Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

Background: Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results: The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306) of our global sample of individuals was infected with the plutWBI isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWBI is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion: The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWBI infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may reflect a bottleneck during their recent introduction to this region.

An update of observed stratospheric temperature trends

An updated analysis of observed stratospheric temperature variability and trends is presented on the basis of satellite, radiosonde, and lidar observations. Satellite data include measurements from the series of NOAA operational instruments, including the Microwave Sounding Unit covering 1979–2007 and the Stratospheric Sounding Unit (SSU) covering 1979–2005. Radiosonde results are compared for six different data sets, incorporating a variety of homogeneity adjustments to account for changes in instrumentation and observational practices. Temperature changes in the lower stratosphere show cooling of 0.5 K/decade over much of the globe for 1979–2007, with some differences in detail among the different radiosonde and satellite data sets. Substantially larger cooling trends are observed in the Antarctic lower stratosphere during spring and summer, in association with development of the Antarctic ozone hole. Trends in the lower stratosphere derived from radiosonde data are also analyzed for a longer record (back to 1958); trends for the presatellite era (1958–1978) have a large range among the different homogenized data sets, implying large trend uncertainties. Trends in the middle and upper stratosphere have been derived from updated SSU data, taking into account changes in the SSU weighting functions due to observed atmospheric CO2 increases. The results show mean cooling of 0.5–1.5 K/decade during 1979–2005, with the greatest cooling in the upper stratosphere near 40–50 km. Temperature anomalies throughout the stratosphere were relatively constant during the decade 1995–2005. Long records of lidar temperature measurements at a few locations show reasonable agreement with SSU trends, although sampling uncertainties are large in the localized lidar measurements. Updated estimates of the solar cycle influence on stratospheric temperatures show a statistically significant signal in the tropics (30N–S), with an amplitude (solar maximum minus solar minimum) of 0.5 K (lower stratosphere) to 1.0 K (upper stratosphere).

The role of competition and state aid policy in financial and monetary law

During the financial crisis, companies and lenders found themselves in distressed situations. Competition authorities across the globe had to deal with controversial issues such as the application of the failing firm defence in merger transactions as well as assessment of emergency aid granted by states. This article considers competition policy in periods of crisis, in particular the failing firm defence in merger control and its state aid policy.

Fast regridding of large, complex geospatial datasets

In the earth sciences, data are commonly cast on complex grids in order to model irregular domains such as coastlines, or to evenly distribute grid points over the globe. It is common for a scientist to wish to re-cast such data onto a grid that is more amenable to manipulation, visualization, or comparison with other data sources. The complexity of the grids presents a significant technical difficulty to the regridding process. In particular, the regridding of complex grids may suffer from severe performance issues, in the worst case scaling with the product of the sizes of the source and destination grids. We present a mechanism for the fast regridding of such datasets, based upon the construction of a spatial index that allows fast searching of the source grid. We discover that the most efficient spatial index under test (in terms of memory usage and query time) is a simple look-up table. A kd-tree implementation was found to be faster to build and to give similar query performance at the expense of a larger memory footprint. Using our approach, we demonstrate that regridding of complex data may proceed at speeds sufficient to permit regridding on-the-fly in an interactive visualization application, or in a Web Map Service implementation. For large datasets with complex grids the new mechanism is shown to significantly outperform algorithms used in many scientific visualization packages.

Uncertainty in climate change impacts on basin-scale freshwater resources – preface to the special issue: the QUEST-GSI methodology and synthesis of results

This paper presents a preface to this Special Issue on the results of the QUEST-GSI (Global Scale Impacts) project on climate change impacts on catchment-scale water resources. A detailed description of the unified methodology, subsequently used in all studies in this issue, is provided. The project method involved running simulations of catchment-scale hydrology using a unified set of past and future climate scenarios, to enable a consistent analysis of the climate impacts around the globe. These scenarios include "policy-relevant" prescribed warming scenarios. This is followed by a synthesis of the key findings. Overall, the studies indicate that in most basins the models project substantial changes to river flow, beyond that observed in the historical record, but that in many cases there is considerable uncertainty in the magnitude and sign of the projected changes. The implications of this for adaptation activities are discussed.

Utopia and education in the seventeenth century: Bacon’s 'Salomon’s House' and its influence

New Worlds Reflected provides a significant contribution both to the history of utopian literature and travel, and to the wider cultural and intellectual history of the time, assembling original essays from scholars interested in representations of the globe and new and ideal worlds in the period from the sixteenth to eighteenth centuries, and in the imaginative reciprocal responsiveness of utopian and travel writing. Chapter 7 looks at the influence of Salomon’s House in Francis Bacon’s New Atlantis (1627) on later seventeenth-century educational utopias.

