Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations

OMA 2011: orthology inference among 1000 complete genomes

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline—in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org

Uncertain groupings: probabilistic combination of grouping data

Probabilistic approaches for data integration have much potential. We view data integration as an iterative process where data understanding gradually increases as the data scientist continuously refines his view on how to deal with learned intricacies like data conflicts. This paper presents a probabilistic approach for integrating data on groupings. We focus on a bio-informatics use case concerning homology. A bio-informatician has a large number of homology data sources to choose from. To enable querying combined knowledge contained in these sources, they need to be integrated. We validate our approach by integrating three real-world biological databases on homology in three iterations

The Early Evolution of Massive Stars: Radio Recombination Line Spectra

Velocity shifts and differential broadening of radio recombination lines are used to estimate the densities and velocities of the ionized gas in several hypercompact and ultracompact HII regions. These small HII regions are thought to be at their earliest evolutionary phase and associated with the youngest massive stars. The observations suggest that these HII regions are characterized by high densities, supersonic flows and steep density gradients, consistent with accretion and outflows that would be associated with the formation of massive stars.Comment: ApJ in pres

Subarcsecond Submillimeter Imaging of the Ultracompact HII Region G5.89-0.39

We present the first subarcsecond submillimeter images of the enigmatic ultracompact HII region (UCHII) G5.89-0.39. Observed with the SMA, the 875 micron continuum emission exhibits a shell-like morphology similar to longer wavelengths. By using images with comparable angular resolution at five frequencies obtained from the VLA archive and CARMA, we have removed the free-free component from the 875 micron image. We find five sources of dust emission: two compact warm objects (SMA1 and SMA2) along the periphery of the shell, and three additional regions further out. There is no dust emission inside the shell, supporting the picture of a dust-free cavity surrounded by high density gas. At subarcsecond resolution, most of the molecular gas tracers encircle the UCHII region and appear to constrain its expansion. We also find G5.89-0.39 to be almost completely lacking in organic molecular line emission. The dust cores SMA1 and SMA2 exhibit compact spatial peaks in optically-thin gas tracers (e.g. 34SO2), while SMA1 also coincides with 11.9 micron emission. In CO(3-2), we find a high-velocity north/south bipolar outflow centered on SMA1, aligned with infrared H2 knots, and responsible for much of the maser activity. We conclude that SMA1 is an embedded intermediate mass protostar with an estimated luminosity of 3000 Lsun and a circumstellar mass of ~1 Msun. Finally, we have discovered an NH3 (3,3) maser 12 arcsec northwest of the UCHII region, coincident with a 44 GHz CH3OH maser, and possibly associated with the Br gamma outflow source identified by Puga et al. (2006).Comment: 41 pages, 11 figures, published in The Astrophysical Journal (2008) Volume 680, Issue 2, pp. 1271-1288. An error in the registration of the marker positions in Figure 11 has been corrected in this versio

CARMA CO(J = 2 - 1) Observations of the Circumstellar Envelope of Betelgeuse

We report radio interferometric observations of the 12C16O 1.3 mm J = 2-1 emission line in the circumstellar envelope of the M supergiant Alpha Ori and have detected and separated both the S1 and S2 flow components for the first time. Observations were made with the Combined Array for Research in Millimeter-wave Astronomy (CARMA) interferometer in the C, D, and E antenna configurations. We obtain good u-v coverage (5-280 klambda) by combining data from all three configurations allowing us to trace spatial scales as small as 0.9\arcsec over a 32\arcsec field of view. The high spectral and spatial resolution C configuration line profile shows that the inner S1 flow has slightly asymmetric outflow velocities ranging from -9.0 km s-1 to +10.6 km s-1 with respect to the stellar rest frame. We find little evidence for the outer S2 flow in this configuration because the majority of this emission has been spatially-filtered (resolved out) by the array. We also report a SOFIA-GREAT CO(J= 12-11) emission line profile which we associate with this inner higher excitation S1 flow. The outer S2 flow appears in the D and E configuration maps and its outflow velocity is found to be in good agreement with high resolution optical spectroscopy of K I obtained at the McDonald Observatory. We image both S1 and S2 in the multi-configuration maps and see a gradual change in the angular size of the emission in the high absolute velocity maps. We assign an outer radius of 4\arcsec to S1 and propose that S2 extends beyond CARMA's field of view (32\arcsec at 1.3 mm) out to a radius of 17\arcsec which is larger than recent single-dish observations have indicated. When azimuthally averaged, the intensity fall-off for both flows is found to be proportional to R^{-1}, where R is the projected radius, indicating optically thin winds with \rho \propto R^{-2}.Comment: 11 pages, 8 figures To be published in the Astronomical Journal (Received 2012 February 10; accepted 2012 May 25

