Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

European Union Cross-Border Cooperation as Conflict Transformation:Potential and Limits

Cross-border cooperation as conflict transformation provides a potential strategy for the European Union (EU) to help realise its founding peacebuilding objective. A wealth of cross-border cooperation activity sponsored by the EU spans a quarter of a century. Although the conflict transformation capacity of that cooperation is questionable in some border regions there is evidence to suggest that it has delivered peacebuilding dividends in other border regions. However, EU cross-border cooperation as conflict transformation faces a number of significant twenty-first century challenges including: ghost borders of the communal imagination; EU external border securitization; perceptions of EU and Russian empire-building; and the Mediterranean transmigrant/refugee crisis. It is argued that these challenges pose significant obstacles to EU cross-border cooperation as conflict transformation and undermine the peacebuilding objective of European integration.

Economic Stability and Economic Governance in the Euro Area:What the European Crisis Can Teach on the Limits of Economic Integration

The recent European economic crisis has dramatically exposed the failures of
the various institutional mechanisms in place to maintain economic stability
in Europe, and has unveiled the difficulty in achieving international coordination
on fiscal and financial stability policies. Drawing on the European<br/>experience, this article analyzes the concept of economic stability in international
law and highlights the peculiar problems connected to its maintenance
or promotion. First, we demonstrate that policies that safeguard and
protect economic stability are largely regulated and managed at the national
level, due to their inextricable relationship with the exercise of national political
power. Until recently, more limited levels of pan-European integration
did not make the coordination of economic stability policies seem necessary.
However, a much deeper level of economic integration makes it very difficult
to tackle an international economic crisis through national responses. If EU
Member states wish to maintain and deepen economic integration, they
must accept an erosion of sovereignty over their economic stability policies.
This will not only deprive states of a fundamental anchor of political power,
but also create a challenge for the maintenance of democratic control over
economic policies. Second, this article argues that soft law approaches are
likely ineffective in enforcing the regulatory disciplines required to ensure
economic stability.

Investigating clinical predictors of arteriovenous fistula functional patency in a European cohort

Background: Arteriovenous fistula (AVF) failure to mature (FTM) rates contribute to excessive dependence on central venous catheters for haemodialysis. Choosing the most appropriate vascular access site for an individual patient is guided largely by their age, co-morbidities and clinical examination. We investigated the clinical predictors of AVF FTM in a European cohort of patients and applied an existing clinical risk prediction model for AVF FTM to this population.
Methods: A prospective cohort study was designed that included all patients undergoing AVF creation between January 2009 and December 2014 in a single centre (Belfast City Hospital) who had a functional AVF outcome observed by March 2015.
Results: A total of 525 patients had a functional AVF outcome recorded and were included in the FTM analysis. In this cohort, 309 (59%) patients achieved functional AVF patency and 216 (41%) patients had FTM. Female gender [P < 0.001, odds ratio (OR) 2.03 (CI 1.37–3.02)] and lower-arm AVF [P < 0.001, OR 4.07 (CI 2.77–5.92)] were associated with AVF FTM. The Lok model did not predict FTM outcomes based on the associated risk stratification in our population.
Conclusions: In this European study, female gender was associated with twice the risk of AVF FTM and a lower-arm AVF with four times the risk of FTM. The FTM risk prediction model was not found to be discriminative in this population. Clinical risk factors for AVF FTM vary between populations;we would recommend that units investigate their own clinical predictors of FTM to maximize AVF functional patency and ultimately survival in dialysis patients. Clinical predictors of AVF FTM may not be sufficient on their own to improve vascular access functional patency rates.

