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  • 1
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    Magnetic field structures in star-forming regions: mid-infrared imaging polarimetry of K3-50 (2015)
    Oxford University Press
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    Publication Date: 2015-09-27
    Description: We report new imaging polarimetry observations of the Galactic compact H ii region K3-50 using CanariCam at the Gran Telescopio Canarias. We use a standard polarimetric analysis technique, first outlined by Aitken, to decompose the observed polarization images centred at 8.7, 10.3, and 12.5 μm into the emissive and absorptive components from silicate grains that are aligned with the local magnetic field. These components reveal the spatially resolved magnetic field structures across the mid-infrared emission area of K3-50. We examine these structures and show that they are consistent with previously observed features and physical models of K3-50, such as the molecular torus and the ionized outflow. We propose a 3D geometry for all the structures seen at different wavelengths. We also compute relevant physical quantities in order to estimate the associated magnetic field strengths that would be implied under various physical assumptions. We compare these results with magnetohydrodynamic simulations of protostar formation that predict the magnetic field strength and configuration. We find that the magnetic field may be dynamically important in the innermost 0.2 pc of the molecular torus, but that the torus is more likely to be rotationally supported against gravity outside this radius. Similarly, magnetic fields are unlikely to dominate the global physics of the ionized outflow, but they may be important in helping confine the flow near the cavity wall in some locations. Ours is the first application of the Aitken technique to spatially resolved magnetic field structures in multiple layers along the line of sight, effectively a method of ‘polarization tomography’.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Insertion DNA Accelerates Meiotic Interchromosomal Recombination in Arabidopsis thaliana (2016)
    Oxford University Press
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    Publication Date: 2016-07-19
    Description: Nucleotide insertions/deletions are ubiquitous in eukaryotic genomes, and the resulting hemizygous (unpaired) DNA has significant, heritable effects on adjacent DNA. However, little is known about the genetic behavior of insertion DNA. Here, we describe a binary transgenic system to study the behavior of insertion DNA during meiosis. Transgenic Arabidopsis lines were generated to carry two different defective reporter genes on nonhomologous chromosomes, designated as "recipient" and "donor" lines. Double hemizygous plants (harboring unpaired DNA) were produced by crossing between the recipient and the donor, and double homozygous lines (harboring paired DNA) via self-pollination. The transfer of the donor’s unmutated sequence to the recipient generated a functional β-glucuronidase gene, which could be visualized by histochemical staining and corroborated by polymerase chain reaction amplification and sequencing. More than 673 million seedlings were screened, and the results showed that meiotic ectopic recombination in the hemizygous lines occurred at a frequency 〉6.49-fold higher than that in the homozygous lines. Gene conversion might have been exclusively or predominantly responsible for the gene correction events. The direct measurement of ectopic recombination events provided evidence that an insertion, in the absence of an allelic counterpart, could scan the entire genome for homologous counterparts with which to pair. Furthermore, the unpaired (hemizygous) architectures could accelerate ectopic recombination between itself and interchromosomal counterparts. We suggest that the ectopic recombination accelerated by hemizygous architectures may be a general mechanism for interchromosomal recombination through ubiquitously dispersed repeat sequences in plants, ultimately contributing to genetic renovation and eukaryotic evolution.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Properties of massive star-forming clumps with infall motions (2016)
    Oxford University Press
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    Publication Date: 2016-07-15
    Description: In this work, we aim to characterize high-mass clumps with infall motions. We selected 327 clumps from the Millimetre Astronomy Legacy Team 90-GHz survey, and identified 100 infall candidates. Combined with the results of He et al., we obtained a sample of 732 high-mass clumps, including 231 massive infall candidates and 501 clumps where infall is not detected. Objects in our sample were classified as pre-stellar, proto-stellar, H ii or photodissociation region (PDR). The detection rates of the infall candidates in the pre-stellar, proto-stellar, H ii and PDR stages are 41.2 per cent, 36.6 per cent, 30.6 per cent and 12.7 per cent, respectively. The infall candidates have a higher H 2 column density and volume density compared with the clumps where infall is not detected at every stage. For the infall candidates, the median values of the infall rates at the pre-stellar, proto-stellar, H ii and PDR stages are 2.6 x 10 –3 , 7.0 x 10 –3 , 6.5 x 10 –3 and 5.5 x 10 –3 M  yr –1 , respectively. These values indicate that infall candidates at later evolutionary stages are still accumulating material efficiently. It is interesting to find that both infall candidates and clumps where infall is not detected show a clear trend of increasing mass from the pre-stellar to proto-stellar, and to the H ii stages. The power indices of the clump mass function are 2.04 ± 0.16 and 2.17 ± 0.31 for the infall candidates and clumps where infall is not detected, respectively, which agree well with the power index of the stellar initial mass function (2.35) and the cold Planck cores (2.0).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species (2016)
