Temporal and geographical distribution of measles virus genotypes

The nucleotide sequence encoding the C terminus of the nucleocapsid protein of measles virus (MV) is the most variable in the genome. The sequence of this region is reported for 21 new MV strains and for virus RNA obtained from cases of subacute panencephalitis (SSPE) tissue. The nucleotide sequence of a total of 65 MV strains has been analysed using the CLUSTAL program to determine the relationships between the strains. An unrooted tree shows that eight different genotypes can be discerned amongst the sequences analysed so far. The data show that the C-terminal coding sequence of the nucleocapsid gene, although highly variable between strains, is stable in a given strain and does not appear to diverge in tissue culture. It therefore provides a good 'signature' sequence for specific genotypes. The sequence of this region can be used to discriminate new imported viruses from old 'endemic' strains of MV in a geographical area. The different genotypes are not geographically restricted although some appear to be the mainly 'endemic' types in large areas of the world. In global terms there appears to be at least four co-circulating genotypes of MV. The low level of divergence in the Edmonston lineage group isolated before 1970 indicates that some isolates are probably laboratory contaminants. This applies to some SSPE isolates such as the Halle, Mantooth and Horta-Barbosa strains as well as some wild-type isolates from that period.

Beaming of High-Order Harmonics Generated from Laser-Plasma Interactions

Beam divergences of high-order extreme ultraviolet harmonics from intense laser interactions with steep plasma density gradients are studied through experiment and Fourier analysis of the harmonic spatial phase. We show that while emission due to the relativistically oscillating mirror mechanism can be explained by ponderomotive surface denting, in agreement with previous results, the divergence of the emission due to the coherent wake emission mechanism requires a combination of the dent phase and an intrinsic emission phase. The temporal dependence of the divergences for both mechanisms is highlighted while it is also shown that the coherent wake emission divergence can be small in circumstances where the phase terms compensate each other. © 2013 American Physical Society.

Tudor staphylococcal nuclease is an evolutionarily conserved component of the programmed cell death degradome

Programmed cell death (PCD) is executed by proteases, which cleave diverse proteins thus modulating their biochemical and cellular functions. Proteases of the caspase family and hundreds of caspase substrates constitute a major part of the PCD degradome in animals(1,2). Plants lack close homologues of caspases, but instead possess an ancestral family of cysteine proteases, metacaspases(3,4). Although metacaspases are essential for PCD(5-7), their natural substrates remain unknown(4,8). Here we show that metacaspase mcII-Pa cleaves a phylogenetically conserved protein, TSN (Tudor staphylococcal nuclease), during both developmental and stress-induced PCD. TSN knockdown leads to activation of ectopic cell death during reproduction, impairing plant fertility. Surprisingly, human TSN (also known as p100 or SND1), a multifunctional regulator of gene expression(9-15), is cleaved by caspase-3 during apoptosis. This cleavage impairs the ability of TSN to activate mRNA splicing, inhibits its ribonuclease activity and is important for the execution of apoptosis. Our results establish TSN as the first biological substrate of metacaspase and demonstrate that despite the divergence of plants and animals from a common ancestor about one billion years ago and their use of distinct PCD pathways, both have retained a common mechanism to compromise cell viability through the cleavage of the same substrate, TSN.

Dynamics of dark hollow Gaussian laser pulses in relativistic plasma

Optical beams with null central intensity have potential applications in the field of atom optics. The spatial and temporal evolution of a central shadow dark hollow Gaussian (DHG) relativistic laser pulse propagating in a plasma is studied in this article for first principles. A nonlinear Schrodinger-type equation is obtained for the beam spot profile and then solved numerically to investigate the pulse propagation characteristics. As series of numerical simulations are employed to trace the profile of the focused and compressed DHG laser pulse as it propagates through the plasma. The theoretical and simulation results predict that higher-order DHG pulses show smaller divergence as they propagate and, thus, lead to enhanced energy transport. © 2013 American Physical Society.

The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial.We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of fivemarkers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. Therecovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.

