ALBERT

Description: The polyconformational behavior of l -iduronic acid (L-IdoA2S) in heparin derivatives has been previously analyzed in terms of intra-ring proton–proton vicinal coupling constants ( 3 J HH ) through mathematical fit of experimental and theoretical values (Ferro DR, Provasoli A, Ragazzi M, Casu B, Torri G, Bossennec V, Perly B, Sinay P, Petitou M, Choay J. 1990. Conformer Populations of l -Iduronic Acid Residues in Glycosaminoglycan Sequences. Carbohydr Res. 195:157–167; Muñoz-García JC, López-Prados J, Angulo J, Díaz-Contreras I, Reichardt N, de Paz JL, Martín-Lomas M, Nieto PM. 2012. Effect of the substituents of the neighboring ring in the conformational equilibrium of iduronate in heparin-like trisaccharides. Chemistry. 18:16319–16331.). However, this methodology is subjected to the experimental uncertainties of the J-coupling measurements, the force field deviations and the goodness of the least-squares fit. In the present work, we have used time-averaged distance restrained molecular dynamics ( tar -MD) to largely reduce these errors, which enables accurate quantification of the population of conformers, or puckers, of the L-IdoA2S residue, in a set of eight heparin-like trisaccharides following the general sequence d -glucosamine (GlcN)-IdoA-GlcN, directly from the time evolution of the puckering coordinates and . Thus, by carrying out tar -MD simulations in explicit water, with the exclusive nuclear overhauser enhancement (NOE)-derived distance H2–H5 of the L-IdoA2S 2 S O conformer as the unique imposed constraint, we have been able to accurately and easily determine the different extents to which the iduronate ring populates the polar ( 1 C 4 chair) and equatorial ( 2 S O skew-boat) areas of the puckering sphere depending on the sulfation pattern of the flanking GlcN residues, under low temperature conditions (278 K). The results indicate that 6-O-sulfation at the reducing-end GlcN residue facilitates the 1 C 4 to 2 S O transitions of the iduronate ring by augmenting the flexibility of the C2–C3 torsion, driving the conformational equilibrium toward a majority of equatorial conformers.

Description: We explore molecular cloud properties and the physics of CO transition lines in z 6 Lyman-break galaxies and predict their CO fluxes using an analytic formalism built from global models of star formation in high-redshift galaxies that minimizes our reliance on local observations. Our model includes a new approach to calculating the molecular gas fraction that takes the total gas density, the star formation rate and the star formation efficiency in clouds as the principal inputs. This method agrees with chemical equilibrium calculations of the molecular fraction based on local chemistry if galaxies at z 6 have metallicities on the order of a few per cent of solar. Such low metallicities in turn imply that much of the carbon in these systems exists in ionized form rather than as CO. Moreover, we find that the higher-order CO transitions observable at high redshift with Atacama Large Millimeter Array (ALMA) will typically be sub-thermally populated but that the details depend sensitively on the presence of turbulent clumps within molecular clouds. Ultimately, we expect current facilities will only be able to observe the CO signal from reionization epoch galaxies with great difficulty. We estimate that at least ~100 h of integration time with ALMA will be required to detect the CO(6–5) transition in z  = 6 systems with rest-frame UV magnitudes of –20.

Description: : We have developed a web-based query tool, Whole-Genome rVISTA (WGRV), that determines enrichment of transcription factors (TFs) and associated target genes in sets of co-regulated genes. WGRV enables users to query databases containing pre-computed genome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promoters (from 100 bp to 5 kb upstream) of human, mouse and Drosophila genomes. TF binding sites are based on position-weight matrices from the TRANSFAC Professional database. For a given set of co-regulated genes, WGRV returns statistically enriched and evolutionarily conserved binding sites, mapped by the regulatory VISTA (rVISTA) algorithm. Users can then retrieve a list of genes from the query set containing the enriched TF binding sites and their location in the query set promoters. Results are exported in a BED format for rapid visualization in the UCSC genome browser. Flat files of mapped conserved sites and their genomic coordinates are also available for analysis with stand-alone software. Availability: http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl . Contact: azambon@ucsd.edu or ildubchak@lbl.gov Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Group signature schemes allow a user, belonging to a specific group of users, to sign a message in an anonymous way on behalf of the group. In general, these schemes need the collaboration of a Key Generation Center or a Trusted Third Party, which can disclose the identity of the actual signer if necessary (e.g. to settle a dispute). In this article, two new group signature schemes are presented, whose security is based upon two Number Theory problems: Integer Factorization Problem and Subgroup Discrete Logarithm Problem (SDLP). The security of both proposals is analysed and their differences are presented as well.

Description: NGC 3201 is a globular cluster (GC) which shows very peculiar kinematic characteristics including an extreme radial velocity and a highly retrograde orbit, strongly suggesting an extragalactic origin. Our aims are to study NGC 3201 in the context of multiple populations (MPs), hoping to constrain possible candidates for the self-enrichment by studying the chemical abundance pattern, as well as adding insight into the origin of this intriguing cluster. We present a detailed chemical abundance analysis of eight red giant branch stars using high-resolution spectroscopy. We measured 29 elements and found [Fe/H] = –1.53±0.01; we cannot rule out a metallicity spread of ~0.12 dex, and an α-enhancement typical of halo GCs. However, significant spreads are observed in the abundances of all light elements except for Mg. We confirm the presence of an extended Na–O anticorrelation. n-capture elements generally are dominated by the r-process, in good agreement with the bulk of Galactic GCs. The total (C+N+O) abundance is slightly supersolar and requires a small downward correction to the isochrone age, yielding 11.4 Gyr. Kinematically, NGC 3201 appears likely to have had an extragalactic origin but its chemical evolution is similar to most other, presumably native, Galactic GCs.

