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  • 1
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    RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-28
    Description: DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Correcting atmospheric effects on InSAR with MERIS water vapour data and elevation-dependent interpolation model (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-15
    Description: SUMMARY The propagation delay when radar signals travel from the troposphere has been one of the major limitations for the applications of high precision repeat-pass Interferometric Synthetic Aperture Radar (InSAR). In this paper, we first present an elevation-dependent atmospheric correction model for Advanced Synthetic Aperture Radar (ASAR—the instrument aboard the ENVISAT satellite) interferograms with Medium Resolution Imaging Spectrometer (MERIS) integrated water vapour (IWV) data. Then, using four ASAR interferometric pairs over Southern California as examples, we conduct the atmospheric correction experiments with cloud-free MERIS IWV data. The results show that after the correction the rms differences between InSAR and GPS have reduced by 69.6 per cent, 29 per cent, 31.8 per cent and 23.3 per cent, respectively for the four selected interferograms, with an average improvement of 38.4 per cent. Most importantly, after the correction, six distinct deformation areas have been identified, that is, Long Beach–Santa Ana Basin, Pomona–Ontario, San Bernardino and Elsinore basin, with the deformation velocities along the radar line-of-sight (LOS) direction ranging from −20 mm yr −1 to −30 mm yr −1 and on average around −25 mm yr −1 , and Santa Fe Springs and Wilmington, with a slightly low deformation rate of about −10 mm yr −1 along LOS. Finally, through the method of stacking, we generate a mean deformation velocity map of Los Angeles over a period of 5 yr. The deformation is quite consistent with the historical deformation of the area. Thus, using the cloud-free MERIS IWV data correcting synchronized ASAR interferograms can significantly reduce the atmospheric effects in the interferograms and further better capture the ground deformation and other geophysical signals.
    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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  • 3
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    Correcting atmospheric effects on InSAR with MERIS water vapour data and elevation-dependent interpolation model (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-28
    Description: SUMMARY The propagation delay when radar signals travel from the troposphere has been one of the major limitations for the applications of high precision repeat-pass Interferometric Synthetic Aperture Radar (InSAR). In this paper, we first present an elevation-dependent atmospheric correction model for Advanced Synthetic Aperture Radar (ASAR—the instrument aboard the ENVISAT satellite) interferograms with Medium Resolution Imaging Spectrometer (MERIS) integrated water vapour (IWV) data. Then, using four ASAR interferometric pairs over Southern California as examples, we conduct the atmospheric correction experiments with cloud-free MERIS IWV data. The results show that after the correction the rms differences between InSAR and GPS have reduced by 69.6 per cent, 29 per cent, 31.8 per cent and 23.3 per cent, respectively for the four selected interferograms, with an average improvement of 38.4 per cent. Most importantly, after the correction, six distinct deformation areas have been identified, that is, Long Beach–Santa Ana Basin, Pomona–Ontario, San Bernardino and Elsinore basin, with the deformation velocities along the radar line-of-sight (LOS) direction ranging from −20 mm yr −1 to −30 mm yr −1 and on average around −25 mm yr −1 , and Santa Fe Springs and Wilmington, with a slightly low deformation rate of about −10 mm yr −1 along LOS. Finally, through the method of stacking, we generate a mean deformation velocity map of Los Angeles over a period of 5 yr. The deformation is quite consistent with the historical deformation of the area. Thus, using the cloud-free MERIS IWV data correcting synchronized ASAR interferograms can significantly reduce the atmospheric effects in the interferograms and further better capture the ground deformation and other geophysical signals.
    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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  • 4
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    Dissection of human MiRNA regulatory influence to subpathway (2012)
    Oxford University Press
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    Publication Date: 2012-04-03
    Description: The global insight into the relationships between miRNAs and their regulatory influences remains poorly understood. And most of complex diseases may be attributed to certain local areas of pathway (subpathway) instead of the entire pathway. Here, we reviewed the studies on miRNA regulations to pathways and constructed a bipartite miRNAs and subpathways network for systematic analyzing the miRNA regulatory influences to subpathways. We found that a small fraction of miRNAs were global regulators, environmental information processing pathways were preferentially regulated by miRNAs, and miRNAs had synergistic effect on regulating group of subpathways with similar function. Integrating the disease states of miRNAs, we also found that disease miRNAs regulated more subpathways than nondisease miRNAs, and for all miRNAs, the number of regulated subpathways was not in proportion to the number of the related diseases. Therefore, the study not only provided a global view on the relationships among disease, miRNA and subpathway, but also uncovered the function aspects of miRNA regulations and potential pathogenesis of complex diseases. A web server to query, visualize and download for all the data can be freely accessed at http://bioinfo.hrbmu.edu.cn/miR2Subpath .