Behaviour-time budget and functional habitat use of a free-ranging European badger (Meles meles)

Background: The European badger (Melesmeles) is involved in the maintenance of bovine tuberculosis infection and onward spread to cattle. However, little is known about how transmission occurs. One possible route could be through direct contact between infected badgers and cattle. It is also possible that indirect contact between cattle and infected badger excretory products such as faeces or urine may occur either on pasture or within and around farm buildings. A better understanding of behaviour patterns in wild badgers may help to develop biosecurity measures to minimise direct and indirect contact between badgers and cattle. However, monitoring the behaviour of free-ranging badgers can be logistically challenging and labour intensive due to their nocturnal and semi-fossorial nature.We trialled a GPS and tri-axial accelerometer-equipped collar on a free-ranging badger to assess its potential value to elucidate behaviour-time budgets and functional habitat use. Results: During the recording period between 16:00 and 08:00 on a single night, resting was the most commonly identified behaviour (67.4%) followed by walking (20.9%), snuffling (9.5%) and trotting (2.3%).When examining accelerometer data associated with each GPS fix and habitat type (occurring 2 min 30 s before and after), walking was themost common behaviour in woodland (40.3%) and arable habitats (53.8%), while snuffling was themost common behaviour in pasture (61.9%). Several nocturnal resting periods were also observed. The total distance travelled was 2.28 km. Conclusions: In the present report, we demonstrate proof of principle in the application of a combined GPS and accelerometer device to collect detailed quantitative data on wild badger behaviour. Behaviour-time budgets allow us to investigate how badgers allocate energy to different activities and how thismight change with disease status. Such information could be useful in the development of measures to reduce opportunities for onward transmission of bovine tuberculosis from badgers to cattle.

ANRIL Variants and Aggressive Periodontitis in European and African Populations

Introduction: The chromosome 9p21 locus has been identified as a marker of coronary artery disease. In this locus studies have focused on variations in the ANRIL gene that has also been identified as a strong candidate for association with aggressive periodontitis (AgP).
Objective: To investigate possible associations between gene variants of ANRIL and AgP in European and African populations.
Methods: European AgP cases (n= 213) and age-matched periodontally healthy controls (n= 81) were recruited from centres in the United Kingdom (Belfast, Glasgow, Newcastle and London). African AgP cases (n= 95) and controls (n= 105) were recruited in Khartoum, Sudan. Five single nucleotide polymorphisms (SNPs) in ANRIL were genotyped using Sequenom and analysed using Haploview with permutation testing to correct for multiple candidates. Odds ratios (OR) and 95% confidence intervals (95%CI) were calculated.
Results: In the European subjects there was a significant association between rs518394 (p=0.0013; OR = 1.81, 95%CI 1.26-2.61) and rs1333049 (p=0.0028; OR = 1.75, 95%CI 1.21-2.52) and AgP. These associations remained significant after permutation testing. In addition there was an association between rs 1360590 (p=0.035) and AgP in females. In the African subjects there was a significant association between only one SNP rs1537415 and AgP (p=0.036; OR = 1.59, 95%CI 1.04-2.43), however, this was not significant following permutation testing. There were no significant associations with rs3217992 in either population.
Conclusions: SNP variants in the ANRIL locus were shown to be significantly associated with AgP in a European population and for the first time in an African population confirming this as the best replicated locus for aggressive periodontitis.

Triggering employee voice under the European Information and Consultation Directive: A non-union case study

The transposition of the 2002/14/EC Directive, establishing a general framework for information and consultation (I&C), has proven contentious in largely voluntarist systems of employment regulation. Receiving particular criticism is the employee ‘opt-in’ mechanism as a means to access I&C rights. For non-union employees in particular, the ability and potential to negotiate rights for I&C is widely seen to be problematic. This article uniquely examines the opt-in mechanism in the context of non-unionism, considering how non-union employers respond to non-union employees invoking their legislative rights to I&C. Drawing upon a case study conducted over four years in a large non-union multinational, the evidence shows how the opt-in and negotiation process function to the advantage of the employer rather than the intended regulatory impact to advance employee rights

Distribution, occurrence and biotoxin composition of the main shellfish toxin producing microalgae within European waters: A comparison of methods of analysis

