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  • 1
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    Electrical resistivity of coal-bearing rocks under high temperature and the detection of coal fires using electrical resistance tomography (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-02
    Description: Coal fires are severe hazards to environment, health and safety throughout the world. Efficient and economical extinguishing of these fires requires that the extent of the subsurface coal fires should be delineated. Electrical and electromagnetic methods have been used to detect coal fires in recent years. However, the resistivity change of coal-bearing rocks at high temperature is rarely investigated. The resistivity characteristics of coal fires at different temperatures and depths are seldomly researched as well. In this paper, we present the results of measurements of several coal-bearing rocks’ resistivity and permeability under high temperature. Two major causes for the change in resistivity with increasing temperature are recognized, there are the increase of charge carriers and thermal fracturing, of which the first one is probably the dominant cause. A set of 2-D simulations is carried out to compare the relation of resolution and efficiency of coal fires detection to temperature and depth when adopting the electrical resistance tomography. The simulation results show that the resolution and efficiency decrease with the decrease of temperature and the increase of depth. Finally, the electrical resistance tomography is used to delineate coal fires in the Anjialing Open Pit Mine. Most low-resistivity regions are verified as coal-fire areas according to the long-term monitoring of borehole temperature. The results indicate that the electrical resistance tomography can be used as a tool for the detection of coal fires.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    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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  • 2
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    Gadd45a promotes DNA demethylation through TDG (2015)
    Oxford University Press
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    Publication Date: 2015-05-03
    Description: Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet)—initiated oxidative demethylation. The connection of Gadd45a with oxidative demethylation is evidenced by the enhanced activation of a methylated reporter gene in HEK293T cells expressing Gadd45a in combination with catalytically active TDG and Tet. Gadd45a interacts with TDG physically and increases the removal of 5fC and 5caC from genomic and transfected plasmid DNA by TDG. Knockout of both Gadd45a and Gadd45b from mouse ES cells leads to hypermethylation of specific genomic loci most of which are also targets of TDG and show 5fC enrichment in TDG-deficient cells. These observations indicate that the demethylation effect of Gadd45a is mediated by TDG activity. This finding thus unites Gadd45a with the recently defined Tet-initiated demethylation pathway.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Jiamusi Pulsar Observations: I. Abnormal emission events of PSR B0919+06 (2016)
    Oxford University Press
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    Publication Date: 2016-01-13
    Description: PSR B0919+06 generally radiates radio pulses in a normal phase range. It is known for its occasional perplexing abnormal emission events wherein individual pulses come to an earlier phase range for a few tens of periods and then it returns to its usual phase. Heretofore, only a few such events have been available for study. We observed PSR B0919+06 for about 30 h using the Jiamusi 66-m telescope at the Jiamusi Deep Space Station at the S band, and we detected 92 abnormal emission events. We identify four types of events based on the abrupted or gradual phase-shifting of individual pulses. The abnormal emission events are seen to occur randomly about every 1000–3000 periods, and they affect the leading edge of the mean profile by up to 2 per cent in amplitude. The abnormal emission events are probably related to gradual changes of emission processing in the pulsar magnetosphere.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    The role of Notch signaling in muscle progenitor cell depletion and the rapid onset of histopathology in muscular dystrophy (2015)
    Oxford University Press
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    Publication Date: 2015-04-23
    Description: Although it has been speculated that stem cell depletion plays a role in the rapid progression of the muscle histopathology associated with Duchenne Muscular Dystrophy (DMD), the molecular and cellular mechanisms responsible for stem cell depletion remain poorly understood. The rapid depletion of muscle stem cells has not been observed in the dystrophin-deficient model of DMD (mdx mouse), which may explain the relatively mild dystrophic phenotype observed in this animal model. In contrast, we have observed a rapid occurrence of stem cell depletion in the dystrophin/utrophin double knockout (dKO) mouse model, which exhibits histopathological features that more closely recapitulate the phenotype observed in DMD patients compared with the mdx mouse. Notch signaling has been found to be a key regulator of stem cell self-renewal and myogenesis in normal skeletal muscle; however, little is known about the role that Notch plays in the development of the dystrophic histopathology associated with DMD. Our results revealed an over-activation of Notch in the skeletal muscles of dKO mice, which correlated with sustained inflammation, impaired muscle regeneration and the rapid depletion and senescence of the muscle progenitor cells (MPCs, i.e. Pax7+ cells). Consequently, the repression of Notch in the skeletal muscle of dKO mice delayed/reduced the depletion and senescence of MPCs, and restored the myogenesis capacity while reducing inflammation and fibrosis. We suggest that the down-regulation of Notch could represent a viable approach to reduce the dystrophic histopathologies associated with DMD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    In vitro selection of DNA-cleaving deoxyribozyme with site-specific thymidine excision activity (2014)
    Oxford University Press
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    Publication Date: 2014-08-15
    Description: Single-nucleotide polymorphisms, either inherited or due to spontaneous DNA damage, are associated with numerous diseases. Developing tools for site-specific nucleotide modification may one day provide a way to alter disease polymorphisms. Here, we describe the in vitro selection and characterization of a new deoxyribozyme called F-8, which catalyzes nucleotide excision specifically at thymidine. Cleavage by F-8 generates 3'- and 5'-phosphate ends recognized by DNA modifying enzymes, which repair the targeted deoxyribonucleotide while maintaining the integrity of the rest of the sequence. These results illustrate the potential of DNAzymes as tools for DNA manipulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants (2016)