Extensive genome duplications in sturgeons:New evidence from microsatellite data

Summary: Genome duplications and polyploidization events are thought to have played relevant roles in the early stages of vertebrate evolution, in particular near the time of divergence of the lamprey lineage. Additional genome duplications, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The role of polyploidization in vertebrate genome evolution is a thriving area of research. Sturgeons (order Acipenseriformes) provide a unique model for the investigation of genome duplication, with existing species possessing 120, 250 or 360 chromosomes. In the present study, data from 240 sturgeon specimens representing 11 species were used for analysis of ploidy levels. Allele numbers were assessed at eleven microsatellite loci. The results provide further evidence for functional diploidy, tetraploidy and hexaploidy in species possessing 120, 250 and 360 chromosomes, respectively. The analysis also uncovered novel evidence for functional hexaploidy in the shortnose sturgeon (Acipenser brevirostrum). In conclusion, the process of functional genome reduction is demonstrated to be an on-going process in this fish lineage. © 2013 Blackwell Verlag GmbH.

On Irish stickleback:Morphological diversification in a secondary contact zone

Question: How parallel is adaptive evolution when it occurs from different genetic backgrounds? Background: Divergent evolutionary lineages of several post-glacial fish species including the threespine stickleback are found together in Ireland. Goals: To investigate the morphological diversity of stickleback populations in Ireland and assess whether morphology evolved in parallel between evolutionary lineages. Methods: We sampled stickleback from lake, river, and coastal habitats across Ireland. Microsatellite and mitochondrial DNA data revealed evolutionary history. Geometric morphometrics and linear trait measurements characterized morphology. We used a multivariate approach to quantify parallel and non-parallel divergence within and between lineages. Results: Repeated evolution of similar morphologies in similar habitats occurred across Ireland, concordant with patterns observed elsewhere in the stickleback distribution. A strong pattern of habitat-specific morphology existed even among divergent lineages. Furthermore, a strong signal of shared morphological divergence occurred along a marine-freshwater axis. Evidently, deterministic natural selection played a more important role in driving freshwater adaptation than independent evolutionary history. © 2013 Mark Ravinet.

Determination of Spontaneous Mutation Frequencies in Measles Virus under Nonselective Conditions

There is a paradox between the remarkable genetic stability of measles virus (MV) in the field and the high mutation rates implied by the frequency of the appearance of monoclonal antibody escape mutants generated when the virus is pressured to revert in vitro (S. J. Schrag, P. A. Rota, and W. J. Bellini, J. Virol. 73: 51-54, 1999). We established a highly sensitive assay to determine frequencies of various categories of mutations in large populations of wild-type and laboratory-adapted MVs using recombinant viruses containing an additional transcription unit (ATU) encoding enhanced green fluorescent protein (EGFP). Single and double mutations were made in the fluorophore of EGFP to ablate fluorescence. The frequencies of reversion mutants in the population were determined by measuring the appearance of fluorescence indicating a revertant virus. This allows mutation rates to be measured under nonselective conditions, as phenotypic reversion to fluorescence requires only either a single-or a double-nucleotide change and amino acid substitution, which does not affect the length of the nonessential reporter protein expressed from the ATU. Mutation rates in MV are the same for wild-type and laboratory-adapted viruses, and they are an order of magnitude lower than the previous measurement assessed under selective conditions. The actual mutation rate for MV is approximately 1.8 x 10(-6) per base per replication event. Copyright © 2013, American Society for Microbiology. All Rights Reserved.

Generalized Laplacian Eigenmaps for Modeling and Tracking Human Motions

This paper presents generalized Laplacian eigenmaps, a novel dimensionality reduction approach designed to address stylistic variations in time series. It generates compact and coherent continuous spaces whose geometry is data-driven. This paper also introduces graph-based particle filter, a novel methodology conceived for efficient tracking in low dimensional space derived from a spectral dimensionality reduction method. Its strengths are a propagation scheme, which facilitates the prediction in time and style, and a noise model coherent with the manifold, which prevents divergence, and increases robustness. Experiments show that a combination of both techniques achieves state-of-the-art performance for human pose tracking in underconstrained scenarios.

Table-Top Laser-Based Source of Femtosecond, Collimated, Ultrarelativistic Positron Beams

The generation of ultrarelativistic positron beams with short duration (τ_e⁺≃30 fs), small divergence (θ_e⁺≃3 mrad), and high density (n _e⁺≃1014-1015 cm^-3) from a fully optical setup is reported. The detected positron beam propagates with a high-density electron beam and γ rays of similar spectral shape and peak energy, thus closely resembling the structure of an astrophysical leptonic jet. It is envisaged that this experimental evidence, besides the intrinsic relevance to laser-driven particle acceleration, may open the pathway for the small-scale study of astrophysical leptonic jets in the laboratory. 

