Molecular Mechanisms of Activation in the Orange Carotenoid Protein Revealed by Molecular Dynamics

Light-harvesting in photosynthesis is accompanied by photoprotective processes. In cyanobacteria, the photoprotective role is played by a specialized complex, the orange carotenoid protein, which is activated by strong blue-green light. This photoactivation involves a unique series of structural changes which terminate with an opening of the complex into two separate domains, one of which acts as a quencher for the light-harvesting complexes. Many experimental studies have tried to reveal the molecular mechanisms through which the energy absorbed by the carotenoid finally leads to the large conformational change of the complex. Here, for the first time, these mechanisms are revealed by simulating at the atomistic level the whole dynamics of the complex through an effective combination of enhanced sampling techniques. On the basis of our findings, we can conclude that the carotenoid does not act as a spring that, releasing its internal strain, induces the dissociation, as was previously proposed, but as a "latch" locking together the two domains. The photochemically triggered displacement of the carotenoid breaks this balance, allowing the complex to dissociate

The X-CLASS - redMaPPer galaxy cluster comparison: I. Identification procedures

We performed a detailed and, for a large part interactive, analysis of the matching output between the X-CLASS and redMaPPer cluster catalogues. The overlap between the two catalogues has been accurately determined and possible cluster positional errors were manually recovered. The final samples comprise 270 and 355 redMaPPer and X-CLASS clusters respectively. X-ray cluster matching rates were analysed as a function of optical richness. In a second step, the redMaPPer clusters were correlated with the entire X-ray catalogue, containing point and uncharacterised sources (down to a few 10^{-15} erg s^{-1} cm^{-2} in the [0.5-2] keV band). A stacking analysis was performed for the remaining undetected optical clusters. Main results show that neither of the wavebands misses any massive cluster (as coded by X-ray luminosity or optical richness). After correcting for obvious pipeline short-comings (about 10% of the cases both in optical and X-ray), ~50% of the redMaPPer (down to a richness of 20) are found to coincide with an X-CLASS cluster; when considering X-ray sources of any type, this fraction increases to ~ 80%; for the remaining objects, the stacking analysis finds a weak signal within 0.5 Mpc around the cluster optical centers. The fraction of clusters totally dominated by AGN-type emission appears to be of the order of a few percent. Conversely ~ 40% of the X-CLASS clusters are identified with a redMaPPer (down to a richness of 20) - part of the non-matches being due to the fact that the X-CLASS sample extends further out than redMaPPer (z<1 vs z<0.6); extending the correlation down to a richness of 5, raises the matching rate to ~ 65%.Comment: 15 pages, 20 figures, 2 table

RR Lyrae in XSTPS: The halo density profile in the North Galactic Cap

We present a catalog of RR Lyrae stars (RRLs) observed by the Xuyi Schmidt Telescope Photometric Survey (XDSS). The area we consider is located in the North Galactic Cap, covering 376.75 sq deg at RA $\approx$ 150 deg and Dec $\approx$ 27 deg down to a magnitude limit of i $\approx$ 19. Using the variability information afforded by the multi-epoch nature of our XDSS data, combined with colors from the Sloan Digital Sky Survey, we are able to identify candidate RRLs. We find 318 candidates, derive distances to them and estimate the detection efficiency. The majority of our candidates have more than 12 observations and for these we are able to calculate periods. These also allows us to estimate our contamination level, which we predict is between 30% to 40%. Finally we use the sample to probe the halo density profile in the 9-49 kpc range and find that it can be well fitted by a double power law. We find good agreement between this model and the models derived for the South Galactic Cap using the Watkins et al. (2009) and Sesar et al. (2010) RRL data-sets, after accounting for possible contamination in our data-set from Sagittarius stream members. We consider non-spherical double power law models of the halo density profile and again find agreement with literature data-sets, although we have limited power to constrain the flattening due to our small survey area. Much tighter constraints will be placed by current and future wide-area surveys, most notably ESA's astrometric Gaia mission. Our analysis demonstrates that surveys with a limited number of epochs can effectively be mined for RRLs. Our complete sample is provided as accompanying online material.Comment: 14 pages, ApJ (in press

Eclipsing binary stars in the Large and Small Magellanic Clouds from the MACHO project: The Sample

We present a new sample of 4634 eclipsing binary stars in the Large Magellanic Cloud (LMC), expanding on a previous sample of 611 objects and a new sample of 1509 eclipsing binary stars in the Small Magellanic Cloud (SMC), that were identified in the light curve database of the MACHO project. We perform a cross correlation with the OGLE-II LMC sample, finding 1236 matches. A cross correlation with the OGLE-II SMC sample finds 698 matches. We then compare the LMC subsamples corresponding to center and the periphery of the LMC and find only minor differences between the two populations. These samples are sufficiently large and complete that statistical studies of the binary star populations are possible.Comment: 67 pages, 40 figure

A Survey of MicroRNA Length Variants Contributing to miRNome Complexity in Peach (Prunus Persica L.)

