Genetic Suppression of Basement Membrane Defects in Caenorhabditis elegans by Gain of Function in Extracellular Matrix and Cell-Matrix Attachment Genes.

Basement membranes are extracellular matrices essential for embryonic development in animals. Peroxidasins are extracellular peroxidases implicated in the unique sulfilimine cross-links between type IV basement membrane collagens. Loss of function in the Caenorhabditis elegans peroxidasin PXN-2 results in fully penetrant embryonic or larval lethality. Using genetic suppressor screening, we find that the requirement for PXN-2 in development can be bypassed by gain of function in multiple genes encoding other basement membrane components, or proteins implicated in cell-matrix attachment. We identify multiple alleles of let-805, encoding the transmembrane protein myotactin, which suppress phenotypes of pxn-2 null mutants and of other basement membrane mutants such as F-spondin/spon-1 These let-805 suppressor alleles cause missense alterations in two pairs of FNIII repeats in the extracellular domain; they act dominantly and have no detectable phenotypes alone, suggesting they cause gain of function. We also identify suppressor missense mutations affecting basement membrane components type IV collagen (emb-9, let-2) and perlecan (unc-52), as well as a mutation affecting spectraplakin (vab-10), a component of the epidermal cytoskeleton. These suppressor alleles do not bypass the developmental requirement for core structural proteins of the basement membrane such as laminin or type IV collagen. In conclusion, putative gain-of-function alterations in matrix proteins or in cell-matrix receptors can overcome the requirement for certain basement membrane proteins in embryonic development, revealing previously unknown plasticity in the genetic requirements for the extracellular matrix

ALMA Observations of Circumnuclear Disks in Early Type Galaxies: 12CO(2-1) and Continuum Properties

We present results from an Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 2 program to map CO(2-1) emission in nearby early-type galaxies (ETGs) that host circumnuclear gas disks. We obtained $\sim0.3''-$resolution Band 6 observations of seven ETGs selected on the basis of dust disks in Hubble Space Telescope images. We detect CO emission in five at high signal-to-noise ratio with the remaining two only faintly detected. All CO emission is coincident with the dust and is in dynamically cold rotation. Four ETGs show evidence of rapid central rotation; these are prime candidates for higher-resolution ALMA observations to measure the black hole masses. In this paper we focus on the molecular gas and continuum properties. Total gas masses and H$_2$ column densities for our five CO-bright galaxies are on average $\sim10^8$ $M_\odot$ and $\sim10^{22.5}$ cm$^{-2}$ over the $\sim$kpc-scale disks, and analysis suggests that these disks are stabilized against gravitational fragmentation. The continuum emission of all seven galaxies is dominated by a central, unresolved source, and in five we also detect a spatially extended component. The $\sim$230 GHz nuclear continua are modeled as power laws ranging from $S_\nu \sim \nu^{-0.4}$ to $\nu^{1.6}$ within the observed frequency band. The extended continuum profiles of the two radio-bright (and CO-faint) galaxies are roughly aligned with their radio jet and suggests resolved synchrotron jets. The extended continua of the CO-bright disks are coincident with optically thick dust absorption and have spectral slopes that are consistent with thermal dust emission.Comment: 20 pages, 10 figures; accepted for publication in Ap

