貝と人とのかかわり : 利用にみる地域資源と文化

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「自然との結びつき」 : ソーニャ・サンチェスのハイクについて

2014-03-28本稿は Luo Lianggong（罗良功）教授の講演テクスト “‘A Connection with nature’:On Soonia Sanchez’s Haiku” の邦訳である。（長畑明利訳）国際シンポジウム「Race and Ethnicity in American Literature and Culture: A Reconsideration（アメリカ文学・文化における人種・民族—再検討）」(2013年3月16日～3月17日、名古屋大学)departmental bulletin pape

鑑賞学習教材としてのアートカードの意義と可能性

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Mutation of RNA-contacting amino acid residues adversely affect PUS1 activity.

(a)) The rate of pseudouridylation (% pseudoU) of PUS1 wildtype and the indicated PUS1 mutants with R169 substrate is shown. Data of two replicas is shown. (b) Heatmaps of the number of oligonucleotide spectra identified by LC-MS/MS analysis in a RNase T1 digest of RNA substrate R397 after incubation with wildtype PUS1 and cluster A mutants showing either a characteristic 207.04 m/z Ψ nucleoside signature ion (bottom) or a 211.00 m/z ribose phosphate ion (top). The fragments containing Ψ are highlighted with red boxes below the heatmaps and red circles in the RNA structure (right). The nucleotides are colored according to the type of structure that they are in (green: stems (canonical helices), yellow: interior loops, blue: hairpin loops, orange: 5’ and 3’ unpaired region). (c) LC-MS/MS analysis of RNA substrate R397 after incubation with wildtype PUS1 and cluster B mutants, showing the characteristic 207.04 m/z Ψ nucleoside signature ion and the 211.00 m/z ribose phosphate ion. Ψ containing fragments are highlighted with red boxes.</p

RNA-substrate binding by PUS1 and TruA.

Superposition of RNA-bound PUS1 (PDB ID: 7R9G; PUS1: rainbow, RNA: pink) with tRNA-bound E. coli TruA (PDB ID: 2NR0; TruA & tRNA: gray) revealed a different orientation of the RNA substrates.</p

Sequence alignment and RNA interactions of <i>S</i>. <i>cerevisiae</i> PUS1 and <i>E</i>. <i>coli</i> TruA.

The conserved catalytic aspartate at position 134 in PUS1 and position 60 in TruA is indicated by a yellow box. RNA-interacting residues are highlighted in green (PUS1) and magenta (TruA) (top panel). Distribution of RNA-contacting residues in the protein-subunit interface for PUS1 (left) and TruA (right; bottom panel). (PDF)</p

Mutation of RNA-contacting amino acid residues adversely affect PUS1 activity.

(a) Table showing the average percent of uridine-to-Ψ conversion of the reactions shown in Fig 3C (from two independent replicates), and the percentage of PUS1 activity, normalized by the percent pseudouridylation in the PUS1wt reaction. (b) Protein gel comparing the input amount and purity of the PUS1 variants in the in vitro reactions. (c) Electrophoretic mobility shift assays of the mutant PUS1 enzymes (PUS1R132A left, PUS1R362A right). (PDF)</p

Protein-RNA contacts.

(a) The first twelve nucleotides of each RNA strand (R263) are visible in the crystal structure, while the last six nucleotides are disordered and unobservable. Each protein subunit displays identical contacts, related by two-fold symmetry, to RNA bases and backbone atoms, and to a tightly coordinated sulfate ion immediately upstream of the upstream base in each bound RNA (contacts made by only one protein subunit are displayed for clarity). Residues that either contact the RNA near the active site (cluster a, blue boxes), or further downstream (cluster b, orange boxes) are indicated. (b) Distribution of RNA-contacting residues in the protein-subunit interface for one PUS1 subunit. Brackets indicate the residues that contact the RNA close to the active site (cluster A, blue) or further downstream (cluster B, orange). (c) Distribution of contacts around the RNA duplex for both enzyme subunits in the dimeric assemblage. RNA-contacting residues in both PUS1 proteins are labeled either black (rainbow colored PUS1) or red (turquoise colored PUS1).</p

Comparison of yeast PUS1 to <i>E</i>. <i>coli</i> TruA and human PUS1.

(a) Human PUS1 apo-enzyme (4J37). The structure includes two bound sulfate ions, one of which aligns with a single sulfate ion near the enzyme active site that was also observed in RNA-bound S. cerevisiae PUS1. (b) S. cerevisiae PUS1D134A bound to duplex RNA. A large insertion in the yeast enzyme, spanning residues S206 to approximately L279 (indicated by the oval), is unique as compared to its homologues in other eukaryotes (S5 Fig). It contains two RNA-contacting residues that are unique to the yeast enzyme. (c) E. coli TruA (2NR0) bound to tRNA. TruA utilizes an equivalent surface to bind its respective target but in a considerably different manner from PUS1.</p

Model and representative electron-density for RNA-bound PUS1.

(a) The contents of the asymmetric unit, for both structures that were solved, corresponds to a single protein subunit (colored as a spectrum, from the blue N-terminal end of the refined model to the red C-terminal end) bound to a single R263 RNA oligonucleotide (black bases). The model of the catalytically inactive D134A enzyme is shown in two orientations related by a 90° rotation around the x-axis (PDB ID: 7R9G). (b) In both structures, the application of a crystallographic 2-fold rotation axis generates a dimeric complex in which two subunits are independently bound to an RNA duplex. The second protein subunit and second RNA strand are colored in dark teal and pale blue, respectively. (c) Representative simulated annealing composite omit 2Fo-Fc electron density contoured across the RNA duplex and (d) at the region of protein-RNA contacts observed at the 5’ end of one RNA strand. The structural features illustrated in this figure are replicated for the wild type enzyme bound to a closely related RNA complex, which was solved in an unrelated crystallographic space group and lattice (S7 Fig). The position of the bound sulfate ion mirrors a similarly placed sulfate in the previously described structure of unbound human PUS1.</p