Crystal structure and stability of gyrase–fluoroquinolone cleaved complexes from Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) infects one-third of the world’s population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone–gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone–enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. These concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance

Molecular Mechanism for the Hofmeister Effect Derived from NMR and DSC Measurements on Barnase

The effects of sodium thiocyanate, sodium chloride, and sodium sulfate on the ribonuclease barnase were studied using differential scanning calorimetry (DSC) and NMR. Both measurements reveal specific and saturable binding at low anion concentrations (up to 250 mM), which produces localized conformational and energetic effects that are unrelated to the Hofmeister series. The binding of sulfate slows intramolecular motions, as revealed by peak broadening in 13 C heteronuclear single quantum coherence spectroscopy. None of the anions shows significant binding to hydrophobic groups. Above 250 mM, the DSC results are consistent with the expected Hofmeister effects in that the chaotropic anion thiocyanate destabilizes barnase. In this higher concentration range, the anions have approximately linear effects on protein NMR chemical shifts, with no evidence for direct interaction of the anions with the protein surface. We conclude that the effects of the anions on barnase are mediated by solvent interactions. The results are not consistent with the predictions of the preferential interaction, preferential hydration, and excluded volume models commonly used to describe Hofmeister effects. Instead, they suggest that the Hofmeister anion effects on both stability and solubility of barnase are due to the way in which the protein interacts with water molecules, and in particular with water dipoles, which are more ordered around sulfate anions and less ordered around thiocyanate anions

Results of geophysical monitoring over a "leaking" natural analogue site in Italy

CO2 storage in the subsurface is becoming more and more attractive as a means to reduce CO2 emissions to the atmosphere and hence minimize human-induced global warming. The ability to monitor and verify these CO2 storage reservoirs is a key element for further implementation of other storage sites. Since the current sites fortunately do not appear to "leak" CO2, it is difficult to test the most suitable monitoring techniques for their ability to detect CO2 migration pathways. In this study different monitoring methods have been evaluated at a site in the Latera caldera (central Italy) where natural, thermo-metamorphically produced CO2 finds its way to the surface. The aim of the study is to identify which monitoring methods can detect the migrating CO2 and to gain understanding of the preferential migration pathways of the CO2. Different geophysical monitoring techniques have been deployed at a small, 200×500 m study area located in the centre of the caldera: 2D reflection seismics (testing different sources), 2D refraction seismics, multi-channel analysis of surface wave (MASW), ground penetrating radar (GPR), micro-gravity, magnetometer, self-potential (SP), 2D and 3D geo-electrical measurements and electro-magnetic (EM31 and EM34) measurements. Furthermore CO2 flux measurements were performed in a dense grid over the study area, and a limited number of soil gas samples collected along two profiles, to "ground-truth" the geophysical results. In general a good correlation has been observed between the different methods and the presence of CO2. Geophysical responses, especially those of the reflection seismic and magnetometer data, change markedly from one side of the proposed main fault to the other, probably linked to a sharp geological boundary. The observed fractures on the seismic data seem to correspond with the preferred migration pathways of the CO2. The GPR and resistivity measurements detect strong variations in conductivity induced by the presence of the CO2 up to about 2 and 20 m depth, respectively, as supported by the soil gas and flux measurements. © 2009 Elsevier Ltd. All rights reserved

Immorality and Irrationality

Does immorality necessarily involve irrationality? The question is often taken to be among the deepest in moral philosophy. But apparently deep questions sometimes admit of deflationary answers. In this case we can make way for a deflationary answer by appealing to dualism about rationality, according to which there are two fundamentally distinct notions of rationality: structural rationality and substantive rationality. I have defended dualism elsewhere. Here, I’ll argue that it allows us to embrace a sensible – I will not say boring – moderate view about the relationship between immorality and irrationality: roughly, that immorality involves substantive irrationality, but not structural irrationality. I defend this moderate view, and argue that many of the arguments for less moderate views turn either on missing the distinction between substantive and structural rationality, or on misconstruing it

Resonant transmission through an open quantum dot

We have measured the low-temperature transport properties of a quantum dot formed in a one-dimensional channel. In zero magnetic field this device shows quantized ballistic conductance plateaus with resonant tunneling peaks in each transition region between plateaus. Studies of this structure as a function of applied perpendicular magnetic field and source-drain bias indicate that resonant structure deriving from tightly bound states is split by Coulomb charging at zero magnetic field.Comment: To be published in Phys. Rev. B (1997). 8 LaTex pages with 5 figure