Harmful algal blooms (HABs) are a natural global phenomena emerging in severity and extent. Incidents have many economic, ecological and human health impacts. Monitoring and providing early warning of toxic HABs are critical for protecting public health. Current monitoring programmes include measuring the number of toxic phytoplankton cells in the water and biotoxin levels in shellfish tissue. As these efforts are demanding and labour intensive, methods which improve the efficiency are essential. This study compares the utilisation of a multitoxin surface plasmon resonance (multitoxin SPR) biosensor with enzyme-linked immunosorbent assay (ELISA) and analytical methods such as high performance liquid chromatography with fluorescence detection (HPLC-FLD) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for toxic HAB monitoring efforts in Europe. Seawater samples (n = 256) from European waters, collected 2009-2011, were analysed for biotoxins: saxitoxin and analogues, okadaic acid and dinophysistoxins 1/2 (DTX1/DTX2) and domoic acid responsible for paralytic shellfish poisoning (PSP), diarrheic shellfish poisoning (DSP) and amnesic shellfish poisoning (ASP), respectively. Biotoxins were detected mainly in samples from Spain and Ireland. France and Norway appeared to have the lowest number of toxic samples. Both the multitoxin SPR biosensor and the RNA microarray were more sensitive at detecting toxic HABs than standard light microscopy phytoplankton monitoring. Correlations between each of the detection methods were performed with the overall agreement, based on statistical 2 × 2 comparison tables, between each testing platform ranging between 32% and 74% for all three toxin families illustrating that one individual testing method may not be an ideal solution. An efficient early warning monitoring system for the detection of toxic HABs could therefore be achieved by combining both the multitoxin SPR biosensor and RNA microarray.

A validated UPLC–MS/MS method for the surveillance of ten aquatic biotoxins in European brackish and freshwater systems

Over the past few decades, there has been an increased frequency and duration of cyanobacterial Harmful Algal Blooms (HABs) in freshwater systems globally. These can produce secondary metabolites called cyanotoxins, many of which are hepatotoxins, raising concerns about repeated exposure through ingestion of contaminated drinking water or food or through recreational activities such as bathing/ swimming. An ultra-performance liquid chromatography tandem mass spectrometry (UPLC–MS/MS) multi-toxin method has been developed and validated for freshwater cyanotoxins; microcystins-LR, -YR, -RR, -LA, -LY and -LF, nodularin, cylindrospermopsin, anatoxin-a and the marine diatom toxin domoic acid. Separation was achieved in around 9 min and dual SPE was incorporated providing detection limits of between 0.3 and 5.6 ng/L of original sample. Intra- and inter-day precision analysis showed relative
standard deviations (RSD) of 1.2–9.6% and 1.3–12.0% respectively. The method was applied to the analysis of aquatic samples (n = 206) from six European countries. The main class detected were the hepatotoxins; microcystin-YR (n = 22), cylindrospermopsin (n = 25), microcystin-RR (n = 17), microcystin-LR (n = 12), microcystin-LY (n = 1), microcystin-LF (n = 1) and nodularin (n = 5). For microcystins, the levels detected ranged from 0.001 to 1.51 mg/L, with two samples showing combined levels above the guideline set by the WHO of 1 mg/L for microcystin-LR. Several samples presented with multiple toxins indicating the potential for synergistic effects and possibly enhanced toxicity. This is the first published pan European survey of freshwater bodies for multiple biotoxins, including two identified for the first time; cylindrospermopsin in Ireland and nodularin in Germany, presenting further incentives for improved monitoring and development of strategies to mitigate human exposure.

Trends in Approval Times for Genetically Engineered Crops in the United States and the European Union

Genetically engineered (GE) crops are subject to regulatory oversight to ensure their safety for humans and the environment. Their approval in the European Union (EU) starts with an application in a given Member State followed by a scientific step (risk assessment), and ends with a political decision-making step (risk management); and in the United States (US) it starts with a scientific (field trial) step and ends with a ‘bureaucratic’ decision-making step. We investigated trends for the time taken for these steps and the overall time taken for approving GE crops in the US and the EU (traders in these commodities). Results show that from 1996-2015 the overall time trend for approval in the EU decreased and then flattened off, with an overall mean completion-time of 1,763 days. In the US in 1998 there was a break in the trend of the overall approval time: Initially, from 1988 until 1997 the trend decreased with a mean approval time of 1,321 days; from 1998-2015, the trend almost stagnated with a mean approval time of 2,467 days.

