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  • 1
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    Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-06
    Description: Coastal areas are land–sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Toward a next-generation atlas of RNA secondary structure (2016)
    Oxford University Press
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    Publication Date: 2016-01-21
    Description: RNA structure plays a crucial role in gene maturation, regulation and function. Determining the form and frequency of RNA folds is essential for a better understanding of how RNA exerts its functions. Low-throughput studies have focused on RNA primary sequences and expression levels, but with an emphasis on relatively small numbers of transcripts. However, with the recent advent of high-throughput technologies, it is realistic to begin analyzing RNA secondary structures on a genome-wide scale. Here, we review genome-wide RNA secondary structure profiles as well as advances in computational structure predictions. We further discuss the novel characteristics of RNA secondary structure across messenger RNAs. Probing RNA secondary structure by high-throughput sequencing will enable us to build atlases of RNA secondary structures, an important step in helping us to understand the versatility of RNA functions in diverse cellular processes.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 3
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    Fully discrete analysis of the heterogeneous multiscale method for elliptic problems with multiple scales (2015)
    Oxford University Press
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    Publication Date: 2015-01-15
    Description: A fully discrete analysis of the finite element heterogeneous multiscale method (FE-HMM) for elliptic problems with N +1 well-separated scales is discussed. The FE-HMM is a numerical homogenization method that relies on a macroscopic scheme (macro FEM) for the approximation of the effective solution corresponding to the multiscale problem. The effective data are recovered from micro scale computation (micro FEM) on sampling domains located at appropriate quadrature points of the macroscopic mesh. At the macroscopic level, the numerical method can be seen as an FEM with numerical quadrature for a modified effective problem, hence variational crimes are made when designing this method. Up to now, the method has been analysed for two scales and the micro FEM was assumed to be conforming. For more than two scales, variational crimes are committed also at the intermediate (meso) scales and the effective data of the macroscopic scheme are obtained from a cascade of FEMs with numerical integration, which require a careful analysis. Numerical experiments for three-scale problems illustrate the theoretical convergence rates.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press
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  • 4
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    An analysis of SS precursors using spectral-element method seismograms (2011)
    Oxford University Press
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    Publication Date: 2011-11-11
    Description: SUMMARY The traveltimes of underside shear wave reflections (i.e. SS precursors) are widely used data for mapping the topography of mantle discontinuities in the upper mantle. Here, we examine the accuracy of ray theory in estimating the contribution of shear velocity heterogeneity in the mantle to SS–S400S, SS–S670S and S400S–S670S traveltimes. We analyse stacks of spectral-element method waveforms computed for 34 shallow earthquakes and 16 020 globally distributed virtual seismometers. The waveforms are computed for three versions of shear velocity model S20RTS with variable strengths of the volumetric shear velocity perturbations within the layered structure of the Preliminary Reference Earth Model. We find that ray-theoretical corrections account for only 50 per cent of the traveltime variation due to large-scale velocity heterogeneity. For current tomographic models, as represented by S20RTS, this translates into unpredictable long- and short-wavelength errors in maps of mantle discontinuity depths of about 5 km. This amounts to roughly 10 per cent of published variations in mantle discontinuity depths. However, relative errors will be significantly larger if ray-theoretical traveltime corrections are based on (forthcoming) models of shear velocity with much stronger heterogeneity at the smallest scales.