Self-referencing spectral interferometric probing of the onset time of relativistic transparency in intense laser-foil interactions

Irradiation of an ultrathin foil target by a high intensity laser pulse drives collective electron motion and the generation of strong electrostatic fields, resulting in ultrabright sources of high-order harmonics and energetic ions. The ion energies can be significantly enhanced if the foil undergoes relativistic self-induced transparency during the interaction, with the degree of enhancement depending in part on the onset time of transparency. We report on a simple and effective approach to diagnose the time during the interaction at which the foil becomes transparent to the laser light, providing a route to optically controlling and optimizing ion acceleration and radiation generation. The scheme involves a self-referencing approach to spectral interferometry, in which coherent transition radiation produced at the foil rear interferes with laser light transmitted through the foil. The relative timing of the onset of transmission with respect to the transition radiation generation is determined from spectral fringe spacing and compared to simultaneous frequency-resolved optical gating measurements. The results are in excellent agreement, and are discussed with reference to particle-in-cell simulations of the interaction physics and an analytical model for the onset time of transparency in ultrathin foils

Analysis of human performance as a measure of mental fatigue

In our day to day, we often experience a sense of being tired due to mental or physical workload. Along with that, there is also a feeling of degrading performance, even after the completion of simple tasks. These mental states however, are often not felt consciously or are ignored. This is an attitude that may result in human error, failure, and may lead to potential health problems together with a decrease in quality of life. States of acute mental fatigue may be detected with the close monitoring of certain indicators, such as productivity, performance and health indicators. In this paper, a model and prototype are proposed to detect and monitor acute acute fatigue, based on non-invasive Humancomputer Interaction (HCI). This approach will enable the development of better working environments, with an impact on the quality of life and the work produced.This work was developed in the context of the project CAMCoF - Contextaware Multimodal Communication Framework funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Funda ção para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-028980

Quantum optics in the phase space - A tutorial on Gaussian states

In this tutorial, we introduce the basic concepts and mathematical tools needed for phase-space description of a very common class of states, whose phase properties are described by Gaussian Wigner functions: the Gaussian states. In particular, we address their manipulation, evolution and characterization in view of their application to quantum information.Comment: Tutorial. 23 pages, 1 figure. Updated version accepted for publication in EPJ - ST devoted to the memory of Federico Casagrand

A tetragonal-to-monoclinic phase transition in a ferroelectric perovskite: the structure of PbZr(0.52)Ti(0.48)O3

The perovskite-like ferroelectric system PbZr(1-x)Ti(x)O3 (PZT) has a nearly vertical morphotropic phase boundary (MPB) around x=0.45-0.50. Recent synchrotron x-ray powder diffraction measurements by Noheda et al. [Appl. Phys. Lett. 74, 2059 (1999)] have revealed a new monoclinic phase between the previously-established tetragonal and rhombohedral regions. In the present work we describe a Rietveld analysis of the detailed structure of the tetragonal and monoclinic PZT phases on a sample with x= 0.48 for which the lattice parameters are respectively: at= 4.044 A, ct= 4.138 A, at 325 K, and am= 5.721 A, bm= 5.708 A, cm= 4.138 A, beta= 90.496 deg., at 20K. In the tetragonal phase the shifts of the atoms along the polar [001] direction are similar to those in PbTiO3 but the refinement indicates that there are, in addition, local disordered shifts of the Pb atoms of ~0.2 A perpendicular to the polar axis.. The monoclinic structure can be viewed as a condensation along one of the directions of the local displacements present in the tetragonal phase. It equally well corresponds to a freezing-out of the local displacements along one of the directions recently reported by Corker et al.[J. Phys. Condens. Matter 10, 6251 (1998)] for rhombohedral PZT. The monoclinic structure therefore provides a microscopic picture of the MPB region in which one of the "locally" monoclinic phases in the "average" rhombohedral or tetragonal structures freezes out, and thus represents a bridge between these two phases.Comment: REVTeX, 7 figures. Modifications after referee's suggestion: new figure (figure 5), comments in 2nd para. (Sect.III) and in 2nd & 3rd para. (Sect. IV-a), in the abstract: "...of ~0.2 A perpendicular to the polar axis.