Evaluation of ice cloud representation in the ECMWF and UK Met Office models using CloudSat and CALIPSO data

Ice cloud representation in general circulation models remains a challenging task, due to the lack of accurate observations and the complexity of microphysical processes. In this article, we evaluate the ice water content (IWC) and ice cloud fraction statistical distributions from the numerical weather prediction models of the European Centre for Medium-Range Weather Forecasts (ECMWF) and the UK Met Office, exploiting the synergy between the CloudSat radar and CALIPSO lidar. Using the last three weeks of July 2006, we analyse the global ice cloud occurrence as a function of temperature and latitude and show that the models capture the main geographical and temperature-dependent distributions, but overestimate the ice cloud occurrence in the Tropics in the temperature range from −60 °C to −20 °C and in the Antarctic for temperatures higher than −20 °C, but underestimate ice cloud occurrence at very low temperatures. A global statistical comparison of the occurrence of grid-box mean IWC at different temperatures shows that both the mean and range of IWC increases with increasing temperature. Globally, the models capture most of the IWC variability in the temperature range between −60 °C and −5 °C, and also reproduce the observed latitudinal dependencies in the IWC distribution due to different meteorological regimes. Two versions of the ECMWF model are assessed. The recent operational version with a diagnostic representation of precipitating snow and mixed-phase ice cloud fails to represent the IWC distribution in the −20 °C to 0 °C range, but a new version with prognostic variables for liquid water, ice and snow is much closer to the observed distribution. The comparison of models and observations provides a much-needed analysis of the vertical distribution of IWC across the globe, highlighting the ability of the models to reproduce much of the observed variability as well as the deficiencies where further improvements are required.

Everything and nothing project

An EPRSC ‘Partnerships for Public Engagement’ scheme 2010. FEC 122,545.56/UoR 10K everything and nothing is a performance and workshop which engages the public creatively with mathematical concepts: the Poincare conjecture, the shape of the universe, topology, and the nature of infinity are explored through an original, thought provoking piece of music theatre. Jorge Luis Borges' short story 'The Library of Babel' and the aviator Amelia Earhart’s attempt to circumnavigate the globe combine to communicate to audience key mathematical concepts of Poincare’s conjecture. The project builds on a 2008 EPSRC early development project (EP/G001650/1) and is led by an interdisciplinary team the19thstep consisting of composer Dorothy Ker, sculptor Kate Allen and mathematician Marcus du Sautoy. everything and nothing has been devised by Dorothy Ker and Kate Allen, is performed by percussionist Chris Brannick, mezzo soprano Lucy Stevens and sound designer Kelcey Swain. The UK tour targets arts-going audiences, from the Green Man Festival to the British Science Festival. Each performance is accompanied with a workshop led by Topologist Katie Steckles. Alongside the performances and workshops is a website, http://www.everythingandnothingproject.com/ The Public engagement evaluation and monitoring for the project are carried out by evaluator Bea Jefferson. The project is significant in its timely relation to contemporary mathematics and arts-science themes delivering an extensive programme of public engagement.

Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages

P>To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal variation in bacteriophage numbers was evident, peaking between June and August. Removal of cattle from the pasture precipitated a reduction in bacteriophage numbers, and during the winter months, no bacteriophage infecting Escherichia coli were detected, a surprising occurrence considering that 1031 tailed-bacteriophages are estimated to populate the globe. To address this discrepancy a culture-independent method based on quantitative PCR was developed. Primers targeting the Q gene and stx genes were designed that accurately and discriminately quantified artificial mixed lambdoid bacteriophage populations. Application of these primer sets to water samples possessing no detectable phages by plaque assay, demonstrated that the number of lambdoid bacteriophage ranged from 4.7 x 104 to 6.5 x 106 ml-1, with one in 103 free lambdoid bacteriophages carrying a Shiga toxin operon (stx). Specific molecular biological tools and discriminatory gene targets have enabled virus populations in the natural environment to be enumerated and similar strategies could replace existing propagation-dependent techniques, which grossly underestimate the abundance of viral entities.

