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  • 1
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    An autonomous observation and control system based on EPICS and RTS2 for Antarctic telescopes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-19
    Description: For unattended telescopes in Antarctic, the remote operation, autonomous observation and control are essential. An EPICS-(Experimental Physics and Industrial Control System) and RTS2-(Remote Telescope System, 2nd Version) based autonomous observation and control system with remoted operation is introduced in this paper. EPICS is a set of open source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments while RTS2 is an open source environment for control of a fully autonomous observatory. Using the advantage of EPICS and RTS2, respectively, a combined integrated software framework for autonomous observation and control is established that use RTS2 to fulfil the function of astronomical observation and use EPICS to fulfil the device control of telescope. A command and status interface for EPICS and RTS2 is designed to make the EPICS IOC (Input/Output Controller) components integrate to RTS2 directly. For the specification and requirement of control system of telescope in Antarctic, core components named Executor and Auto-focus for autonomous observation is designed and implemented with remote operation user interface based on browser-server mode. The whole system including the telescope is tested in Lijiang Observatory in Yunnan Province for practical observation to complete the autonomous observation and control, including telescope control, camera control, dome control, weather information acquisition with the local and remote operation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization (2013)
    Oxford University Press
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    Publication Date: 2013-06-08
    Description: All orthobunyaviruses possess three genome segments of single-stranded negative sense RNA that are encapsidated with the virus-encoded nucleocapsid (N) protein to form a ribonucleoprotein (RNP) complex, which is uncharacterized at high resolution. We report the crystal structure of both the Bunyamwera virus (BUNV) N–RNA complex and the unbound Schmallenberg virus (SBV) N protein, at resolutions of 3.20 and 2.75 Å, respectively. Both N proteins crystallized as ring-like tetramers and exhibit a high degree of structural similarity despite classification into different orthobunyavirus serogroups. The structures represent a new RNA-binding protein fold. BUNV N possesses a positively charged groove into which RNA is deeply sequestered, with the bases facing away from the solvent. This location is highly inaccessible, implying that RNA polymerization and other critical base pairing events in the virus life cycle require RNP disassembly. Mutational analysis of N protein supports a correlation between structure and function. Comparison between these crystal structures and electron microscopy images of both soluble tetramers and authentic RNPs suggests the N protein does not bind RNA as a repeating monomer; thus, it represents a newly described architecture for bunyavirus RNP assembly, with implications for many other segmented negative-strand RNA viruses.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: NONCODE ( http://www.bioinfo.org/noncode/ ) is an interactive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs). The recently reduced cost of RNA sequencing has produced an explosion of newly identified data. Revolutionary third-generation sequencing methods have also contributed to more accurate annotations. Accumulative experimental data also provides more comprehensive knowledge of lncRNA functions. In this update, NONCODE has added six new species, bringing the total to 16 species altogether. The lncRNAs in NONCODE have increased from 210 831 to 527,336. For human and mouse, the lncRNA numbers are 167,150 and 130,558, respectively. NONCODE 2016 has also introduced three important new features: (i) conservation annotation; (ii) the relationships between lncRNAs and diseases; and (iii) an interface to choose high-quality datasets through predicted scores, literature support and long-read sequencing method support. NONCODE is also accessible through http://www.noncode.org/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    BLM unfolds G-quadruplexes in different structural environments through different mechanisms (2015)
    Oxford University Press
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    Publication Date: 2015-05-20
    Description: Mutations in the RecQ DNA helicase gene BLM give rise to Bloom's syndrome, which is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition. BLM helicase is highly active in binding and unwinding G-quadruplexes (G4s), which are physiological targets for BLM, as revealed by genome-wide characterizations of gene expression of cells from BS patients. With smFRET assays, we studied the molecular mechanism of BLM-catalyzed G4 unfolding and showed that ATP is required for G4 unfolding. Surprisingly, depending on the molecular environments of G4, BLM unfolds G4 through different mechanisms: unfolding G4 harboring a 3'-ssDNA tail in three discrete steps with unidirectional translocation, and unfolding G4 connected to dsDNA by ssDNA in a repetitive manner in which BLM remains anchored at the ss/dsDNA junction, and G4 was unfolded by reeling in ssDNA. This indicates that one BLM molecule may unfold G4s in different molecular environments through different mechanisms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Changepoint estimation: another look at multiple testing problems (2015)
    Oxford University Press
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    Publication Date: 2015-11-28
    Description: We consider large scale multiple testing for data that have locally clustered signals. With this structure, we apply techniques from changepoint analysis and propose a boundary detection algorithm so that the clustering information can be utilized. Consequently the precision of the multiple testing procedure is substantially improved. We study tests with independent as well as dependent $p$ -values. Monte Carlo simulations suggest that the methods perform well with realistic sample sizes and show improved detection ability compared with competing methods. Our procedure is applied to a genome-wide association dataset of blood lipids.
