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  • Oxford University Press  (817)
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  • 11
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    Galaxy And Mass Assembly (GAMA): the bright void galaxy population in the optical and mid-IR (2015)
    Oxford University Press
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    Publication Date: 2015-09-11
    Description: We examine the properties of galaxies in the Galaxies and Mass Assembly (GAMA) survey located in voids with radii 〉10 h –1  Mpc. Utilizing the GAMA equatorial survey, 592 void galaxies are identified out to z   0.1 brighter than M r  = –18.4, our magnitude completeness limit. Using the W Hα versus [N  ii ]/Hα (WHAN) line strength diagnostic diagram, we classify their spectra as star forming, AGN, or dominated by old stellar populations. For objects more massive than 5  x  10 9 M , we identify a sample of 26 void galaxies with old stellar populations classed as passive and retired galaxies in the WHAN diagnostic diagram, else they lack any emission lines in their spectra. When matched to Wide-field Infrared Survey Explorer mid-IR photometry, these passive and retired galaxies exhibit a range of mid-IR colour, with a number of void galaxies exhibiting [4.6] – [12] colours inconsistent with completely quenched stellar populations, with a similar spread in colour seen for a randomly drawn non-void comparison sample. We hypothesize that a number of these galaxies host obscured star formation, else they are star forming outside of their central regions targeted for single-fibre spectroscopy. When matched to a randomly drawn sample of non-void galaxies, the void and non-void galaxies exhibit similar properties in terms of optical and mid-IR colour, morphology, and star formation activity, suggesting comparable mass assembly and quenching histories. A trend in mid-IR [4.6] – [12] colour is seen, such that both void and non-void galaxies with quenched/passive colours 〈1.5 typically have masses higher than 10 10 M , where internally driven processes play an increasingly important role in galaxy evolution.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 12
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    Discovery of a low-mass companion to the F7V star HD 984 (2015)
    Oxford University Press
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    Publication Date: 2015-09-27
    Description: We report the discovery of a low-mass companion to the nearby ( d = 47 pc) F7V star HD 984. The companion is detected 0.19 arcsec away from its host star in the L ' band with the Apodized Phase Plate on NaCo/Very Large Telescope and was recovered by L '-band non-coronagraphic imaging data taken a few days later. We confirm the companion is comoving with the star with SINFONI integral field spectrograph H + K data. We present the first published data obtained with SINFONI in pupil-tracking mode. HD 984 has been argued to be a kinematic member of the 30 Myr-old Columba group, and its HR diagram position is not altogether inconsistent with being a zero-age main sequence star of this age. By consolidating different age indicators, including isochronal age, coronal X-ray emission, and stellar rotation, we independently estimate a main-sequence age of 115 ± 85 Myr (95 per cent CL) which does not rely on this kinematic association. The mass of directly imaged companions are usually inferred from theoretical evolutionary tracks, which are highly dependent on the age of the star. Based on the age extrema, we demonstrate that with our photometric data alone, the companion's mass is highly uncertain: between 33 and 96 M Jup (0.03–0.09 M ) using the COND evolutionary models. We compare the companion's SINFONI spectrum with field dwarf spectra to break this degeneracy. Based on the slope and shape of the spectrum in the H band, we conclude that the companion is an M6.0 ± 0.5 dwarf. The age of the system is not further constrained by the companion, as M dwarfs are poorly fit on low-mass evolutionary tracks. This discovery emphasizes the importance of obtaining a spectrum to spectral type companions around F-stars.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 13
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    Searching for gas giant planets on Solar system scales - a NACO/APP L'-band survey of A- and F-type main-sequence stars (2015)
    Oxford University Press
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    Publication Date: 2015-09-27
    Description: We report the results of a direct imaging survey of A- and F-type main-sequence stars searching for giant planets. A/F stars are often the targets of surveys, as they are thought to have more massive giant planets relative to solar-type stars. However, most imaging is only sensitive to orbital separations 〉30 au, where it has been demonstrated that giant planets are rare. In this survey, we take advantage of the high-contrast capabilities of the Apodizing Phase Plate coronagraph on NACO at the Very Large Telescope. Combined with optimized principal component analysis post-processing, we are sensitive to planetary-mass companions (2–12 M Jup ) at Solar system scales (≤30 au). We obtained data on 13 stars in the L ' band and detected one new companion as part of this survey: an M6.0 ± 0.5 dwarf companion around HD 984. We re-detect low-mass companions around HD 12894 and HD 20385, both reported shortly after the completion of this survey. We use Monte Carlo simulations to determine new constraints on the low-mass (〈80 M Jup ) companion frequency, as a function of mass and separation. Assuming solar-type planet mass and separation distributions, normalized to the planet frequency appropriate for A-stars, and the observed companion mass-ratio distribution for stellar companions extrapolated to planetary masses, we derive a truncation radius for the planetary mass companion surface density of 〈135 au at 95 per cent confidence.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 14
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    Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish (2015)
    Oxford University Press
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    Publication Date: 2015-11-22
    Description: Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (d N /d S ) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits—suggesting an important role for NC network architecture during the diversification in vertebrates.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 15
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    Transcription yield of fully 2'-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-29
    Description: On average, mutations are deleterious to proteins. Mutations conferring new function to a protein often come at the expense of protein folding or stability, reducing overall activity. Over the years, a panel of T7 RNA polymerases have been designed or evolved to accept nucleotides with modified ribose moieties. These modified RNAs have proven useful, especially in vivo , but the transcriptional yields tend to be quite low. Here we show that mutations previously shown to increase the thermal tolerance of T7 RNA polymerase can increase the activity of mutants with expanded substrate range. The resulting polymerase mutants can be used to generate 2' -O- methyl modified RNA with yields much higher than enzymes currently employed.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 16
