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  • 1
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    Infalling clouds on to supermassive black hole binaries - I. Formation of discs, accretion and gas dynamics (2015)
    Oxford University Press
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    Publication Date: 2015-11-21
    Description: There is compelling evidence that most – if not all – galaxies harbour a supermassive black hole (SMBH) at their nucleus; hence binaries of these massive objects are an inevitable product of the hierarchical evolution of structures in the Universe, and represent an important but thus-far elusive phase of galaxy evolution. Gas accretion via a circumbinary disc is thought to be important for the dynamical evolution of SMBH binaries, as well as in producing luminous emission that can be used to infer their properties. One plausible source of the gaseous fuel is clumps of gas formed due to turbulence and gravitational instabilities in the interstellar medium, that later fall towards and interact with the binary. In this context, we model numerically the evolution of turbulent clouds in near-radial infall on to equal-mass SMBH binaries, using a modified version of the SPH (smoothed particle hydrodynamics) code gadget -3. We present a total of 12 simulations that explore different possible pericentre distances and relative inclinations, and show that the formation of circumbinary discs and discs around each SMBH (‘mini-discs’) depend on those parameters. We also study the dynamics of the formed discs, and the variability of the feeding rate on to the SMBHs in the different configurations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Intermediate-mass black holes from Population III remnants in the first galactic nuclei (2016)
    Oxford University Press
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    Publication Date: 2016-06-26
    Description: We report the formation of intermediate-mass black holes (IMBHs) in suites of numerical N -body simulations of Population III remnant black holes (BHs) embedded in gas-rich protogalaxies at redshifts z 10. We model the effects of gas drag on the BHs’ orbits, and allow BHs to grow via gas accretion, including a mode of hyper-Eddington accretion in which photon trapping and rapid gas inflow suppress any negative radiative feedback. Most initial BH configurations lead to the formation of one (but never more than one) IMBH in the centre of the protogalaxy, reaching a mass of 10 3–5 M through hyper-Eddington growth. Our results suggest a viable pathway to forming the earliest massive BHs in the centres of early galaxies. We also find that the nuclear IMBH typically captures a stellar-mass BH companion, making these systems observable in gravitational waves as extreme mass-ratio inspirals with eLISA .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    5-Aminoimidazole-4-carboxyamide-1-{beta}-D-ribofranoside stimulates the rat enhancer of split- and hairy-related protein-2 gene via atypical protein kinase C lambda (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: The 5'-AMP-activated protein kinase (AMPK) functions as a cellular energy sensor. 5-Aminoimidazole-4-carboxyamide-1-β-D-ribofranoside (AICAR) is a chemical activator of AMPK. In the liver, AICAR suppresses expression of the phosphoenolpyruvate carboxykinase ( PEPCK ) gene. The rat enhancer of split- and hairy-related protein-2 (SHARP-2) is an insulin-inducible transcriptional repressor and its target is the PEPCK gene. In this study, we examined an issue of whether the SHARP-2 gene expression is regulated by AICAR via the AMPK. AICAR increased the level of SHARP-2 mRNA in H4IIE cells. Whereas an AMPK inhibitor, compound-C, had no effects on the AICAR-induction, inhibitors for both phosphoinositide 3-kinase (PI 3-K) and protein kinase C (PKC) completely diminished the effects of AICAR. Western blot analyses showed that AICAR rapidly activated atypical PKC lambda (aPKC). In addition, when a dominant negative form of aPKC was expressed, the induction of SHARP-2 mRNA level by AICAR was inhibited. Calcium ion is not required for the activation of aPKC. A calcium ion-chelating reagent had no effects on the AICAR-induction. Furthermore, the AICAR-induction was inhibited by treatment with an RNA polymerase inhibitor or a protein synthesis inhibitor. Thus, we conclude that the AICAR-induction of the SHARP-2 gene is mediated at transcription level by a PI 3-K/aPKC pathway.
