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Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis (2015)

Asano, N., Kato, K., Nakamura, A., Komoda, K., Tanaka, I., Yao, M.

Oxford University Press

In: Nucleic Acids Research

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Publikationsdatum: 2015-05-20

Beschreibung: Proteins Rpf2 and Rrs1 are required for 60S ribosomal subunit maturation. These proteins are necessary for the recruitment of three ribosomal components (5S ribosomal RNA [rRNA], RpL5 and RpL11) to the 90S ribosome precursor and subsequent 27SB pre-rRNA processing. Here we present the crystal structure of the Aspergillus nidulans ( An ) Rpf2-Rrs1 core complex. The core complex contains the tightly interlocked N-terminal domains of Rpf2 and Rrs1. The Rpf2 N-terminal domain includes a Brix domain characterized by similar N- and C-terminal architecture. The long α-helix of Rrs1 joins the C-terminal half of the Brix domain as if it were part of a single molecule. The conserved proline-rich linker connecting the N- and C-terminal domains of Rrs1 wrap around the side of Rpf2 and anchor the C-terminal domain of Rrs1 to a specific site on Rpf2. In addition, gel shift analysis revealed that the Rpf2-Rrs1 complex binds directly to 5S rRNA. Further analysis of Rpf2-Rrs1 mutants demonstrated that Saccharomyces cerevisiae Rpf2 R236 (corresponds to R238 of An Rpf2) plays a significant role in this binding. Based on these studies and previous reports, we have proposed a model for ribosomal component recruitment to the 90S ribosome precursor.

Print ISSN: 0305-1048

Digitale ISSN: 1362-4962

Thema: Biologie

Publiziert von Oxford University Press

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The suppression of direct collapse black hole formation by soft X-ray irradiation (2015)

Inayoshi, K., Tanaka, T. L.

Oxford University Press

In: Monthly Notices of the Royal Astronomical Society

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Publikationsdatum: 2015-05-23

Beschreibung: 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

Digitale ISSN: 1365-2966

Thema: Physik

Publiziert von Oxford University Press

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The environments of Ly {alpha} blobs - I. Wide-field Ly {alpha} imaging of TN J1338-1942, a powerful radio galaxy at z ~= 4.1 associated with a giant Ly {alpha} nebula (2015)

Saito, T., Matsuda, Y., Lacey, C. G., Smail, I., Orsi, A., Baugh, C. M., Inoue, A. K., Tanaka, I., Yamada, T., Ohta, K., De Breuck, C., Kodama, T., Taniguchi, Y.

Oxford University Press

In: Monthly Notices of the Royal Astronomical Society

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Publikationsdatum: 2015-01-16

Beschreibung: We exploit wide-field Ly α imaging with Subaru to probe the environment around TN J1338–1942, a powerful radio galaxy with a 〉 100 kpc Ly α halo at z = 4.11. We used a sample of Ly α emitters (LAEs) down to log ( L Lyα [ erg s –1 ]) ~ 42.8 to measure the galaxy density around TN J1338–1942, compared to a control sample from a blank field taken with the same instrument. We found that TN J1338–1942 resides in a region with a peak overdensity of LAE = 2.8 ± 0.5 on scales of 8 h – 1 Mpc (on the sky) and 112 h – 1 Mpc (line of sight) in comoving coordinates. Adjacent to this overdensity, we found a strong underdensity where virtually no LAEs are detected. We used a semi-analytical model of LAEs derived from the Millennium Simulation to compare our results with theoretical predictions. While the theoretical density distribution is consistent with the blank field, overdense regions such as that around TN J1338–1942 are very rare, with a number density of 6.4 x 10 – 8 Mpc – 3 (comoving), corresponding to the densest 〈0.4 percentile at z ~= 4.1. We also found that the Ly α luminosity function in the TN J1338–1942 field differs from that in the blank field: the number of bright LAEs (log ( L Lyα [ erg s – 1 ]) 43.3) is enhanced, while the number of fainter LAEs is relatively suppressed. These results suggest that some powerful radio galaxies associated with Ly α nebulae reside in extreme overdensities on ~3–6 Mpc scales, where star formation and AGN activity may be enhanced via frequent galaxy mergers or high rates of gas accretion from the surroundings.