Generation of neutral and high-density electron–positron pair plasmas in the laboratory

Electron–positron pair plasmas represent a unique state of matter, whereby there exists an intrinsic and complete symmetry between negatively charged (matter) and positively charged (antimatter) particles. These plasmas play a fundamental role in the dynamics of ultra-massive astrophysical objects and are believed to be associated with the emission of ultra-bright gamma-ray bursts. Despite extensive theoretical modelling, our knowledge of this state of matter is still speculative, owing to the extreme difficulty in recreating neutral matter–antimatter plasmas in the laboratory. Here we show that, by using a compact laser-driven setup, ion-free electron–positron plasmas with unique characteristics can be produced. Their charge neutrality (same amount of matter and antimatter), high-density and small divergence finally open up the possibility of studying electron–positron plasmas in controlled laboratory experiments.

Laser-driven generation of collimated ultra-relativistic positron beams

We report on recent experimental results concerning the generation of collimated (divergence of the order of a few mrad) ultra-relativistic positron beams using a fully optical system. The positron beams are generated exploiting a quantum-electrodynamic cascade initiated by the propagation of a laser-accelerated, ultra-relativistic electron beam through high-Z solid targets. As long as the target thickness is comparable to or smaller than the radiation length of the material, the divergence of the escaping positron beam is of the order of the inverse of its Lorentz factor. For thicker solid targets the divergence is seen to gradually increase, due to the increased number of fundamental steps in the cascade, but it is still kept of the order of few tens of mrad, depending on the spectral components in the beam. This high degree of collimation will be fundamental for further injection into plasma-wakefield afterburners.

Effects of buried high-Z layers on fast electron propagation

By extending a prior model [A. R. Bell, J.R. Davies, S. M. Guerin, Phys. Rev. E 58, 2471 (1998)], the magnetic field generated during the transport of a fast electron beam driven by an ultraintense laser in a solid target is derived analytically and applied to estimate the effect of such field on fast electron propagation through a buried high-Z layer in a lower-Z target. It is found that the effect gets weaker with the increase of the depth of the buried layer, the divergence of the fast electrons, and the laser intensity, indicating that magnetic field effects on the fast electron divergence as measured from K-a X-ray emission may need to be considered for moderate laser intensities. On the basis of the calculations, some considerations are made on how one can mitigate the effect of the magnetic field generated at the interface.

The challenge to health professionals when carers resist truth telling at the end of life: a qualitative secondary analysis

Aims and objectives: To draw out the similar complexities faced by staff around
truth-telling in a children’s and adult population and to interrogate the dilemmas faced by staff when informal carers act to block truth-telling.

Background: Policy encourages normalisation of death, but carers may act to protect or prevent the patient from being told the truth. Little is known about the impact on staff.

Design: Secondary analysis of data using a supra-analysis design to identify commonality of experiences.

Methods: Secondary ‘supra-analysis’ was used to transcend the focus of two primary studies in the UK, which examined staff perspectives in a palliative children’s and a palliative adult setting, respectively. The analysis examined new theoretical questions relating to the commonality of issues independently derived in each primary study. Both primary studies used focus groups. Existing empirical data were analysed thematically and compared across the studies.

Results: Staff reported a hiding of the truth by carers and sustained use of activities aimed at prolonging life. Carers frequently ignored the advance of end of life, and divergence between staff and carer approaches to truth-telling challenged professionals. Not being truthful with patients had a deleterious effect on staff, causing anger and feelings of incompetence.

Conclusions: Both children’s and adult specialist palliative care staff found themselves caught in a dilemma, subject to policies that promoted openness in planning for death and informal carers who often prevented them from being truthful with patients about terminal prognosis. This dilemma had adverse psychological effects upon many staff.

Relevance to clinical practice: There remains a powerful death-denying culture in
many societies, and carers of dying patients may prevent staff from being truthful with their patients. The current situation is not ideal, and open discussion of this problem is the essential first step in finding a solution.