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    Draft Genome of the Scarab Beetle Oryctes borbonicus on La Reunion Island (2016)
    Oxford University Press
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    Publication Date: 2016-07-14
    Description: Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus , which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus , a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae . We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus . The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 17
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    INstruct: a database of high-quality 3D structurally resolved protein interactome networks (2013)
    Oxford University Press
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    Publication Date: 2013-06-06
    Description: : INstruct is a database of high-quality, 3D, structurally resolved protein interactome networks in human and six model organisms. INstruct combines the scale of available high-quality binary protein interaction data with the specificity of atomic-resolution structural information derived from co-crystal evidence using a tested interaction interface inference method. Its web interface is designed to allow for flexible search based on standard and organism-specific protein and gene-naming conventions, visualization of protein architecture highlighting interaction interfaces and viewing and downloading custom 3D structurally resolved interactome datasets. Availability: INstruct is freely available on the web at http://instruct.yulab.org with all major browsers supported. Contact: haiyuan.yu@cornell.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 18
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    Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria (2013)
    Oxford University Press
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    Publication Date: 2013-04-02
    Description: In Escherichia coli , 12 distinct RNA structures within the transcripts encoding ribosomal proteins interact with specific ribosomal proteins to allow autogenous regulation of expression from large multi-gene operons, thus coordinating ribosomal protein biosynthesis across multiple operons. However, these RNA structures are typically not represented in the RNA Families Database or annotated in genomic sequences databases, and their phylogenetic distribution is largely unknown. To investigate the extent to which these RNA structures are conserved across eubacterial phyla, we created multiple sequence alignments representing 10 of these messenger RNA (mRNA) structures in E. coli . We find that while three RNA structures are widely distributed across many phyla of bacteria, seven of the RNAs are narrowly distributed to a few orders of Gammaproteobacteria. To experimentally validate our computational predictions, we biochemically confirmed dual L1-binding sites identified in many Firmicute species. This work reveals that RNA-based regulation of ribosomal protein biosynthesis is used in nearly all eubacterial phyla, but the specific RNA structures that regulate ribosomal protein biosynthesis in E. coli are narrowly distributed. These results highlight the limits of our knowledge regarding ribosomal protein biosynthesis regulation outside of E. coli, and the potential for alternative RNA structures responsible for regulating ribosomal proteins in other eubacteria.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 19
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    Molecular mechanism of CHRDL1-mediated X-linked megalocornea in humans and in Xenopus model (2015)
    Oxford University Press
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    Publication Date: 2015-05-09
    Description: Chordin-Like 1 ( CHRDL1 ) mutations cause non-syndromic X-linked megalocornea (XMC) characterized by enlarged anterior eye segments. Mosaic corneal degeneration, presenile cataract and secondary glaucoma are associated with XMC. Beside that CHRDL1 encodes Ventroptin, a secreted bone morphogenetic protein (BMP) antagonist, the molecular mechanism of XMC is not well understood yet. In a family with broad phenotypic variability of XMC, we identified the novel CHRDL1 frameshift mutation c.807_808delTC [p.H270Wfs*22] presumably causing CHRDL1 loss of function. Using Xenopus laevis as model organism, we demonstrate that chrdl1 is specifically expressed in the ocular tissue at late developmental stages. The chrdl1 knockdown directly resembles the human XMC phenotype and confirms CHRDL1 deficiency to cause XMC. Interestingly, secondary to this bmp4 is down-regulated in the Xenopus eyes. Moreover, phospho-SMAD1/5 is altered and BMP receptor 1A is reduced in a XMC patient. Together, we classify these observations as negative-feedback regulation due to the deficient BMP antagonism in XMC. As CHRDL1 is preferentially expressed in the limbal stem cell niche of adult human cornea, we assume that CHRDL1 plays a key role in cornea homeostasis. In conclusion, we provide novel insights into the molecular mechanism of XMC as well as into the specific role of CHRDL1 during cornea organogenesis, among others by the establishment of the first XMC in vivo model. We show that unravelling monogenic cornea disorders like XMC—with presumably disturbed cornea growth and differentiation—contribute to the identification of potential limbal stem cell niche factors that are promising targets for regenerative therapies of corneal injuries.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 20
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    Asymmetric supernova remnants generated by Galactic, massive runaway stars (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-13
    Description: After the death of a runaway massive star, its supernova shock wave interacts with the bow shocks produced by its defunct progenitor, and may lose energy, momentum and its spherical symmetry before expanding into the local interstellar medium (ISM). We investigate whether the initial mass and space velocity of these progenitors can be associated with asymmetric supernova remnants. We run hydrodynamical models of supernovae exploding in the pre-shaped medium of moving Galactic core-collapse progenitors. We find that bow shocks that accumulate more than about 1.5 M generate asymmetric remnants. The shock wave first collides with these bow shocks 160-750 yr after the supernova, and the collision lasts until 830-4900 yr. The shock wave is then located 1.35-5 pc from the centre of the explosion, and it expands freely into the ISM, whereas in the opposite direction it is channelled into the region of undisturbed wind material. This applies to an initially 20 M progenitor moving with velocity 20 km s -1 and to our initially 40 M progenitor. These remnants generate mixing of ISM gas, stellar wind and supernova ejecta that is particularly important upstream from the centre of the explosion. Their light curves are dominated by emission from optically thin cooling and by X-ray emission of the shocked ISM gas. We find that these remnants are likely to be observed in the [O iii ] 5007 spectral line emission or in the soft energy-band of X-rays. Finally, we discuss our results in the context of observed Galactic supernova remnants such as 3C 391 and the Cygnus Loop.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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