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  • 11
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    The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-05-05
    Description: Acidification of seawater caused by anthropogenic carbon dioxide (CO 2 ) is anticipated to influence the growth of dinitrogen (N 2 )–fixing phytoplankton, which contribute a large fraction of primary production in the tropical and subtropical ocean. We found that growth and N 2 -fixation of the ubiquitous cyanobacterium Trichodesmium decreased under acidified conditions, notwithstanding a beneficial effect of high CO 2 . Acidification resulted in low cytosolic pH and reduced N 2 -fixation rates despite elevated nitrogenase concentrations. Low cytosolic pH required increased proton pumping across the thylakoid membrane and elevated adenosine triphosphate production. These requirements were not satisfied under field or experimental iron-limiting conditions, which greatly amplified the negative effect of acidification.
    Keywords: Microbiology
    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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  • 12
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    Polarization of Rayleigh scattered Ly{alpha} in active galactic nuclei (2016)
    Oxford University Press
    Details
    Publication Date: 2016-11-29
    Description: The unification scheme of active galactic nuclei invokes an optically thick molecular torus component hiding the broad emission line region. Assuming the presence of a thick neutral component in the molecular torus characterized by a H  i column density 〉10 22 cm –2 , we propose that far-UV radiation around Lyα can be significantly polarized through Rayleigh scattering. Adopting a Monte Carlo technique, we compute polarization of Rayleigh scattered radiation near Lyα in a thick neutral region in the shape of a slab and a cylindrical shell. It is found that radiation near Lyα Rayleigh reflected from a very thick slab can be significantly polarized in a fairly large range of wavelength  ~ 50 Å exhibiting a flux profile similar to the incident one. Rayleigh transmitted radiation in a slab is characterized by the central dip with a complicated polarization behaviour. The optically thick part near Lyα centre is polarized in the direction perpendicular to the slab normal, which is in contrast to weakly polarized wing parts in the direction parallel to the slab normal. A similar polarization flip phenomenon is also found in the case of a tall cylindrical shell, in which the spatial diffusion along the vertical direction near the inner cylinder wall for core photons leads to a tendency of the electric field aligned to the direction perpendicular to the vertical axis. Observational implications are briefly discussed including spectropolarimetry of the quasar PG 1630+377 by Koratkar et al. in 1990 where Lyα is strongly polarized with no other emission lines polarized.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 13
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    YM500: a small RNA sequencing (smRNA-seq) database for microRNA research (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: MicroRNAs (miRNAs) are small RNAs ~22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database, the YM500 ( http://ngs.ym.edu.tw/ym500/ ), containing analysis pipelines and analysis results for 609 human and mice smRNA-seq results, including public data from the Gene Expression Omnibus (GEO) and some private sources. YM500 collects analysis results for miRNA quantification, for isomiR identification (incl. RNA editing), for arm switching discovery, and, more importantly, for novel miRNA predictions. Wetlab validation on 〉100 miRNAs confirmed high correlation between miRNA profiling and RT-qPCR results ( R = 0.84). This database allows researchers to search these four different types of analysis results via our interactive web interface. YM500 allows researchers to define the criteria of isomiRs, and also integrates the information of dbSNP to help researchers distinguish isomiRs from SNPs. A user-friendly interface is provided to integrate miRNA-related information and existing evidence from hundreds of sequencing datasets. The identified novel miRNAs and isomiRs hold the potential for both basic research and biotech applications.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 14
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    rSNPBase: a database for curated regulatory SNPs (2013)
    Oxford University Press
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    Publication Date: 2013-12-29
    Description: In recent years, human regulatory SNPs (rSNPs) have been widely studied. Here, we present database rSNPBase, freely available at http://rsnp.psych.ac.cn/ , to provide curated rSNPs that analyses the regulatory features of all SNPs in the human genome with reference to experimentally supported regulatory elements. In contrast with previous SNP functional annotation databases, rSNPBase is characterized by several unique features. (i) To improve reliability, all SNPs in rSNPBase are annotated with reference to experimentally supported regulatory elements. (ii) rSNPBase focuses on rSNPs involved in a wide range of regulation types, including proximal and distal transcriptional regulation and post-transcriptional regulation, and identifies their potentially regulated genes. (iii) Linkage disequilibrium (LD) correlations between SNPs were analysed so that the regulatory feature is annotated to SNP-set rather than a single SNP. (iv) rSNPBase provides the spatio-temporal labels and experimental eQTL labels for SNPs. In summary, rSNPBase provides more reliable, comprehensive and user-friendly regulatory annotations on rSNPs and will assist researchers in selecting candidate SNPs for further genetic studies and in exploring causal SNPs for in-depth molecular mechanisms of complex phenotypes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 15
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    High-performance perovskite/Cu(In,Ga)Se2 monolithic tandem solar cells (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-08-31
    Description: The combination of hybrid perovskite and Cu(In,Ga)Se 2 (CIGS) has the potential for realizing high-efficiency thin-film tandem solar cells because of the complementary tunable bandgaps and excellent photovoltaic properties of these materials. In tandem solar device architectures, the interconnecting layer plays a critical role in determining the overall cell performance, requiring both an effective electrical connection and high optical transparency. We used nanoscale interface engineering of the CIGS surface and a heavily doped poly[bis(4-phenyl)(2,4,6-trimethylphenyl)amine] (PTAA) hole transport layer between the subcells that preserves open-circuit voltage and enhances both the fill factor and short-circuit current. A monolithic perovskite/CIGS tandem solar cell achieved a 22.43% efficiency, and unencapsulated devices under ambient conditions maintained 88% of their initial efficiency after 500 hours of aging under continuous 1-sun illumination.
