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  • 1
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physica C: Superconductivity and its applications 209 (1993), S. 167-170 
    ISSN: 0921-4534
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2015-07-15
    Description: Recent advances in RNA library preparation methods, platform accessibility and cost efficiency have allowed high-throughput RNA sequencing (RNAseq) to replace conventional hybridization microarray platforms as the method of choice for mRNA profiling and transcriptome analyses. RNAseq is a powerful technique to profile both long and short RNA expression, and the depth of information gained from distinct RNAseq methods is striking and facilitates discovery. In addition to expression analysis, distinct RNAseq approaches also allow investigators the ability to assess transcriptional elongation, DNA variance and exogenous RNA content. Here we review the current state of the art in transcriptome sequencing and address epigenetic regulation, quantification of transcription activation, RNAseq output and a diverse set of applications for RNAseq data. We detail how RNAseq can be used to identify allele-specific expression, single-nucleotide polymorphisms and somatic mutations and discuss the benefits and limitations of using RNAseq to monitor DNA characteristics. Moreover, we highlight the power of combining RNA- and DNAseq methods for genomic analysis. In summary, RNAseq provides the opportunity to gain greater insight into transcriptional regulation and output than simply miRNA and mRNA profiling.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 3
    Publication Date: 2015-12-02
    Description: Selenocysteine (Sec) is found in the catalytic centers of many selenoproteins and plays important roles in living organisms. Malfunctions of selenoproteins lead to various human disorders including cancer. Known as the 21st amino acid, the biosynthesis of Sec involves unusual pathways consisting of several stages. While the later stages of the pathways are well elucidated, the molecular basis of the first stage—the serylation of Sec-specific tRNA (tRNA Sec ) catalyzed by seryl-tRNA synthetase (SerRS)—is unclear. Here we present two cocrystal structures of human SerRS bound with tRNA Sec in different stoichiometry and confirm the formation of both complexes in solution by various characterization techniques. We discovered that the enzyme mainly recognizes the backbone of the long variable arm of tRNA Sec with few base-specific contacts. The N-terminal coiled-coil region works like a long-range lever to precisely direct tRNA 3' end to the other protein subunit for aminoacylation in a conformation-dependent manner. Restraints of the flexibility of the coiled-coil greatly reduce serylation efficiencies. Lastly, modeling studies suggest that the local differences present in the D- and T-regions as well as the characteristic U20:G19:C56 base triple in tRNA Sec may allow SerRS to distinguish tRNA Sec from closely related tRNA Ser substrate.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2019
    Description: Abstract By using global MHD simulation, we present the large scale characteristics of flux transfer events (FTEs) on the dayside magnetopause during periods of generic southward interplanetary magnetic field (IMF). It is revealed that FTEs can be generated both at lower and higher latitudes, and also at almost all local times. The occurrence rate of FTEs has an apparent longitudinal/latitudinal dependence, with a higher occurrence rate near noon/at lower latitudes. It is further shown that even under constant solar wind conditions, the azimuthal lengths of FTEs can have large variability, changing from as short as 〈1RE to as long as 〉10RE for different FTEs. Moreover, FTEs generated closer to the subsolar point tend to have longer extensions along their axes. These new knowledge of large scale properties of FTEs will improve our understanding of the solar wind ‐ magnetosphere interaction.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
    Publication Date: 2016-10-20
    Description: We study the evolution and properties of giant clumps in high- z disc galaxies using adaptive mesh refinement cosmological simulations at redshifts z ~ 6–1. Our sample consists of 34 galaxies, of halo masses 10 11 –10 12 M at z = 2, run with and without radiation pressure (RP) feedback from young stars. While RP has little effect on the sizes and global stability of discs, it reduces the amount of star-forming gas by a factor of ~2, leading to a similar decrease in stellar mass by z ~ 2. Both samples undergo extended periods of violent disc instability continuously forming giant clumps of masses 10 7 –10 9 M at a similar rate, though RP significantly reduces the number of long-lived clumps (LLCs). When RP is (not) included, clumps with circular velocity 40 (20) km s – 1 , baryonic surface density 200 (100)M pc – 2 and baryonic mass 10 8.2 (10 7.3 ) M are short-lived, disrupted in a few free-fall times. More massive and dense clumps survive and migrate towards the disc centre over a few disc orbital times. In the RP simulations, the distribution of clump masses and star formation rates (SFRs) normalized to their host disc is similar at all redshifts, exhibiting a truncated power law with a slope slightly shallower than –2. The specific SFR (sSFR) of the LLCs declines with age as they migrate towards the disc centre, producing gradients in mass, stellar age, gas fraction, sSFR and metallicity that distinguish them from the short-lived clumps which tend to populate the outer disc. Ex situ mergers comprise ~37 per cent of the mass in clumps and ~29 per cent of the SFR. They are more massive and with older stellar ages than the in situ clumps, especially near the disc edge. Roughly half the galaxies at redshifts z = 4–1 are clumpy, with ~3–30 per cent of their SFR and ~0.1–3 per cent of their stellar mass in clumps.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2014-08-01
    Description: Transposable elements (TE) have both negative and positive impact on the biology of their host. As a result, a balance is struck between the host and the TE that relies on directing integration to specific genome territories. The extraordinary capacity of DNA sequencing can create ultra dense maps of integration that are being used to study the mechanisms that position integration. Unfortunately, the great increase in the numbers of insertion sites detected comes with the cost of not knowing which positions are rare targets and which sustain high numbers of insertions. To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions. We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position. Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration. The serial number system is a general method that can be applied to determine precise integration maps for retroviruses and gene therapy vectors.
    Keywords: Recombination, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
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