials (160⩽η/mV⩽200) a smooth Ni film is formed ia a 2D step-flow growth process, commencing at steps of the Ag substrate. At medium overpotentials (200η/mV300) a transformation from 2D step-flow to 3D growth occurs, resulting in the selective formation of Ni multilayer islands along the Ag steps. At even higher overpotentials (η300 mV) 3D islands are formed at the steps and on the substrate terraces. The size of the Ni multilayer islands is independent of the terrace widths, indicating that Ni growth proceeds ia direct discharge at step sites (“direct deposition”). The transition from 2D to 3D growth as well as the change in island shape with overpotential can be rationalized by a different potential dependence of the various microscopic nucleation and growth processes. The multilayer growth at steps is attributed to next-layer nucleation at the structural defect induced by the Ag–Ni boundary and can be described quantitatively as a function of deposition time by a simple 2D model. In addition, place-exchange of Ni with Ag surface atoms and encapsulation of Ni islands by Ag is observed. Dissolution of the electrodeposited multilayer Ni films proceeds ia step-flow etching, with a higher dissolution rate for the Ni monolayer as compared to higher Ni layers.

Comparative In Situ STM Studies on the Electrodeposition of Ultrathin Nickel Films on Ag(111) and Au(111) Electrodes

Results of an in situ scanning-tunneling microscopy (STM) study on the initial stages of Ni electrodeposition on Ag(111) are presented and compared with previous results on Au(111). In the submonolayer range the STM results indicate substantial place exchange of Ni with Ag surface atoms. Submonolayer Ni islands are formed almost exclusively at the step edges, they are partly embedded into the upper terrace. In contrast, on Au(111) place exchange of Ni adatoms with the Au substrate occurs exclusively at the elbow sites of the herringbone reconstruction, and adlayer nickel islands nucleate selectively on top of the embedded Ni atoms (low overpotential) or also at steps (high overpotential). At multilayer coverages atomically smooth Ni deposits are found on both metal substrates with a lattice constant similar to that in metallic Ni. On Ag(111) large, quasi-two-dimensional Ni islands are observed, contrasting the almost perfect layer-by-layer growth on Ni/Au(1 11). The density of structural defects within the Ni islands on Ag( 111) is significantly lower than for the Ni film on Au( 111 ).

Admetal-induced substrate surface restructuring during metal-on-metal electrochemical deposition studied by in situ scanning tunneling microscopy

Abstract Based on time-dependent in situ scanning tunneling microscopy (STM) studies, we demonstrate that for Ni on Ag(111) and Ru on Au(111), electrochemical metal-on-metal deposition can result in pronounced substrate surface restructuring. For Ni/Ag(111), we observe that at low deposition flux and low coverage, Ni submonolayer islands at steps are partly embedded in the Ag terraces, whereas at higher deposition flux and higher coverage, substrate restructuring results in the formation of monolayer bays in the Ag terraces. We suggest that this restructuring process proceeds predominantly via step edge diffusion of Ag atoms. For Ru/Au(111), the formation of fjords and monolayer holes in the Au terraces is observed at low and high Ru coverage, respectively. The importance of the Au surface mobility for the restructuring process is demonstrated by comparing experiments in H2SO4 and HCl solutions, in which Au exhibits strongly different surface mobilities. For this system, restructuring involves Au diffusion along Au steps, Au atom detachment from the Au steps, and upward exchange diffusion. According to these observations and their comparison with similar findings for vacuum deposition, we conclude that this restructuring requires (i) a high substrate surface mobility and (ii) a stronger bonding of substrate atoms to deposit islands than to the substrate.

Siliconized triarylamines as redox mediator in dye-sensitized solar cells.

A new class of triarylamine compound functionalized with bulky triisopropylsilyl ether (-OTIPS) groups is used as a hole transport material in dye-sensitized solar cells (DSSCs). Using both optical and photoelectrochemical techniques, we compared the performance of this compound with that of a parent compound containing methyl ethers as well as the conventional I₃⁻/I⁻ redox couple. DSSCs fabricated with the triisopropylsilyl ether-substituted triarylamine exhibited high open circuit potentials (V(oc) > 0.9 V on average) and efficiencies of up to 1.9%. However, cells fabricated with triarylamine containing methyl ethers performed very poorly, pointing to the importance of -OTIPS in the overall performance of this material.

