The impact of genome defense on mobile elements in Microbotryum

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a ‘genome defense’ which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.

Mapping the human record in the British early Palaeolithic: evidence from the Solent River system

The lithic record from the Solent River and its tributaries is re-examined in the light of recent interpretations about the changing demography of Britain during the Lower and early Middle Palaeolithic. Existing models of the terrace stratigraphies in the Solent and its tributary areas are reviewed and the corresponding archaeological record (specifically handaxes) for each terrace is assessed to provide models for the relative changes in human occupation through time. The Bournemouth area is studied in detail to examine the effects of quarrying and urbanisation on collection history and on the biases it introduces to the record. In addition, the effects of reworking of artefacts from higher into lower terraces are assessed, and shown to be a significant problem. Although there is very little absolute dating available for the Solent area, a cautious interpretation of the results from these analyses would suggest a pre-Marine Isotope Stage (MIS) 12 date for the first appearance of humans, a peak in population between MIS 12 and 10, and a decline in population during MIS 9 and 8. Owing to poor contextual data and small sample sizes, it is not clear when Levallois technology was introduced. This record is compared and contrasted to that from the Thames Valley. It is suggested that changes in the palaeogeography of Britain, in particular land connections to the continent, might have contributed to differences in the archaeological records from the Solent and Thames regions.

Evaluating the ability of a numerical weather prediction model to forecast tracer concentrations during ETEX 2

In this paper the meteorological processes responsible for transporting tracer during the second ETEX (European Tracer EXperiment) release are determined using the UK Met Office Unified Model (UM). The UM predicted distribution of tracer is also compared with observations from the ETEX campaign. The dominant meteorological process is a warm conveyor belt which transports large amounts of tracer away from the surface up to a height of 4 km over a 36 h period. Convection is also an important process, transporting tracer to heights of up to 8 km. Potential sources of error when using an operational numerical weather prediction model to forecast air quality are also investigated. These potential sources of error include model dynamics, model resolution and model physics. In the UM a semi-Lagrangian monotonic advection scheme is used with cubic polynomial interpolation. This can predict unrealistic negative values of tracer which are subsequently set to zero, and hence results in an overprediction of tracer concentrations. In order to conserve mass in the UM tracer simulations it was necessary to include a flux corrected transport method. Model resolution can also affect the accuracy of predicted tracer distributions. Low resolution simulations (50 km grid length) were unable to resolve a change in wind direction observed during ETEX 2, this led to an error in the transport direction and hence an error in tracer distribution. High resolution simulations (12 km grid length) captured the change in wind direction and hence produced a tracer distribution that compared better with the observations. The representation of convective mixing was found to have a large effect on the vertical transport of tracer. Turning off the convective mixing parameterisation in the UM significantly reduced the vertical transport of tracer. Finally, air quality forecasts were found to be sensitive to the timing of synoptic scale features. Errors in the position of the cold front relative to the tracer release location of only 1 h resulted in changes in the predicted tracer concentrations that were of the same order of magnitude as the absolute tracer concentrations.

Reactive Halogens in the Marine Boundary Layer (RHaMBLe): the tropical North Atlantic experiments

