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  • 1
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    Widespread purifying selection on RNA structure in mammals (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies 〉4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1 . This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    SN Ia host galaxy properties from Sloan Digital Sky Survey-II spectroscopy (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: We study the stellar populations of Type Ia supernova (SN Ia) host galaxies using Sloan Digital Sky Survey (SDSS)-II spectroscopy. The main focus is on the relationships of SN Ia properties with stellar velocity dispersion and the stellar population parameters age, metallicity and element abundance ratios. We concentrate on a sub-sample of 84 SNe Ia from the SDSS-II Supernova Survey and find that SALT2 stretch factor values show the strongest dependence on stellar population age. Hence, more luminous SNe Ia appear in younger stellar progenitor systems. No statistically significant trends in the Hubble residual with any of the stellar population parameters studied are found. Moreover, the method of photometric stellar mass derivation affects the Hubble residual–mass relationship. For an extended sample (247 objects), including SNe Ia with SDSS host galaxy photometry only, the Hubble residual–mass relationship behaves as a sloped step function. In the high-mass regime, probed by our host spectroscopy sample, this relationship is flat. Below a stellar mass of ~2 10 10 M , i.e. close to the evolutionary transition mass of low-redshift galaxies, the trend changes dramatically such that lower mass galaxies possess lower luminosity SNe Ia after light-curve corrections. The sloped step function of the Hubble residual–mass relationship should be accounted for when using stellar mass as a further parameter for minimizing the Hubble residuals.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Star formation and dust heating in the FIR bright sources of M83 (2013)
    Oxford University Press
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    Publication Date: 2013-06-09
    Description: We investigate star formation and dust heating in the compact far-infrared (FIR) bright sources detected in the Herschel maps of M83. We use the source extraction code getsources to detect and extract sources in the FIR, as well as their photometry in the mid-infrared and Hα. By performing infrared spectral energy distribution fitting and applying an Hα-based star formation rate (SFR) calibration, we derive the dust masses and temperatures, SFRs, gas masses and star formation efficiencies (SFEs). The detected sources lie exclusively on the spiral arms and represent giant molecular associations, with gas masses and sizes of 10 6 –10 8  M and 200–300 pc, respectively. The inferred parameters show little to no radial dependence and there is only a weak correlation between the SFRs and gas masses, which suggests that more massive clouds are less efficient at forming stars. Dust heating is mainly due to local star formation. However, although the sources are not optically thick, the total intrinsic young stellar population luminosity can almost completely account for the dust luminosity. This suggests that other radiation sources also contribute to the dust heating and approximately compensate for the unabsorbed fraction of UV light.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    A Herschel-ATLAS study of dusty spheroids: probing the minor-merger process in the local Universe (2013)
    Oxford University Press
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    Publication Date: 2013-09-26
    Description: We use multiwavelength (0.12–500 μm) photometry from Herschel -ATLAS, WISE , UKIDSS , SDSS and GALEX to study 23 nearby spheroidal galaxies with prominent dust lanes (DLSGs). DLSGs are considered to be remnants of recent minor mergers, making them ideal laboratories for studying both the interstellar medium (ISM) of spheroids and minor-merger-driven star formation in the nearby Universe. The DLSGs exhibit star formation rates (SFRs) between 0.01 and 10 M yr –1 , with a median of 0.26 M yr –1 (a factor of 3.5 greater than the average SG). The median dust mass, dust-to-stellar mass ratio and dust temperature in these galaxies are around 10 7.6 M , 0.05 per cent and 19.5 K, respectively. The dust masses are at least a factor of 50 greater than that expected from stellar mass loss and, like the SFRs, show no correlation with galaxy luminosity, suggesting that both the ISM and the star formation have external drivers. Adopting literature gas-to-dust ratios and star formation histories derived from fits to the panchromatic photometry, we estimate that the median current and initial gas-to-stellar mass ratios in these systems are 4 and 7 per cent, respectively. If, as indicated by recent work, minor mergers that drive star formation in spheroids with (NUV – r ) 〉 3.8 (the colour range of our DLSGs) have stellar mass ratios between 1:6 and 1:10, then the satellite gas fractions are likely ≥50 per cent.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Modeling the dispersal of Cape hake ichthyoplankton (2012)
    Oxford University Press
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    Publication Date: 2012-06-26
    Description: The two Cape hake species of the southern Benguela ecosystem, the shallow-water and deep-water hakes Merluccius capensis and M. paradoxus , are economically the most important marine resources in South Africa. Recruitment is a key process in the dynamics of marine organisms, yet very little is known about the early life history of Cape hakes, especially the location of spawning grounds and transport of eggs and larvae. For each species, ichthyoplankton dispersal off South Africa is simulated by coupling oceanographic simulations to an individual-based model in order to track virtual individuals. Results indicate that the most favorable spawning areas for transport to nursery areas are located off the south-western coast and the eastern Agulhas Bank, and highlight partly different drift routes followed by the two ichthyoplankton species off Cape Columbine. Transport from spawning to nursery areas is the highest in austral winter for a spawning depth ranging between 0 and 100 m. These modeling results are in broad agreement with available knowledge on the ecology of Cape hakes. The present work on Cape hakes complements previous modeling studies on anchovy and sardine in the same area. Taken together, these studies underline the correspondence between cross-shore (for hakes) or alongshore (for anchovy and sardine) transport mechanisms and the spawning strategies used by these key species of the southern Benguela ecosystem.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Knowledge production and learning for sustainable forest management on the ground: Pan-European landscapes as a time machine (2011)