Psychological determinants of consumer acceptance of personalised nutrition in 9 European countries

OBJECTIVE: To develop a model of the psychological factors which predict people's intention to adopt personalised nutrition. Potential determinants of adoption included perceived risk and benefit, perceived self-efficacy, internal locus of control and health commitment.

METHODS: A questionnaire, developed from exploratory study data and the existing theoretical literature, and including validated psychological scales was administered to N=9381 participants from 9 European countries (Germany, Greece, Ireland, Poland, Portugal, Spain, the Netherlands, the UK, and Norway).

RESULTS: Structural equation modelling indicated that the greater participants' perceived benefits to be associated with personalised nutrition, the more positive their attitudes were towards personalised nutrition, and the greater their intention to adopt it. Higher levels of nutrition self-efficacy were related to more positive attitudes towards, and a greater expressed intention to adopt, personalised nutrition. Other constructs positively impacting attitudes towards personalised nutrition included more positive perceptions of the efficacy of regulatory control to protect consumers (e.g. in relation to personal data protection), higher self-reported internal health locus of control, and health commitment. Although higher perceived risk had a negative relationship with attitude and an inverse relationship with perceived benefit, its effects on attitude and intention to adopt personalised nutrition was less influential than perceived benefit. The model was stable across the different European countries, suggesting that psychological factors determining adoption of personalised nutrition have generic applicability across different European countries.

CONCLUSION: The results suggest that transparent provision of information about potential benefits, and protection of consumers' personal data is important for adoption, delivery of public health benefits, and commercialisation of personalised nutrition.

The Extra-territorial Obligations of European States regarding Human Rights in the Context of Terrorism

This chapter focuses on the growing tendency of international human rights law to require states to protect the rights of non-nationals who are in the state unlawfully and of nationals and non-nationals who are outside the state, especially when any of these people are involved in terrorist or counter-terrorist activity. It reviews these additional obligations within a European context, focusing on EU law and the law of the European Convention on Human Rights and drawing on the case law of UK courts. Part 1 considers when a European state must grant asylum to alleged terrorists on the basis that otherwise they would suffer human rights abuses in the state from which they are fleeing. Part 2 examines whether, outside of asylum claims, a European state must not deport or extradite an alleged terrorist because he or she might suffer an abuse of human rights in the receiving state. Part 3 looks at whether a European state whose security forces are engaged in counter-terrorism activities abroad is obliged to protect the human rights of the individuals serving in those forces and/or the human rights of the alleged terrorists they are confronting. While welcoming the extension of state responsibility, the chapter notes that it is occurring in a way which introduces three aspects of relativity into the protection of human rights. First, European law protects only some human rights extra-territorially. Second, it protects those rights only when there is ‘a real risk’ of their being violated. Third, sometimes it protects those rights only when there is a real risk of their being violated ‘flagrantly’.

Eurozone Network Connectedness During Calm and Crisis: Evidence from the MTS Platform for Interdealer Trading of European Sovereign Debt

This paper examines the connectedness of the Eurozone sovereign debt market over the period 2005–2011. By employing measures built from the variance decompositions of approximating models we are able to define weighted, directed networks that enable a deeper understanding of the relationships between the Eurozone countries. We find that connectedness in the Eurozone was very high during the calm market conditions preceding the global financial crisis but decreased dramatically when the crisis took hold, and worsened as the Eurozone sovereign debt crisis emerged. The drop in connectedness was especially prevalent in the case of the peripheral countries with some of the most peripheral countries deteriorating into isolation. Our results have implications for both market participants and regulators.