The Ferritin-like superfamily: evolution of the biological iron storeman from a rubrerythrin-like ancestor

Background: The Ferritins are part of the extensive ‘Ferritin-like superfamily’ which have diverse functions but are linked by the presence of a common four-helical bundle domain. The role performed by Ferritins as the cellular repository of excess iron is unique. In many ways Ferritins act as tiny organelles in their ability to secrete iron away from the delicate machinery of the cell, and then to release it again in a controlled fashion avoiding toxicity. The Ferritins are ancient proteins, being common in all three domains of life. This ubiquity reflects the key contribution that Ferritins provide in achieving iron homeostasis. Scope of the review: This review compares the features of the different Ferritins and considers how they, and other members of the Ferritin-like superfamily, have evolved. It also considers relevant features of the eleven other known families within the Ferritin-like superfamily, particularly the highly diverse rubrerythrins. Major conclusions: The Ferritins have travelled a considerable evolutionary journey, being derived from far more simplistic rubrerythrin-like molecules which play roles in defence against toxic oxygen species. The forces of evolution have moulded such molecules into three distinct types of iron storing (or detoxifying) protein: the classical and universal 24-meric ferritins; the haem-containing 24-meric bacterioferritins of prokaryotes; and the prokaryotic 12-meric Dps proteins. These three Ferritin types are similar, but also possess unique properties that distinguish them and enable then to achieve their specific physiological purposes. General significance: A wide range of biological functions have evolved from a relatively simple structural unit.

Parents' verbal communication and childhood anxiety: a systematic review

Parents’ verbal communication to their child, particularly the expression of fear-relevant information (e.g., attributions of threat to the environment), is considered to play a key role in children’s fears and anxiety. This review considers the extent to which parental verbal communication is associated with child anxiety by examining research that has employed objective observational methods. Using a systematic search strategy, we identified 15 studies that addressed this question. These studies provided some evidence that particular fear-relevant features of parental verbal communication are associated with child anxiety under certain conditions. However, the scope for drawing reliable, general conclusions was limited by extensive methodological variation between studies, particularly in terms of the features of parental verbal communication examined and the context in which communication took place, how child anxiety was measured, and inconsistent consideration of factors that may moderate the verbal communication–child anxiety relationship. We discuss ways in which future research can contribute to this developing evidence base and reduce further methodological inconsistency so as to inform interventions for children with anxiety problems.

On the significance of the basic structure: a priori baseline views and luck egalitarianism

This paper uses the exploration of the grounds of a common criticism of luck egalitarianism to try to make an argument about both the proper subject of theorising about justice and how to approach that subject. It draws a distinction between what it calls basic structure views and a priori baseline views, where the former take the institutional aspects of political prescriptions seriously and the latter do not. It argues that objections to luck egalitarianism on the grounds of its harshness can in part be explained by this blindness to relevant features of institutions. Further, it may be that luck egalitarianism cannot regard its own enactment as just. A related objection to Dworkin’s equality of resources, which claims that it cannot pick a particular institutional background to set the costs of resources and so is radically indeterminate, is also presented. These results, I argue, give us good reason to reject all a priori baseline views.

Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

Is the OECD acute worm toxicity test environmentally relevant? The effect of mineral form on calculated lead toxicity

In a series of experiments the toxicity of lead to worms in soil was determined following the draft OECD earthworm reproduction toxicity protocol except that lead was added as solid lead nitrate, carbonate and sulphide rather than as lead nitrate solution as would normally be the case. The compounds were added to the test soil to give lead concentrations of 625-12500 pg Pb g-1 of soil. Calculated toxicities of the lead decreased in the order nitrate > carbonate > sulphide, the same order as the decrease in the solubility of the metal compounds used. The 7-day LC50 (lethal concentration when 50% of the population is killed) for the nitrate was 5321 +/- 275 mug Pb g(-1) of soil and this did not change with time. The LC50 values for carbonate and sulphide could not be determined at the concentration ranges used. The only parameter sensitive enough to distinguish the toxicities of the three compounds was cocoon (egg) production. The EC50S for cocoon production (the concentration to produce a 50% reduction in cocoon production) were 993, 8604 and 10 246 mug Pb g(-1) of soil for lead nitrate, carbonate and sulphide, respectively. Standard toxicity tests need to take into account the form in which the contaminant is present in the soil to be of environmental relevance. (C) 2002 Elsevier Science Ltd. All rights reserved.