Print ISSN: 0035-8711

Digitale ISSN: 1365-2966

Thema: Physik

Publiziert von Oxford University Press

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A fast and accurate numerical method for symmetric Levy processes based on the Fourier transform and sinc-Gauss sampling formula (2016)

Tanaka, K.

Oxford University Press

In: IMA Journal of Numerical Analysis

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Publikationsdatum: 2016-07-13

Beschreibung: In this paper, we propose a fast and accurate numerical method based on Fourier transforms to solve Kolmogorov forward equations of symmetric scalar Lévy processes. The method is based on the accurate numerical formulas for Fourier transforms proposed by Ooura. These formulas are combined with nonuniform fast Fourier transforms (FFT) and fractional FFT to speed up the numerical computations. Moreover, we propose a formula for numerical indefinite integration on equispaced grids as a component of the method. The proposed integration formula is based on the sinc-Gauss sampling formula, which is a function approximation formula. This integration formula is also combined with the FFT. Therefore, all steps of the proposed method are executed using the FFT and its variants. The proposed method allows us to be free from some special treatments for a nonsmooth initial condition and numerical time integration. The numerical solutions obtained by the proposed method appear to be exponentially convergent on the interval if the corresponding exact solutions do not have sharp cusps. Furthermore, the real computational times are approximately consistent with the theoretical estimates.

Print ISSN: 0272-4979

Digitale ISSN: 1464-3642

Thema: Mathematik

Publiziert von Oxford University Press

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Multispecies Analysis of Expression Pattern Diversification in the Recently Expanded Insect Ly6 Gene Family (2015)

Tanaka, K., Diekmann, Y., Hazbun, A., Hijazi, A., Vreede, B., Roch, F., Sucena, E.

Oxford University Press

In: Molecular Biology and Evolution

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Publikationsdatum: 2015-06-22

Beschreibung: Gene families often consist of members with diverse expression domains reflecting their functions in a wide variety of tissues. However, how the expression of individual members, and thus their tissue-specific functions, diversified during the course of gene family expansion is not well understood. In this study, we approached this question through the analysis of the duplication history and transcriptional evolution of a rapidly expanding subfamily of insect Ly6 genes. We analyzed different insect genomes and identified seven Ly6 genes that have originated from a single ancestor through sequential duplication within the higher Diptera. We then determined how the original embryonic expression pattern of the founding gene diversified by characterizing its tissue-specific expression in the beetle Tribolium castaneum , the butterfly Bicyclus anynana, and the mosquito Anopheles stephensi and those of its duplicates in three higher dipteran species, representing various stages of the duplication history ( Megaselia abdita, Ceratitis capitata, and Drosophila melanogaster ). Our results revealed that frequent neofunctionalization episodes contributed to the increased expression breadth of this subfamily and that these events occurred after duplication and speciation events at comparable frequencies. In addition, at each duplication node, we consistently found asymmetric expression divergence. One paralog inherited most of the tissue-specificities of the founder gene, whereas the other paralog evolved drastically reduced expression domains. Our approach attests to the power of combining a well-established duplication history with a comprehensive coverage of representative species in acquiring unequivocal information about the dynamics of gene expression evolution in gene families.

Print ISSN: 0737-4038

Digitale ISSN: 1537-1719

Thema: Biologie

Publiziert von Oxford University Press

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GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry (2015)

Morimoto, K., Nishikaze, T., Yoshizawa, A. C., Kajihara, S., Aoshima, K., Oda, Y., Tanaka, K.

