Phage inducible islands in the gram-positive cocci

The SaPIs are a cohesive subfamily of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer frequencies, which they enhance by interfering with helper phage reproduction. As the SaPIs represent a highly successful biological strategy, with many natural Staphylococcus aureus strains containing two or more, we assumed that similar elements would be widespread in the Gram-positive cocci. On the basis of resemblance to the paradigmatic SaPI genome, we have readily identified large cohesive families of similar elements in the lactococci and pneumococci/streptococci plus a few such elements in Enterococcus faecalis. Based on extensive ortholog analyses, we found that the PICI elements in the four different genera all represent distinct but parallel lineages, suggesting that they represent convergent evolution towards a highly successful lifestyle. We have characterized in depth the enterococcal element, EfCIV583, and have shown that it very closely resembles the SaPIs in functionality as well as in genome organization, setting the stage for expansion of the study of elements of this type. In summary, our findings greatly broaden the PICI family to include elements from at least three genera of cocci

LEGUS and Halpha-LEGUS Observations of Star Clusters in NGC 4449: Improved Ages and the Fraction of Light in Clusters as a Function of Age

We present a new catalog and results for the cluster system of the starburst galaxy NGC 4449 based on multi-band imaging observations taken as part of the LEGUS and Halpha-LEGUS surveys. We improve the spectral energy fitting method used to estimate cluster ages and find that the results, particularly for older clusters, are in better agreement with those from spectroscopy. The inclusion of Halpha measurements, the role of stochasticity for low mass clusters, the assumptions about reddening, and the choices of SSP model and metallicity all have important impacts on the age-dating of clusters. A comparison with ages derived from stellar color-magnitude diagrams for partially resolved clusters shows reasonable agreement, but large scatter in some cases. The fraction of light found in clusters relative to the total light (i.e., T_L) in the U, B, and V filters in 25 different ~kpc-size regions throughout NGC 4449 correlates with both the specific Region Luminosity, R_L, and the dominant age of the underlying stellar population in each region. The observed cluster age distribution is found to decline over time as dN/dt ~ t^g, with g=-0.85+/-0.15, independent of cluster mass, and is consistent with strong, early cluster disruption. The mass functions of the clusters can be described by a power law with dN/dM ~ M^b and b=-1.86+/-0.2, independent of cluster age. The mass and age distributions are quite resilient to differences in age-dating methods. There is tentative evidence for a factor of 2-3 enhancement in both the star and cluster formation rate ~100 - 300 Myr ago, indicating that cluster formation tracks star formation generally. The enhancement is probably associated with an earlier interaction event

The properties, origin and evolution of stellar clusters in galaxy simulations and observations

We investigate the properties and evolution of star particles in two simulations of isolated spiral galaxies, and two galaxies from cosmological simulations. Unlike previous numerical work, where typically each star particle represents one ‘cluster’, for the isolated galaxies we are able to model features we term ‘clusters’ with groups of particles. We compute the spatial distribution of stars with different ages, and cluster mass distributions, comparing our findings with observations including the recent LEGUS survey. We find that spiral structure tends to be present in older (100s Myrs) stars and clusters in the simulations compared to the observations. This likely reflects differences in the numbers of stars or clusters, the strength of spiral arms, and whether the clusters are allowed to evolve. Where we model clusters with multiple particles, we are able to study their evolution. The evolution of simulated clusters tends to follow that of their natal gas clouds. Massive, dense, long-lived clouds host massive clusters, whilst short-lived clouds host smaller clusters which readily disperse. Most clusters appear to disperse fairly quickly, in basic agreement with observational findings. We note that embedded clusters may be less inclined to disperse in simulations in a galactic environment with continuous accretion of gas onto the clouds than isolated clouds and correspondingly, massive young clusters which are no longer associated with gas tend not to occur in the simulations. Caveats of our models include that the cluster densities are lower than realistic clusters, and the simplistic implementation of stellar feedback

Arp 220: A Post-Starburst Galaxy With Little Star Formation Outside of It's Nuclear Disks

The ultra-luminous infrared galaxy Arp2 20 is a late-stage merger with several tidal structures in the outskirts and two very compact, dusty nuclei that show evidence for extreme star formation and host at least one AGN. New and archival high-resolution images taken by the Hubble Space Telescope provide a state-of-the-art view of the structures, dust, and stellar clusters in Arp 220. We find that ~90% of the Halpha emission arises from a shock-ionized bubble emanating from the AGN in the western nucleus, while the nuclear disks dominate the Pbeta emission. Four very young (~3-6 Myr) but lower mass (< 10^4 Msun) clusters are detected in Halpha within a few arcsec of the nuclei, but produce less than 1% of the line emission. We see little evidence for a population of massive clusters younger than 100Myr anywhere in Arp 220. From the masses and ages of the detected clusters, we find that star formation took place more-or-less continuously starting ~few Gyr ago with a rate between ~3-12 Msun/yr. Approximately 100Myr ago, star formation shut off suddenly everywhere, except in the nuclear disks. A very recent flicker of weak star formation produced the four young, low-mass clusters, while the rest of the galaxy appears to have remained in a post-starburst state. Cluster ages indicate that the tidal structures on the west side of the galaxy are older than those on the east side, but all appear to pre-date the shutoff of star formation. Arp 220 has many of the characteristics expected of a 'Shocked Post-Starburst Galaxy' or SPOG, since most of the system has been in a post-starburst state for the past ~100Myr and the detected Halpha emission arises from shocked rather than photo-ionized gas.Comment: accepted for publication in the Astrophysical Journa

