Suppression of Viral RNA Binding and the Assembly of Infectious Hepatitis C Virus Particles In Vitro by Cyclophilin Inhibitors

Nonstructural protein 5A (NS5A) of hepatitis C virus (HCV) is an indispensable component of the HCV replication and assembly machineries. Although its precise mechanism of action is not yet clear, current evidence indicates that its structure and function are regulated by the cellular peptidylprolyl isomerase cyclophilin A (CyPA). CyPA binds to proline residues in the C-terminal half of NS5A, in a distributed fashion, and modulates the structure of the disordered domains II and III. Cyclophilin inhibitors (CPIs), including cyclosporine (CsA) and its nonimmunosuppressive derivatives, inhibit HCV infection of diverse genotypes, both in vitro and in vivo. Here we report a mechanism by which CPIs inhibit HCV infection and demonstrate that CPIs can suppress HCV assembly in addition to their well-documented inhibitory effect on RNA replication. Although the interaction between NS5A and other viral proteins is not affected by CPIs, RNA binding by NS5A in cell culture-based HCV (HCVcc)-infected cells is significantly inhibited by CPI treatment, and sensitivity of RNA binding is correlated with previously characterized CyPA dependence or CsA sensitivity of HCV mutants. Furthermore, the difference in CyPA dependence between a subgenomic and a full-length replicon of JFH-1 was due, at least in part, to an additional role that CyPA plays in HCV assembly, a conclusion that is supported by experiments with the clinical CPI alisporivir. The host-directed nature and the ability to interfere with more than one step in the HCV life cycle may result in a higher genetic barrier to resistance for this class of HCV inhibitors.     

Effect of tower base painting on willow ptarmigan collision rates with wind turbines

1. Birds colliding with turbine rotor blades is a well‐known negative consequence of wind‐power plants. However, there has been far less attention to the risk of birds colliding with the turbine towers, and how to mitigate this risk.
2. Based on data from the Smøla wind‐power plant in Central Norway, it seems highly likely that willow ptarmigan (the only gallinaceous species found on the island) is prone to collide with turbine towers. By employing a BACI‐approach, we tested if painting the lower parts of turbine towers black would reduce the collision risk.
3. Overall, there was a 48% reduction in the number of recorded ptarmigan carcasses per search at painted turbines relative to neighboring control (unpainted) ones, with significant variation both within and between years.
4. Using contrast painting to the turbine towers resulted in significantly reduced number of ptarmigan carcasses found, emphasizing the effectiveness of such a relatively simple mitigation measure.

     

Fine‐scale variation within urban landscapes affects marking patterns and gastrointestinal parasite diversity in red foxes

1. Urban areas are often considered to be a hostile environment for wildlife as they are highly fragmented and frequently disturbed. However, these same habitats can contain abundant resources, while lacking many common competitors and predators. The urban environment can have a direct impact on the species living there but can also have indirect effects on their parasites and pathogens. To date, relatively few studies have measured how fine‐scale spatial heterogeneity within urban landscapes can affect parasite transmission and persistence.
2. Here, we surveyed 237 greenspaces across the urban environment of Edinburgh (UK) to investigate how fine‐scale variation in socio‐economic and ecological variables can affect red fox (Vulpes vulpes) marking behavior, gastrointestinal (GI) parasite prevalence, and parasite community diversity.
3. We found that the presence and abundance of red fox fecal markings were nonuniformly distributed across greenspaces and instead were dependent on the ecological characteristics of a site. Specifically, common foraging areas were left largely unmarked, which indicates that suitable resting and denning sites may be limiting factor in urban environments. In addition, the amount of greenspace around each site was positively correlated with overall GI parasite prevalence, species richness, and diversity, highlighting the importance of greenspace (a commonly used measure of landscape connectivity) in determining the composition of the parasite community in urban areas.
4. Our results suggest that fine‐scale variation within urban environments can be important for understanding the ecology of infectious diseases in urban wildlife and could have wider implication for the management of urban carnivores.

     

Environment versus dispersal in the assembly of western Amazonian palm communities

Aim It is a central issue in ecology and biogeography to understand what governs community assembly and the maintenance of biodiversity in tropical rain forest ecosystems. A key question is the relative importance of environmental species sorting (niche assembly) and dispersal limitation (dispersal assembly), which we investigate using a large dataset from diverse palm communities. Location Lowland rain forest, western Amazon River Basin, Peru. Methods We inventoried palm communities, registering all palm individuals and recording environmental conditions in 149 transects of 5 m × 500 m. We used ordination, Mantel tests and indicator species analysis (ISA) to assess compositional patterns, species responses to geographical location and environmental factors. Mantel tests were used to assess the relative importance of geographical distance (as a proxy for dispersal limitation) and environmental differences as possible drivers of dissimilarity in palm species composition. We repeated the Mantel tests for subsets of species that differ in traits of likely importance for habitat specialization and dispersal (height and range size). Results We found a strong relationship between compositional dissimilarity and environmental distance and a weaker but also significant relationship between compositional dissimilarity and geographical distance. Consistent with expectations, relationships with environmental and geographical distance were stronger for understorey species than for canopy species. Geographical distance had a higher correlation with compositional dissimilarity for small‐ranged species compared with large‐ranged species, whereas the opposite was true for environmental distance. The main environmental correlates were inundation and soil nutrient levels. Main conclusions The assembly of palm communities in the western Amazon appears to be driven primarily by species sorting according to hydrology and soil, but with dispersal limitation also playing an important role. The importance of environmental characteristics and geographical distance varies depending on plant height and geographical range size in agreement with functional predictions, increasing our confidence in the inferred assembly mechanisms.     

