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  • 1
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    Dissecting the chromatin interactome of microRNA genes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-13
    Description: Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes ( MIRs ) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs . We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II–associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA–target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR–MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Diversity of electronic transitions and photoluminescence properties of p-type cuprous oxide films: A temperature-dependent spectral transmittance study (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-01-23
    Description: Cuprous oxide films have been deposited on quartz substrates by a sol-gel method under various annealing temperatures. The X-ray diffraction analysis and Raman scattering show that all the films are of pure Cu 2 O phase. From comparison of photoluminescence with 488 and 325 nm laser excitations, the electronic transition energies and intensities present the annealing-temperature dependent behavior. The electronic band structures of the Cu 2 O film annealed at 800 °C, especially for the contribution of exciton series and high energy transitions, have been investigated by temperature dependent transmittance. The extracted refraction index and the high frequency dielectric constant both abruptly decrease until the temperature rises up to 100 K. Six transitions can be clearly identified and the red shift trend of E o3 - E o5 transition energies with increasing the temperature can be found. Moreover, the anomalous behavior takes place at about 200 K from the E o6 transition. The singularities indicate that the change in the crystalline and electronic band structure occurs as the temperature near 100 K and 200 K for the film.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    HYDROCARBON POTENTIAL AND PALAEO‐DEPOSITIONAL ENVIRONMENT OF LACUSTRINE SOURCE ROCKS: MIDDLE JURASSIC SHIMENGOU FORMATION, NORTHERN QAIDAM BASIN, NW CHINA (2018)
    Details
    Publication Date: 2018
    Description: The Middle Jurassic Shimengou Formation in the Qaidam Basin, NW China, includes coals and lacustrine source rocks which locally reach oil shale quality (i.e. yielding 〉3.5 % oil on low‐temperature distillation). In the present study, the palaeo‐depositional environment and hydrocarbon potential of the 84.5 m thick Shale Member of the Shimengou Formation are investigated based on bulk geochemical parameters, organic petrographic data, biomarker analysis, and stable isotope geochemistry of 88 core samples. The Shale Member was deposited in an anoxic freshwater lake which formed following the drowning of a precursor low‐lying mire. Variations in bulk geochemical parameters allow four informal units to be identified, referred to (from the base up) as Units 1 to 4. These contain intervals of oil shale of varying thicknesses. In Unit 1, mudstones in the interval referred to as oil shale Layer 1 (true thickness [TD]: 2.06 m) are OM‐rich as a result of algal blooms and photic zone anoxia, and correspond to an initial flooding event. Subsequently, productivity of aquatic organisms decreased, resulting in the deposition of organic‐lean mudstones in Unit 2. Oil shale Layers 2 (TD: 2.03 m) and 3 (TD: 8.03 m) near the base of Unit 3 were deposited during maximum water depths. As with Layer 1, high productivity by algal blooms resulted in photic zone anoxia in a stratified water column. The shales in the upper part of Unit 3 are characterized by high TOC contents and a gradual increased input of terrigenous OM, and were deposited in a stable semi‐deep lake. Finally, organic‐lean mudstones in Unit 4 were deposited in shallow lacustrine conditions. The reconstruction of depositional environments in thick, non‐marine shale‐rich successions by mineralogical, petrographic and inorganic geochemical methods may be challenging as a result of the homogenous composition of component mudstones. The results of this study indicate, however, that sub‐division and basin‐wide correlation of such intervals can be achieved by organic geochemical analyses. Oil shales and organic‐rich mudstones in Units 1 and 3 of the Shimengou Formation Shale Member are excellent oil‐prone source‐rocks with a Source Potential Index of 3.2 t HC/m2. Considering the large area covered by the Shimengou Formation in the northern Qaidam Basin (∼34,000 km2), the results of this study highlight the regional significance for future petroleum exploration. They indicate that variations in organic productivity and dilution by minerals are key factors controlling the abundance and type of organic matter in the formation. An understanding of these factors will assist with the identification of exploration targets.
