Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease

Nidoviruses (arteriviruses, coronaviruses, and roniviruses) are a phylogenetically compact but diverse group of positive-strand RNA viruses that includes important human and animal pathogens. Nidovirus RNA synthesis is mediated by a cytoplasmic membrane-associated replication/transcription complex that includes up to 16 viral nonstructural proteins (nsps), which carry common enzymatic activities, like the viral RNA polymerase, but also unusual and poorly understood RNA-processing functions. Of these, a conserved endoribonuclease (NendoU) is a major genetic marker that is unique to nidoviruses. NendoU activity was previously verified in vitro for the coronavirus nsp15, but not for any of its distantly related orthologs from other nidovirus lineages, like the arterivirus nsp11. Here, we show that the bacterially expressed nsp11 proteins of two arteriviruses, equine arteritis virus and porcine respiratory and reproductive syndrome virus, possess pyrimidine-specific endoribonuclease activity. RNA cleavage was independent of divalent cations in vitro and was greatly reduced by replacement of residues previously implicated in catalysis. Comparative characterization of the NendoU activity in arteriviruses and severe acute respiratory syndrome coronavirus revealed common and distinct features of their substrate requirements and reaction mechanism. Our data provide the first biochemical evidence of endoribonuclease activity associated with arterivirus nsp11 and support the conclusion that this remarkable RNA-processing enzyme, whose substrate in the infected cell remains to be identified, distinguishes nidoviruses from all other RNA viruses.

Shedding Light on the light bulb puzzle: the role of attitudes and perceptions in the adoption of energy efficient light bulbs

Despite the potential energy savings and economic benefits associated with compact fluorescent light bulbs, their adoption by the residential sector has been limited to date. In this paper, we present a theoretical model that focuses on the agents' ability to perceive the correct cost of lighting and on the role of environmental attitudes as key determinants of the adoption decision. We use original data from Ireland to test our theoretical predictions. Our results emphasize the importance of education, information and environmental awareness in the adoption decision.

Efficacy of sod removal in regenerating fen vegetation for the conservation of the marsh fritillary butterfly Euphydryas aurinia, Montiaghs Moss Nature Reserve, County Antrim, Northern Ireland.

The efficacy of ‘sod removal’ as a fenland restoration technique was tested using an experimental approach at Montiaghs Moss Nature Reserve, Northern Ireland, from 2006 to 2008. The site suffered from rank growth of purple moor-grass Molinia caerulea which was out-competing herbaceous species. Soil was removed up to a depth of 15 cm completely denuding vegetation in the experimental plot exposing bare peat. By July 2007, 15.2% of sod-removal areas were revegetated; by October 2008 cover had risen to 64.6%. Of this cover, purple moor-grass accounted for only 9-11% compared to 78- 79% on control plots. Cover of other rank-forming grass species was also significantly reduced. Sod removal significantly increased the cover of species characteristic of fenlands including sedges Carex spp., rushes Juncus spp., marsh pennywort Hydrocotyle vulgaris and lesser spearwort Ranunculus flammula. It seems likely that sod removal, which lowered the surface of the peat, restored minerotrophic conditions and exposed the historical seed bank stimulating regeneration of some fenland specialists and pioneer species; this resulted in significantly higher species richness on sod removal plots than control plots two years after treatment. There was no demonstrable effect of sod removal on abundance of devil’s-bit scabious Succisa pratensis, the larval food plant of the Annex II listed marsh fritillary butterfly Euphydryas aurinia. We recommend that consideration should be given to artificially seeding devil’s-bit scabious soon after sod removal treatment to promote early recolonisation and to increase plant abundance on the site.

The impact of personal resources and their goal relevance on satisfaction with food-related life among the elderly.

The study explored how actual resources, perceived levels of different types of resources and goal relevance of these resources affect older people's satisfaction with food-related life using a survey in eight European countries, where 3291 participants above 65 years of age and living in their own homes took part. Satisfaction with food-related life was measured using Satisfaction With Food-related Life (SWFL) scale developed by Grunert, Raats, Dean, Nielsen, Lumbers and The Food in Later Life Team. [(2007). A measure of satisfaction with food-related life. Appetite, 49, 486–493]. Results showed that older people rated the resources that they believed to have plentiful of as being highly relevant to achieve their goals. The individuals who rated the relevance and their level of different resources as high were also more satisfied with their food-related quality of life. Further, satisfaction with food-related life, as was expected, was predicted by income, health measures and living circumstances. However, the study also showed that perceived levels of other resources such as support of family and friends, food knowledge, storage facilities also added to the individuals’ satisfaction with food-related life. In addition, the congruence between perceived level and relevance of a resource was also shown to add to people's satisfaction with food-related life, implying that older people's satisfaction with food-related life depends not only on the level of resources they think they have but also on their goals and how important they think these resources are to achieving their goals.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Ion channel gates: comparative analysis of energy barriers.

The energetic profile of an ion translated along the axis of an ion channel should reveal whether the structure corresponds to a functionally open or closed state of the channel. In this study, we explore the combined use of Poisson–Boltzmann electrostatic calculations and evaluation of van der Waals interactions between ion and pore to provide an initial appraisal of the gating state of a channel. This approach is exemplified by its application to the bacterial inward rectifier potassium channel KirBac3.1, where it reveals the closed gate to be formed by a ring of leucine (L124) side chains. We have extended this analysis to a comparative survey of gating profiles, including model hydrophobic nanopores, the nicotinic acetylcholine receptor, and a number of potassium channel structures and models. This enables us to identify three gating regimes, and to show the limitation of this computationally inexpensive method. For a (closed) gate radius of 0.4 nm

Physical model for the generation of ideal resources in multipartite quantum networking

We propose a physical model for generating multipartite entangled states of spin-s particles that have important applications in distributed quantum information processing. Our protocol is based on a process where mobile spins induce the interaction among remote scattering centers. As such, a major advantage lies in the management of stationary and well-separated spins. Among the generable states, there is a class of N-qubit singlets allowing for optimal quantum telecloning in a scalable and controllable way. We also show how to prepare Aharonov, W, and Greenberger-Horne-Zeilinger states.

Towards a strategy for the conservation of the freshwater pearl mussel Margaritifera margaritifera in County Donegal, Ireland

This study attempts to identify the habitat requirements of the pearl mussel Margaritifea margaritifera in County Donegal, in north west Ireland, an area with little urban, industrial or intensive agricultural development. No mussels occur in rivers where calcium and conductivity levels are high or where the substratum is predominantly bedrock or fine sediment but it was not possible to distinguish clearly between mussel and non-mussel sites on the basis of ordination analysis. However, rivers which still support mussels and rivers with historical records of mussels are loosely grouped. Rivers which formerly supported mussels but lack living M. margaritifera appear to have suitable habitat for mussels; pearl fishing is the most likely reason for the extinction of these mussel populations. Where population densities are high, for example in locations on the rivers Eske, Clady and Owenea, conservation may necessitate the establishment of reserves. The prospect for the successful reintroduction of mussels into former mussel rivers such as the Finn and Eany Water, where suitable habitat exists and water quality is high, is very good.

UTILISATION OF MOLLUSC RESOURCES IN N. IRELAND

Mussel beds in N. Ireland contain about 3–400 000 tonnes of molluscs of which 6–7% is edible flesh. Most of these resources are not suitable for direct human consumption and attempts are currently being made at Queen's University, to perfect a process to separate mussel shell and flesh aimed at the production of high grade products from a low grade source. This report deals with the likely consequences of large scale harvesting of mussels and offers possible alternatives.