    Oxford University Press
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    Publication Date: 2016-08-05
    Description: The plastid genome (plastome) of heterotrophic plants like mycoheterotrophs and parasites shows massive gene losses in consequence to the relaxation of functional constraints on photosynthesis. To understand the patterns of this convergent plastome reduction syndrome in heterotrophic plants, we studied 12 closely related orchids of three different lifeforms from the tribe Neottieae (Orchidaceae). We employ a comparative genomics approach to examine structural and selectional changes in plastomes within Neottieae. Both leafy and leafless heterotrophic species have functionally reduced plastid genome. Our analyses show that genes for the NAD(P)H dehydrogenase complex, the photosystems, and the RNA polymerase have been lost functionally multiple times independently. The physical reduction proceeds in a highly lineage-specific manner, accompanied by structural reconfigurations such as inversions or modifications of the large inverted repeats. Despite significant but minor selectional changes, all retained genes continue to evolve under purifying selection. All leafless Neottia species, including both visibly green and nongreen members, are fully mycoheterotrophic, likely evolved from leafy and partially mycoheterotrophic species. The plastomes of Neottieae span many stages of plastome degradation, including the longest plastome of a mycoheterotroph, providing invaluable insights into the mechanisms of plastome evolution along the transition from autotrophy to full mycoheterotrophy.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    An extensive spectroscopic time series of three Wolf-Rayet stars - I. The lifetime of large-scale structures in the wind of WR 134 (2016)
    Oxford University Press
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    Publication Date: 2016-06-23
    Description: During the summer of 2013, a 4-month spectroscopic campaign took place to observe the variabilities in three Wolf–Rayet stars. The spectroscopic data have been analysed for WR 134 (WN6b), to better understand its behaviour and long-term periodicity, which we interpret as arising from corotating interaction regions (CIRs) in the wind. By analysing the variability of the He ii 5411 emission line, the previously identified period was refined to P  = 2.255 ± 0.008 (s.d.) d. The coherency time of the variability, which we associate with the lifetime of the CIRs in the wind, was deduced to be 40 ± 6 d, or ~18 cycles, by cross-correlating the variability patterns as a function of time. When comparing the phased observational grey-scale difference images with theoretical grey-scales previously calculated from models including CIRs in an optically thin stellar wind, we find that two CIRs were likely present. A separation in longitude of ~= 90° was determined between the two CIRs and we suggest that the different maximum velocities that they reach indicate that they emerge from different latitudes. We have also been able to detect observational signatures of the CIRs in other spectral lines (C iv 5802,5812 and He i 5876). Furthermore, a DAC was found to be present simultaneously with the CIR signatures detected in the He i 5876 emission line which is consistent with the proposed geometry of the large-scale structures in the wind. Small-scale structures also show a presence in the wind, simultaneously with the larger scale structures, showing that they do in fact co-exist.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Higher-mode ambient-noise Rayleigh waves in sedimentary basins (2016)
    Oxford University Press
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    Publication Date: 2016-07-16
    Description: We show that higher modes are an important component of high-frequency Rayleigh waves in the cross-correlations over sedimentary basins. The particle motions provide a good test for distinguishing and separating the fundamental from the first higher mode, with the fundamental mode having retrograde and the first higher mode having prograde motion in the 1–10 s period of interest. The basement depth controls the cut-off period of the first higher mode, which coincides with a rapid increase (over period) in the particle-motion ellipticity or H / V ratio of the fundamental mode. The strong higher mode we observed is not only due to the low-velocity sedimentary layer but also due to the noise sources with significant radial component such as the basin edge scattering. It is important to correctly identify the mode order when inverting the dispersion curves because misidentifying the higher mode as fundamental will lead to an anomalous high V SV velocity.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
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    The DcpS inhibitor RG3039 improves motor function in SMA mice (2013)
    Oxford University Press
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    Publication Date: 2013-09-25
