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  • Oxford University Press  (30)
  • American Association for the Advancement of Science (AAAS)  (6)
  • 1
    Publication Date: 2016-07-25
    Description: 1H 0707–495 is the most convincing example of a supermassive black hole with an X-ray spectrum being dominated by extremely smeared, relativistic reflection, with the additional requirement of strongly supersolar iron abundance. However, here we show that the iron features in its 2–10 keV spectrum are rather similar to the archetypal wind dominated source, PDS 456. We fit all the 2–10 keV spectra from 1H 0707–495 using the same wind model as used for PDS 456, but viewed at higher inclination so that the iron absorption line is broader but not so blueshifted. This gives a good overall fit to the data from 1H 0707–495, and an extrapolation of this model to higher energies also gives a good match to the NuSTAR data. Small remaining residuals indicate that the iron line emission is stronger than in PDS 456. This is consistent with the wider angle wind expected from a continuum-driven wind from the super-Eddington mass accretion rate in 1H 0707–495, and/or the presence of residual reflection from the underlying disc though the presence of the absorption line in the model removes the requirement for highly relativistic smearing, and highly supersolar iron abundance. We suggest that the spectrum of 1H 0707–495 is sculpted more by absorption in a wind than by extreme relativistic effects in strong gravity.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2013-09-19
    Description: Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging human pathogen that causes life-threatening invasive infections such as streptococcal toxic shock syndrome. Recent epidemiological studies reveal that invasive SDSE infections have been increasing in Asia, Europe, and the United States. Almost all SDSE carry Lancefield group G or C antigen. We have determined the complete genome sequence of a human group C SDSE 167 strain. A comparison of its sequence with that of four SDSE strains, three in Lancefield group G and one in Lancefield group A, showed approximately 90% coverage. Most regions showing little or no homology were located in the prophages. There was no evidence of massive rearrangement in the genome of SDSE 167. Bayesian phylogeny using entire genome sequences showed that the most recent common ancestor of the five SDSE strains appeared 446 years ago. Interestingly, we found that SDSE 167 harbors sugar metabolizing enzymes in a unique region and streptodornase in the phage region, which presumably contribute to the degradation of host tissues and the prompted covRS mutation, respectively. A comparison of these five SDSE strains, which differ in Lancefield group antigens, revealed a gene cluster presumably responsible for the synthesis of the antigenic determinant. These results may provide the basis for molecular epidemiological research of SDSE.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 3
    Publication Date: 2015-07-12
    Description: Efficient pre-replication complex (pre-RC) formation on chromatin templates is crucial for the maintenance of genome integrity. However, the regulation of chromatin dynamics during this process has remained elusive. We found that a conserved protein, GRWD1 (glutamate-rich WD40 repeat containing 1), binds to two representative replication origins specifically during G1 phase in a CDC6- and Cdt1-dependent manner, and that depletion of GRWD1 reduces loading of MCM but not CDC6 and Cdt1. Furthermore, chromatin immunoprecipitation coupled with high-throughput sequencing (Seq) revealed significant genome-wide co-localization of GRWD1 with CDC6. We found that GRWD1 has histone-binding activity. To investigate the effect of GRWD1 on chromatin architecture, we used formaldehyde-assisted isolation of regulatory elements (FAIRE)-seq or FAIRE-quantitative PCR analyses, and the results suggest that GRWD1 regulates chromatin openness at specific chromatin locations. Taken together, these findings suggest that GRWD1 may be a novel histone-binding protein that regulates chromatin dynamics and MCM loading at replication origins.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2016-09-09
    Description: The study of polymorphisms is particularly informative for enhancing our understanding of phenotypic and genetic diversity. The persistence of polymorphism in a population is generally explained by balancing selection. Color polymorphisms that are often found in many insects and arthropods are prime examples of the maintenance of polymorphisms via balancing selection. In some aphids, color morphs are maintained through frequency-dependent predation by two predatory insects. However, the presence of color polymorphism in ant-attended aphids cannot be explained by traditional balancing selection because these aphids are free from predation. We examined the selective advantages of the existence of two color (red and green) morphs in the ant-attended aphid, Macrosiphoniella yomogicola , in fields. We measured the degree of ant attendance on aphid colonies with different proportions of color morphs. The results show that the ants strongly favor aphid colonies with intermediate proportions of the two color morphs. The relationship between the degree of ant attendance and the proportion of color morphs in the field is convex when aphid colony size and ant colony size are controlled. This function has a peak of approximately 65% of green morphs in a colony. This system represents the first case of a balancing polymorphism that is not maintained by opposing factors but by a symbiotic relationship.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 5
    Publication Date: 2015-02-18
    Description: Upstream open reading frames (uORFs) are often found in the 5'-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2019