Evaluation of imprint DESI-MS substrates for the analysis of fungal metabolites

Mass spectrometry (MS) has become an important tool in microbiology for the identification of microorganisms and for monitoring the production of microbial secondary metabolites. Therefore, several ambient mass spectrometry techniques have been applied in the last few years. Although desorption electrospray ionization mass spectrometry (DESI-MS) is the most popular ambient MS technique, its application in the direct analysis of fungal compounds is still not well established. The irregular or uneven nature of the colony, the absorbent properties of the growth medium and the need for a firm surface for effective ionization hinder the direct screening of metabolites in fungal cultures by DESI-MS analysis. To overcome these limitations, in this study, we tested different surfaces, such as tape, porous polytetrafluoroethylene (PTFE), thin layer chromatography (TLC) surfaces, filter paper, flat silicon wafers and porous silicon (pSi), to obtain the best imprint-DESI-MS outcome with fungal cultures of Trichoderma harzianum for metabolite screening. We also evaluated the efficiency of the surfaces for the DESI-MS of small polar fungal metabolites in regard to signal intensity, signal stability and imaging suitability. The silicon surfaces provided the highest signal intensity for the fungal metabolites. PTFE and filter paper demonstrated relatively high signal stabilities that could be useful for prolonged DESI-MS/MS experiments, whereas tape was found to be the best option for DESI-MS imaging. The imprint on a tape surface was the only one capable of maintaining the structural features of the concentric conidial rings of T. harzianum.

Binding interactions in early- and late-stage amyloid aggregates of TTR(105–115)

One of the central aims of amyloid research is to identify chemical and structural features that confer amyloidogenic propensity. In this study, we use Saturation Transfer Difference (STD) NMR spectroscopy to acquire an atom-specific map of the interactions between soluble and aggregated Transthyretin peptide (TTR(105-115)) in early- and late-stage amyloidogenesis. Atomic Force Microscopy (AFM) was used to monitor the transition of early-stage samples, containing protofilaments, to late-stage samples composed of fully-mature fibrils. Progressive aggregation was accompanied by an increase in the correlation time tau(c) of soluble TTR(105-115) as indicated by (1)H NMR line broadening, but no significant change in the (1)H chemical shifts. The STD profile of backbone amide protons is in good agreement with an earlier computational study predicting hydrogen bonding propensity for each residue in small TTR(105-115) aggregates (Paci et al., J. Mol. Biol. (2004) 555-569). The STD profiles of C(alpha) and C(beta) protons identify a central aliphatic region of the peptide, Ala108-Leu111, that plays a crucial, but different role in early- and late-stage amyloidogenesis. In general, the STD profiles of early and fully-mature samples are dissimilar, suggesting different mechanisms of self-assembly in protofilaments and mature amyloid fibrils. The early-stage mechanism appears to be more dependent on main-chain hydrogen bonding, while the late-stage mechanism involves an increased number of interactions between bulky side chains.

Electrochemical cell for in situ magneto-optic Kerr effect measurements

A unique electrochemical cell allows in situ magneto-optic Kerr effect measurements for magnetic characterization of ultrathin films, concurrently with electrochemical control. This durable, compact, and easy to assemble cell is mounted on a rotatable base which enables magnetic measurements in both the longitudinal (in plane) and polar (perpendicular to plane) configurations. Its utility in the reproducible preparation and in situ magnetic characterization of thin films is demonstrated with electrochemical and ferromagnetic hysteresis data for ultrathin Ni films (⩽15 monolayers) electrodeposited on Ag(111) and Au(111) single crystal substrates.

Catalysis and Multi-Component Reactions

We have been studying the development of new asymmetric two-center catalysis using rare earth alkoxides and bifunctional sugar and related ligands. In The Fourth International Conference on Multi-Component Reactions and Related Chemistry (MCR 2009), new catalytic asymmetric reactions using catalysts 1 and 2 and catalytic asymmetric syntheses of ranirestat 3 and tamiflu 4 will be presented.