Spatial variation of the physical conditions of molecular gas in galaxies

Multi-line studies of CO-12, CO-13, C-18O, HCN, and HCO(+) at 3 mm, 1.3 mm, and 0.8 mm using the Institute for Radio Astronomy in the Millimeter range (IRAM) 30 m telescope, with the IRAM superconductor insulator superconductor (SIS) receivers and the Max Planck Institute for External Physics (MPE) 350 GHz SIS receiver, show that the densities and temperatures of molecular gas in external galaxies change significantly with position. CO-12 measures the densities and temperature of diffuse interclump molecular gas, but not the bulk of the molecular gas. Simple one-component models, with or without external heating, cannot account for the weakness of the CO-12 J = 3 to 2 line relative to J = 2 to 1 and J = 1 to 0. CO-12 does not trace the bulk of the molecular gas, and optical depth effects obviate a straightforward interpretation of CO-12 data. Instead, researchers turned to the optically thin CO isotopes and other molecular species. Isotopic CO lines measure the bulk of the molecular gas, and HCN and HCO(+) pick out denser regions. Researchers find a warm ridge of gas in IC 342 (Eckart et al. 1989), denser gas in the starburst nucleus of IC 342, and a possible hot-spot in NGC 2903. In IC 342, NGC 2146, and NGC 6764, the CO-13 J = 2 to 1 line is subthermally populated, implying gas densities less than or equal to 10(exp 4) cm(-3)

Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data

BackgroundThe prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research.MethodsArtificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool’s output.ResultsVIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception.ConclusionsThis study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools

Titanium Nitride Films for Ultrasensitive Microresonator Detectors

Titanium nitride (TiNx) films are ideal for use in superconducting microresonator detectors because: a) the critical temperature varies with composition (0 < Tc < 5 K); b) the normal-state resistivity is large, \rho_n ~ 100 $\mu$Ohm cm, facilitating efficient photon absorption and providing a large kinetic inductance and detector responsivity; and c) TiN films are very hard and mechanically robust. Resonators using reactively sputtered TiN films show remarkably low loss (Q_i > 10^7) and have noise properties similar to resonators made using other materials, while the quasiparticle lifetimes are reasonably long, 10-200 $\mu$s. TiN microresonators should therefore reach sensitivities well below 10^-19 WHz^(-1/2).Comment: to be published in AP

Order Effects of Ballot Position without Information-Induced Confirmatory Bias

Candidate list positions have been shown to influence decision making when voters have limited candidate information (e.g. Miller and Krosnick, 1998; Brockington, 2003). Here, a primacy advantage is observed due to a greater number of positive arguments generated for early list candidates (Krosnick, 1991). The present study examined list position effects when an absence of information precludes such a confirmatory bias heuristic. We report the first large scale low-information experimental election where candidate position is fully counterbalanced. Seven hundred and twenty participants voted in a mock election where the position of 6 fictitious and meaningless parties was counterbalanced across the electorate. Analysis by position revealed that significantly fewer votes were allocated to the terminal parties (Experiment 1). In addition, Experiment 1 reported preliminary evidence of an alphabetical bias (consistent with Bagley, 1966). However, this positional bias was not present in a methodological replication using six genuine UK political parties (Experiment 2). This suggests that in situations of pure guessing, the heuristic shifts from the primacy benefiting confirmatory bias to an alternative heuristic that prejudices the first and last parties. These findings suggest that whilst the UK general electoral process may be largely immune to positional prejudice, English local elections (in which there can be multiple candidates from the same party) and multiple preference ranking systems (Scottish Local Government and London Mayoral Elections) could be susceptible to both positional and alphabetical biases

Molecular Tracers of the Central 12 pc of the Galactic Center

We have used the BIMA array to image the Galactic Center with a 19-pointing mosaic in HCN(1-0), HCO+(1-0), and H 42-alpha emission with 5 km/s velocity resolution and 13'' x 4'' angular resolution. The 5' field includes the circumnuclear ring (CND) and parts of the 20 and 50 km/s clouds. HCN(1-0) and HCO+ trace the CND and nearby giant molecular clouds while the H 42-alpha emission traces the ionized gas in Sgr A West. We find that the CND has a definite outer edge in HCN and HCO+ emission at ~45'' radius and appears to be composed of two or three distinct streams of molecular gas rotating around the nucleus. Outside the CND, HCN and HCO+ trace dense clumps of high-velocity gas in addition to optically thick emission from the 20 and 50 km/s clouds. A molecular ridge of compressed gas and dust, traced in NH3 emission and self-absorbed HCN and HCO+, wraps around the eastern edge of Sgr A East. Just inside this ridge are several arcs of gas which have been accelerated by the impact of Sgr A East with the 50 km/s cloud. HCN and HCO+ emission trace the extension of the northern arm of Sgr A West which appears to be an independent stream of neutral and ionized gas and dust originating outside the CND. Broad line widths and OH maser emission mark the intersection of the northern arm and the CND. Comparison to previous NH3 and 1.2mm dust observations shows that HCN and HCO+ preferentially trace the CND and are weaker tracers of the GMCs than NH3 and dust. We discuss possible scenarios for the emission mechanisms and environment at the Galactic center which could explain the differences in these images.Comment: 24 pages, including 17 figures; to appear in The Astrophysical Journa