    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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  • 5
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    Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies (2014)
    Oxford University Press
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    Publication Date: 2014-04-23
    Description: Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed "transcriptomic shock." To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice ( Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis -factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of "whole genome doubling" has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery (2013)
    Oxford University Press
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    Publication Date: 2013-09-06
    Description: The 3' untranslated region (3'UTR) of hepatitis C virus (HCV) messenger RNA stimulates viral translation by an undetermined mechanism. We identified a high affinity interaction, conserved among different HCV genotypes, between the HCV 3'UTR and the host ribosome. The 3'UTR interacts with 40S ribosomal subunit proteins residing primarily in a localized region on the 40S solvent-accessible surface near the messenger RNA entry and exit sites. This region partially overlaps with the site where the HCV internal ribosome entry site was found to bind, with the internal ribosome entry site-40S subunit interaction being dominant. Despite its ability to bind to 40S subunits independently, the HCV 3'UTR only stimulates translation in cis , without affecting the first round translation rate . These observations support a model in which the HCV 3'UTR retains ribosome complexes during translation termination to facilitate efficient initiation of subsequent rounds of translation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Upper mantle density modelling for Large-Scale Moho gravity inversion: Case study on the Atlantic Ocean (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Moho geometry is an important parameter for geodynamic understanding. Seismic methods can provide accurate burial depths, but the coverage is low; the widely used CRUST1.0 model under oceans is greatly restricted by a low coverage of seismic data. Gravity inversion can provide high coverage of Moho undulations, but the accuracy is relatively low. Observed gravity anomalies integrate gravity effects induced by 3D density perturbations in the Earth. For studies of the geometry of a specific density interface based on gravity, all gravity effects caused by other interfaces should be removed from the total anomaly map based on 3D density distributions. We use temperature-based and velocity-based methods to model lithospheric/upper mantle density; two temperature-calculation parameter models (PSM and GDH1), three thermal expansion coefficients (alpha) and three scaling ratio models are tested for each method. PSM and GDH1 result in a similar mantle gravity anomaly (MGA) pattern but different MGA average values when the alpha model is the same. Different alpha and scaling ratio models result in different Moho inversion results, and the optimal result from the temperature-based method has a 3.2 km RMS with the CRUST1.0 model. A comparison between this inversion result and the CRUST1.0 model shows that the temperature-based method performs well for reproducing Moho geometry in the main part of the Atlantic Ocean, especially the central basin. The optimal result from the velocity-based method has a 4.3 km RMS with the CRUST1.0 model. Compared with the temperature-based method, the velocity-based method performs worse in the central basin but better in regions with low-velocity and low-density mantle away from the mid-ocean ridge.〈/span〉
    Print ISSN: 2051-1965
    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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  • 8
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    Diversity and distribution of catechol 2, 3-dioxygenase genes in surface sediments of the Bohai Sea (2016)
    Oxford University Press
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    Publication Date: 2016-05-05
    Description: Catechol 2, 3-dioxygenase (C23O) is the key enzyme for aerobic aromatic degradation. Based on clone libraries and quantitative real-time polymerase chain reaction, we characterized diversity and distribution patterns of C23O genes in surface sediments of the Bohai Sea. The results showed that sediments of the Bohai Sea were dominated by genes related to C23O subfamily I.2.A. The samples from wastewater discharge area (DG) and aquaculture farm (KL) showed distinct composition of C23O genes when compared to the samples from Bohai Bay (BH), and total organic carbon was a crucial determinant accounted for the composition variation. C6BH12-38 and C2BH2-35 displayed the highest gene copies and highest ratios to the 16S rRNA genes in KL, and they might prefer biologically labile aromatic hydrocarbons via aquaculture inputs. Meanwhile, C7BH3-48 showed the highest gene copies and highest ratios to the 16S rRNA genes in DG, and this could be selective effect of organic loadings from wastewater discharge. An evident increase in C6BH12-38 and C7BH3-48 gene copies and reduction in diversity of C23O genes in DG and KL indicated composition perturbations of C23O genes and potential loss in functional redundancy. We suggest that ecological habitat and trophic specificity could shape the distribution of C23O genes in the Bohai Sea sediments.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    A method for selecting M dwarfs with an increased likelihood of unresolved ultracool companionship (2016)
    Oxford University Press
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    Publication Date: 2016-02-12
    Description: Locating ultracool companions to M dwarfs is important for constraining low-mass formation models, the measurement of substellar dynamical masses and radii, and for testing ultracool evolutionary models. We present an optimized method for identifying M dwarfs which may have unresolved ultracool companions. We construct a catalogue of 440 694 M dwarf candidates, from Wide-Field Infrared Survey Explorer, Two Micron All-Sky Survey and Sloan Digital Sky Survey, based on optical- and near-infrared colours and reduced proper motion. With strict reddening, photometric and quality constraints we isolate a subsample of 36 898 M dwarfs and search for possible mid-infrared M dwarf + ultracool dwarf candidates by comparing M dwarfs which have similar optical/near-infrared colours (chosen for their sensitivity to effective temperature and metallicity). We present 1082 M dwarf + ultracool dwarf candidates for follow-up. Using simulated ultracool dwarf companions to M dwarfs, we estimate that the occurrence of unresolved ultracool companions amongst our M dwarf + ultracool dwarf candidates should be at least four times the average for our full M dwarf catalogue. We discuss possible contamination and bias and predict yields of candidates based on our simulations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-30
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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