    Description: Spinal muscular atrophy (SMA) is caused by mutations of the survival motor neuron 1 ( SMN1 ) gene, retention of the survival motor neuron 2 ( SMN2 ) gene and insufficient expression of full-length survival motor neuron (SMN) protein. Quinazolines increase SMN2 promoter activity and inhibit the ribonucleic acid scavenger enzyme DcpS. The quinazoline derivative RG3039 has advanced to early phase clinical trials. In preparation for efficacy studies in SMA patients, we investigated the effects of RG3039 in severe SMA mice. Here, we show that RG3039 distributed to central nervous system tissues where it robustly inhibited DcpS enzyme activity, but minimally activated SMN expression or the assembly of small nuclear ribonucleoproteins. Nonetheless, treated SMA mice showed a dose-dependent increase in survival, weight and motor function. This was associated with improved motor neuron somal and neuromuscular junction synaptic innervation and function and increased muscle size. RG3039 also enhanced survival of conditional SMA mice in which SMN had been genetically restored to motor neurons. As this systemically delivered drug may have therapeutic benefits that extend beyond motor neurons, it could act additively with SMN-restoring therapies delivered directly to the central nervous system such as antisense oligonucleotides or gene therapy.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    High-efficiency and heritable gene targeting in mouse by transcription activator-like effector nucleases (2013)
    Oxford University Press
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    Publication Date: 2013-06-08
    Description: Transcription activator-like effector nucleases (TALENs) are a powerful new approach for targeted gene disruption in various animal models, but little is known about their activities in Mus musculus, the widely used mammalian model organism. Here, we report that direct injection of in vitro transcribed messenger RNA of TALEN pairs into mouse zygotes induced somatic mutations, which were stably passed to the next generation through germ-line transmission. With one TALEN pair constructed for each of 10 target genes, mutant F0 mice for each gene were obtained with the mutation rate ranged from 13 to 67% and an average of ~40% of total healthy newborns with no significant differences between C57BL/6 and FVB/N genetic background. One TALEN pair with single mismatch to their intended target sequence in each side failed to yield any mutation. Furthermore, highly efficient germ-line transmission was obtained, as all the F0 founders tested transmitted the mutations to F1 mice. In addition, we also observed that one bi-allele mutant founder of Lepr gene, encoding Leptin receptor, had similar diabetic phenotype as db/db mouse. Together, our results suggest that TALENs are an effective genetic tool for rapid gene disruption with high efficiency and heritability in mouse with distinct genetic background.
    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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  • 9
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    Infall motions in massive star-forming regions: results from years 1 and 2 of the MALT90 survey (2015)
    Oxford University Press
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    Publication Date: 2015-05-01
    Description: Massive star-forming regions with observed infall motions are good sites for studying the birth of massive stars. In this paper, 405 compact sources have been extracted from the APEX Telescope Large Area Survey of the Galaxy (ATLASGAL) compact sources that also have been observed in the Millimetre Astronomy Legacy Team 90-GHz (MALT90) survey during years 1 and 2. These observations are complemented with Spitzer GLIMPSE/MIPSGAL mid-IR survey data to help classify the elected star-forming clumps into three evolutionary stages: pre-stellar, proto-stellar and UCHII regions. The results suggest that 0.05 g cm –2 is a reliable empirical lower bound for the clump surface densities required for massive-star formation to occur. The optically thick HCO + (1-0) and HNC(1-0) lines, as well as the optically thin N 2 H + (1-0) line were used to search for infall motions towards these sources. By analysing the asymmetries of the optically thick HCO + (1-0) and HNC(1-0) lines and the mapping observations of HCO + (1-0), a total of 131 reliable infall candidates have been identified. The HCO + (1-0) line shows the highest occurrence of obvious asymmetric features, suggesting that it may be a better infall motion tracer than other lines such as HNC(1-0). The detection rates of infall candidates towards pre-stellar, proto-stellar and UCHII clumps are 0.3452, 0.3861 and 0.2152, respectively. The relatively high detection rate of infall candidates towards UCHII clumps indicates that many UCHII regions are still accreting matter. The peak column densities and masses of the infall candidates, in general, display an increasing trend with progressing evolutionary stages. However, the rough estimates of the mass infall rate show no obvious variation with evolutionary stage.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph (2015)
    Oxford University Press
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    Publication Date: 2015-05-12
    Description: : MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement. Availability and implementation: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact: rb@l3-bioinfo.com or twlam@cs.hku.hk 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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