Stability of local secondary structure determines selectivity of viral RNA chaperones

To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA–RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus σNS. Here, we compared the abilities of NSP2 and σNS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while σNS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, resulting in efficient intramolecular RNA helix disruption. Hexameric σNS oligomerizes into an octamer that binds two RNAs, yet it exhibits only limited RNA-unwinding activity compared to NSP2. Thus, the formation of intersegment RNA–RNA interactions is governed by both helix-unwinding capacity of the chaperones and stability of RNA structure. We propose that this protein-mediated RNA selection mechanism may underpin the high fidelity assembly of multi-segmented RNA genomes in Reoviridae

Geokinematics of Central Europe: New insights from the CERGOP-2/Environment Project

The Central European Geodynamics Project CERGOP/2, funded by the European Union from 2003to 2006 under the 5th Framework Programme, benefited from repeated measurements of thecoordinates of epoch and permanent GPS stations of the Central European GPS Reference Network(CEGRN), starting in 1994. Here we report on the results of the systematic processing of availabledata up to 2005. The analysis has yielded velocities for some 60 sites, covering a variety of CentralEuropean tectonic provinces, from the Adria indenter to the Tauern window, the Dinarides, thePannonian Basin, the Vrancea seismic zone and the Carpathian Mountains. The estimated velocitiesdefine kinematical patterns which outline, with varying spatial resolution depending on the stationdensity and history, the present day surface kinematics in Central Europe. Horizontal velocities areanalyzed after removal from the ITRF2000 estimated velocities of a rigid rotation accounting forthe mean motion of Europe: a ~2.3 mm/yr north-south oriented convergence rate between Adria andthe Southern Alps that can be considered to be the present day velocity of the Adria indenterrelative to the European foreland. An eastward extrusion zone initiates at the Tauern Window. Thelateral eastward flow towards the Pannonian Basin exhibits a gentle gradient from 1-1.5 mm/yrimmediately east of the Tauern Window to zero in the Pannonian Basin. This kinematic continuityimplies that the Pannonian plate fragment recently suggested by seismic data does not require aspecific Eulerian pole. On the southeastern boundary of the Adria microplate, we report a velocitydrop from 4-4.5 mm/yr motion near Matera to ~1 mm/yr north of the Dinarides, in the southwesternpart of the Pannonian Basin. A positive velocity gradient as one moves south from West Ukraineacross Rumania and Bulgaria is estimated to be 2 mm/yr on a scale of 600-800 km, as if the crustwere dragged by the counterclockwise rotation along the North Anatolian Fault Zone. This regimeapparently does not interfere with the Vrancea seismic zone: earthquakes there are sufficiently deep(> 100 km) that the brittle deformation at depth can be considered as decoupled from the creep atthe surface. We conclude that models of the Quaternary tectonics of Central and Eastern Europeshould not neglect the long wavelength, nearly aseismic deformation affecting the upper crust in theRomanian and Bulgarian regions

Leaf anatomical plasticity of Brachypodium pinnatum (L.) Beauv. growing in contrasting microenvironments in a semiarid loess forest-steppe vegetation mosaic

After clearcutting xerothermic oakwoods once natural in the forest-steppe loess regions of Hungary, the perennial understorey grass Brachypodium pinnatum has been persisting for decades by establishing microhabitats from shade to full sun. In this paper, we explore variation in leaf anatomy for plants growing in different microhabitat light regimes (full shade under oak canopy, half shade near shrubs, and in unshaded grassland) in situ, and for plants reciprocally transplanted between these microhabitats. Leaf lamina thickness and mesophyll thickness were about 1.5 times greater in the grassland in situ than in oak subcanopy due to an additional layer of mesophyll cells and to 25-32% taller mesophyll cells. Mesophyll thickness and the proportion of veins plus sclerenchyma were lower for plants transplanted from either full or half shade to full sun than in situ plants in the grassland. Parenchymatous bundle sheath tended to be thicker in the grassland than in the two other microhabitats. Mean intervenial distance remained invariable among microsites. These adjustments in leaf anatomy may be a considerable part, but presumably not the dominant component of the medium-term (one year) light acclimation of B. pinnatum and the species success in microsites with contrasting light climate appearing side-by-side during secondary vegetation succession

