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  • 1
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    From birth to death of protoplanetary discs: modelling their formation, evolution and dispersal (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: The formation, evolution and dispersal processes of protoplanetary discs are investigated and the disc lifetime is estimated. The gravitational collapse of a pre-stellar core forms both a central star and a protoplanetary disc. The central star grows by accretion from the disc and irradiation by the central star heats up the disc and generates a thermal wind, which results in the disc's dispersal. Using the one-dimensional diffusion equation, we calculate the evolution of protoplanetary discs numerically. To calculate the disc evolution from formation to dispersal, we add source and sink terms that represent gas accretion from pre-stellar cores and photoevaporation, respectively. We find that the disc lifetimes of typical pre-stellar cores are around 2–4 million years (Myr). A pre-stellar core with high angular momentum forms a larger disc with a long lifetime, while a disc around an X-ray-luminous star has a short lifetime. Integrating disc lifetimes under various masses and angular velocities of pre-stellar cores and X-ray luminosities of young stellar objects, we obtain the disc fraction at a given stellar age and mean lifetime of the disc. Our model indicates that the mean lifetime of a protoplanetary disc is 3.7 Myr, which is consistent with the observational estimate from young stellar clusters. We also find that the dispersion of X-ray luminosity is needed to reproduce the observed disc fraction.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Structure and function of human histone H3.Y nucleosome (2016)
    Oxford University Press
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    Publication Date: 2016-07-28
    Description: Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stable in vitro and in vivo . Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30 (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Pho Pop5 and Pho Rpp30 in the hyperthermophilic archaeon Pyrococcus horikoshii , homologues of human ribonuclease P (RNase P) proteins hPop5 and Rpp30, respectively, fold into a heterotetramer [ Pho Rpp30–( Pho Pop5) 2 – Pho Rpp30], which plays a crucial role in the activation of RNase P RNA ( Pho pRNA). Here, we examined the functional implication of Pho Pop5 and Pho Rpp30 in the tetramer. Surface plasmon resonance (SPR) analysis revealed that the tetramer strongly interacts with an oligonucleotide including the nucleotide sequence of a stem-loop SL3 in Pho pRNA. In contrast, Pho Pop5 had markedly reduced affinity to SL3, whereas Pho Rpp30 had little affinity to SL3. SPR studies of Pho Pop5 mutants further revealed that the C-terminal helix (α4) in Pho Pop5 functions as a molecular recognition element for SL3. Moreover, gel filtration indicated that Pho Rpp30 exists as a monomer, whereas Pho Pop5 is an oligomer in solution, suggesting that Pho Rpp30 assists Pho Pop5 in attaining a functionally active conformation by shielding hydrophobic surfaces of Pho Pop5. These results, together with available data, allow us to generate a structural and mechanistic model for the Pho pRNA activation by Pho Pop5 and Pho Rpp30, in which the two C-terminal helices (α4) of Pho Pop5 in the tetramer whose formation is assisted by Pho Rpp30 act as binding elements and bridge SL3 and SL16 in Pho pRNA.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 4
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    Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons (2016)
    Oxford University Press
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    Publication Date: 2016-01-30
    Description: Post-transcriptional modifications at the anticodon first (wobble) position of tRNA play critical roles in precise decoding of genetic codes. 5-carboxymethoxyuridine (cmo 5 U) and its methyl ester derivative 5-methoxycarbonylmethoxyuridine (mcmo 5 U) are modified nucleosides found at the anticodon wobble position in several tRNAs from Gram-negative bacteria. cmo 5 U and mcmo 5 U facilitate non-Watson–Crick base pairing with guanosine and pyrimidines at the third positions of codons, thereby expanding decoding capabilities. By mass spectrometric analyses of individual tRNAs and a shotgun approach of total RNA from Escherichia coli , we identified mcmo 5 U as a major modification in tRNA Ala1 , tRNA Ser1 , tRNA Pro3 and tRNA Thr4 ; by contrast, cmo 5 U was present primarily in tRNA Leu3 and tRNA Val1 . In addition, we discovered 5-methoxycarbonylmethoxy-2'- O -methyluridine (mcmo 5 Um) as a novel but minor modification in tRNA Ser1 . Terminal methylation frequency of mcmo 5 U in tRNA Pro3 was low (30%) in the early log phase of cell growth, gradually increased as growth proceeded and reached nearly 100% in late log and stationary phases. We identified CmoM (previously known as SmtA), an AdoMet-dependent methyltransferase that methylates cmo 5 U to form mcmo 5 U. A luciferase reporter assay based on a +1 frameshift construct revealed that terminal methylation of mcmo 5 U contributes to the decoding ability of tRNA Ala1 .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus (2016)
    Oxford University Press
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    Publication Date: 2016-02-24
