Alvira : comparative genomics of viral strains

The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution

Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution

Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race

Full spectral fitting of Milky Way and M31 globular clusters: ages and metallicities

Context: The formation and evolution of disk galaxies are long standing questions in Astronomy. Understanding the properties of globular cluster systems can lead to important insights on the evolution of its host galaxy. Aims: We aim to obtain the stellar population parameters - age and metallicity - of a sample of M31 and Galactic globular clusters. Studying their globular cluster systems is an important step towards understanding their formation and evolution in a complete way. Methods: Our analysis employs a modern pixel-to-pixel spectral fitting technique to fit observed integrated spectra to updated stellar population models. By comparing observations to models we obtain the ages and metallicities of their stellar populations. We apply this technique to a sample of 38 globular clusters in M31 and to 41 Galactic globular clusters, used as a control sample. Results: Our sample of M31 globular clusters spans ages from 150 Myr to the age of the Universe. Metallicities [Fe/H] range from -2.2 dex to the solar value. The age-metallicity relation obtained can be described as having two components: an old population with a flat age-[Fe/H] relation, possibly associated with the halo and/or bulge, and a second one with a roughly linear relation between age and metallicity, higher metallicities corresponding to younger ages, possibly associated with the M31 disk. While we recover the very well known Galactic GC metallicity bimodality, our own analysis of M31's metallicity distribution function (MDF) suggests that both GC systems cover basically the same [Fe/H] range yet M31's MDF is not clearly bimodal. These results suggest that both galaxies experienced different star formation and accretion histories.Comment: A&A, in pres

Fractional Branes, Confinement, and Dynamically Generated Superpotentials

We examine the effects of instantons in four dimensional N=1 supersymmetric gauge theory by including D0-branes in type IIA brane constructions. We examine instanton generated superpotentials in supersymmetric QCD and find that they are due to a repulsive force between D4-branes bound to D0-branes ending on NS 5-branes. We study situations where instanton effects break supersymmetry such as the Intriligator-Thomas-Izawa-Yangagida model and relate this to a IIA brane construction. We also argue how confinement due to a condensate of fractional instantons manifests itself in Super Yang-Mills theory using fractional D0 branes, D4 branes, and NS strings.Comment: 19 pages, 2 figures, uses harvmac. References adde

Structure and Mass of a Young Globular Cluster in NGC 6946

Using the Wide Field Planetary Camera 2 on board the Hubble Space Telescope, we have imaged a luminous young star cluster in the nearby spiral galaxy NGC 6946. The cluster has an absolute visual magnitude M(V)=-13.2, comparable to the brightest young `super-star clusters' in the Antennae merger galaxy. UBV colors indicate an age of about 15 Myr. The cluster has a compact core (core radius = 1.3 pc), surrounded by an extended envelope. We estimate that the effective radius (Reff) = 13 pc, but this number is uncertain because the outer parts of the cluster profile gradually merge with the general field. Combined with population synthesis models, the luminosity and age of the cluster imply a mass of 8.2x10^5 Msun for a Salpeter IMF extending down to 0.1 Msun, or 5.5x10^5 Msun if the IMF is log-normal below 0.4 Msun. Depending on model assumptions, the central density of the cluster is between 5300 Msun pc^-3 and 17000 Msun pc^-3, comparable to other high-density star forming regions. We also estimate a dynamical mass for the cluster, using high-dispersion spectra from the HIRES spectrograph on the Keck I telescope. The velocity dispersion is 10.0 +/- 2.7 km/s, implying a total cluster mass within 65 pc of (1.7 +/- 0.9) x 10^6 Msun. Comparing the dynamical mass with the mass estimates based on the photometry and population synthesis models, the mass-to-light ratio is at least as high as for a Salpeter IMF extending down to 0.1 Msun, although a turn-over in the IMF at 0.4 Msun is still possible within the errors. The cluster will presumably remain bound, evolving into a globular cluster-like object.Comment: 33 pages, including 10 figures and 3 tables. Accepted for publication in the Astrophysical Journa

Extragalactic Globular Clusters in the Near-Infrared II. The Globular Clusters Systems of NGC 3115 and NGC 4365

We combine near-infrared photometry obtained with the VLT/ISAAC instrument and archival HST/WFPC2 optical images to determine VIK magnitudes and colours of globular clusters in two early-type galaxies, NGC 3115 and NGC 4365. The combination of near-IR and optical photometry provides a way to lift the age-metallicity degeneracy. For NGC 3115, the globular cluster colours reveal two major sub-populations, consistent with previous studies. By comparing the V-I, V-K colours of the NGC 3115 globular clusters with SSP models, we find that the colour difference between the two >10 Gyr old major sub-populations is primarily due to a difference in metallicity. We find \Delta[Fe/H] = 1.0 +/- 0.3 dex and the blue and red globular cluster sub-populations being coeval within 3 Gyr. In contrast to the NGC 3115 globular clusters, the globular cluster system in NGC 4365 exhibits a more complex age and metallicity structure. We find a significant population of intermediate-age very metal-rich globular clusters along with an old population of both metal-rich and metal-poor clusters. Specifically, we observe a large population of globular clusters with V-K and V-I colours, for which all current SSP models give ages and metallicities in the range ~2-8 Gyr and ~0.5-3 Z_solar, respectively. After 10 Gyr of passive evolution, the intermediate-age globular clusters in NGC 4365 will have colours which are consistent with the very metal-rich population of globular clusters in giant elliptical galaxies, such as M87. Our results for both globular cluster systems are consistent with previous age and metallicity studies of the diffuse galactic light. In addition to the major globular cluster populations in NGC 3115 and NGC 4365 we report on the detection of objects with extremely red colours.Comment: accepted for publication in A&A, 19 pages, incl. 9 figure

Species conservation in the Pacific Islands: taking effective steps forward

Pacific species face heightened levels of threat due to the relatively small size, fragility and rapid environmental changes from human development and invasive species in many Pacific Island Countries and Territories. The geographic isolation of many islands is also a major barrier to the spread of scientific and traditional knowledge on threatened species, and facilitation of supportive networks for strengthening collaboration on species conservation. An additional block is the lack of consolidated approaches to many species conservation issues within the Pacific Island Countries and Territories, particularly for noncharismatic species that are often overlooked or are low on the agenda. Furthermore, the capacity and availability of resources for conservation – including both people and available scientific information – are known to be heavily biased towards developed countries in Oceania. The combined impacts of these gaps and blocks are clearly evident in several related public outputs including: national and regional species inventories, National Biodiversity and Strategic Action Plans, and progress on undertaking and implementing IUCN Red-List species assessments for the Pacific Islands

Respiratory drive in the acute respiratory distress syndrome: pathophysiology, monitoring, and therapeutic interventions

Neural respiratory drive, i.e., the activity of respiratory centres controlling breathing, is an overlooked physiologic variable which affects the pathophysiology and the clinical outcome of acute respiratory distress syndrome (ARDS). Spontaneous breathing may offer multiple physiologic benefits in these patients, including decreased need for sedation, preserved diaphragm activity and improved cardiovascular function. However, excessive effort to breathe due to high respiratory drive may lead to patient self-inflicted lung injury (P-SILI), even in the absence of mechanical ventilation. In the present review, we focus on the physiological and clinical implications of control of respiratory drive in ARDS patients. We summarize the main determinants of neural respiratory drive and the mechanisms involved in its potentiation, in health and ARDS. We also describe potential and pitfalls of the available bedside methods for drive assessment and explore classical and more \u201cfuturistic\u201d interventions to control drive in ARDS patients