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  • 1
    Publication Date: 2020-07-13
    Description: We report the detection of phase-locked polarization in the bright (mV = 2.98−3.24) semidetached eclipsing binary μ1 Sco (HD 151890). The phenomenon was observed in multiple photometric bands using two different HIPPI-class (HIgh Precision Polarimetric Instrument) polarimeters with telescopes ranging in size from 35 cm to 3.9 m. The peak-to-trough amplitude of the polarization is wavelength dependent and large, ∼700 ppm in green light, and is easily seen with even the smallest telescope. We fit the polarization phase curve with a synspec/vlidort polarized radiative transfer model and a Wilson–Devinney geometric formalism, which we describe in detail. Light from each star reflected by the photosphere of the other, together with a much smaller contribution from tidal distortion and eclipse effects, wholly accounts for the polarization amplitude. In the past, polarization in semidetached binaries has been attributed mostly to scattering from extra-stellar gas. Our new interpretation facilitates determining masses of such stars in non-eclipsing systems.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2015-09-30
    Description: In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli , short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 Å x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro . Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2015-11-21
    Description: Assessments of the risk posed by near-Earth objects ignore the possibility of a giant comet entering the inner solar system. Bill Napier, David Asher, Mark Bailey and Duncan Steel examine the likelihood and potential consequences of the appearance of such a centaur.
    Print ISSN: 1366-8781
    Electronic ISSN: 1468-4004
    Topics: Geosciences , Physics
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  • 4
    Publication Date: 2015-11-25
    Description: We present radial velocities, stellar parameters, and detailed abundances of 39 elements derived from high-resolution spectroscopic observations of red giant stars in the luminous, metal-poor globular cluster NGC 5824. We observe 26 stars in NGC 5824 using the Michigan/Magellan Fiber System (M2FS) and two stars using the Magellan Inamori Kyocera Echelle spectrograph. We derive a mean metallicity of [Fe/H] = –1.94 ± 0.02 (statistical) ±0.10 (systematic). The metallicity dispersion of this sample of stars, 0.08 dex, is in agreement with previous work and does not exceed the expected observational errors. Previous work suggested an internal metallicity spread only when fainter samples of stars were considered, so we cannot exclude the possibility of an intrinsic metallicity dispersion in NGC 5824. The M2FS spectra reveal a large internal dispersion in [Mg/Fe], 0.28 dex, which is found in a few other luminous, metal-poor clusters. [Mg/Fe] is correlated with [O/Fe] and anticorrelated with [Na/Fe] and [Al/Fe]. There is no evidence for internal dispersion among the other α- or Fe-group abundance ratios. 25 of the 26 stars exhibit a n -capture enrichment pattern dominated by r -process nucleosynthesis (〈[Eu/Fe]〉 = +0.11 ± 0.12; 〈[Ba/Eu]〉 = –0.66 ± 0.05). Only one star shows evidence of substantial s -process enhancement ([Ba/Fe] = +0.56 ± 0.12; [Ba/Eu] = +0.38 ± 0.14), but this star does not exhibit other characteristics associated with s -process enhancement via mass transfer from a binary companion. The Pb and other heavy elements produced by the s -process suggest a time-scale of no more than a few hundred Myr for star formation and chemical enrichment, like the complex globular clusters M2, M22, and NGC 5286.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2016-07-30
    Description: Motivation: We present an update to the pathway enrichment analysis tool ‘Pathway Analysis by Randomization Incorporating Structure (PARIS)’ that determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy to evaluate the genomic structure of interrogated pathways, through permutation testing of genomic features, thus eliminating many of the over-testing concerns arising with other pathway analysis approaches. Results: We have updated PARIS to incorporate expanded pathway definitions through the incorporation of new expert knowledge from multiple database sources, through customized user provided pathways, and other improvements in user flexibility and functionality. Availability and implementation: PARIS is freely available to all users at https://ritchielab.psu.edu/software/paris-download . Contact: jnc43@case.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2013-06-07
    Description: Visual refractive errors (REs) are complex genetic traits with a largely unknown etiology. To date, genome-wide association studies (GWASs) of moderate size have identified several novel risk markers for RE, measured here as mean spherical equivalent (MSE). We performed a GWAS using a total of 7280 samples from five cohorts: the Age-Related Eye Disease Study (AREDS); the KORA study (‘Cooperative Health Research in the Region of Augsburg’); the Framingham Eye Study (FES); the Ogliastra Genetic Park-Talana (OGP-Talana) Study and the Multiethnic Study of Atherosclerosis (MESA). Genotyping was performed on Illumina and Affymetrix platforms with additional markers imputed to the HapMap II reference panel. We identified a new genome-wide significant locus on chromosome 16 (rs10500355, P = 3.9 x 10 –9 ) in a combined discovery and replication set (26 953 samples). This single nucleotide polymorphism (SNP) is located within the RBFOX1 gene which is a neuron-specific splicing factor regulating a wide range of alternative splicing events implicated in neuronal development and maturation, including transcription factors, other splicing factors and synaptic proteins.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2016-04-08