    Description: The crystal structures of the wild type and catalytic mutant Asp-312-〉Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (β/α) 8 -barrel and two β-domains located at both N- and C-terminal ends. The isomaltohexaose–complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (–4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 6
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    Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its Set2–Rpb1 interaction (SRI) domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser 2 and Ser 5 (CTD-S2,5-P). H3K36me2 is sufficient for recruitment of the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2P-dependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts mainly through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 was not enough for silencing. Clr6 complex II appeared not to be responsible for heterochromatic silencing by H3K36me3. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insights into the distinct roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    On the photoelectric quantum yield of small dust particles (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: Photoelectron emission is crucial to electric charging of dust particles around main-sequence stars and gas heating in various dusty environments. An estimate of the photoelectric processes contains an ill-defined parameter called the photoelectric quantum yield, which is the total number of electrons ejected from a dust particle per absorbed photon. Here we revisit the so-called small particle effect of photoelectron emission and provide an analytical model to estimate photoelectric quantum yields of small dust particles in sizes down to nanometers. We show that the small particle effect elevates the photoelectric quantum yields of nanoparticles up to by a factor of 10 3 for carbon, water ice, and organics, and a factor of 10 2 for silicate, silicon carbide, and iron. We conclude the surface curvature of the particles is a quantity of great importance to the small particle effect, unless the particles are submicrometers in radius or larger.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Evolution of an accretion disc in binary black hole systems (2016)
    Oxford University Press
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    Publication Date: 2016-12-28
    Description: We investigate evolution of an accretion disc in binary black hole (BBH) systems and possible electromagnetic counterparts of the gravitational waves from mergers of BBHs. Perna et al. proposed a novel evolutionary scenario of an accretion disc in BBHs in which a disc eventually becomes ‘dead’, i.e. the magnetorotational instability (MRI) becomes inactive. In their scenario, the dead disc survives until a few seconds before the merger event. We improve the dead disc model and propose another scenario, taking account of effects of the tidal torque from the companion and the critical ionization degree for MRI activation more carefully. We find that the mass of the dead disc is much lower than that in the Perna's scenario. When the binary separation sufficiently becomes small, the mass inflow induced by the tidal torque reactivates MRI, restarting mass accretion on to the black hole. We also find that this disc ‘revival’ happens more than thousands of years before the merger. The mass accretion induced by the tidal torque increases as the separation decreases, and a relativistic jet could be launched before the merger. The emissions from these jets are too faint compared to gamma-ray bursts, but detectable if the merger events happen within 10 Mpc or if the masses of the black holes are as massive as ~10 5 M .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Loss and Gain of Human Acidic Mammalian Chitinase Activity by Nonsynonymous SNPs (2016)
    Oxford University Press
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    Publication Date: 2016-11-09
    Description: Acidic mammalian chitinase (AMCase) is implicated in asthma, allergic inflammation, and food processing. Little is known about genetic and evolutional regulation of chitinolytic activity of AMCase. Here, we relate human AMCase polymorphisms to the mouse AMCase, and show that the highly active variants encoded by nonsynonymous single-nucleotide polymorphisms (nsSNPs) are consistent with the mouse AMCase sequence. The chitinolytic activity of the recombinant human AMCase was significantly lower than that of the mouse counterpart. By creating mouse-human chimeric AMCase protein we found that the presence of the N-terminal region of human AMCase containing conserved active site residues reduced the enzymatic activity of the molecule. We were able to significantly increase the activity of human AMCase by amino acid substitutions encoded by nsSNPs (N45, D47, and R61) with those conserved in the mouse homologue (D45, N47, and M61). For abolition of the mouse AMCase activity, introduction of M61R mutation was sufficient. M61 is conserved in most of primates other than human and orangutan as well as in other mammals. Orangutan has I61 substitution, which also markedly reduced the activity of the mouse AMCase, indicating that the M61 is a crucial residue for the chitinolytic activity. Altogether, our data suggest that human AMCase has lost its chitinolytic activity by integration of nsSNPs during evolution and that the enzyme can be reactivated by introducing amino acids conserved in the mouse counterpart.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-20
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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