Luminous Infrared Galaxies with the Submillimeter Array: I. Survey Overview and the Central Gas to Dust Ratio

We present new data obtained with the Submillimeter Array for a sample of fourteen nearby luminous and ultraluminous infrared galaxies. The galaxies were selected to have luminosity distances D < 200 Mpc and far-infrared luminosities log(L_FIR) > 11.4. The galaxies were observed with spatial resolutions of order 1 kpc in the CO J=3-2, CO J=2-1, 13CO J=2-1, and HCO+ J=4-3 lines as well as the continuum at 880 microns and 1.3 mm. We have combined our CO and continuum data to measure an average gas-to-dust mass ratio of 120 +/- 28 (rms deviation 109) in the central regions of these galaxies, very similar to the value of 150 determined for the Milky Way. This similarity is interesting given the more intense heating from the starburst and possibly accretion activity in the luminous infrared galaxies compared to the Milky Way. We find that the peak H_2 surface density correlates with the far-infrared luminosity, which suggests that galaxies with higher gas surface densities inside the central kiloparsec have a higher star formation rate. The lack of a significant correlation between total H_2 mass and far-infrared luminosity in our sample suggests that the increased star formation rate is due to the increased availability of molecular gas as fuel for star formation in the central regions. In contrast to previous analyses by other authors, we do not find a significant correlation between central gas surface density and the star formation efficiency, as trace by the ratio of far-infrared luminosity to nuclear gas mass. Our data show that it is the star formation rate, not the star formation efficiency, that increases with increasing central gas surface density in these galaxies.Comment: 66 pages, 39 figures, aastex preprint format; to be published in ApJ Supplements. Version of paper with full resolution figures available at http://www.physics.mcmaster.ca/~wilson/www_xfer/ULIRGS_publi

ASCA Observations of "Type 2" LINERs: Evidence for a Stellar Source of Ionization

We present ASCA observations of LINERs without broad H$\alpha$ emission in their optical spectra. The sample of "type 2" LINERs consists of NGC 404, 4111, 4192, 4457, and 4569. We have detected X-ray emission from all the objects except for NGC 404; among the detected objects are two so-called transition objects (NGC 4192 and NGC 4569), which have been postulated to be composite nuclei having both an HII region and a LINER component. The images of NGC 4111 and NGC 4569 in the soft (0.5-2 keV) and hard (2-7 keV) X-ray bands are extended on scales of several kpc. The X-ray spectra of NGC 4111, NGC 4457 and NGC 4569 are well fitted by a two-component model that consists of soft thermal emission with $kT\sim0.65$ keV and a hard component represented by a power law (photon index $\sim$ 2) or by thermal bremsstrahlung emission ($kT\sim$ several keV). The extended hard X-rays probably come from discrete sources, while the soft emission most likely originates from hot gas produced by active star formation in the host galaxy. We have found no clear evidence for the presence of active galactic nuclei (AGNs) in the sample. If an AGN component is the primary ionization source of the optical emission lines, then it must be heavily obscured with a column density significantly larger than $10^{23}$ cm$^{-2}$. Alternatively, the optical emission could be ionized by a population of exceptionally hot stars.Comment: 13 pages, 5 figures, emulateapj.sty, Accepted for publication in the Astrophysical Journa