Description: In this paper, we introduce a low-cost, high-order stabilized method for the numerical solution of incompressible flow problems. This is a particular type of projection-stabilized method where each targeted operator, such as the pressure gradient or the convection, is stabilized by least-squares terms added to the Galerkin formulation. The main methodological originality is that we replace the projection-stabilized structure by an interpolation-stabilized structure, with reduced computational cost for some choices of the interpolation operator. This stabilization has one level, in the sense that it is defined on a single mesh. We prove the stability of our formulation by means of a specific inf–sup condition, which is the main technical innovation of our paper. We perform a convergence and error estimates analysis, proving the optimal order of accuracy of our method. We include some numerical tests that confirm our theoretical expectations.

Description: Rapid phosphorylation of histone variant H2AX proximal to DNA breaks is an initiating event and a hallmark of eukaryotic DNA damage responses. Three mammalian kinases are known to phosphorylate H2AX in response to DNA damage. However, the mechanism(s) for damage-localized phosphorylation remains incompletely understood. The DNA-dependent protein kinase (DNA-PK) is the most abundant H2AX-modifying kinases and uniquely activated by binding DNA termini. Here, we have developed a novel approach to examine enzyme activity and substrate properties by executing biochemical assays on intact cellular structures. We apply this approach to examine the mechanisms of localized protein modification in chromatin within fixed cells. DNA-PK retains substrate specificity and independently generates break-localized H2AX foci in chromatin. In situ DNA-PK activity recapitulates localization and intensity of in vivo H2AX phosphorylation and requires no active cellular processes. Nuclease treatments or addition of exogenous DNA resulted in genome-wide H2AX phosphorylation, showing that DNA termini dictated the locality of H2AX phosphorylation in situ . DNA-PK also reconstituted focal phosphorylation of structural maintenance of chromatin protein 1, but not activating transcription factor 2. Allosteric regulation of DNA-PK by DNA termini protruding from chromatin constitutes an autonomous mechanism for break-localized protein phosphorylation that generates sub-nuclear foci. We discuss generalized implications of this mechanism in localizing mammalian DNA damage responses.

Description: We present a 30-day monitoring campaign of the optical counterpart of the bright X-ray transient Swift J1745–26, starting only 19 min after the discovery of the source. We observe the system peaking at i '  ~ 17.6 on day six (MJD 561 92) to then decay at a rate of ~0.04 mag d –1 . We show that the optical peak occurs at least 3 d later than the hard X-ray (15–50 keV) flux peak. Our measurements result in an outburst amplitude greater than 4.3 mag, which favours an orbital period 21 h and a companion star with a spectral type later than ~A0. Spectroscopic observations taken with the Gran Telescopio de Canarias 10.4 m telescope reveal a broad (full width at half-maximum ~1100 km s –1 ), double-peaked Hα emission line from which we constrain the radial velocity semi-amplitude of the donor to be K 2  〉 250 km s –1 . The breadth of the line and the observed optical and X-ray fluxes suggest that Swift J1745–26 is a new black hole candidate located closer than ~7 kpc.

Description: We have systematically studied the effect of the orbital inclination in the outburst evolution of black hole transients. We have included all the systems observed by the Rossi X-ray Timing Explorer in which the thermal, accretion disc component becomes strongly dominant at some point of the outburst. Inclination is found to modify the shape of the tracks that these systems display in the colour/luminosity diagrams traditionally used for their study. Black hole transients seen at low inclination reach softer spectra and their accretion discs look cooler than those observed closer to edge-on. This difference can be naturally explained by considering inclination-dependent relativistic effects on accretion discs.

Description: Aims Studying plant ecological succession provides insights into the spatiotemporal processes underlying community assembly and is of primary importance for restoration ecology. We investigate here colonization events and local community assembly over an original primary succession occurring on roadcuts after roadwork. For this, we addressed both the changes in species presence-absence (incidence data) to highlight pre-establishment filters and in species relative abundances to further assess the influence of local biotic processes. Methods We studied 43 limestone roadcuts in Mediterranean France, covering five age classes up to an age of 80 years, along with 13 natural cliffs as a reference, and we counted 14322 plant individuals on these sites. We applied a constrained nonsymmetric correspondence analysis of both the incidence (presence-absence) and abundance data to assess the variation of these data along the chronosequence. Important Findings Along the first 30 years, the initially abundant short-lived species declined both in terms of incidence and abundance and were replaced by longer lived herbaceous and woody species. This first phase was characterized by species that are widespread in the surrounding scrublands and was comparable to an early secondary succession there. After 30 years, there were continuing changes in incidence data with age, but no more significant change in species’ abundances. This second phase was marked by the late colonization of specialists that did not become dominant. Although colonization and establishment limitation was thereby apparent for specialist species, a slow convergence of community composition toward the situation of natural cliffs could be detected in the older stages of the chronosequence. These findings convey insights into the natural dynamics of man-made outcrop plant communities and may be useful for the ecological management and restoration of such contexts. It also illustrates the interest of comparing incidence and abundance data to investigate the relative influence of ecological determinants on the assembly of plant communities.