    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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    Formation, disruption and energy output of Population III X-ray binaries (2015)
    Oxford University Press
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    Publication Date: 2015-12-16
    Description: The first astrophysical objects shaped the cosmic environment by reionizing and heating the intergalactic medium (IGM). Particularly, X-rays are very efficient at heating the IGM before reionization is complete. High-mass X-ray binaries (HMXBs) in early stellar populations are prime candidates for driving the thermal evolution of the IGM at redshifts z 20; however, their formation efficiency is not well understood. Using N -body simulations, we estimate the HMXB formation rate via mutual gravitational interactions of nascent, small groups of the Population III stars. We run two sets of calculations: (i) stars formed in small groups of five in nearly Keplerian initial orbits and (ii) collision of two such groups (an expected outcome of mergers of host protogalaxies). We find that HMXBs form at a rate of one per 10 4 M in newly born stars, and that they emit with a power of ~10 41 erg s –1 in the 2–10 keV band per star formation rate. This value is a factor of ~10 2 larger than what is observed in star-forming galaxies at lower redshifts; the X-ray production from early HMXBs would have been even more copious, if they also formed in situ or via migration in protostellar discs. Combining our results with earlier studies suggests that early HMXBs were highly effective at heating the IGM and leaving a strong 21-cm signature. We discuss broader implications of our results, such as the rate of long gamma-ray bursts from Population III stars and the direct collapse channel for massive black hole formation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Confirming the "Rapid phosphorus transfer from microorganisms to mesozooplankton in the Eastern Mediterranean Sea" scenario through a mesocosm experiment (2016)
    Oxford University Press
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    Publication Date: 2016-06-04
    Description: P-transport through the microbial food web was investigated in a mesocosm experiment in which orthophosphate was added to oligotrophic Cretan Sea water. As non-exclusive alternatives to traditional phytoplankton–zooplankton succession, two mechanisms for P-transport have previously been proposed: a stoichiometric shift in food quality (Tunnelling); and a transport through a predatory food chain from heterotrophic bacteria, bypassing phytoplankton (Bypass). Following P-addition, particulate C:P-ratio dropped from 436 to 44 (molar) within 1 day, and egg production increased after 2 days. This confirms the hypothesized stoichiometric shift and rapid copepod response of a "Tunnelling" scenario. Bacterial abundance responded positively to P-addition on Day 1, ciliates increased after Day 5 and new egg production peaks occurred on Days 5 and 9; a succession suggesting additional Bypass transport although the response expected in heterotrophic flagellate abundance was not confirmed. A small, but statistically not significant, increase in Chl a in the 0.6- to 2-µm size fraction also suggests possible additional P-transport through a phytoplankton–zooplankton succession. On the basis of the magnitude of the stoichiometric change and the short delay in egg production response, we consider the Tunnelling mechanism to be the most likely signal initiating egg production, but a Bypass, and possibly a traditional succession, may have contributed to maintain the elevated egg production.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    The suppression of direct collapse black hole formation by soft X-ray irradiation (2015)
    Oxford University Press
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    Publication Date: 2015-05-23
    Description: The origin of supermassive black holes (SMBHs) in galactic nuclei is one of the major unsolved problems in astrophysics. One hypothesis is that they grew from 10 5 M black holes that formed in the ‘direct collapse’ of massive gas clouds that have low concentrations of both metals and molecular hydrogen (H 2 ). Such clouds could form in the early ( z 10) Universe if pre-galactic gas is irradiated by H 2 -photodissociating, far-ultraviolet (FUV) light from a nearby star-forming galaxy. In this work, we re-examine the critical FUV flux J crit that is required to keep H 2 photodissociated and lead to direct collapse. We submit that the same galaxies that putatively supply the extraordinary FUV fluxes required for direct collapse should also produce copious amounts of soft X-rays, which work to offset H 2 photodissociation by increasing the ionization fraction and promoting H 2 formation. Accounting for this effect increases the value of J crit by a factor of at least 3–10, depending on the brightness temperature of FUV radiation. This enhancement of J crit suppresses the abundance of potential direct collapse sites at z  〉 10 by several orders of magnitude. Recent studies – without accounting for the soft X-rays from the FUV source galaxies – had already arrived at large values of J crit that implied that direct collapse may occur too rarely to account for the observed abundance of high-redshift quasars. Our results suggest that J crit should be even higher than previously estimated, and pose an additional challenge for the direct collapse scenario via strong FUV radiation to explain the high-redshift quasar population.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes (2015)
    Oxford University Press
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    Publication Date: 2015-02-10
    Description: Initial results from sequencing studies suggest that there are relatively few low-frequency (〈5%) variants associated with large effects on common phenotypes. We performed low-pass whole-genome sequencing in 680 individuals from the InCHIANTI study to test two primary hypotheses: (i) that sequencing would detect single low-frequency–large effect variants that explained similar amounts of phenotypic variance as single common variants, and (ii) that some common variant associations could be explained by low-frequency variants. We tested two sets of disease-related common phenotypes for which we had statistical power to detect large numbers of common variant–common phenotype associations—11 132 cis -gene expression traits in 450 individuals and 93 circulating biomarkers in all 680 individuals. From a total of 11 657 229 high-quality variants of which 6 129 221 and 5 528 008 were common and low frequency (〈5%), respectively, low frequency–large effect associations comprised 7% of detectable cis -gene expression traits [89 of 1314 cis -eQTLs at P 〈 1 x 10 –06 (false discovery rate ~5%)] and one of eight biomarker associations at P 〈 8 x 10 –10 . Very few (30 of 1232; 2%) common variant associations were fully explained by low-frequency variants. Our data show that whole-genome sequencing can identify low-frequency variants undetected by genotyping based approaches when sample sizes are sufficiently large to detect substantial numbers of common variant associations, and that common variant associations are rarely explained by single low-frequency variants of large effect.