Evolution of the modern Nile delta promontories: development of accretional features during shoreline retreat

The active accretional features that have developed along the modern Nile Delta promontories during shoreline retreat are analysed using topographic maps, remote imagery, ground and hydrographic surveys, together providing 15 time-slice maps (1922-2000) at Rosetta and 14 time-slice maps (1909-2000) at Damietta. Small double sandy spits developed and persisted at Rosetta between 1986 and 1991. At Damietta, a much larger single spit, 9 km long, formed approximately east of the mouth of the Damietta Nile branch between 1955 and 1972, although its source has now been depleted. Both the Rosetta and Damietta inlets are associated with submerged mouth bars that accumulated prior to the damming of the Nile, but that continue to contribute to local sedimentation problems, particularly at Rosetta. The development of the active accretional features along the Nile promontories reflects a combination of factors including sediment availability, transport pathways from source areas, a decrease in the magnitude of Nile flood discharges, as well as the impact of protective structures at the river mouths.

Key features of the IPSL ocean atmosphere model and its sensitivity to atmospheric resolution

This paper presents the major characteristics of the Institut Pierre Simon Laplace (IPSL) coupled ocean–atmosphere general circulation model. The model components and the coupling methodology are described, as well as the main characteristics of the climatology and interannual variability. The model results of the standard version used for IPCC climate projections, and for intercomparison projects like the Paleoclimate Modeling Intercomparison Project (PMIP 2) are compared to those with a higher resolution in the atmosphere. A focus on the North Atlantic and on the tropics is used to address the impact of the atmosphere resolution on processes and feedbacks. In the North Atlantic, the resolution change leads to an improved representation of the storm-tracks and the North Atlantic oscillation. The better representation of the wind structure increases the northward salt transports, the deep-water formation and the Atlantic meridional overturning circulation. In the tropics, the ocean–atmosphere dynamical coupling, or Bjerknes feedback, improves with the resolution. The amplitude of ENSO (El Niño-Southern oscillation) consequently increases, as the damping processes are left unchanged.

Arctic oscillation or North Atlantic oscillation?

The definition and interpretation of the Arctic oscillation (AO) are examined and compared with those of the North Atlantic oscillation (NAO). It is shown that the NAO reflects the correlations between the surface pressure variability at its centers of action, whereas this is not the case for the AO. The NAO pattern can be identified in a physically consistent way in principal component analysis applied to various fields in the Euro-Atlantic region. A similar identification is found in the Pacific region for the Pacific–North American (PNA) pattern, but no such identification is found here for the AO. The AO does reflect the tendency for the zonal winds at 35° and 55°N to anticorrelate in both the Atlantic and Pacific regions associated with the NAO and PNA. Because climatological features in the two ocean basins are at different latitudes, the zonally symmetric nature of the AO does not mean that it represents a simple modulation of the circumpolar flow. An increase in the AO or NAO implies strong, separated tropospheric jets in the Atlantic but a weakened Pacific jet. The PNA has strong related variability in the Pacific jet exit, but elsewhere the zonal wind is similar to that related to the NAO. The NAO-related zonal winds link strongly through to the stratosphere in the Atlantic sector. The PNA-related winds do so in the Pacific, but to a lesser extent. The results suggest that the NAO paradigm may be more physically relevant and robust for Northern Hemisphere variability than is the AO paradigm. However, this does not disqualify many of the physical mechanisms associated with annular modes for explaining the existence of the NAO.

Initial results from Phase 2 of the international urban energy balance model comparison

Urban land surface schemes have been developed to model the distinct features of the urban surface and the associated energy exchange processes. These models have been developed for a range of purposes and make different assumptions related to the inclusion and representation of the relevant processes. Here, the first results of Phase 2 from an international comparison project to evaluate 32 urban land surface schemes are presented. This is the first large-scale systematic evaluation of these models. In four stages, participants were given increasingly detailed information about an urban site for which urban fluxes were directly observed. At each stage, each group returned their models' calculated surface energy balance fluxes. Wide variations are evident in the performance of the models for individual fluxes. No individual model performs best for all fluxes. Providing additional information about the surface generally results in better performance. However, there is clear evidence that poor choice of parameter values can cause a large drop in performance for models that otherwise perform well. As many models do not perform well across all fluxes, there is need for caution in their application, and users should be aware of the implications for applications and decision making.

Features of the Atlantic diet and its healthiness: Theory and evidence from social science

In order to understand diets, why and how they change and can be influenced, it is important to understand how food choices are made. The has been the subject of, considerable study within many of the social science disciplines and the humanities. The paper draws on the theoretical and empirical work of psychologists, sociologists, economists, market researchers, anthropologists, geographers and historians to understand better the forces behind food choice, derive some general empirical messages from the literature, to shed light on food choice in a European context and to address the question of whether there is, or has been, a recognisably Atlantic diet. The paper proceeds to analyse the characteristics of the food consumption patterns in the Atlantic diet countries, examines whether their food consumption patterns are homogenous (i.e. similar across the countries of this group), whether they are specific (i.e. different from the ones in other country groups) and finally evaluates the nutritional composition of the Atlantic diet against the WHO/FAO recommendations for a healthy and wholesome diet.