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 5
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    A robust goodness-of-fit test for generalized autoregressive conditional heteroscedastic models (2018)
    Oxford University Press
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    Publication Date: 2018-03-06
    Description:   The estimation of time series models with heavy-tailed innovations has been widely discussed, but corresponding goodness-of-fit tests have attracted less attention, primarily because the autocorrelation function commonly used in constructing goodness-of-fit tests necessarily imposes certain moment conditions on the innovations. As a bounded random variable has finite moments of all orders, we address the problem by first transforming the residuals with a bounded function. More specifically, we consider the sample autocorrelation function of the transformed absolute residuals of a fitted generalized autoregressive conditional heteroscedastic model. With the corresponding residual empirical distribution function naturally employed as the transformation, a robust goodness-of-fit test is then constructed. The asymptotic distributions of the test statistic under the null hypothesis and local alternatives are derived, and Monte Carlo experiments are conducted to examine finite-sample properties. The proposed test is shown to be more powerful than existing tests when the innovations are heavy-tailed.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
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  • 6
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    Approximate non-linear multiparameter inversion with single and double scattering seismic wavefields in acoustic media (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-21
    Description: An approach for approximate direct quadratic non-linear inversion in two-parameter (density and bulk modulus) heterogeneous acoustic media is being presented and discussed in this paper. The approach consists of two parts: the first is a linear generalized Radon transform (GRT) migration procedure based on the weighted true-amplitude summation of pre-stack seismic scattered data that is adapted to a virtually arbitrary observing system, and the second is a non-iterative quadratic inversion operation, produced from the explicit expression of amplitude radiation pattern that is acting on the migrated data. This ensures the asymptotic inversion can continue to simultaneously locate the discontinuities and reconstruct the size of the discontinuities in the perturbation parameters describing the acoustic media. We identify that the amplitude radiation pattern is the binary quadratic combination of the parameters in the process of formulating non-linear inverse scattering problems based on second-order Born approximation. The coefficients of the quadratic terms are computed by appropriately handling the double scattering effects. These added quadratic terms provide a better amplitude correction for the parameters inversion. Through numerical tests, we show that for strong perturbations, the errors of the linear inversion are significant and unacceptable. In contrast, the quadratic non-linear inversion can give fairly accurate inversion results and keep almost the same computational complexity as conventional GRT liner inversion.
    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 Futalosine Pathway Played an Important Role in Menaquinone Biosynthesis during Early Prokaryote Evolution (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-24
    Description: Menaquinone (MK) is an important component of the electron-transfer system in prokaryotes. One of its precursors, 1,4-dihydroxy-2-naphthoate, can be synthesized from chorismate by the classical MK pathway. Interestingly, in some bacteria, chorismate can also be converted to 1,4-dihydroxy-6-naphthoate by four enzymes encoded by mqnABCD in an alternative futalosine pathway. In this study, six crucial enzymes belonging to these two independent nonhomologous pathways were identified in the predicted proteomes of prokaryotes representing a broad phylogenetic distribution. Although the classical MK pathway was found in 32.1% of the proteomes, more than twice the proportion containing the futalosine pathway, the latter was found in a broader taxonomic range of organisms (18 of 31 phyla). The prokaryotes equipped with the classical MK pathway were almost all aerobic or facultatively anaerobic, but those with the futalosine pathway were not only aerobic or facultatively anaerobic but also anaerobic. Phylogenies of enzymes of the classical MK pathway indicated that its genes in archaea were probably acquired by an ancient horizontal gene transfer from bacterial donors. Therefore, the organization of the futalosine pathway likely predated that of the classical MK pathway in the evolutionary history of prokaryotes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-03
    Description: G-quadruplex (G4) with stacked G-tetrads structure is able to bind hemin (iron (III)-protoporphyrin IX) to form a unique type of DNAzyme/RNAzyme with peroxidase-mimicking activity, which has been widely employed in multidisciplinary fields. However, its further applications are hampered by its relatively weak activity compared with protein enzymes. Herein, we report a unique intramolecular enhancement effect of the adjacent adenine (EnEAA) at 3' end of G4 core sequences that significantly improves the activity of G4 DNAzymes. Through detailed investigations of the EnEAA, the added 3' adenine was proved to accelerate the compound I formation in catalytic cycle and thus improve the G4 DNAzyme activity. EnEAA was found to be highly dependent on the unprotonated state of the N1 of adenine, substantiating that adenine might function as a general acid–base catalyst. Further adenine analogs analysis supported that both N1 and exocyclic 6-amino groups in adenine played key role in the catalysis. Moreover, we proved that EnEAA was generally applicable for various parallel G-quadruplex structures and even G4 RNAzyme. Our studies implied that adenine might act analogously as the distal histidine in protein peroxidases, which shed light on the fundamental understanding and rational design of G4 DNAzyme/RNAzyme catalysts with enhanced functions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Impacts of human activities on distribution of sulfate-reducing prokaryotes and antibiotic resistance genes in marine coastal sediments of Hong Kong (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-16
    Description: Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments ( P -value 〈 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    A long non-coding RNA, APOA4-AS, regulates APOA4 expression depending on HuR in mice (2016)
    Oxford University Press
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    Publication Date: 2016-07-28
    Description: Long non-coding RNAs (lncRNAs) have been shown to be critical biomarkers or therapeutic targets for human diseases. However, only a small number of lncRNAs were screened and characterized. Here, we identified 15 lncRNAs, which are associated with fatty liver disease. Among them, APOA 4-AS is shown to be a concordant regulator of Apolipoprotein A-IV (APOA4) expression. APOA4 -AS has a similar expression pattern with APOA4 gene. The expressions of APOA4 -AS and APOA4 are both abnormally elevated in the liver of ob/ob mice and patients with fatty liver disease. Knockdown of APOA4 -AS reduces APOA4 expression both in vitro and in vivo and leads to decreased levels of plasma triglyceride and total cholesterol in ob/ob mice. Mechanistically, APOA4 -AS directly interacts with mRNA stabilizing protein HuR and stabilizes APOA4 mRNA. Deletion of HuR dramatically reduces both APOA4 -AS and APOA4 transcripts. This study uncovers an anti-sense lncRNA ( APOA4 -AS), which is co-expressed with APOA4 , and concordantly and specifically regulates APOA4 expression both in vitro and in vivo with the involvement of HuR.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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