    Oxford University Press
    In: Forestry
    Details
    Publication Date: 2011-11-24
    Description: While sustainable forest management (SFM) policy processes are well developed, implementation on the ground remains a challenge. Given the diversity of biophysical conditions, economic histories and governance systems on the European continent, regionally and temporally adapted and adaptive solutions are needed for both social and ecological systems. To illustrate this, we apply (1) a biographic forest and woodland history approach to central Sweden’s Bergslagen region, where boreal sustained yield forestry was widely applied first and (2) a comparative case study approach using five European landscapes that represent different forest history phases in Scotland, Germany, Ukraine and Russia. Additionally, we illustrate the need to learn from reference landscapes for natural forest and cultural woodland systems such as in economically remote regions in Romania, Russia and on the Iberian Peninsula. We conclude that there is great opportunity for innovative knowledge production about both governance and management for different SFM dimensions based on comparisons among concrete landscapes. In addition, there is a need to develop local place-based social learning processes that are characterized by a focus on a geographical area, commitment to SFM policy visions and collaborative approaches to development that include both ecological and social systems.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 7
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    Precession of the Sagittarius stream (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-06
    Description: Using a variety of stellar tracers – blue horizontal branch stars, main-sequence turn-off stars and red giants – we follow the path of the Sagittarius (Sgr) stream across the sky in Sloan Digital Sky Survey data. Our study presents new Sgr debris detections, accurate distances and line-of-sight velocities that together help to shed new light on the puzzle of the Sgr tails. For both the leading and the trailing tails, we trace the points of their maximal extent, or apocentric distances, and find that they lie at R L  = 47.8 ± 0.5 kpc and R T  = 102.5 ± 2.5 kpc, respectively. The angular difference between the apocentres is 93 $_{.}^{\circ}$ 2 ± 3 $_{.}^{\circ}$ 5, which is smaller than predicted for logarithmic haloes. Such differential orbital precession can be made consistent with models of the Milky Way in which the dark matter density falls more quickly with radius. However, currently, no existing Sgr disruption simulation can explain the entirety of the observational data. Based on its position and radial velocity, we show that the unusually large globular cluster NGC 2419 can be associated with the Sgr trailing stream. We measure the precession of the orbital plane of the Sgr debris in the Milky Way potential and show that, surprisingly, Sgr debris in the primary (brighter) tails evolves differently from the secondary (fainter) tails, both in the north and the south.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Herschel-ATLAS: properties of dusty massive galaxies at low and high redshifts (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-06
    Description: We present a comparison of the physical properties of a rest-frame 250-μm-selected sample of massive, dusty galaxies from 0 〈 z  〈 5.3. Our sample comprises 29 high-redshift submillimetre galaxies (SMGs) from the literature and 843 dusty galaxies at z  〈 0.5 from the Herschel -Astrophysical TeraHertz Large Area Survey (H-ATLAS), selected to have a similar stellar mass to the SMGs. The z  〉 1 SMGs have an average star formation rate (SFR) of $390^{+80}_{-70}\,$  M  yr –1 , which is 120 times that of the low-redshift sample matched in stellar mass to the SMGs (SFR = 3.3 ± 0.2 M  yr –1 ). The SMGs harbour a substantial mass of dust ( $1.2^{+0.3}_{-0.2}\times {10}^9\,$  M ), compared to (1.6 ± 0.1) 10 8  M for low-redshift dusty galaxies. At low redshifts, the dust luminosity is dominated by the diffuse interstellar medium, whereas a large fraction of the dust luminosity in SMGs originates from star-forming regions. At the same dust mass, SMGs are offset towards a higher SFR compared to the low-redshift H-ATLAS galaxies. This is not only due to the higher gas fraction in SMGs but also because they are undergoing a more efficient mode of star formation, which is consistent with their bursty star formation histories. The offset in SFR between SMGs and low-redshift galaxies is similar to that found in CO studies, suggesting that dust mass is as good a tracer of molecular gas as CO.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-28
    Description: Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP / attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    PACS photometry of the Herschel Reference Survey - far-infrared/submillimetre colours as tracers of dust properties in nearby galaxies (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-02
    Description: We present Herschel /PACS 100 and 160 μm integrated photometry for the 323 galaxies in the Herschel Reference Survey (HRS), a K -band, volume-limited sample of galaxies in the local Universe. Once combined with the Herschel /SPIRE observations already available, these data make the HRS the largest representative sample of nearby galaxies with homogeneous coverage across the 100–500 μm wavelength range. In this paper, we take advantage of this unique data set to investigate the properties and shape of the far-infrared/submillimetre spectral energy distribution in nearby galaxies. We show that, in the stellar mass range covered by the HRS (8  log ( M * /M )  12), the far-infrared/submillimetre colours are inconsistent with a single modified blackbody having the same dust emissivity index β for all galaxies. In particular, either β decreases or multiple temperature components are needed, when moving from metal-rich/gas-poor to metal-poor/gas-rich galaxies. We thus investigate how the dust temperature and mass obtained from a single modified blackbody depend on the assumptions made on β. We show that, while the correlations between dust temperature, galaxy structure and star formation rate are strongly model dependent, the dust mass scaling relations are much more reliable, and variations of β only change the strength of the observed trends.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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