An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D

Background: The phenotypic effects of sequence variations in protein-coding regions come about primarily via their effects on the resulting structures, for example by disrupting active sites or affecting structural stability. In order better to understand the mechanisms behind known mutant phenotypes, and predict the effects of novel variations, biologists need tools to gauge the impacts of DNA mutations in terms of their structural manifestation. Although many mutations occur within domains whose structure has been solved, many more occur within genes whose protein products have not been structurally characterized.Results: Here we present 3DSim (3D Structural Implication of Mutations), a database and web application facilitating the localization and visualization of single amino acid polymorphisms (SAAPs) mapped to protein structures even where the structure of the protein of interest is unknown. The server displays information on 6514 point mutations, 4865 of them known to be associated with disease. These polymorphisms are drawn from SAAPdb, which aggregates data from various sources including dbSNP and several pathogenic mutation databases. While the SAAPdb interface displays mutations on known structures, 3DSim projects mutations onto known sequence domains in Gene3D. This resource contains sequences annotated with domains predicted to belong to structural families in the CATH database. Mappings between domain sequences in Gene3D and known structures in CATH are obtained using a MUSCLE alignment. 1210 three-dimensional structures corresponding to CATH structural domains are currently included in 3DSim; these domains are distributed across 396 CATH superfamilies, and provide a comprehensive overview of the distribution of mutations in structural space.Conclusion: The server is publicly available at http://3DSim.bioinfo.cnio.es/. In addition, the database containing the mapping between SAAPdb, Gene3D and CATH is available on request and most of the functionality is available through programmatic web service access

Colloidal templating at a cholesteric - oil interface: Assembly guided by an array of disclination lines

We simulate colloids (radius $R \sim 1\mu$m) trapped at the interface between a cholesteric liquid crystal and an immiscible oil, at which the helical order (pitch p) in the bulk conflicts with the orientation induced at the interface, stabilizing an ordered array of disclinations. For weak anchoring strength W of the director field at the colloidal surface, this creates a template, favoring particle positions eitheron top of or midway between defect lines, depending on $\alpha = R/p$. For small $\alpha$, optical microscopy experiments confirm this picture, but for larger $\alpha$ no templating is seen. This may stem from the emergence at moderate W of a rugged energy landscape associated with defect reconnections.Comment: 5 pages, 4 figure

Infrared astronomical satellite (IRAS) catalogs and atlases. Volume 1: Explanatory supplement

The Infrared Astronomical Satellite (IRAS) was launched on January 26, 1983. During its 300-day mission, IRAS surveyed over 96 pct of the celestial sphere at four infrared wavelengths, centered approximately at 12, 25, 60, and 100 microns. Volume 1 describes the instrument, the mission, and data reduction

Applying institutional theories to managing megaprojects

© 2017 Elsevier Ltd, APM and IPMA This paper contributes to Rodney Turner's initiative to develop a theory of project management from practice. Organizational scholars studying strategy suggest that more attention needs to be paid to practices involved in organizing, as well as the institutional contexts in which these practices are embedded. Taking a cue from strategy-in-practice approaches, it is proposed that institutional theories can be used to address some questions that have not been answered adequately regarding megaprojects. Institutional theories also seem to be gaining the attention of scholars investigating large, global, infrastructure projects as reported in engineering, management and construction journals. Increasingly, it is evident that the problem areas attached to these projects stretch beyond technical issues: they must be considered as socio-technical endeavours embedded in complex institutional frames. The authors suggest that studying how to deal with institutional differences in the environment of megaprojects has both theoretical and practical implications

