Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies

The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.
A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes. These large superfamilies are generally very diverse, spanning a wide range of functions, both in terms of molecular activities and biological processes. Some of these superfamilies, such as the Rossmann-fold P-loop nucleotide hydrolases or the TIM-barrel glycosidases, have been the subject of extensive structural studies which in turn have shed light on how evolution of the sequence and structure properties produce functional diversity amongst homologues. Recently, the Structure-Function Linkage Database (SFLD) has been setup with the aim of helping the study of structure-function correlations in such superfamilies. Since the evolutionary success of these large superfamilies suggests biological importance, several Structural Genomics Centers have focused on providing full structural coverage for representatives of all sequence families in these superfamilies.
In this work we evaluate structure/function diversity in a set of these large superfamilies and attempt to assess the quality and quantity of biological information gained from Structural Genomics.
&#xa

Loss of mass and stability of galaxies in MOND

The self-binding energy and stability of a galaxy in MOND-based gravity are curiously decreasing functions of its center of mass acceleration towards neighbouring mass concentrations. A tentative indication of this breaking of the Strong Equivalence Principle in field galaxies is the RAVE-observed escape speed in the Milky Way. Another consequence is that satellites of field galaxies will move on nearly Keplerian orbits at large radii (100 - 500 kpc), with a declining speed below the asymptotically constant naive MOND prediction. But consequences of an environment-sensitive gravity are even more severe in clusters, where member galaxies accelerate fast: no more Dark-Halo-like potential is present to support galaxies, meaning that extended axisymmetric disks of gas and stars are likely unstable. These predicted reappearance of asymptotic Keplerian velocity curves and disappearance of "stereotypic galaxies" in clusters are falsifiable with targeted surveys.Comment: 4 pages, 2 figures, ApJ Letter

Localization, Coulomb interactions and electrical heating in single-wall carbon nanotubes/polymer composites

Low field and high field transport properties of carbon nanotubes/polymer composites are investigated for different tube fractions. Above the percolation threshold f_c=0.33%, transport is due to hopping of localized charge carriers with a localization length xi=10-30 nm. Coulomb interactions associated with a soft gap Delta_CG=2.5 meV are present at low temperature close to f_c. We argue that it originates from the Coulomb charging energy effect which is partly screened by adjacent bundles. The high field conductivity is described within an electrical heating scheme. All the results suggest that using composites close to the percolation threshold may be a way to access intrinsic properties of the nanotubes by experiments at a macroscopic scale.Comment: 4 pages, 5 figures, Submitted to Phys. Rev.

CPT symmetry and antimatter gravity in general relativity

The gravitational behavior of antimatter is still unknown. While we may be confident that antimatter is self-attractive, the interaction between matter and antimatter might be either attractive or repulsive. We investigate this issue on theoretical grounds. Starting from the CPT invariance of physical laws, we transform matter into antimatter in the equations of both electrodynamics and gravitation. In the former case, the result is the well-known change of sign of the electric charge. In the latter, we find that the gravitational interaction between matter and antimatter is a mutual repulsion, i.e. antigravity appears as a prediction of general relativity when CPT is applied. This result supports cosmological models attempting to explain the Universe accelerated expansion in terms of a matter-antimatter repulsive interaction.Comment: 6 pages, to be published in EPL (http://epljournal.edpsciences.org/

Low frequency Raman studies of multi-wall carbon nanotubes: experiments and theory

In this paper, we investigate the low frequency Raman spectra of multi-wall carbon nanotubes (MWNT) prepared by the electric arc method. Low frequency Raman modes are unambiguously identified on purified samples thanks to the small internal diameter of the MWNT. We propose a model to describe these modes. They originate from the radial breathing vibrations of the individual walls coupled through the Van der Waals interaction between adjacent concentric walls. The intensity of the modes is described in the framework of bond polarization theory. Using this model and the structural characteristics of the nanotubes obtained from transmission electron microscopy allows to simulate the experimental low frequency Raman spectra with an excellent agreement. It suggests that Raman spectroscopy can be as useful regarding the characterization of MWNT as it is in the case of single-wall nanotubes.Comment: 4 pages, 2 eps fig., 2 jpeg fig., RevTex, submitted to Phys. Rev.

Lopsidedness of cluster galaxies in modified gravity

We point out an interesting theoretical prediction for elliptical galaxies residing inside galaxy clusters in the framework of modified Newtonian dynamics (MOND), that could be used to test this paradigm. Apart from the central brightest cluster galaxy, other galaxies close enough to the centre experience a strong gravitational influence from the other galaxies of the cluster. This influence manifests itself only as tides in standard Newtonian gravity, meaning that the systematic acceleration of the centre of mass of the galaxy has no consequence. However, in the context of MOND, a consequence of the breaking of the strong equivalence principle is that the systematic acceleration changes the own self-gravity of the galaxy. We show here that, in this framework, initially axisymmetric elliptical galaxies become lopsided along the external field's direction, and that the centroid of the galaxy, defined by the outer density contours, is shifted by a few hundreds parsecs with respect to the densest point.Comment: accepted for publication in JCA

Universal scaling of nonlocal and local resistance fluctuations in small wires

Resistance fluctuations in small metal samples result from coherent transport of the carriers. The wave functions of the carriers extend into regions which are not accessible classically. We have directly measured the length dependence of the nonlocal magnetoresistance fluctuations in Sb and Au wires by studying regions of our samples separated from the classical current path by a distance L which varied from 3Lcphi down to 0.2Lcphi (where Lcphi is the phase coherence length for the carriers in the metal). These fluctuations decay exponentially with L/Lcphi. Measurements along the classical current paths scale more slowly with L/Lcphi than predicted by the analytical theory but are in agreement with numerical simulations. We have also studied the length dependence of the magnetic field correlation scale BC, and we find that it is in qualitative agreement with a recent model calculation that accounts for the voltage probes

Fusion Crust and the Measurement of Surface Ages of Antarctic Ordinary Chondrites

Natural thermoluminescence (TL) reflects radiation exposure and storage temperature. Meteorites generally exhibit thermoluminescence acquired during their long exposure to galactic cosmic rays in space. During atmospheric passage, temperatures are high enough to completely drain the TL, in the first mm of material under the fusion crust. We therefore refer to this surface layer as "fusion crust" although it does include some unmelted material just below the crust. When the meteorite lands on earth this drained layer will begin to build up natural TL once again due to radiation from cosmic rays and internal radionuclides. Cosmic ray annual dose is estimated to be between 0.04 and 0.06 rad/yr on the earth's surface in Antarctica while the internal radionuclides contribute only about 0.01 rad/yr. Therefore the total annual dose received by the meteorite while it is on the surface is between 0.05 and 0.07 rad/yr. If the meteorite is buried deeply in the ice it is effectively shielded from most cosmic rays and thus only internal radioactivity contributes to the annual dose