Oxford University Press

In: Bioinformatics

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Publikationsdatum: 2015-06-27

Beschreibung: : Tandem mass spectrometry (MS/MS or MS n ) is a potent technique for characterizing N -glycan structures. GlycanAnalysis searches a glycan database to support the identification of glycan structures from MS/MS spectra. It also calculates diagnostic ions of glycan structures registered in a glycan database (GlycomeDB or KEGG GLYCAN) and searches for MS/MS spectra of N -glycans that match diagnostic ions to determine the structures. This program functions as a plug-in for Mass++, a freeware mass spectrum visualization and analysis program. Availability and implementation: The executable files of Mass++ are available for free at http://www.first-ms3d.jp/english/ . The GlycanAnalysis plug-in is included in the standard package of Mass++ for Windows. Contact: k-morimt@shimadzu.co.jp or nishikaz@shimadzu.co.jp or acyshzw@shimadzu.co.jp Supplementary information: Supplementary material are available at Bioinformatics online.

Print ISSN: 1367-4803

Digitale ISSN: 1460-2059

Thema: Biologie , Informatik , Medizin

Publiziert von Oxford University Press

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Exploring the glycan interaction in vivo: Future prospects of neo-glycoproteins for diagnostics (2016)

Ogura, A., Kurbangalieva, A., Tanaka, K.

Oxford University Press

In: Glycobiology

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Publikationsdatum: 2016-09-11

Beschreibung: Herein the biodistributions and in vivo kinetics of chemically prepared neoglycoproteins are reviewed. Chemical methods can be used to conjugate various mono- and oligosaccharides onto a protein surface. The kinetics and organ-specific accumulation profiles of these glycoconjugates, which are introduced through intravenous injections, have been analyzed using conventional dissection studies as well as noninvasive methods such as single photon emission computed tomography, positron emission tomography and fluorescence imaging. These studies suggest that glycan-dependent protein distribution kinetics may be useful for pharmacological and diagnostic applications.

Print ISSN: 0959-6658

Digitale ISSN: 1460-2423

Thema: Biologie , Medizin

Publiziert von Oxford University Press

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Absence of lactobacilli containing glycolipids with the {alpha}-galactose epitope and the enhanced fucosylation of a receptor glycolipid GA1 in the digestive tracts of immune-deficient scid mice (2015)

Iwamori, M., Tanaka, K., Adachi, S., Aoki, D., Nomura, T.

Oxford University Press

In: Journal of Biochemistry

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Publikationsdatum: 2015-07-01

Beschreibung: The Lactobacillus species in the digestive tracts of immune-deficient scid mice was distinct from that in control mice, i.e. Lactobacillus murinus in scid and L. johnsonii in control mice, according to their 16S-rRNA, indicating that a symbiotic relationship between lactobacilli and a host is established under pressure from the immune system. The caecal and colonal contents rich in L. murinus of scid mice were loose with a strong sour smell, resulting in diarrhoea, and those with L. johnsonii in control mice included abundant solid materials. Lactobacillus glycolipids were revealed to be recognized by the immune system, and by TLC-immunostaining, LacTetH-DG (Galα1-6Galα1-6Galα1-2Glcα1-3’DG) of L. johnsonii was detected in the stomach, caecum and colon of control mice, but not in those of scid ones, in which fucosylation of a receptor GA1 for L. johnsonii was enhanced more than 4-fold compared with in the control mice. Thus, structural modification of receptor glycolipids was revealed to occur in the process of establishment of a symbiotic relationship between lactobacilli and a host. LacTetH-DG was also immunogenic to human, because of the presence of natural antibodies against it, and the antibody binding to it was comparable to that of blood group- and species-related glycosphingolipids.

Print ISSN: 0021-924X

Digitale ISSN: 1756-2651

Thema: Biologie , Chemie und Pharmazie

Publiziert von Oxford University Press im Namen von The Japanese Biochemical Society (JBS).

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