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one ground-based platforms. The heavily instrumented cruise D319 on the RRS Discovery from Lisbon, Portugal to São Vicente, Cape Verde and back to Falmouth, UK was used to characterise the spatial distribution of boundary layer components likely to play a role in reactive halogen chemistry. Measurements onboard the ARSF Dornier aircraft were used to allow the observations to be interpreted in the context of their vertical distribution and to confirm the interpretation of atmospheric structure in the vicinity of the Cape Verde islands. Long-term ground-based measurements at the Cape Verde Atmospheric Observatory (CVAO) on São Vicente were supplemented by long-term measurements of reactive halogen species and characterisation of additional trace gas and aerosol species during the intensive experimental period. This paper presents a summary of the measurements made within the RHaMBLe remote experiments and discusses them in their meteorological and chemical context as determined from these three platforms and from additional meteorological analyses. Air always arrived at the CVAO from the North East with a range of air mass origins (European, Atlantic and North American continental). Trace gases were present at stable and fairly low concentrations with the exception of a slight increase in some anthropogenic components in air of North American origin, though NOx mixing ratios during this period remained below 20 pptv (note the non-IUPAC adoption in this manuscript of pptv and ppbv, equivalent to pmol mol−1 and nmol mol−1 to reflect common practice). Consistency with these air mass classifications is observed in the time series of soluble gas and aerosol composition measurements, with additional identification of periods of slightly elevated dust concentrations consistent with the trajectories passing over the African continent. The CVAO is shown to be broadly representative of the wider North Atlantic marine boundary layer; measurements of NO, O3 and black carbon from the ship are consistent with a clean Northern Hemisphere marine background. Aerosol composition measurements do not indicate elevated organic material associated with clean marine air. Closer to the African coast, black carbon and NO levels start to increase, indicating greater anthropogenic influence. Lower ozone in this region is possibly associated with the increased levels of measured halocarbons, associated with the nutrient rich waters of the Mauritanian upwelling. Bromide and chloride deficits in coarse mode aerosol at both the CVAO and on D319 and the continuous abundance of inorganic gaseous halogen species at CVAO indicate significant reactive cycling of halogens. Aircraft measurements of O3 and CO show that surface measurements are representative of the entire boundary layer in the vicinity both in diurnal variability and absolute levels. Above the inversion layer similar diurnal behaviour in O3 and CO is observed at lower mixing ratios in the air that had originated from south of Cape Verde, possibly from within the ITCZ. ECMWF calculations on two days indicate very different boundary layer depths and aircraft flights over the ship replicate this, giving confidence in the calculated boundary layer depth.

Gas-phase kinetics of chlorosilylene reactions. I. ClSiH + Me3SiH: absolute rate measurements and theoretical calculations for prototype Si−H insertion reactions

Time-resolved studies of chlorosilylene, CISiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane, Me3SiH, in the gas phase. The reaction was studied at total pressures up to 100 torr (with and without added SF6) over the temperature range 297-407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-13.97 +/- 0.25) + (12.57 +/- 1.64) kJ mol(-1)/RT In 10. The Arrhenius parameters are consistent with a mechanism involving an intermediate complex, whose rearrangement is the rate-determining step. Quantum chemical calculations of the potential energy surface for this reaction and also the reactions of CISiH with SiH4 and the other methylsilanes support this conclusion. Comparisons of both experiment and theory with the analogous Si-H insertion processes of SiH2 and SiMe2 show that the main factor causing the lower reactivity of ClSiH is the secondary energy barrier. The calculations also show the existence of a novel intramolecular H-atom exchange process in the complex of ClSiH with MeSiH3.

The implications of climate policy for the impacts of climate change on global water resources

This paper assesses the implications of climate policy for exposure to water resources stresses. It compares a Reference scenario which leads to an increase in global mean temperature of 4oC by the end of the 21st century with a Mitigation scenario which stabilises greenhouse gas concentrations at around 450ppm CO2e and leads to a 2oC increase in 2100. Associated changes in river runoff are simulated using a global hydrological model, for four spatial patterns of change in temperature and rainfall. There is a considerable difference in hydrological change between these four patterns, but the percentages of change avoided at the global scale are relatively robust. By the 2050s, the Mitigation scenario typically avoids between 16 and 30% of the change in runoff under the Reference scenario, and by 2100 it avoids between 43 and 65%. Two different measures of exposure to water resources stress are calculated, based on resources per capita and the ratio of withdrawals to resources. Using the first measure, the Mitigation scenario avoids 8-17% of the impact in 2050 and 20-31% in 2100; with the second measure, the avoided impacts are 5-21% and 15-47% respectively. However, at the same time, the Mitigation scenario also reduces the positive impacts of climate change on water scarcity in other areas. The absolute numbers and locations of people affected by climate change and climate policy vary considerably between the four climate model patterns.

Can carbon surface oxidation shift the pore size distribution curve calculated from Ar, N(2) and CO(2) adsorption isotherms? Simulation results for a realistic carbon model

Using the virtual porous carbon model proposed by Harris et al, we study the effect of carbon surface oxidation on the pore size distribution (PSD) curve determined from simulated Ar, N(2) and CO(2) isotherms. It is assumed that surface oxidation is not destructive for the carbon skeleton, and that all pores are accessible for studied molecules (i.e., only the effect of the change of surface chemical composition is studied). The results obtained show two important things, i.e., oxidation of the carbon surface very slightly changes the absolute porosity (calculated from the geometric method of Bhattacharya and Gubbins (BG)); however, PSD curves calculated from simulated isotherms are to a greater or lesser extent affected by the presence of surface oxides. The most reliable results are obtained from Ar adsorption data. Not only is adsorption of this adsorbate practically independent from the presence of surface oxides, but, more importantly, for this molecule one can apply the slit-like model of pores as the first approach to recover the average pore diameter of a real carbon structure. For nitrogen, the effect of carbon surface chemical composition is observed due to the quadrupole moment of this molecule, and this effect shifts the PSD curves compared to Ar. The largest differences are seen for CO2, and it is clearly demonstrated that the PSD curves obtained from adsorption isotherms of this molecule contain artificial peaks and the average pore diameter is strongly influenced by the presence of electrostatic adsorbate-adsorbate as well as adsorbate-adsorbent interactions.