Teixeiria lusitanica, a new fossil flower from the Early Cretaceous of Portugal with affinities to Ranunculales

A charcoalified fossil flower bud of a new genus and species (Teixeiria lusitanica) is described from the Early Cretaceous of Portugal. The flower is actinomorphic and unisexually male. At the base of the bud there are several bracts of different sizes, which are followed by sepal-like and petal-like tepals. Bracts and perianth organs seem to be arranged spirally and to exhibit transitions between different organ categories. The androecium has numerous stamens in two sizes, but with unclear arrangement. Pollen is small and tricolpate with a perforate tectum and a densely columellate infratectal layer. No carpels or remains of carpels could be observed on the floral axis. Teixeiria lusitanica shows most affinities to members of Ranunculales. There are also some similarities with Berberidopsis (Berberidopsidaceae, Berberidopsidales) and members of the Saxifragales (Hamamelidaceae and Daphniphyllaceae).     

Interstitial bone stress distributions accompanying ingrowth of a screen-like prosthesis anchorage layer

Recent development of screen-like bonded weaves of titanium wire for orthopaedic implant anchorage affords a unique opportunity for analytic studies of porous ingrowth micromechanics. The regular geometry of individual wires and the periodicity of the mesh weave are exploited in a series of two-dimensional finite element models, mapping interstitial bone stress fields as a function of ingrowth depth and wire size, shape, and spacing.

When the depth of bone ingrowth was less than one wire diameter, peak bone stresses always occurred at the leading (i.e. deepest) edge of bone ingrowth, immediately adjacent to the wire. As ingrowth depth approached a full wire diameter, peak local bone stresses were 2–9 times the nominal applied host bone stress, with greater stresses occurring for lower screen weave densities. Within multiple screen layers, the top layer consistently experienced the peak stress and transmitted most of the applied load, regardless of the number of underlying screen layers surrounded by bone. Neither wire size variations nor partial wire flattening substantially affected general trends in stress predictions.     

Nitrogenase activity,hydrogen evolution and biomass production in different Casuarina symbioses

Nitrogenase activity, hydrogen evolution, biomass production and nodulation were studied in threeCasuarina species,C. equisetifolia Forst.,C. glauca Sieber ex Spreng andC. obesa Miq., either inoculated with a crushed nodule inoculum prepared fromC. glauca nodules or inoculated with the pure cultureHFP CcI3. Nodulation was also studied inC. cristata Miq. inoculated with the above mentionedFrankia sources. C. equisetifolia, C. glauca andC. obesa were nodulated when inoculated with both of theFrankia inoculum, whileC. cristata was very poorly nodulated. Nitrogenase activity per plant and on a nodule dry weight basis was significantly highest inC. glauca inoculated withC. glauca inoculum after 150 days from planting. This difference decreased and at 217 days from planting there was no significant difference between the symbioses, except forC. obesa inoculated withC. glauca inoculum which showed the significantly lowest nitrogenase activity. After 150 days from planting relative efficiency of nitrogenase was lowest inC. equisetifolia inoculated withHFP CcI3 and inC. equisetifolia inoculated withC. glauca inoculum. Biomass production was similar inC. glauca inoculated withC. glauca inoculum, inC. equisetifolia inoculated withHFP CcI3 and inC. obesa inoculated withHFP CcI3 at the final harvest. The data presented here show that there is a strong interrelationship between host plant and endobiont. This interrelationship is of considerable importance when introducing Casuarina symbioses for production of fuel wood.     

A unique,thermostable dimer linkage structure of RD114 retroviral RNA

Retroviruses package their genome as RNA dimers linked together primarily by base-pairing between palindromic stem–loop (psl) sequences at the 5′ end of genomic RNA. Retroviral RNA dimers usually melt in the range of 55°C–70°C. However, RNA dimers from virions of the feline endogenous gammaretrovirus RD114 were reported to melt only at 87°C. We here report that the high thermal stability of RD114 RNA dimers generated from in vitro synthesized RNA is an effect of multiple dimerization sites located in the 5′ region from the R region to sequences downstream from the splice donor (SD) site. By antisense oligonucleotide probing we were able to map at least five dimerization sites. Computational prediction revealed a possibility to form stems with autocomplementary loops for all of the mapped dimerization sites. Three of them were located upstream of the SD site. Mutant analysis supported a role of all five loop sequences in the formation and thermal stability of RNA dimers. Four of the five psls were also predicted in the RNA of two baboon endogenous retroviruses proposed to be ancestors of RD114. RNA fragments of the 5′ R region or prolonged further downstream could be efficiently dimerized in vitro. However, this was not the case for the 3′ R region linked to upstream U3 sequences, suggesting a specific mechanism of negative regulation of dimerization at the 3′ end of the genome, possibly explained by a long double-stranded RNA region at the U3-R border. Altogether, these data point to determinants of the high thermostability of the dimer linkage structure of the RD114 genome and reveal differences from other retroviruses.