Leaf morphology and anatomy in two contrasting environments for C3 and C4 grasses of different invasion potential

Leaf morphology, coarse structure and anatomy were compared for two invasive C4, two non-invasive C4, and two expanding native C3 grass species grown in their original, high-light semiarid temperate habitat, and in a growth room under variable moderate light and favourable supply of water and nutrients. It was hypothesised that (H1) among C4 grasses leaf structural response will be greater for invasive than for non-invasive species, and (H2) for plants of high spreading capacity C4 species will be less responsive than C3 species. Leaf mass per area was lower in the growth room than in the field by 43.4–54% and 5.7–21.2% for grasses of high spreading capacity and for non-invasive C4 species, respectively. Little or no response was observed in the proportion of epidermis and mesophyll, but the proportional area of veins plus sclerenchyma was greater in the field than in the growth room for the invasive C4 Sorghum halepense, and the spreading C3 Bromus inermis and Calamagrostis epigeios, while it did not differ for the two non-invasive C4 grasses and the invasive C4 Cynodon dactylon. Leaf intervential distance was invariant for C4 grasses (except for the non-invasive Chrysopogon gryllus) and the C3 C. epigeios, but changed by 25.1% for the C3 B. inermis . These results suggest that among C4 grasses invasive species expceed non-invasive ones in the plasticity of leaf coarse structure, but not that of leaf morphology and anatomy. However, leaf structure was not less plastic in invasive C4 than in expanding C3 grasses except for intervential distance

Direct Measurements of Arsenic and Phosphorus Evolution During Cap-Annealing of Gold-Based Metallizations on GaAs and InP

Evolution of arsenic and phosphorus during heat treatment of unprotected and encapsulated Au, AuZn and AuGeNi contacts on GaAs and InP has been examined and correlated with their ohmic behavior

Excited States of Water-Soluble Metal Porphyrins as Microenvironmental Probes for DNA and DNA-Model Compounds: Time-Resolved Transient Absorption and Resonance Raman Studies of Ni(TMpy-P4) in [Poly(dG-dC)]2 and [Poly(dA-dT)]2

The dynamics and mechanisms of photoexcitation relaxation of the water-soluble cationic metalloporphyrin nickel(II) 5,10,15,20-tetrakis[4-(N-methylpyridyl)]porphyrin (Ni(TMpy-P4)) bound to DNA-model polynucleotides, i.e. poly(dG-dC)2 and poly(dA-dT)2, and free in a mere phosphate buffer, have been studied in detail by using time-resolved picosecond transient absorption (TA) and nanosecond resonance Raman (RR) spectroscopies. For the Ni(TMpy-P4)−poly(dG-dC)2 complex, double-exponential kinetics of relaxation has been found, with time constants of ≤10 and 350 ± 20 ps, and absolute absorption spectra have been reconstructed from experimentally measured difference spectra. The long-lived transient species has been assigned to the excited intramolecular metal-centered (d,d) state 3B1g of the 4-coordinate Ni porphyrin intercalated between G-C base pairs. Transient RR spectra originating from this state have also been obtained and discussed. A much more complicated process of excitation relaxation has been found for the Ni(TMpy-P4)−poly(dA-dT)2 complex, where at least four relaxation components can be separated with time constants of ≤10, ∼100, ∼450 ps, and ≫1 ns. Our studies support the existence of at least two types of Ni(TMpy-P4) interaction with poly(dA-dT)2, each having its own kinetics of TA decay and transient RR spectra. Both TA and RR sets of data show that a major part of Ni porphyrin molecules yields a photophysical behavior typical for a 4-coordinate species, the excited (d,d) state 3B1g playing the key role in relaxation processes, while a minor part of Ni(TMpy-P4) also participates in axial ligand binding/release photoprocesses. Comparative analysis of transient RR spectra of Ni(TMpy-P4) bound to the A-T sequence and free in a phosphate buffer shows that no 6-coordinate 3B1g(L)2 transient species is photogenerated in the complex with poly(dA-dT)2, and therefore, axial coordination of only one extra-ligand molecule (most probably from the surrounding water solution) to the porphyrin central Ni ion is proposed to explain the experimental results. Possible processes of Ni(TMpy-P4) binding to poly(dA-dT)2 are discussed on the basis of the current photophysical data