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

Rheumatoid arthritis (RA) is a prevalent systemic autoimmune disease, caused by a combination of genetic and environmental factors. Animal models suggest a role for intestinal bacteria in supporting the systemic immune response required for joint inflammation. Here we performed 16S sequencing on 114 stool samples from rheumatoid arthritis patients and controls, and shotgun sequencing on a subset of 44 such samples. We identified the presence of Prevotella copri as strongly correlated with disease in new-onset untreated rheumatoid arthritis (NORA) patients. Increases in Prevotella abundance correlated with a reduction in Bacteroides and a loss of reportedly beneficial microbes in NORA subjects. We also identified unique Prevotella genes that correlated with disease. Further, colonization of mice revealed the ability of P. copri to dominate the intestinal microbiota and resulted in an increased sensitivity to chemically induced colitis. This work identifies a potential role for P. copri in the pathogenesis of RA. DOI: http://dx.doi.org/10.7554/eLife.01202.00

Star Formation Histories of the LEGUS Dwarf Galaxies (I): recent History of NGC1705, NGC4449 and Holmberg II

We use HST observations from the Legacy Extragalactic UV Survey to reconstruct the recent star formation histories (SFHs) of three actively star-forming dwarf galaxies, NGC4449, Holmberg II and NGC1705, from their UV color-magnitude diagrams (CMDs). We apply a CMD fitting technique using two independent sets of stellar isochrones, PARSEC-COLIBRI and MIST, to assess the uncertainties related to stellar evolution modelling. Irrespective of the adopted stellar models, all the three dwarfs are found to have had almost constant star formation rates (SFRs) in the last 100-200 Myr, with modest enhancements (a factor of $\sim$2) above the 100 Myr-averaged-SFR. Significant differences among the three dwarfs are found in the overall SFR, the timing of the most recent peak and the SFR$/$area. The Initial Mass Function (IMF) of NGC1705 and Holmberg II is consistent with a Salpeter slope down to $\approx$ 5 M$_{\odot}$, whereas it is slightly flatter, s$=-2.0$, in NGC4449. The SFHs derived with the two different sets of stellar models are consistent with each other, except for some quantitative details, attributable to their input assumptions. They also share the drawback that all synthetic diagrams predict a clear separation in color between upper main sequence and helium burning stars, which is not apparent in the data. Since differential reddening, significant in NGC4449, or unresolved binaries don't appear to be sufficient to fill the gap, we suggest this calls for a revision of both sets of stellar evolutionary tracks.Comment: 22 pages, 17 figures, accepted for publication on Ap

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

The emissivity of foam-covered water surface at L-band: theoretical modeling and experimental results from the FROG 2003 field experiment

Sea surface salinity can be measured by microwave radiometry at L-band (1400–1427 MHz). This frequency is a compromise between sensitivity to the salinity, small atmospheric perturbation, and reasonable pixel resolution. The description of the ocean emission depends on two main factors: 1) the sea water permittivity, which is a function of salinity, temperature, and frequency, and 2) the sea surface state, which depends on the wind-induced wave spectrum, swell, and rain-induced roughness spectrum, and by the foam coverage and its emissivity. This study presents a simplified two-layer emission model for foam-covered water and the results of a controlled experiment to measure the foam emissivity as a function of salinity, foam thickness, incidence angle, and polarization. Experimental results are presented, and then compared to the two-layer foam emission model with the measured foam parameters used as input model parameters. At 37 psu salt water the foam-induced emissivity increase is 0.007 per millimeter of foam thickness (extrapolated to nadir), increasing with increasing incidence angles at vertical polarization, and decreasing withPostprint (published version

The properties, origin and evolution of stellar clusters in galaxy simulations and observations

Published onlineWe investigate the properties and evolution of star particles in two simulations of isolated spiral galaxies, and two galaxies from cosmological simulations. Unlike previous numerical work, where typically each star particle represents one ‘cluster’, for the isolated galaxies we are able to model features we term ‘clusters’ with groups of particles. We compute the spatial distribution of stars with different ages, and cluster mass distributions, comparing our findings with observations including the recent LEGUS survey. We find that spiral structure tends to be present in older (100s Myr) stars and clusters in the simulations compared to the observations. This likely reflects differences in the numbers of stars or clusters, the strength of spiral arms, and whether the clusters are allowed to evolve. Where we model clusters with multiple particles, we are able to study their evolution. The evolution of simulated clusters tends to follow that of their natal gas clouds. Massive, dense, long-lived clouds host massive clusters, whilst short-lived clouds host smaller clusters which readily disperse. Most clusters appear to disperse fairly quickly, in basic agreement with observational findings. We note that embedded clusters may be less inclined to disperse in simulations in a galactic environment with continuous accretion of gas on to the clouds than isolated clouds and correspondingly, massive young clusters which are no longer associated with gas tend not to occur in the simulations. Caveats of our models include that the cluster densities are lower than realistic clusters, and the simplistic implementation of stellar feedback.We thank the referee for a useful report. The calculations for this paper were performed primarily on the DiRAC machine ‘Complexity’, as well as the supercomputer at Exeter, which is jointly funded by STFC, the Large Facilities Capital Fund of BIS, and the University of Exeter. We would like to thank Michele Fumagalli for work putting together the LEGUS cluster catalogues. CLD and CGF acknowledge funding from the European Research Council for the FP7 ERC starting grant project LOCALSTAR. CGF thanks Ben Thompson for performing data reduction. DG kindly acknowledges financial support by the German Research Foundation (DFG) through grant GO 1659/3-2. Figures in this paper were produced using splash (Price 2007)