Integrating nitrogen fluxes at the European scale

Executive summary Nature of the problem • Environmental problems related to nitrogen concern all economic sectors and impact all media: atmosphere, pedosphere, hydrosphere and anthroposphere. • Therefore, the integration of fluxes allows an overall coverage of problems related to reactive nitrogen (Nr) in the environment, which is not accessible from sectoral approaches or by focusing on specific media. Approaches • This chapter presents a set of high resolution maps showing key elements of the N flux budget across Europe, including N2 and Nr fluxes. • Comparative nitrogen budgets are also presented for a range of European countries, highlighting the most efficient strategies for mitigating Nr problems at a national scale. A new European Nitrogen Budget (EU-27) is presented on the basis of state-of-the-art Europe-wide models and databases focusing on different segments of Europe’s society. Key findings • From c. 18 Tg Nr yr −1 input to agriculture in the EU-27, only about 7 Tg Nr yr− 1 find their way to the consumer or are further processed by industry. • Some 3.7 Tg Nr yr−1 is released by the burning of fossil fuels in the EU-27, whereby the contribution of the industry and energy sectors is equal to that of the transport sector. More than 8 Tg Nr yr−1 are disposed of to the hydrosphere, while the EU-27 is a net exporter of reactive nitrogen through atmospheric transport of c. 2.3 Tg Nr yr−1. • The largest single sink for Nr appears to be denitrifi cation to N2 in European coastal shelf regions (potentially as large as the input of mineral fertilizer, about 11 Tg N yr–1 for the EU-27); however, this sink is also the most uncertain, because of the uncertainty of Nr import from the open ocean. Major uncertainties • National nitrogen budgets are diffi cult to compile using a large range of data sources and are currently available only for a limited number of countries. • Modelling approaches have been used to fill in the data gaps in some of these budgets, but it became obvious during this study that further research is needed in order to collect necessary data and make national nitrogen budgets inter-comparable across Europe. • In some countries, due to inconsistent or contradictory information coming from different data sources, closure of the nitrogen budget was not possible. Recommendations • The large variety of problems associated with the excess of Nr in the European environment,including adverse impacts, requires an integrated nitrogen management approach that would allow for creation and closure of N budgets within European environments. • Development of nitrogen budgets nationwide, their assessment and management could become an effective tool to prioritize measures and prevent unwanted side effects.

Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Radical left-wing Euroscepticism in the 2014 elections: a cross-European comparison

This article examines the varied performance of radical left-wing Eurosceptic parties during the 2014 EP elections. While the performance of the radical right during this 'earthquake' election has been widely discussed, little attention has been paid to the radical left. The article examines the result comparatively, and identifies that: (1) across Europe, radical left-wing euroscepticism is limited to few countries, including Greece, Cyprus, France and Portugal; (2) the countries that have experienced the worst of the economic crisis did not experience a significant rise in far right-wing party support but did experience the rise of left-wing euroscepticism; (3) from this sample only Greece experienced the rise of both the radical right and radical left.