Health-related quality of life in Huntington’s Disease patients: a comparison of proxy assessment and patient self-rating using the disease-specific Huntington’s Disease health-related quality of life questionnaire (HDQoL)

Huntington’s disease (HD) is a fatal, neurodegenerative disease for which there is no known cure. Proxy evaluation is relevant for HD as its manifestation might limit the ability of persons to report their health-related quality of life (HrQoL). This study explored patient–proxy ratings of HrQoL of persons at different stages of HD, and examined factors that may affect proxy ratings. A total of 105 patient–proxy pairs completed the Huntington’s disease health-related quality of life questionnaire (HDQoL) and other established HrQoL measures (EQ-5D and SF-12v2). Proxy–patient agreement was assessed in terms of absolute level (mean ratings) and intraclass correlation. Proxies’ ratings were at a similar level to patients’ self-ratings on an overall Summary Score and on most of the six Specific Scales of the HDQoL. On the Specific Hopes and Worries Scale, proxies on average rated HrQoL as better than patients’ self-ratings, while on both the Specific Cognitive Scale and Specific Physical and Functional Scale proxies tended to rate HrQoL more poorly than patients themselves. The patient’s disease stage and mental wellbeing (SF-12 Mental Component scale) were the two factors that primarily affected proxy assessment. Proxy scores were strongly correlated with patients’ self-ratings of HrQoL, on the Summary Scale and all Specific Scales. The patient–proxy correlation was lower for patients at moderate stages of HD compared to patients at early and advanced stages. The proxy report version of the HDQoL is a useful complementary tool to self-assessment, and a promising alternative when individual patients with advanced HD are unable to self-report.

Thermodynamic efficiency and entropy production in the climate system

We present an outlook on the climate system thermodynamics. First, we construct an equivalent Carnot engine with efficiency and frame the Lorenz energy cycle in a macroscale thermodynamic context. Then, by exploiting the second law, we prove that the lower bound to the entropy production is times the integrated absolute value of the internal entropy fluctuations. An exergetic interpretation is also proposed. Finally, the controversial maximum entropy production principle is reinterpreted as requiring the joint optimization of heat transport and mechanical work production. These results provide tools for climate change analysis and for climate models’ validation.

Change & flexibility: the role of serviced office space in corporate real estate portfolios and office markets

With the increasing pace of change, organisations have sought new real estate solutions which provide greater flexibility. What appears to be required is not flexibility for all uses but appropriate flexibility for the volatile, risky and temporal part of a business. This is the essence of the idea behind the split between the core and periphery portfolio. The serviced office has emerged to fill the need for absolute flexibility. This market is very diverse in terms of the product, services and target market. It has grown and gained credibility with occupiers and more recently with the property investment market. Occupiers similarly use this space in a variety of ways. Some solely occupy serviced space while others use it to complement their more permanent space. It therefore appears that the market is fulfilling the role of providing periphery space for at least some of the occupiers. In all instances the key to this space is a focus on financial and tenurial flexibility which is not provided by other types of business space offered.

Investigating global tropical cyclone activity with a hierarchy of AGCMs: the role of model resolution