VLA H53alpha observations of the central region of the Super Star Cluster Galaxy NGC 5253

We present observations in the H53alpha line and radio continuum at 43 GHz carried out with the VLA in the D array (2'' angular resolution) toward the starburst galaxy NGC 5253. VLA archival data have been reprocessed to produce a uniform set of 2, 1.3 and 0.7 cm high angular (0.''2 X 0.''1) radio continuum images. The RRL H53alpha, a previously reported measurement of the H92alpha RRL flux density and the reprocessed high angular resolution radio continuum flux densities have been modeled using a collection of HII regions. Based on the models, the ionized gas in the nuclear source has an electron density of ~6 X 10^4 cm^-3 and an volume filling factor of 0.05. A Lyman continuum photon production rate of 2 X 10^52 s^-1 is necessary to sustain the ionization in the nuclear region. The number of required O7 stars in the central 1.5 pc of the supernebula is ~ 2000. The H53alpha velocity gradient 10 km s^-1 arcsec^-1) implies a dynamical mass of ~3X10^5 Msun; this mass suggests the supernebula is confined by gravity.Comment: Accepted in Astrophysical Journal 7 figure

GMRT observations of the field of INTEGRAL X-ray sources- II (newly discovered hard X-ray sources)

We have conducted low-frequency radio observations with the Giant Metrewave Radio Telescope (GMRT) of 40 new hard X-ray sources discovered by the INTEGRAL satellite. This survey was conducted in order, to study radio emissions from these sources, to provide precise position and to identify new microquasar candidates. From our observations we find that 24 of the X-ray sources have radio candidates within the INTEGRAL error circle. Based on the radio morphology, variability and information available from different wavelengths, we categorize them as seventeen Galactic sources (4 unresolved, 7 extended, 6 extended sources in diffuse region) and seven extragalactic sources (2 unresolved, 5 extended). Detailed account for seventeen of these sources was presented in earlier paper. Based on the radio data for the remaining sources at 0.61 GHz, and the available information from NVSS, DSS, 2MASS and NED, we have identified possible radio counterparts for the hard X-ray sources. The three unresolved sources, viz IGR J17303$-$0601, IGR J17464$-$3213, and IGR J18406$-$0539 are discussed in detail. These sources have been identified as X-ray binaries with compact central engine and variable in X-ray and in the radio, and are most likely microquasar candidates. The remaining fourteen sources have extended radio morphology and are either diffuse Galactic regions or extragalactic in origin.Comment: 9 pages, 7 figures, submitted to A&A. submitted to A&

Combined BIMA and OVRO observations of comet C/1999 S4 (LINEAR)

We present results from an observing campaign of the molecular content of the coma of comet C/1999 S4 (LINEAR) carried out jointly with the millimeter-arrays of the Berkeley-Illinois-Maryland Association (BIMA) and the Owens Valley Radio Observatory (OVRO). Using the BIMA array in autocorrelation (`single-dish') mode, we detected weak HCN J=1-0 emission from comet C/1999 S4 (LINEAR) at 14 +- 4 mK km/s averaged over the 143" beam. The three days over which emission was detected, 2000 July 21.9-24.2, immediately precede the reported full breakup of the nucleus of this comet. During this same period, we find an upper limit for HCN 1-0 of 144 mJy/beam km/s (203 mK km/s) in the 9"x12" synthesized beam of combined observations of BIMA and OVRO in cross-correlation (`imaging') mode. Together with reported values of HCN 1-0 emission in the 28" IRAM 30-meter beam, our data probe the spatial distribution of the HCN emission from radii of 1300 to 19,000 km. Using literature results of HCN excitation in cometary comae, we find that the relative line fluxes in the 12"x9", 28" and 143" beams are consistent with expectations for a nuclear source of HCN and expansion of the volatile gases and evaporating icy grains following a Haser model.Comment: 18 pages, 3 figures. Uses aastex. AJ in pres

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the “ortholog conjecture”, or standard model of phylogenomics, protein function changes rapidly after duplication, leading to paralogs with different functions, while orthologs retain the ancestral function. We report here that a comparison of experimentally supported functional annotations among homologs from 13 genomes mostly supports this model. We show that to analyze GO annotation effectively, several confounding factors need to be controlled: authorship bias, variation of GO term frequency among species, variation of background similarity among species pairs, and propagated annotation bias. After controlling for these biases, we observe that orthologs have generally more similar functional annotations than paralogs. This is especially strong for sub-cellular localization. We observe only a weak decrease in functional similarity with increasing sequence divergence. These findings hold over a large diversity of species; notably orthologs from model organisms such as E. coli, yeast or mouse have conserved function with human proteins