The transfer of energy between electrons and ions in solids

In this review we consider those processes in condensed matter that involve the irreversible flow of energy between electrons and nuclei that follows from a system being taken out of equilibrium. We survey some of the more important experimental phenomena associated with these processes, followed by a number of theoretical techniques for studying them. The techniques considered are those that can be applied to systems containing many nonequivalent atoms. They include both perturbative approaches (Fermi's Golden Rule and non-equilibrium Green's functions) and molecular dynamics based (the Ehrenfest approximation, surface hopping, semi-classical Gaussian wavefunction methods and correlated electron-ion dynamics). These methods are described and characterized, with indications of their relative merits.

Culturing freshwater pearl mussel Margaritifera margaritifera: a breakthrough in the conservation of an endangered species.

1. The freshwater pearl mussel Margaritifera margaritifera L. is globally endangered and is threatened by commercial exploitation, pollution and habitat loss throughout its range. Captive breeding would be a valuable tool in enhancing the status of M. margaritifera in the UK. 2. We have developed a semi-natural system for successfully infecting juvenile brown trout with glochidial M. margaritifera, and culturing juvenile mussels in experimental tanks where glochidial M. margaritifera can excyst from fish gills and settle into sediment. 3. Infected fish had less than 1% mortality. Levels of infection varied among fish. Two yearly cohorts of juvenile M. margaritifera were identified from samples of sediment taken from each experimental tank. Individuals range in size from 1.4 mm (2000 cohort) to >3 mm in length (1999 cohort). 4. The number of juvenile M. margaritifera present in the two experimental tanks are estimated to be between 3600 (tank A) and 0 (tank B) for the putative 1999 cohort and between 6000 (tank A) and 13 000 (tank B) for the putative 2000 cohort. 5. This pioneering method for large-scale cultivation of juvenile M. margaritifera is intermediate between the release of infected fish into rivers and the intensive cultivation systems developed in continental Europe and the USA for other species of unionid. This is the first time that large numbers of M. margaritifera have been cultured and represents a significant breakthrough in the conservation of this globally endangered Red Data List species. The method is straightforward and is most cost-effective when undertaken alongside established hatchery processes.

Conservation of substrate specificities among coronavirus main proteases.

The key enzyme in coronavirus replicase polyprotein processing is the coronavirus main protease, 3CL(pro). The substrate specificities of five coronavirus main proteases, including the prototypic enzymes from the coronavirus groups I, II and III, were characterized. Recombinant main proteases of human coronavirus (HCoV), transmissible gastroenteritis virus (TGEV), feline infectious peritonitis virus, avian infectious bronchitis virus and mouse hepatitis virus (MHV) were tested in peptide-based trans-cleavage assays. The determination of relative rate constants for a set of corresponding HCoV, TGEV and MHV 3CL(pro) cleavage sites revealed a conserved ranking of these sites. Furthermore, a synthetic peptide representing the N-terminal HCoV 3CL(pro) cleavage site was shown to be effectively hydrolysed by noncognate main proteases. The data show that the differential cleavage kinetics of sites within pp1a/pp1ab are a conserved feature of coronavirus main proteases and lead us to predict similar processing kinetics for the replicase polyproteins of all coronaviruses.

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.

European hare (Lepus europaeus) invasion ecology: Implication for the conservation of the endemic Irish hare (Lepus timidus hibernicus)

European hare Lepus europaeus populations have undergone recent declines but the species has successfully naturalised in many countries outside its native range. It was introduced to Ireland during the mid-late nineteenth century for field sport and is now well established in Northern Ireland. The native Irish hare Lepus timidus hibernicus is an endemic subspecies of mountain hare L. timidus and has attracted major conservation concern following a long-term population decline during the twentieth century and is one of the highest priority species for conservation action in Ireland. Little is known about the European hare in Ireland or whether it poses a significant threat to the native mountain hare subspecies by compromising its ecological security or genetic integrity. We review the invasion ecology of the European hare and examine evidence for interspecific competition with the mountain hare for habitat space and food resources, interspecific hybridisation, disease and parasite transmission and possible impacts of climate change. We also examine the impact that introduced hares can have on native non-lagomorph species. We conclude that the European hare is an emerging and significant threat to the conservation status of the native Irish hare. Invasive mammal species have been successfully eradicated from Ireland before and immediate action is often the only opportunity for cost-effective eradication. An urgent call is issued for further research whilst the need for a European hare invasive Species Action Plan (iSAP) and Eradication strategy are discussed.