Variation in the global-scale impacts of climate change on crop productivity due to climate model uncertainty and adaptation

Crop production is inherently sensitive to fluctuations in weather and climate and is expected to be impacted by climate change. To understand how this impact may vary across the globe many studies have been conducted to determine the change in yield of several crops to expected changes in climate. Changes in climate are typically derived from a single to no more than a few General Circulation Models (GCMs). This study examines the uncertainty introduced to a crop impact assessment when 14 GCMs are used to determine future climate. The General Large Area Model for annual crops (GLAM) was applied over a global domain to simulate the productivity of soybean and spring wheat under baseline climate conditions and under climate conditions consistent with the 2050s under the A1B SRES emissions scenario as simulated by 14 GCMs. Baseline yield simulations were evaluated against global country-level yield statistics to determine the model's ability to capture observed variability in production. The impact of climate change varied between crops, regions, and by GCM. The spread in yield projections due to GCM varied between no change and a reduction of 50%. Without adaptation yield response was linearly related to the magnitude of local temperature change. Therefore, impacts were greatest for countries at northernmost latitudes where warming is predicted to be greatest. However, these countries also exhibited the greatest potential for adaptation to offset yield losses by shifting the crop growing season to a cooler part of the year and/or switching crop variety to take advantage of an extended growing season. The relative magnitude of impacts as simulated by each GCM was not consistent across countries and between crops. It is important, therefore, for crop impact assessments to fully account for GCM uncertainty in estimating future climates and to be explicit about assumptions regarding adaptation.

An extreme case of plant-insect co-diversification: figs and fig-pollinating wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale co-phylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on average, wasps had sequences from 77% of six genes (5.6kb), figs had sequences from 60% of five genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based co-phylogenetic analyses further support the co-diversification hypothesis. Biogeographic analyses indicate that the presentday distribution of fig and pollinator lineages is consistent with an Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term co-diversification.

Revisiting Asian monsoon formation and change associated with Tibetan Plateau forcing: I. Formation

Numerical experiments with different idealized land and mountain distributions are carried out to study the formation of the Asian monsoon and related coupling processes. Results demonstrate that when there is only extratropical continent located between 0 and 120°E and between 20/30°N and the North Pole, a rather weak monsoon rainband appears along the southern border of the continent, coexisting with an intense intertropical convergence zone (ITCZ). The continuous ITCZ surrounds the whole globe, prohibits the development of near-surface cross-equatorial flow, and collects water vapor from tropical oceans, resulting in very weak monsoon rainfall. When tropical lands are integrated, the ITCZ over the longitude domain where the extratropical continent exists disappears as a consequence of the development of a strong surface cross-equatorial flow from the winter hemisphere to the summer hemisphere. In addition, an intense interaction between the two hemispheres develops, tropical water vapor is transported to the subtropics by the enhanced poleward flow, and a prototype of the Asian monsoon appears. The Tibetan Plateau acts to enhance the coupling between the lower and upper tropospheric circulations and between the subtropical and tropical monsoon circulations, resulting in an intensification of the East Asian summer monsoon and a weakening of the South Asian summer monsoon. Linking the Iranian Plateau to the Tibetan Plateau substantially reduces the precipitation over Africa and increases the precipitation over the Arabian Sea and the northern Indian subcontinent, effectively contributing to the development of the South Asian summer monsoon.

Detection and attribution of climate change: a regional perspective

The Intergovernmental Panel on Climate Change fourth assessment report, published in 2007 came to a more confident assessment of the causes of global temperature change than previous reports and concluded that ‘it is likely that there has been significant anthropogenic warming over the past 50 years averaged over each continent except Antarctica.’ Since then, warming over Antarctica has also been attributed to human influence, and further evidence has accumulated attributing a much wider range of climate changes to human activities. Such changes are broadly consistent with theoretical understanding, and climate model simulations, of how the planet is expected to respond. This paper reviews this evidence from a regional perspective to reflect a growing interest in understanding the regional effects of climate change, which can differ markedly across the globe. We set out the methodological basis for detection and attribution and discuss the spatial scales on which it is possible to make robust attribution statements. We review the evidence showing significant human-induced changes in regional temperatures, and for the effects of external forcings on changes in the hydrological cycle, the cryosphere, circulation changes, oceanic changes, and changes in extremes. We then discuss future challenges for the science of attribution. To better assess the pace of change, and to understand more about the regional changes to which societies need to adapt, we will need to refine our understanding of the effects of external forcing and internal variability

Boosting the globalization of plant proteomics through INPPO: current developments 3 and future prospects

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO’s official launch in 2011 via its website (www.inppo.com) and publication of the ‘viewpoint paper’ in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) toward achieving the INPPO objectives by its proposed initiatives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO’s primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a new section has been introduced to plant proteomics starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January & July) newsletter entitled “INPPO Express: News & Views” with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, or Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO family, and also due to the wide encouragement and support from the communities (scientific and non-scientific).