    Description: 〈p〉The Hayabusa2 spacecraft arrived at the near-Earth carbonaceous asteroid 162173 Ryugu in 2018. We present Hayabusa2 observations of Ryugu’s shape, mass, and geomorphology. Ryugu has an oblate ‘spinning top’ shape with a prominent circular equatorial ridge. Its bulk density, 1.19 ± 0.02 g cm〈sup〉–3〈/sup〉, indicates a high porosity (〉50%) interior. Large surface boulders suggest a rubble-pile structure. Surface slope analysis shows Ryugu’s shape may have been produced if it once spun at twice the current rate. Coupled with the observed global material homogeneity, this suggests that Ryugu was reshaped by centrifugally induced deformation during a period of rapid rotation. From these remote-sensing investigations, we identify a suitable sample collection site on the equatorial ridge.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Natural Sciences in General
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  • 7
    Publication Date: 2014-11-14
    Description: Ultrafast outflows (UFOs) are seen in many AGN, giving a possible mode for AGN feedback on to the host galaxy. However, the mechanism(s) for the launch and acceleration of these outflows are currently unknown, with UV line driving apparently strongly disfavoured as the material along the line of sight is so highly ionized that it has no UV transitions. We revisit this issue using the Suzaku X-ray data from PDS 456, an AGN with the most powerful UFO seen in the local Universe. We explore conditions in the wind by developing a new 3D Monte Carlo code for radiation transport. The code only handles highly ionized ions, but the data show the ionization state of the wind is high enough that this is appropriate, and this restriction makes it fast enough to explore parameter space. We reproduce the results of earlier work, confirming that the mass-loss rate in the wind is around 30 per cent of the inferred inflow rate through the outer disc. We show for the first time that UV line driving is likely to be a major contribution to the wind acceleration. The mass-loss rate in the wind matches that predicted from a purely line driven system, and this UV absorption can take place out of the line of sight. Continuum driving should also play a role as the source is close to Eddington. This predicts that the most extreme outflows will be produced from the highest mass accretion rate flows on to high-mass black holes, as observed.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2019
    Description: 〈p〉The Hayabusa2 spacecraft arrived at the near-Earth carbonaceous asteroid 162173 Ryugu in 2018. We present Hayabusa2 observations of Ryugu’s shape, mass, and geomorphology. Ryugu has an oblate "spinning top" shape, with a prominent circular equatorial ridge. Its bulk density, 1.19 ± 0.02 grams per cubic centimeter, indicates a high-porosity (〉50%) interior. Large surface boulders suggest a rubble-pile structure. Surface slope analysis shows Ryugu’s shape may have been produced from having once spun at twice the current rate. Coupled with the observed global material homogeneity, this suggests that Ryugu was reshaped by centrifugally induced deformation during a period of rapid rotation. From these remote-sensing investigations, we identified a suitable sample collection site on the equatorial ridge.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2018
    Description: 〈p〉Over the past decade, the cause of sociality has been much debated. Inclusive fitness [〈b〉br〈/b〉 in Hamilton’s rule (〈b〉br〈/b〉 – 〈b〉c〈/b〉 〉 0)] has been criticized but is still useful in the organization of a framework by elucidating mechanisms through which 〈b〉br〈/b〉 (benefit x relatedness) becomes larger than 〈b〉c〈/b〉 (cost). The bee 〈i〉Lasioglossum baleicum〈/i〉 is suitable for investigation of this issue because of the sympatric occurrence of both social and solitary nesting in its populations. We show that a large part (approximately 92%) of the inclusive fitness of a eusocial worker can be attributed to the benefits of grouping. A 1.5-fold relatedness asymmetry benefit in singly mated haplo-diploids explains a small part (approximately 8.5%) of the observed inclusive fitness. Sociality enables this species to conduct foraging and nest defense simultaneously, which is not the case in solitary nests. Our results indicate that this benefit of grouping is the main source of the increased inclusive fitness of eusocial workers.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 10
    Publication Date: 2013-04-20
    Description: DNA alkylation damage can be repaired by nucleotide excision repair (NER), base excision repair (BER) or by direct removal of alkyl groups from modified bases by O 6 -alkylguanine DNA alkyltransferase (AGT; E.C. 2.1.1.63). DNA mismatch repair (MMR) is also likely involved in this repair. We have investigated alkylation-induced mutagenesis in a series of NER- or AGT-deficient Escherichia coli strains, alone or in combination with defects in the MutS, MutL or MutH components of MMR. All strains used contained the F' prolac from strain CC102 (F'CC102) episome capable of detecting specifically lac GC to AT reverse mutations resulting from O 6 -alkylguanine. The results showed the repair of O 6 -methylguanine to be performed by AGT 〉〉 MMR 〉 NER in order of importance, whereas the repair of O 6 -ethylguanine followed the order NER 〉 AGT 〉 MMR. Studies with double mutants showed that in the absence of AGT or NER repair pathways, the lack of MutS protein generally increased mutant frequencies for both methylating and ethylating agents, suggesting a repair or mutation avoidance role for this protein. However, lack of MutL or MutH protein did not increase alkylation-induced mutagenesis under these conditions and, in fact, reduced mutagenesis by the N -alkyl- N -nitrosoureas MNU and ENU. The combined results suggest that little or no alkylation damage is actually corrected by the mutHLS MMR system; instead, an as yet unspecified interaction of MutS protein with alkylated DNA may promote the involvement of a repair system other than MMR to avoid a mutagenic outcome. Furthermore, both mutagenic and antimutagenic effects of MMR were detected, revealing a dual function of the MMR system in alkylation-exposed cells.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
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