MicroRNAs (miRNAs) are short non-coding RNA molecules produced from hairpin structures and involved in gene expression regulation with major roles in plant development and stress response. Although each annotated miRNA in miRBase (www.mirbase.org) is a single defined sequence with no further details on possible variable sequence length, isomiRs – namely the population of variants of miRNAs coming from the same precursors – have been identified in several species and could represent a way of broadening the regulatory network of the cell. Next-gen-based sequencing makes it possible to comprehensively and accurately assess the entire miRNA repertoire including isomiRs. The aim of this work was to survey the complexity of the peach miRNome by carrying out Illumina high-throughput sequencing of miRNAs in three replicates of five biological samples arising from a set of different peach organs and/or phenological stages. Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed. The presence of the same isomiRs in different biological replicates of a sample and in different tissues demonstrates that the generation of most of the detected isomiRs is not random. The degree of mature sequence heterogeneity is very different for each individual locus. Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators

Evidence for Companion-Induced Secular Changes in the Turbulent Disk of a Be Star in the LMC MACHO Database

The light curve of a blue variable in the MACHO LMC database (FTS ID 78.5979.72) appeared nearly unvarying for ~4 years (quasi-flat segment) but then rapidly changed to become periodic with noisy minima for the remaining 4 years (periodic segment); there are no antecedent indications of a gradual approach to this change. Lomb Periodogram analyses indicate the presence of two distinct periods of ~61 days and 8 days in both the quasi-flat and the periodic segments. Minima of the periodic segment cover at least 50% of the orbital period and contain spikes of light with the 8-day period; maxima do not show this short period. The system typically shows maxima to be redder than minima. The most recent OGLE-III light curve shows only a 30-day periodicity. The variable's V and R magnitudes and color are those of a Be star, and recent sets of near infrared spectra four days apart, secured during the time of the OGLE-III data, show H-alpha emission near and at a maximum, confirming its Be star characteristics. The model that best fits the photometric behavior consists of a thin ring-like circumstellar disk of low mass with four obscuring sectors orbiting the central B star in unison at the 61-day period. The central star peers through the three equi- spaced separations between the four sectors producing the 8-day period. The remainder of the disk contains hydrogen in emission making maxima appear redder. A companion star of lower mass in an inclined and highly eccentric orbit produces an impulsive perturbation near its periastron to change the disk's orientation, changing eclipses from partial to complete within ~ 10 days.Comment: 42 pages, 14 figures, and 2 tables Submitted to AJ v3: Title changed, figures added, model modifie

Post Main Sequence Orbital Circularization of Binary Stars in the Large and Small Magellanic Clouds

We present results from a study of the orbits of eclipsing binary stars (EBs) in the Magellanic Clouds. The samples comprise 4510 EBs found in the Large Magellanic Cloud (LMC) by the MACHO project, 2474 LMC EBs found by the OGLE-II project (of which 1182 are also in the MACHO sample), 1380 in the Small Magellanic Cloud (SMC) found by the MACHO project, and 1317 SMC EBs found by the OGLE-II project (of which 677 are also in the MACHO sample); we also consider the EROS sample of 79 EBs in the bar of the LMC. Statistics of the phase differences between primary and secondary minima allow us to infer the statistics of orbital eccentricities within these samples. We confirm the well-known absence of eccentric orbit in close binary stars. We also find evidence for rapid circularization in longer period systems when one member evolves beyond the main sequence, as also found by previous studies.Comment: 37 pages, 16 figures, accepted for publication in ApJ. Added a new reference and updated information on on line materia

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Discovery of an Unusual Optical Transient with the Hubble Space Telescope

We present observations of SCP 06F6, an unusual optical transient discovered during the Hubble Space Telescope Cluster Supernova Survey. The transient brightened over a period of ~;;100 days, reached a peak magnitude of ~;;21.0 in both i_775 and z_850, and then declined over a similar timescale. There is no host galaxy or progenitor star detected at the location of the transient to a 3 sigma upper limit of i_775 = 26.4 and z_850 = 26.1, giving a corresponding lower limit on the flux increase of a factor of ~;;120. Multiple spectra show five broad absorption bands between 4100 AA and 6500 AA and a mostly featureless continuum longward of 6500 AA. The shape of the lightcurve is inconsistent with microlensing. The transient's spectrum, in addition to being inconsistent with all known supernova types, is not matched to any spectrum in the Sloan Digital Sky Survey (SDSS) database. We suggest that the transient may be one of a new class