    Keywords: Engineering, Materials Science
    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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  • 16
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    PES1 is a critical component of telomerase assembly and regulates cellular senescence (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Telomerase defers the onset of telomere shortening and cellular senescence by adding telomeric repeat DNA to chromosome ends, and its activation contributes to carcinogenesis. Telomerase minimally consists of the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR). However, how telomerase assembles is largely unknown. Here, we demonstrate that PES1 (Pescadillo), a protein overexpressed in many cancers, forms a complex with TERT and TR through direct interaction with TERT, regulating telomerase activity, telomere length maintenance, and senescence. PES1 does not interact with the previously reported telomerase components Reptin, Pontin, p23, and Hsp90. PES1 facilitates telomerase assembly by promoting direct interaction between TERT and TR without affecting TERT and TR levels. PES1 expression correlates positively with telomerase activity and negatively with senescence in patients with breast cancer. Thus, we identify a previously unknown telomerase complex, and targeting PES1 may open a new avenue for cancer therapy.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 17
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    Modelling gamma-ray light curves of phase-aligned millisecond pulsars (2018)
    Oxford University Press
    Details
    Publication Date: 2018-03-06
    Description: Three gamma-ray millisecond pulsars (MSPs), PSR J1939+2134, PSR J1959+2048, and PSR J0034-0534, have been confirmed to have a common feature of phase-aligned in radio and gamma-ray bands. With a geometric (two-pole caustic) model and a physical outer gap model (revised 3D outer gap model) in a three dimensional (3D) retarded magnetic dipole with a perturbation magnetic field, the observed features of these MSPs are studied. In order to obtained the best-fitting model parameters, the Markov chain Monte Carlo technique is used and reasonable GeV band light curves for three MSPs are given. Our calculations indicate that MSPs emit high energy photons with smaller inclination angles (α ≈ 10°–50°), larger view angles (ζ ≈ 65°–100°), and smaller perturbation factor (ε ≈ −0.15–0.1). Note that the factor ε, describing the strength of the perturbed magnetic field, is all less than zero in these two models, so the magnetic field caused by current-induced play a leading role in the pulsed location of MSPs.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 18
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    Selective formation of {gamma}-lactams via C-H amidation enabled by tailored iridium catalysts (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-03-06
    Description: Intramolecular insertion of metal nitrenes into carbon-hydrogen bonds to form -lactam rings has traditionally been hindered by competing isocyanate formation. We report the application of theory and mechanism studies to optimize a class of pentamethylcyclopentadienyl iridium(III) catalysts for suppression of this competing pathway. Modulation of the stereoelectronic properties of the auxiliary bidentate ligands to be more electron-donating was suggested by density functional theory calculations to lower the C–H insertion barrier favoring the desired reaction. These catalysts transform a wide range of 1,4,2-dioxazol-5-ones, carbonylnitrene precursors easily accessible from carboxylic acids, into the corresponding -lactams via sp 3 and sp 2 C–H amidation with exceptional selectivity. The power of this method was further demonstrated by the successful late-stage functionalization of amino acid derivatives and other bioactive molecules.
    Keywords: Chemistry
    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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  • 19
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    YM500v3: a database for small RNA sequencing in human cancer research (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: We previously presented the YM500 database, which contains 〉8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database ( http://ngs.ym.edu.tw/ym500/ ) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated 〉10 000 cancer-related RNA-seq and 〉3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, ‘Survival' and ‘Cancer', in this updated version. The ‘Survival’ section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The ‘Cancer’ section provides the results of differential expression analyses, miRNA–gene interactions and cancer miRNA-related pathways. In the ‘Expression’ section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 20
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    FRB microstructure revealed by the real-time detection of FRB170827 (2018)
    Oxford University Press
    Details
    Publication Date: 2018-05-03
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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