NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints

Nuclear magnetic resonance (NMR) spectroscopy together with X-ray crystallography, are the main techniques used for the determination of high-resolution 3D structures of biological molecules. The output of an NMR experiment includes a set of lower and upper limits for the distances (constraints) between pairs of atoms. If the number of constraints is high enough, there will be a finite number of possible conformations (models) of the macromolecule satisfying the data. Thus, the more constraints are measured, the better defined these structures will be. The availability of a user-friendly tool able to help in the analysis and interpretation of the number of experimental constraints per residue, is thus of valuable importance when assessing the levels of structure definition of NMR solved biological macromolecules, in particular, when high-quality structures are needed in techniques such as, computational biology approaches, site-directed mutagenesis experiments and/or drug design. Here, we present a free publicly available web-server, i.e. NMR Constraints Analyser, which is aimed at providing an automatic graphical analysis of the NMR experimental constraints atom by atom. The NMR Constraints Analyser server is available from the web-page http://molsim.sci.univr.it/constrain

Characterization of Tryptophanase from Vibrio cholerae O1

AbstractTryptophanase (Trpase) encoded by the tnaA gene catalyzes the conversion of tryptophan to indole, which is an extracellular signaling molecule detected in various bacteria including Vibrio cholerae. Indole has been demonstrated to regulate biofilm formation, drug resistance, plasmid maintenance and spore formation of bacteria. In the present study, the tnaA gene from V. cholerae O1 (VcTrpase) was cloned and expressed in E. coli BL21(DE3) tn5:tnaA (a Trpase-deficient competent). VcTrpase was purified by Ni2+-NTA chromatography. The obtained VcTrpase had a molecular mass of approximately 49 kDa, a specific activity of 3 U/mg protein, and absorption peaks at 330 and 435nm. Using a site-directed mutagenesis technique, replacement of Arg419 by Val resulted in a VcTrpase completely devoid of activity. Thus, this site can be a target for drug design for controlling V. cholerae

A non-catecholamine-producing sympathetic paraganglioma of the spermatic cord: the importance of performing candidate gene mutation analysis

textabstractBackground: Catecholamine-producing tumours are called pheochromocytomas when they are located in the adrenal gland and sympathetic paragangliomas when they are located elsewhere in the abdomen. Rarely these tumours do not produce catecholamines and even more rarely they arise in the spermatic cord. Over the past decade, systematic mutation analysis of apparently sporadic cases of pheochromocytomas and paragangliomas has elucidated the frequent presence of germ line mutations in one of five candidate genes, including RET, VHL, SDHB, SDHC, and SDHD. Clinical history and methods: We describe a 45-year-old man with a non catecholamine-producing paraganglioma of the spermatic cord. We performed SDHB immunohistochemistry and performed mutation analysis of the SDHB, SDHC, and SDHD genes. Results: There was no staining of tumour cells with SDHB immunohistochemistry, indicative of an SDH mutation. Mutation analysis demonstrated a germ line SDHD mutation (p.Val147Met). Conclusions: Systematic mutation analysis is required in paraganglioma patients for the detection of germ line mutations. This should be preceded by SDHB immunohistochemistry to limit the number of genes to be tested

Spectroscopic Evidence for the Localization of Skyrmions near Nu=1 as T->0

Optically pumped nuclear magnetic resonance measurements of Ga-71 spectra were carried out in an n-doped GaAs/Al0.1Ga0.9As multiple quantum well sample near the integer quantum Hall ground state Nu=1. As the temperature is lowered (down to T~0.3 K), a ``tilted plateau'' emerges in the Knight shift data, which is a novel experimental signature of quasiparticle localization. The dependence of the spectra on both T and Nu suggests that the localization is a collective process. The frozen limit spectra appear to rule out a 2D lattice of conventional skyrmions.Comment: 4 pages (REVTEX), 5 eps figures embedded in text, published versio

The Third wave in globalization theory

This essay examines a proposition made in the literature that there are three waves in globalization theory—the globalist, skeptical, and postskeptical or transformational waves—and argues that this division requires a new look. The essay is a critique of the third of these waves and its relationship with the second wave. Contributors to the third wave not only defend the idea of globalization from criticism by the skeptics but also try to construct a more complex and qualified theory of globalization than provided by first-wave accounts. The argument made here is that third-wave authors come to conclusions that try to defend globalization yet include qualifications that in practice reaffirm skeptical claims. This feature of the literature has been overlooked in debates and the aim of this essay is to revisit the literature and identify as well as discuss this problem. Such a presentation has political implications. Third wavers propose globalist cosmopolitan democracy when the substance of their arguments does more in practice to bolster the skeptical view of politics based on inequality and conflict, nation-states and regional blocs, and alliances of common interest or ideology rather than cosmopolitan global structures

Below the Belt? Territory and Development in China’s International Rise

China’s internationalization has been heralded by some as a new era of South–South cooperation. Yet such framings of development are pitched at an abstract space of the ‘global South’ which conceals more than it reveals. With some theory moving towards ontologies of ‘global development’, we need to capture both the connectedness and the local specificity of increasingly diffuse processes. This article sets out a more fine-grained understanding of how political territories and processes are imagined and produced by and through China’s internationalization, focusing on infrastructure as a ‘technology’ of territorialization. Much of the focus on China’s internationalization has been on state-to-state relations, but this obscures the ‘omni-channel politics’ that China practises. Using a critical literature review and illustrative case study, this article develops the idea of omni-channel politics to posit a view of ‘twisted’ territories in which political processes and development outcomes are more complex and contingent