    Oxford University Press
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    Publication Date: 2016-02-12
    Description: Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Knockout of RP2 decreases GRK1 and rod transducin subunits and leads to photoreceptor degeneration in zebrafish (2015)
    Oxford University Press
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    Publication Date: 2015-07-24
    Description: Retinitis pigmentosa (RP) affects about 1.8 million individuals worldwide. X-linked retinitis pigmentosa (XLRP) is one of the most severe forms of RP. Nearly 85% of XLRP cases are caused by mutations in the X-linked retinitis pigmentosa 2 ( RP2 ) and RPGR . RP2 has been considered to be a GTPase activator protein for ARL3 and to play a role in the traffic of ciliary proteins. The mechanism of how RP2 mutations cause RP is still unclear. In this study, we generated an RP2 knockout zebrafish line using transcription activator-like effector nuclease technology. Progressive retinal degeneration could be observed in the mutant zebrafish. The degeneration of rods' outer segments (OSs) is predominant, followed by the degeneration of cones' OS. These phenotypes are similar to the characteristics of RP2 patients, and also partly consistent with the phenotypes of RP2 knockout mice and morpholino-mediated RP2 knockdown zebrafish. For the first time, we found RP2 deletion leads to decreased protein levels and abnormal retinal localizations of GRK1 and rod transducin subunits (GNAT1 and GNB1) in zebrafish. Furthermore, the distribution of the total farnesylated proteins in zebrafish retina is also affected by RP2 ablation. These molecular alterations observed in the RP2 knockout zebrafish might probably be responsible for the gradual loss of the photoreceptors' OSs. Our work identified the progression of retinal degeneration in RP2 knockout zebrafish, provided a foundation for revealing the pathogenesis of RP caused by RP2 mutations, and would help to develop potential therapeutics against RP in further studies.
    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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    Model parameters of molecular evolution explain genomic correlations (2017)
    Oxford University Press
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    Publication Date: 2017-01-10
    Description: One long-standing research focus in evolutionary genomics is trying to resolve how biological variables (expression, essentiality, protein–protein interaction, structural stability, etc.) determine the rate of protein evolution. While these studies have considerably deepened our understanding of molecular evolution, many issues remain unsolved. In this opinion article, after having a brief survey of literatures, we establish relationships between model parameters of molecular evolution and genomic variables, based on which, most-observed genomic correlations and confounds can be explained by model parameter combinations under different conditions, which include the strength of stabilizing selection, mutational variance, expression sufficiency, gene pleiotropy, as well as the effective population size. We suggest that the problem to discern biological variable(s) that may determine the rate of protein evolution can be tackled at two levels. The first level, as discussed here, is to demonstrate how the model of molecular evolution can predict potential genomic correlations under various conditions. And the second level is to estimate genome-wide variations of model parameters (or combinations) that help to identify canonical biological variables that may underlie the rate variation among genes that ranges up to at least three magnitudes.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 9
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    22 GHz H2O maser survey towards 221 BGPS sources (2015)
    Oxford University Press
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    Publication Date: 2015-09-16
    Description: We performed a 22 GHz H 2 O maser survey towards 221 Bolocam Galactic Plane Survey (BGPS) sources. We detected 107 H 2 O masers, of which 12 are new. The detection rate is 48.4 per cent for our sample. We obtained the positions of five new H 2 O masers via On The Fly (OTF) observations. The detection rate of H 2 O masers is correlated with continuum emission fluxes of BGPS sources at far-infrared, sub-millimetre and millimetre wavelengths. We employed the classification of Dunham et al. to classify the evolutionary stage of BGPS sources into Group 0, 1, 2, and 3. The detection rate and velocity range of H 2 O masers increases as the BGPS sources evolve from Group 1 to Group 3. The BGPS sources associated with both H 2 O and CH 3 OH masers are more compact than that associated with either only H 2 O or only CH 3 OH masers. This indicates that the sources associated with both H 2 O and CH 3 OH masers are in relative later evolutionary stage. The detection rate of H 2 O masers towards BGPS sources displaying evidence of the collapse phenomenon is 62.1 per cent, which suggests that most BGPS sources showing indications of collapse phenomena contain ongoing active star formation activities.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    22 GHz H2O maser survey towards 221 BGPS sources (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-27
    Description: We performed a 22 GHz H 2 O maser survey towards 221 Bolocam Galactic Plane Survey (BGPS) sources. We detected 107 H 2 O masers, of which 12 are new. The detection rate is 48.4 per cent for our sample. We obtained the positions of five new H 2 O masers via On The Fly (OTF) observations. The detection rate of H 2 O masers is correlated with continuum emission fluxes of BGPS sources at far-infrared, sub-millimetre and millimetre wavelengths. We employed the classification of Dunham et al. to classify the evolutionary stage of BGPS sources into Group 0, 1, 2, and 3. The detection rate and velocity range of H 2 O masers increases as the BGPS sources evolve from Group 1 to Group 3. The BGPS sources associated with both H 2 O and CH 3 OH masers are more compact than that associated with either only H 2 O or only CH 3 OH masers. This indicates that the sources associated with both H 2 O and CH 3 OH masers are in relative later evolutionary stage. The detection rate of H 2 O masers towards BGPS sources displaying evidence of the collapse phenomenon is 62.1 per cent, which suggests that most BGPS sources showing indications of collapse phenomena contain ongoing active star formation activities.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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