Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype–phenotype mapping.

A single-column model ensemble approach applied to the TWP-ICE experiment

Single-column models (SCM) are useful test beds for investigating the parameterization schemes of numerical weather prediction and climate models. The usefulness of SCM simulations are limited, however, by the accuracy of the best estimate large-scale observations prescribed. Errors estimating the observations will result in uncertainty in modeled simulations. One method to address the modeled uncertainty is to simulate an ensemble where the ensemble members span observational uncertainty. This study first derives an ensemble of large-scale data for the Tropical Warm Pool International Cloud Experiment (TWP-ICE) based on an estimate of a possible source of error in the best estimate product. These data are then used to carry out simulations with 11 SCM and two cloud-resolving models (CRM). Best estimate simulations are also performed. All models show that moisture-related variables are close to observations and there are limited differences between the best estimate and ensemble mean values. The models, however, show different sensitivities to changes in the forcing particularly when weakly forced. The ensemble simulations highlight important differences in the surface evaporation term of the moisture budget between the SCM and CRM. Differences are also apparent between the models in the ensemble mean vertical structure of cloud variables, while for each model, cloud properties are relatively insensitive to forcing. The ensemble is further used to investigate cloud variables and precipitation and identifies differences between CRM and SCM particularly for relationships involving ice. This study highlights the additional analysis that can be performed using ensemble simulations and hence enables a more complete model investigation compared to using the more traditional single best estimate simulation only.

The elements of well-being

This essay contends that the constitutive elements of well-being are plural, partly objective, and separable. The essay argues that these elements are pleasure, friendship, significant achievement, important knowledge, and autonomy, but not either the appreciation of beauty or the living of a morally good life. The essay goes on to attack the view that elements of well-being must be combined in order for well-being to be enhanced. The final section argues against the view that, because anything important to say about well-being could be reduced to assertions about these separable elements, the concept of well-being or personal good is ultimately unimportant.

The 'ratione temporis' elements of self-defence

This article focuses on one particular factor that is of crucial importance to all self-defence actions. It is a factor that is almost always present in the application and appraisal of the right, but one that is not always explicitly engaged with: time. There are various ratione temporis elements underpinning the lawful exercise of the right of self-defence, and questions related to the timing of both an attack being responded to in self-defence and the response itself are notably controversial. The self-defence timeline is therefore charted, and the key legal debates encountered along its trajectory are identified. In particular, there is a focus on three temporal ‘stages’ of the right of self-defence: (i) the much-debated question of preventative forms of self-defence (the ‘before’); (ii) the timeliness of a state's defensive action, or what is sometimes called the need for the response to be ‘immediate’ (the ‘during’); and (iii) the duration of self-defence actions, including the crucial issue of when they must end (the ‘after’). The aim of this article is not to break new substantive ground with regard to these ‘stages’ as such, but is, rather, to draw together the temporal strands of self-defence in a more focused manner than is often the case in the literature.

Reducing noise associated with the Monte Carlo Independent Column Approximation for weather forecasting models

The Monte Carlo Independent Column Approximation (McICA) is a flexible method for representing subgrid-scale cloud inhomogeneity in radiative transfer schemes. It does, however, introduce conditional random errors but these have been shown to have little effect on climate simulations, where spatial and temporal scales of interest are large enough for effects of noise to be averaged out. This article considers the effect of McICA noise on a numerical weather prediction (NWP) model, where the time and spatial scales of interest are much closer to those at which the errors manifest themselves; this, as we show, means that noise is more significant. We suggest methods for efficiently reducing the magnitude of McICA noise and test these methods in a global NWP version of the UK Met Office Unified Model (MetUM). The resultant errors are put into context by comparison with errors due to the widely used assumption of maximum-random-overlap of plane-parallel homogeneous cloud. For a simple implementation of the McICA scheme, forecasts of near-surface temperature are found to be worse than those obtained using the plane-parallel, maximum-random-overlap representation of clouds. However, by applying the methods suggested in this article, we can reduce noise enough to give forecasts of near-surface temperature that are an improvement on the plane-parallel maximum-random-overlap forecasts. We conclude that the McICA scheme can be used to improve the representation of clouds in NWP models, with the provision that the associated noise is sufficiently small.

Solvothermal synthesis of one-dimensional chalcogenides containing group 13 elements

The solvothermal synthesis and characterisation of [C6H16N2][GaS2]2 (1), [C6H16N2][Ga2Se3(Se2)] (2), and mixed-metal phases with composition [C6H16N2][Ga2–xInxSe3(Se2)] (0 < x < 2)(3–5), is described. These materials have been characterised by single-crystal and powder X-ray diffraction, thermogravimetric analysis and UV/Vis diffuse reflectance spectroscopy. The materials contain one-dimensional anionic chains. In 1, these chains consist of edge-linked GaS4 tetrahedra, whilst in 2–5, the chains contain perselenide (Se2)2– units and comprise alternating four-membered [M2Se2] and five-membered [M2Se3] rings (where M = Ga, In). Compounds 3–5 represent the first examples of ternary mixed-metal [M2Se3(Se2)]2– chains.