The Gaussian Plasma Lens in Astrophysics. Refraction

We consider the geometrical optics for refraction of a distant radio source by an interstellar plasma lens, with application to a lens with a Gaussian electron column density profile. The refractive properties of the lens are specified completely by a dimensionless parameter, alpha, which is a function of the wavelength of observation, the lens' electron column density, the lens-observer distance, and the transverse diameter of the lens. Relative motion of the observer and lens produces modulations in the source's light curve. Plasma lenses are diverging so the light curve displays a minimum, when the lens is on-axis, surrounded by enhancements above the unlensed flux density. Lensing can also produce caustics, multiple imaging, and angular position wander of the background source. If caustics are formed, the separation of the outer caustics can constrain alpha, while the separation of the inner caustics can constrain the size of the lens. We apply our analysis to 0954+654, a source for which we can identify caustics in its light curve, and 1741-038, for which polarization observations were obtained during and after the scattering event. We find general agreement between modelled and observed light curves at 2.25 GHz, but poor agreement at 8.1 GHz. The discrepancies may result from a combination of lens substructure or anisotropic shape, a lens that only grazes the source, or unresolved source substructure. Our analysis places the following constraints on the lenses: Toward 0954+654 (1741-038) the lens was 0.38 AU (0.065 AU) in diameter, with a peak column density of 0.24 pc cm^{-3} (1E-4 pc cm^{-3}) and an electron density of 1E5 cm^{-3} (300 cm^{-3}). The angular wander caused by the lens was 250 mas (0.4 mas) at 2.25 GHz. For 1741-038, we place an upper limit of 100 mG on the lens' magnetic field.Comment: 26 pages, LaTeX2e using AASTeX macro aaspp4, 11 PostScript figures; to be published in Ap

Spin-Correlation Coefficients and Phase-Shift Analysis for p+3^3He Elastic Scattering

Angular Distributions for the target spin-dependent observables A$_{0y}$, A$_{xx}$, and A$_{yy}$ have been measured using polarized proton beams at several energies between 2 and 6 MeV and a spin-exchange optical pumping polarized $^3$He target. These measurements have been included in a global phase-shift analysis following that of George and Knutson, who reported two best-fit phase-shift solutions to the previous global p+$^3$He elastic scattering database below 12 MeV. These new measurements, along with measurements of cross-section and beam-analyzing power made over a similar energy range by Fisher \textit{et al.}, allowed a single, unique solution to be obtained. The new measurements and phase-shifts are compared with theoretical calculations using realistic nucleon-nucleon potential models.Comment: Submitted to Phys. Rev.

The 1997 event in the Crab pulsar revisited

A complex event observed in the radio pulses from the Crab pulsar in 1997 included echoes, a dispersive delay, and large changes in intensity. It is shown that these phenomena were due to refraction at the edge of a plasma cloud in the outer region of the Crab Nebula. Several similar events have been observed, although in less detail. It is suggested that the plasma cloud is in the form of filaments with diameter around 3 x 10^11m and electron density of order 10^4 cm-3Comment: 5 pages 4 figs Accepted by MNRA

12^{12}C/13^{13}C ratio in planetary nebulae from the IUE archives

We investigated the abundance ratio of $^{12}$C/$^{13}$C in planetary nebulae by examining emission lines arising from \ion{C}{3} 2s2p ^3P_{2,1,0} \to 2s^2 ^1S_0. Spectra were retrieved from the International Ultraviolet Explorer archives, and multiple spectra of the same object were coadded to achieve improved signal-to-noise. The $^{13}$C hyperfine structure line at 1909.6 \AA was detected in NGC 2440. The $^{12}$C/$^{13}$C ratio was found to be $\sim4.4\pm$1.2. In all other objects, we provide an upper limit for the flux of the 1910 \AA line. For 23 of these sources, a lower limit for the $^{12}$C/$^{13}$C ratio was established. The impact on our current understanding of stellar evolution is discussed. The resulting high signal-to-noise \ion{C}{3} spectrum helps constrain the atomic physics of the line formation process. Some objects have the measured 1907/1909 flux ratio outside the low-electron density theoretical limit for $^{12}$C. A mixture of $^{13}$C with $^{12}$C helps to close the gap somewhat. Nevertheless, some observed 1907/1909 flux ratios still appear too high to conform to the presently predicted limits. It is shown that this limit, as well as the 1910/1909 flux ratio, are predominantly influenced by using the standard partitioning among the collision strengths for the multiplet $^1S_0$--$^3P_J$ according to the statistical weights. A detailed calculation for the fine structure collision strengths between these individual levels would be valuable.Comment: ApJ accepted: 19 pages, 3 Figures, 2 Table