Geokinematics of Central Europe: new insights from CERGOP-2/Environment Project

The CERGOP2 project funded by the European Union from 2003 to 2006 under the 5th Framework Programme benefits from repeated measurements of the coordinates of epoch and permanent GPS stations forming the CEGRN network in Central Europe, starting 1994. We report on the results of the systematic processing of the available data up to 2005. The analysis work has yielded the velocities of some 60 sites, covering a variety of Central European tectonic provinces, from the Adria indenter to the Tauern window, the Pannonian basin, the Vrancea Seismic Zone and the Carpathian Mountains. The estimated velocities define kinematical patterns which outline, with varying spatial resolution depending on the station density and history, the present day tectonic flow in Central Europe.The CEGRN data show that the majority of active contraction originating from the Eurasia Nubia plate boundary and the microplate between them is taken up primarily in the Eastern Alps, the Dinarides, and the Pannonian Basin. After removal from the ITRF2000 velocities of a rigid rotation accounting for the mean motion of stable Europe, the residual velocities have random orientations with 0.3 mm/yr scatter. This Iow figure provides an upper estimate for the level of rigidity of the European Platform. A 2.3 mm/yr north-south oriented convergence rate is implied by our data between Adria and the Southern Alps, and a narrow - -60 km wide- contraction zone in the Southern Alps is identified, consistently with earlier results. An eastward extrusion north of the contraction zone corresponds with the extension of the Tauern Window. In the southeastern boundary of the microplate, 4-4.5 mm/yr motion of Adria decreases to -1 mm/yr through the microplate, its boundary, and the Dinarides mountain range towards the southwestern part of the Pannonian Basin. Our data suggest that if the Pannonian Basin is subject to deformation, then it is most likely to be compressional than extensional. We conclude that compression and associated contraction due to the Adria collision with the Alps and the Dinarides is likely to fade away in the Western and Northern Carpathians, where our velocities and strain rates show no significant deformation

A comparative study of surface-enhanced Raman scattering from silver-coated anodic aluminum oxide and porous silicon

International audienceThree types of Ag-coated arrays from porous anodic aluminum oxide (AAO) were prepared and studied as substrates for surface-enhanced Raman scattering (SERS). They were compared with Ag-coated porous silicon (PSi) samples. AAO-based substrates were prepared by the vapor deposition of silver directly onto the surface of porous AAO with different morphologies of the pores, whereas SERS-active island films on the PSi were prepared by immersion plating. The resulting metallic nanostructures were characterized by UV-vis absorption spectroscopy and scanning electron microscopy (SEM). Thermal evaporation leads to the formation of granular arrays of Ag nanoparticles on the surface of AAO. SERS activity of the substrates was tested using water-soluble cationic Zn(II)-tetrakis (4-N-methylpyridyl) porphyrin (ZnTMPyP4) as a probe molecule. The results indicate that all AAO-based substrates studied here exhibit some degree of SERS activity. Noteworthy, for excitation at 532 nm, signals from AAO-based substrates were comparable with those from the PSi-based ones, whereas for 441.6 nm excitation they were about twice higher. The strongest SERS- enhancement at 441.6 nm excitationwas provided by the AAO substrates with silver deposited on the monolith (originally nonporous) side of AAO. Preferential SERS-enhancement of the bands ascribed to the vibrations of the N-methylpyridinium group of ZnTMPyP4 when going to blue excitation was found