    Print ISSN: 0141-6421
    Electronic ISSN: 1747-5457
    Topics: Geosciences
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  • 4
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    Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-30
    Description: The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-12
    Description: The roles of virus-derived small RNAs (vsRNAs) have been studied in plants and insects. However, the generation and function of small RNAs from cytoplasmic RNA viruses in mammalian cells remain unexplored. This study describes four vsRNAs that were detected in enterovirus 71-infected cells using next-generation sequencing and northern blots. Viral infection produced substantial levels (〉10 5 copy numbers per cell) of vsRNA1, one of the four vsRNAs. We also demonstrated that Dicer is involved in vsRNA1 generation in infected cells. vsRNA1 overexpression inhibited viral translation and internal ribosomal entry site (IRES) activity in infected cells. Conversely, blocking vsRNA1 enhanced viral yield and viral protein synthesis. We also present evidence that vsRNA1 targets stem-loop II of the viral 5' untranslated region and inhibits the activity of the IRES through this sequence-specific targeting. Our study demonstrates the ability of a cytoplasmic RNA virus to generate functional vsRNA in mammalian cells. In addition, we also demonstrate a potential novel mechanism for a positive-stranded RNA virus to regulate viral translation: generating a vsRNA that targets the IRES.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    SP6616 as a new Kv2.1 channel inhibitor efficiently promotes β-cell survival involving both PKC/Erk1/2 and CaM/PI3K/Akt signaling pathways (2016)
    Springer Nature
    Details
    Publication Date: 2016-05-06
    Description: SP6616 as a new Kv2.1 channel inhibitor efficiently promotes β-cell survival involving both PKC/Erk1/2 and CaM/PI3K/Akt signaling pathways Cell Death and Disease 7, e2216 (May 2016). doi:10.1038/cddis.2016.119 Authors: T T Zhou, L L Quan, L P Chen, T Du, K X Sun, J C Zhang, L Yu, Y Li, P Wan, L L Chen, B H Jiang, L H Hu, J Chen & X Shen
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 7
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    Clothing image feature extraction based on SURF (2018)
    Institute of Physics (IOP)
    Details
    Publication Date: 2018-11-07
    Description: The SURF (Speeded Up Robust Features) is one of the most commonly used artificial feature extraction algorithms and has a good robustness. SURF is widely used in image processing and machine vision. This paper introduces the implementation of SURF in a more comprehensive way, and applies it to the feature extraction of clothing images. The clothing features extracted by using SURF can be applied in clothing classification, identification, retrieval and matching in combination with machine learning method. It can also be used as input sample of deep neural network to improve classification or recognition accuracy.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 8
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    A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21 (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-15
    Description: The rice Xa21 gene, which confers resistance to Xanthomonas oryzae pv. oryzae race 6, was isolated by positional cloning. Fifty transgenic rice plants carrying the cloned Xa21 gene display high levels of resistance to the pathogen. The sequence of the predicted protein, which carries both a leucine-rich repeat motif and a serine-threonine kinase-like domain, suggests a role in cell surface recognition of a pathogen ligand and subsequent activation of an intracellular defense response. Characterization of Xa21 should facilitate understanding of plant disease resistance and lead to engineered resistance in rice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, W Y -- Wang, G L -- Chen, L L -- Kim, H S -- Pi, L Y -- Holsten, T -- Gardner, J -- Wang, B -- Zhai, W X -- Zhu, L H -- Fauquet, C -- Ronald, P -- New York, N.Y. -- Science. 1995 Dec 15;270(5243):1804-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of California, Davis 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8525370" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; *Genes, Plant ; Genetic Linkage ; Molecular Sequence Data ; Oryza/enzymology/*genetics/microbiology ; Plant Diseases ; Plant Proteins/*genetics/metabolism ; Plants, Genetically Modified ; Protein-Serine-Threonine Kinases/*genetics/metabolism ; Receptor Protein-Tyrosine Kinases ; Receptors, Cell Surface/*genetics/metabolism ; Xanthomonas/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Enhancing the RNA engineering toolkit (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-11-24
    Keywords: Molecular Biology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Implementation of Four-Phase Interleaved Balance Charger for Series-Connected Batteries with Power Factor Correction (2017)
    Institute of Physics (IOP)
    Details
    Publication Date: 2017-11-29
    Description: A four-phase interleaved balance charger for series-connected batteries with power factor correction is proposed in this dissertation. In the two phases of two buckboost converters, the rectified ac power is firstly converted to a dc link capacitor. In the other two phases of two flyback converters, the rectified ac power is directly converted to charge the corresponding batteries. Additionally, the energy on the leakage inductance of flyback converter is bypassed to the dc link capacitor. Then, a dual-output balance charging circuit is connected to the dc link to deliver the dc link power to charge two batteries in the series-connected batteries module. The constant-current/constant-voltage charging strategy is adopted. Finally, a prototype of the proposed charger with rated power 500 W is constructed. From the experimental results, the performance and validity of the proposed topology are verified. Compared to the conventional topology with passive RCD snubber, the effi...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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