Origin of British and Irish mammals: disparate post-glacial colonisation and species introductions

Global climate changes during the Quaternary reveal much about broader evolutionary effects of environmental change. Detailed regional studies reveal how evolutionary lineages and novel communities and ecosystems, emerge through glacial bottlenecks or from refugia. There have been significant advances in benthic imaging and dating, particularly with respect to the movements of the British (Scottish) and Irish ice sheets and associated changes in sea level during and after the Last Glacial Maximum (LGM). Ireland has been isolated as an island for approximately twice as long as Britain with no evidence of any substantial, enduring land bridge between these islands after ca 15 kya. Recent biogeographical studies show that Britain's mammal community is akin to those of southern parts of Scandinavia, The Netherlands and Belgium, but the much lower mammal species richness of Ireland is unique and needs explanation. Here, we consider physiographic, archaeological, phylogeographical i.e. molecular genetic, and biological evidence comprising ecological, behavioural and morphological data, to review how mammal species recolonized western Europe after the LGM with emphasis on Britain and, in particular, Ireland. We focus on why these close neighbours had such different mammal fauna in the early Holocene, the stability of ecosystems after LGM subject to climate change and later species introductions.

There is general concordance of archaeological and molecular genetic evidence where data allow some insight into history after the LGM. Phylogeography reveals the process of recolonization, e.g. with respect to source of colonizers and anthropogenic influence, whilst archaeological data reveal timing more precisely through carbon dating and stratigraphy. More representative samples and improved calibration of the ‘molecular clock’ will lead to further insights with regards to the influence of successive glaciations. Species showing greatest morphological, behavioural and ecological divergence in Ireland in comparison to Britain and continental Europe, were also those which arrived in Ireland very early in the Holocene either with or without the assistance of people. Cold tolerant mammal species recolonized quickly after LGM but disappeared, potentially as a result of a short period of rapid warming. Other early arrivals were less cold tolerant and succumbed to the colder conditions during the Younger Dryas or shortly after the start of the Holocene (11.5 kya), or the area of suitable habitat was insufficient to sustain a viable population especially in larger species. Late Pleistocene mammals in Ireland were restricted to those able to colonize up to ca 15 kya, probably originating from adjacent areas of unglaciated Britain and land now below sea level, to the south and west (of Ireland). These few, early colonizers retain genetic diversity which dates from before the LGM. Late Pleistocene Ireland, therefore, had a much depleted complement of mammal species in comparison to Britain.

Mammal species, colonising predominantly from southeast and east Europe occupied west Europe only as far as Britain between ca 15 and 8 kya, were excluded from Ireland by the Irish and Celtic Seas. Smaller species in particular failed to colonise Ireland. Britain being isolated as an island from ca. 8 kya has similar species richness and composition to adjacent lowland areas of northwest continental Europe and its mammals almost all show strongest genetic affinity to populations in neighbouring continental Europe with a few retaining genotypes associated with earlier, western lineages.

The role of people in the deliberate introduction of mammal species and distinct genotypes is much more significant with regards to Ireland than Britain reflecting the larger species richness of the latter and its more enduring land link with continental Europe. The prime motivation of early people in moving mammals was likely to be resource driven but also potentially cultural; as elsewhere, people exploring uninhabited places introduced species for food and the materials they required to survive. It is possible that the process of introduction of mammals to Ireland commenced during the Mesolithic and accelerated with Neolithic people. Irish populations of these long established, introduced species show some unique genetic variation whilst retaining traces of their origins principally from Britain but in some cases, Scandinavia and Iberia. It is of particular interest that they may retain genetic forms now absent from their source populations. Further species introductions, during the Bronze and late Iron Ages, and Viking and Norman invasions, follow the same pattern but lack the time for genetic divergence from their source populations. Accidental introductions of commensal species show considerable genetic diversity based on numerous translocations along the eastern Atlantic coastline. More recent accidental and deliberate introductions are characterised by a lack of genetic diversity other than that explicable by more than one introduction.

The substantial advances in understanding the postglacial origins and genetic diversity of British and Irish mammals, the role of early people in species translocations, and determination of species that are more recently introduced, should inform policy decisions with regards to species and genetic conservation. Conservation should prioritise early, naturally recolonizing species and those brought in by early people reflecting their long association with these islands. These early arrivals in Britain and Ireland and associated islands show genetic diversity that may be of value in mitigating anthropogenic climate change across Europe. In contrast, more recent introductions are likely to disturb ecosystems greatly, lead to loss of diversity and should be controlled. This challenge is more severe in Ireland where the number and proportion of invasive species from the 19th century to the present has been greater than in Britain.