    Description: : Precise regulatory control of genes, particularly in eukaryotes, frequently requires the joint action of multiple sequence-specific transcription factors. A cis -regulatory module (CRM) is a genomic locus that is responsible for gene regulation and that contains multiple transcription factor binding sites in close proximity. Given a collection of known transcription factor binding motifs, many bioinformatics methods have been proposed over the past 15 years for identifying within a genomic sequence candidate CRMs consisting of clusters of those motifs. Results: The MCAST algorithm uses a hidden Markov model with a P -value-based scoring scheme to identify candidate CRMs. Here, we introduce a new version of MCAST that offers improved graphical output, a dynamic background model, statistical confidence estimates based on false discovery rate estimation and, most significantly, the ability to predict CRMs while taking into account epigenomic data such as DNase I sensitivity or histone modification data. We demonstrate the validity of MCAST’s statistical confidence estimates and the utility of epigenomic priors in identifying CRMs. Availability and implementation: MCAST is part of the MEME Suite software toolkit. A web server and source code are available at http://meme-suite.org and http://alternate.meme-suite.org . Contact: t.bailey@imb.uq.edu.au or william-noble@uw.edu Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2015-05-30
    Description: Across the great diversity of life, there are many compelling examples of parallel and convergent evolution—similar evolutionary changes arising in independently evolving populations. Parallel evolution is often taken to be strong evidence of adaptation occurring in populations that are highly constrained in their genetic variation. Theoretical models suggest a few potential factors driving the probability of parallel evolution, but experimental tests are needed. In this study, we quantify the degree of parallel evolution in 15 replicate populations of Pseudomonas fluorescens evolved in five different environments that varied in resource type and arrangement. We identified repeat changes across multiple levels of biological organization from phenotype, to gene, to nucleotide, and tested the impact of 1) selection environment, 2) the degree of adaptation, and 3) the degree of heterogeneity in the environment on the degree of parallel evolution at the gene-level. We saw, as expected, that parallel evolution occurred more often between populations evolved in the same environment; however, the extent of parallel evolution varied widely. The degree of adaptation did not significantly explain variation in the extent of parallelism in our system but number of available beneficial mutations correlated negatively with parallel evolution. In addition, degree of parallel evolution was significantly higher in populations evolved in a spatially structured, multiresource environment, suggesting that environmental heterogeneity may be an important factor constraining adaptation. Overall, our results stress the importance of environment in driving parallel evolutionary changes and point to a number of avenues for future work for understanding when evolution is predictable.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 9
    Publication Date: 2015-10-21
    Description: Motivation: The advent of next-generation sequencing (NGS) has created unprecedented opportunities to examine viral populations within individual hosts, among infected individuals and over time. Comparing sequence variability across viral genomes allows for the construction of complex population structures, the analysis of which can yield powerful biological insights. However, the simultaneous display of sequence variation, coverage depth and quality scores across thousands of bases presents a unique visualization challenge that has not been fully met by current NGS analysis tools. Results: Here, we present LayerCake, a self-contained visualization tool that allows for the rapid analysis of variation in viral NGS data. LayerCake enables the user to simultaneously visualize variations in multiple viral populations across entire genomes within a highly customizable framework, drawing attention to pertinent and interesting patterns of variation. We have successfully deployed LayerCake to assist with a variety of different genomics datasets. Availability and implementation: Program downloads and detailed instructions are available at http://graphics.cs.wisc.edu/WP/layercake under a modified MIT license. LayerCake is a cross-platform tool written in the Processing framework for Java. Contact: mcorrell@cs.wisc.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 2015-10-19
    Description: We report detections and constraints for the near-infrared K s band secondary eclipses of seven hot-Jupiters using the IRIS2 infrared camera on the Anglo-Australian Telescope. Eclipses in the K s band for WASP-18b and WASP-36b have been measured for the first time. We also present new measurements for the eclipses of WASP-4b, WASP-5b, and WASP-46b, as well as upper limits for the eclipse depths of WASP-2b and WASP-76b. In particular, two full eclipses of WASP-46b were observed, allowing us to demonstrate the repeatability of our observations via independent analyses on each eclipse. Significant numbers of eclipse depths for hot-Jupiters have now been measured in both K s and the four Spitzer IRAC bandpasses. We discuss these measurements in the context of the broad-band colours and brightness temperatures of the hot-Jupiter atmosphere distribution. Specifically, we re-examine the proposed temperature dichotomy between the most irradiated, and mildly irradiated planets. We find no evidence for multiple clusters in the brightness temperature–equilibrium temperature distributions in any of these bandpasses, suggesting a continuous distribution of heat re-emission and circulation characteristics for these planets.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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