    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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    Bacillus subtilis degSU operon is regulated by the ClpXP-Spx regulated proteolysis system (2015)
    Oxford University Press
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    Publication Date: 2015-04-29
    Description: The DegS-DegU two-component regulatory system regulates many cellular events in Bacillus subtilis . Genes for DegSU constitutes an operon directed by the P1 promoter and downstream degU is autoregulated via the P3 promoter activated by phosphorylated DegU. In the Gram-positive bacteria, Spx plays a major role in the protection system against oxidative stresses as a transcriptional regulator. Spx is a substrate of the ATP-dependent ClpXP protease. It regulates diamide-stress regulon in addition to many genes with unknown functions. We have found that null mutations for clpX and clpP , which encode the subunits for the protease ClpXP, enhanced the DegU level through activation of the P1 promoter. We isolated four suppressors for the clpP -enhancing effect. Whole-genome sequencing of the suppressors revealed that two have a point mutation in spx and the rest have a deletion of spx . The clpP -enhancing effect on degS-lacZ expression was abolished in the spx disruptant . These results show that the degSU operon is a new target of Spx-mediated positive regulation. Furthermore, we found that the P1 promoter was induced by glucose and that this induction was greatly reduced in the spx mutant. These results suggested that Spx-mediated glucose induction at the P1 promoter.
    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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  • 9
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    The imprint of the cosmic supermassive black hole growth history on the 21 cm background radiation (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: The redshifted 21 cm transition line of hydrogen tracks the thermal evolution of the neutral intergalactic medium (IGM) at ‘cosmic dawn’, during the emergence of the first luminous astrophysical objects (~100 Myr after the big bang) but before these objects ionized the IGM (~400–800 Myr after the big bang). Because X-rays, in particular, are likely to be the chief energy courier for heating the IGM, measurements of the 21 cm signature can be used to infer knowledge about the first astrophysical X-ray sources. Using analytic arguments and a numerical population synthesis algorithm, we argue that the progenitors of supermassive black holes (SMBHs) should be the dominant source of hard astrophysical X-rays – and thus the primary driver of IGM heating and the 21 cm signature – at redshifts z 20, if (i) they grow readily from the remnants of Population III stars and (ii) produce X-rays in quantities comparable to what is observed from active galactic nuclei and high-mass X-ray binaries. We show that models satisfying these assumptions dominate over contributions to IGM heating from stellar populations, and cause the 21 cm brightness temperature to rise at z 20. An absence of such a signature in the forthcoming observational data would imply that SMBH formation occurred later (e.g. via so-called direct collapse scenarios), that it was not a common occurrence in early galaxies and protogalaxies, or that it produced far fewer X-rays than empirical trends at lower redshifts, either due to intrinsic dimness (radiative inefficiency) or Compton-thick obscuration close to the source.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Critical roles of the mitochondrial complex II in oocyst formation of rodent malaria parasite Plasmodium berghei (2012)
    Oxford University Press
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    Publication Date: 2012-08-29
    Description: It is generally accepted that the mitochondria play central roles in energy production of most eukaryotes. In contrast, it has been thought that Plasmodium spp., the causative agent of malaria, rely mainly on cytosolic glycolysis but not mitochondrial oxidative phosphorylation for energy production during blood stages. However, Plasmodium spp. possesses all genes necessary for the tricarboxylic acid (TCA) cycle and most of the genes for electron transport chain (ETC) enzymes. Therefore, it remains elusive whether oxidative phosphorylation is essential for the parasite survival. To elucidate the role of TCA metabolism and ETC in malaria parasites, we deleted the gene for flavoprotein (Fp) subunit, Pbsdha , one of four components of complex II, a catalytic subunit for succinate dehydrogenase activity. The Pbsdha(-) parasite grew normally at blood stages in mouse. In contrast, ookinete formation of Pbsdha(-) parasites in the mosquito stage was severely impaired. Finally, Pbsdha(-) ookinetes failed in oocyst formation, leading to complete malaria transmission blockade. These results suggest that malaria parasite may switch the energy metabolism from glycolysis to oxidative phosphorylation to adapt to the insect vector where glucose is not readily available for ATP production.
    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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