The ability to run General Circulation Models (GCMs) at ever-higher horizontal resolutions has meant that tropical cyclone simulations are increasingly credible. A hierarchy of atmosphere-only GCMs, based on the Hadley Centre Global Environmental Model (HadGEM1), with horizontal resolution increasing from approximately 270km to 60km (at 50N), is used to systematically investigate the impact of spatial resolution on the simulation of global tropical cyclone activity, independent of model formulation. Tropical cyclones are extracted from ensemble simulations and reanalyses of comparable resolutions using a feature-tracking algorithm. Resolution is critical for simulating storm intensity and convergence to observed storm intensities is not achieved with the model hierarchy. Resolution is less critical for simulating the annual number of tropical cyclones and their geographical distribution, which are well captured at resolutions of 135km or higher, particularly for Northern Hemisphere basins. Simulating the interannual variability of storm occurrence requires resolutions of 100km or higher; however, the level of skill is basin dependent. Higher resolution GCMs are increasingly able to capture the interannual variability of the large-scale environmental conditions that contribute to tropical cyclogenesis. Different environmental factors contribute to the interannual variability of tropical cyclones in the different basins: in the North Atlantic basin the vertical wind shear, potential intensity and low-level absolute vorticity are dominant, while in the North Pacific basins mid-level relative humidity and low-level absolute vorticity are dominant. Model resolution is crucial for a realistic simulation of tropical cyclone behaviour, and high-resolution GCMs are found to be valuable tools for investigating the global location and frequency of tropical cyclones.

Proteomic analyses of a Listeria monocytogenes mutant lacking σB identify new components of the σB regulon and highlight a role for σB in the utilization of glycerol

In Listeria monocytogenes the alternative sigma factor σB plays important roles in both virulence and stress tolerance. In this study a proteomic approach was used to define components of the σB regulon in L. monocytogenes 10403S (serotype 1/2a). Using two-dimensional gel electrophoresis and the recently developed isobaric tags for relative and absolute quantitation technique, the protein expression profiles of the wild type and an isogenic ΔsigB deletion strain were compared. Overall, this study identified 38 proteins whose expression was σB dependent; 17 of these proteins were found to require the presence of σB for full expression, while 21 were expressed at a higher level in the ΔsigB mutant background. The data obtained with the two proteomic approaches showed limited overlap (four proteins were identified by both methods), a finding that highlights the complementarity of the two technologies. Overall, the proteomic data reaffirmed a role for σB in the general stress response and highlighted a probable role for σB in metabolism, especially in the utilization of alternative carbon sources. Proteomic and physiological data revealed the involvement of σB in glycerol metabolism. Five newly identified members of the σB regulon were shown to be under direct regulation of σB using reverse transcription-PCR (RT-PCR), while random amplification of cDNA ends-PCR was used to map four σB-dependent promoters upstream from lmo0796, lmo1830, lmo2391, and lmo2695. Using RT-PCR analysis of known and newly identified σB-dependent genes, as well as proteomic analyses, σB was shown to play a major role in the stationary phase of growth in complex media.

Absolute high spectral resolution measurements of surface solar radiation for detection of water vapour continuum absorption

Solar-pointing Fourier transform infrared (FTIR) spectroscopy offers the capability to measure both the fine scale and broadband spectral structure of atmospheric transmission simultaneously across wide spectral regions. It is therefore suited to the study of both water vapour monomer and continuum absorption behaviours. However, in order to properly address this issue, it is necessary to radiatively calibrate the FTIR instrument response. A solar-pointing high-resolution FTIR spectrometer was deployed as part of the ‘Continuum Absorption by Visible and Infrared radiation and its Atmospheric Relevance’ (CAVIAR) consortium project. This paper describes the radiative calibration process using an ultra-high-temperature blackbody and the consideration of the related influence factors. The result is a radiatively calibrated measurement of the solar irradiation at the ground across the IR region from 2000 to 10 000 cm−1 with an uncertainty of between 3.3 and 5.9 per cent. This measurement is shown to be in good general agreement with a radiative-transfer model. The results from the CAVIAR field measurements are being used in ongoing studies of atmospheric absorbers, in particular the water vapour continuum.

A global assessment of the effects of climate policy on the impacts of climate change

This study presents the first global-scale multi-sectoral regional assessment of the magnitude and uncertainty in the impacts of climate change avoided by emissions policies. The analysis suggests that the most stringent emissions policy considered here – which gives a 50% chance of remaining below a 2oC temperature rise target - reduces impacts by 20-65% by 2100 relative to a ‘business-as-usual’ pathway (A1B) which reaches 4oC, and can delay impacts by several decades. Effects vary between sector and region, and there are few noticeable effects of mitigation policy by 2030. The impacts avoided by 2100 are more strongly influenced by the date and level at which emissions peak than the rate of decline of emissions, with an earlier and lower emissions peak avoiding more impacts. The estimated proportion of impacts avoided at the global scale is relatively robust despite uncertainty in the spatial pattern of climate change, but the absolute amount of avoided impacts is considerably more variable and therefore uncertain.