    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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    Abnormal p38{alpha} mitogen-activated protein kinase signaling in dilated cardiomyopathy caused by lamin A/C gene mutation (2012)
    Oxford University Press
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    Publication Date: 2012-09-14
    Description: We previously interrogated the transcriptome in heart tissue from Lmna H222P/H222P mice, a mouse model of cardiomyopathy caused by lamin A/C gene ( LMNA ) mutation, and found that the extracellular signal-regulated kinase 1/2 and Jun N -terminal kinase branches of the mitogen-activated protein (MAP) kinase signaling pathway were abnormally hyperactivated prior to the onset of significant cardiac impairment. We have now used an alternative gene expression analysis tool to reanalyze this transcriptome and identify hyperactivation of a third branch of the MAP kinase cascade, p38α signaling. Biochemical analysis of hearts from Lmna H222P/H222P mice showed enhanced p38α activation prior to and after the onset of heart disease as well as in hearts from human subjects with cardiomyopathy caused by LMNA mutations. Treatment of Lmna H222P/H222P mice with the p38α inhibitor ARRY-371797 prevented left ventricular dilatation and deterioration of fractional shortening compared with placebo-treated mice but did not block the expression of collagen genes involved in cardiac fibrosis. These results demonstrate that three different branches of the MAP kinase signaling pathway with overlapping consequences are involved in the pathogenesis of cardiomyopathy caused by LMNA mutations. They further suggest that pharmacological inhibition of p38α may be useful in the treatment of this disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Depletion of extracellular signal-regulated kinase 1 in mice with cardiomyopathy caused by lamin A/C gene mutation partially prevents pathology before isoenzyme activation (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-11
    Description: Mutations in the lamin A/C gene ( LMNA ) encoding A-type nuclear lamins cause dilated cardiomyopathy with variable muscular dystrophy. These mutations enhance mitogen-activated protein kinase signaling in the heart and pharmacological inhibition of extracellular signal-regulated kinase (ERK) 1 and 2 improves cardiac function in Lmna H222P/H222P mice. In the current study, we crossed mice lacking ERK1 to Lmna H222P/H222P mice and examined cardiac performance and survival. Male Lmna H222P/H222P / Erk1 –/– mice lacking ERK1 had smaller left ventricular end systolic diameters and increased fractional shortening (FS) at 16 weeks of age than Lmna H222P/H222P/ Erk1 +/+ mice. Their mean survival was also significantly longer. However, the improved cardiac function was abrogated at 20 weeks of age concurrent with an increased activity of ERK2. Lmna H222P/H222P / Erk1 –/– mice treated with an inhibitor of ERK1/2 activation had smaller left ventricular diameters and increased FS at 20 weeks of age. These results provide genetic evidence that ERK1 and ERK2 contribute to the development of cardiomyopathy caused by LMNA mutations and reveal interplay between these isoenzymes in maintaining a combined pathological activity in heart.
    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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    Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-13
    Description: All positive-stranded RNA viruses with genomes 〉~7 kb encode helicases, which generally are poorly characterized. The core of the nidovirus superfamily 1 helicase (HEL1) is associated with a unique N-terminal zinc-binding domain (ZBD) that was previously implicated in helicase regulation, genome replication and subgenomic mRNA synthesis. The high-resolution structure of the arterivirus helicase (nsp10), alone and in complex with a polynucleotide substrate, now provides first insights into the structural basis for nidovirus helicase function. A previously uncharacterized domain 1B connects HEL1 domains 1A and 2A to a long linker of ZBD, which further consists of a novel RING-like module and treble-clef zinc finger, together coordinating three Zn atoms. On substrate binding, major conformational changes were evident outside the HEL1 domains, notably in domain 1B. Structural characterization, mutagenesis and biochemistry revealed that helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-03
    Description: Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Motif analysis revealed that SRSF10 binding to cassette exons was associated with exon inclusion, whereas the binding of SRSF10 within downstream constitutive exons was associated with exon exclusion. This positional effect was further demonstrated by the mutagenesis of potential SRSF10 binding motifs in two minigene constructs. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Consistent with this observation, cells depleted of SRSF10 expression were far more susceptible to endoplasmic reticulum stress-induced apoptosis than control cells. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Certificateless Signatures: New Schemes and Security Models (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-28
    Description: We present a study of security in certificateless signatures. We divide potential adversaries according to their attack power, and for the first time, three new kinds of adversaries are introduced into certificateless signatures. They are Normal Adversary, Strong Adversary and Super Adversary (ordered by their attack power). Combined with the known Type I Adversary and Type II Adversary in certificateless cryptography, we then define the security of certificateless signatures in different attack scenarios. Our new security models, together with others in the literature, provide a clear definition of the security in certificateless signatures. Two concrete schemes with different security levels are also proposed in this paper. The first scheme, which is proven secure (in the random oracle model) against Normal Type I and Super Type II adversaries, has the shortest signature length among all known certificateless signature schemes. The second scheme is secure (in the random oracle model) against Super Type I and Type II adversaries. Compared with another scheme that has a similar security level, our second scheme requires less operational cost but a little longer signature length. Two server-aided verification protocols are also proposed to reduce the verification cost on the verifier.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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