Fantasies of subjugation: a discourse theoretical account of British policy on the European Union

The decision by the UK government to hold a referendum on Britain’s membership of the European Union (EU) marks an important development in policy towards the EU. Policy changes of this kind must be understood in the historical and political context in which they occur. This includes the framing of the policy issues within public discourse. In the UK, policies are formed in a discursive environment which is overwhelmingly hostile towards the EU. Debates are structured by a predominantly Euroskeptic discourse which emphasizes the UK’s separation and heterogeneity from the rest of the EU. Drawing on the logics of critical explanation, this article examines the structure and affective power of Euroskeptic discourses which dictate the terms of the EU debate. It presents a case study of the recent EU treaty revision process, culminating in the Treaty of Lisbon. In so doing, it enables a deeper understanding of recent policy developments

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms

Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein–protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism

The international face of Thessaloniki: the “Greek crisis,” the entrepreneurial mayor, and mainstream media discourses

Thessaloniki and its mayor have been portrayed quite favourably in international mainstream media compared to the Greek state after the 2008 economic crisis. The dominant (media) discourses on Greece interpret the crisis as the result of the failure of the Greek state to reform due to the prevalence of a traditional political culture over a modern one and the moral failures of the population. In the international media representations of Thessaloniki, the local government has been described as “exceptional” in its crisis management compared to the state and other local governments, and the city's mayor, Yiannis Boutaris, has been portrayed as a reform hero, due to the implemented entrepreneurial development strategy and the revamp of the city's image through place branding. Analysing the key role of international media in the production and reproduction of a place-branding campaign of Thessaloniki in international media by employing critical discourse analysis, the paper questions the favourable representations of the city compared to the Greek state during the same period. I argue that the serial repetition of positive images contributed to Thessaloniki being perceived as an example to be followed by other Greek local governments and the central state, acting as a best practice example for transformations envisioned on wider scales. The paper contributes to place-branding debates by illustrating the important role of international media in the dissemination of place brands, and by analysing how media representations of place may serve the legitimation of processes of neoliberalisation on scales wider than the concrete urban setting where they occur

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

Interaction proteomics of synapse protein complexes

The brain integrates complex types of information, and executes a wide range of physiological and behavioral processes. Trillions of tiny organelles, the synapses, are central to neuronal communication and information processing in the brain. Synaptic transmission involves an intricate network of synaptic proteins that forms the molecular machinery underlying transmitter release, activation, and modulation of transmitter receptors and signal transduction cascades. These processes are dynamically regulated and underlie neuroplasticity, crucial to learning and memory formation. In recent years, interaction proteomics has increasingly been used to elucidate the constituents of synaptic protein complexes. Unlike classic hypothesis-based assays, interaction proteomics detects both known and novel interactors without bias. In this trend article, we focus on the technical aspects of recent proteomics to identify synapse protein complexes, and the complementary methods used to verify the protein–protein interaction. Moreover, we discuss the experimental feasibility of performing global analysis of the synapse protein interactome

Accumulating discursive capital, valuating subject positions. From Marx to Foucault

Whenever people use language, they participate in valuation practices, i.e. they give value to themselves as well as to others. To account for the construction of social inequality through discursive valuation practices, discourse theorists need Marxist theory and Marxists need discourse theory. By going from the early Marx to the late Foucault, I will revisit Marx?s value theory in light of practice-oriented approaches to social inequality. I will discuss examples from two distinct arenas, the monopolization of attention by populist leaders and the academic star system, both of which are accounted for in terms of the accumulation of discursive capital. This perspective asks how the value of subject positions is constructed and hierarchies between them are established in discursive practices. Investigating the construction of valuable subject positions in discourse communities, this perspective attempts to overcome the traditional division between language, the economic and the social. Discourse not only represents value and the social order but, through representation, it also contributes to constituting the social as a hierarchical world of more or less valued subject positions

Circular Permutation in Proteins

This is a ‘‘Topic Page’ ’ article for PLoS Computational Biology. Circular permutation describes a type of relationship between proteins, whereby the proteins have a changed order of amino acids in their protein sequence, such that the sequence of the first portion of one protein (adjacent to the N-terminus) is related to that of the second portion of the other protein (near its C-terminus), and vice versa (see Figure 1). This is directly analogous to the mathematical notion of a cyclic permutation over the set of residues in a protein. Circular permutation can be the result of evolutionary events, post-translational modifications, or artificially engineered mutations. The result is a protein structure with different connectivity, but overall similar three-dimensional (3D) shape. The homology between portions of the proteins can be established by observing similar sequences between N- and C-terminal portions of the tw

VASCo: computation and visualization of annotated protein surface contacts

<p>Abstract</p> <p>Background</p> <p>Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions.</p> <p>Results</p> <p>VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in.</p> <p>Conclusion</p> <p>VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.</p

A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions