Tomoya Fujita

RIKEN

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Nobuo Iyi

National Institute for Materials Science

Shintaro Iwasaki

Pioneer (Japan)

Atsushi Kubo

The University of Tokyo

Seiji Tateyama

Japan Advanced Institute of Science and Technology

James C. Ogbonna

University of Nigeria

Tomoo Katsura

University of Bayreuth

Adam Gaweł

AGH University of Krakow

Yoshifumi Mishina

The University of Tokyo

Lisa Osada

University of Tsukuba

Tatsuo Kaneko

Japan Advanced Institute of Science and Technology

Cooperative Institutions

The University of Tokyo

University of Tsukuba

RIKEN Center for Sustainable Resource Science

RIKEN

Institute of Applied Biochemistry

National Institute for Materials Science

Synthetic Genomics (United States)

Okayama University

Japan Advanced Institute of Science and Technology

Japan Science and Technology Agency

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Structural heterogeneity of alkylammonium-exchanged, synthetic fluorotetrasilicic mica

Clay Minerals (2003)

Zenon Kłapyta Adam Gaweł Tomoya Fujita Nobuo Iyi

Abstract A series of organo-silicates was obtained from synthetic Na-fluorotetrasilicic mica (Na-TSM) by ion exchange with dodecyl-, tetradecyl-, hexadecyl- and octadecyltrimethylammonium (C12, C14, C16 and C18) bromides. When the concentration of the alkylammonium ions has varied from 0.43 to 3.4 mmol/g of the silicate, the maximum amount adsorbed on the mica was 0.92 mmol/g. As shown by 23 Na MAS NMR, ∼0.30 mmol/g of Na + ions were non-exchangeable, even if a large excess of the organic ions was used. The XRD patterns of all the samples obtained show that alkylammonium ions are distributed inhomogeneously within the mica interlayers. As a consequence, the organo-micas contain several phases consisting of randomly and regularly interstratified layers differing in terms of the amount of alkylammonium ions adsorbed. These different layers swell in ethylene glycol in the same manner and form new interlayers with identical spacings. The d 001 values of individual organo-TSMs after glycolation suggest that the alkylammonium ions are oriented perpendicular or almost perpendicular to the mica layers. The Na-TSM layers were not detected in organo-TSMs by XRD. The presence of organic and inorganic (Na) mixed-ion interlayers with spacings controlled by the arrangements of the organic ions is consistent with the results obtained. These data also suggest that the alkylammonium/Na + ion ratios vary in alternate interlayers.

Inorganic ions

10.1180/0009855033820085

Cite

Citations (14)

Effect of mixed organic substrate on α-tocopherol production by Euglena gracilis in photoheterotrophic culture

Applied Microbiology and Biotechnology (2008)

Tomoya Fujita Hideki Aoyagi James C. Ogbonna Hideo Tanaka

Euglena gracilis

Photobioreactor

Euglena

Strain (injury)

10.1007/s00253-008-1443-0

Cite

Citations (50)

Quality control of protein synthesis in the early elongation stage

Nature Communications (2023)

Asuteka Nagao Yui Nakanishi Yutaro Yamaguchi Yoshifumi Mishina Minami Karoji

Abstract In the early stage of bacterial translation, peptidyl-tRNAs frequently dissociate from the ribosome (pep-tRNA drop-off) and are recycled by peptidyl-tRNA hydrolase. Here, we establish a highly sensitive method for profiling of pep-tRNAs using mass spectrometry, and successfully detect a large number of nascent peptides from pep-tRNAs accumulated in Escherichia coli pth ts strain. Based on molecular mass analysis, we found about 20% of the peptides bear single amino-acid substitutions of the N-terminal sequences of E. coli ORFs. Detailed analysis of individual pep-tRNAs and reporter assay revealed that most of the substitutions take place at the C-terminal drop-off site and that the miscoded pep-tRNAs rarely participate in the next round of elongation but dissociate from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.

Ribosome profiling

Peptidyl transferase

EF-Tu

10.1038/s41467-023-38077-5

Cite

Citations (15)

Microbial monomers custom-synthesized to build true bio-derived aromatic polymers

Applied Microbiology and Biotechnology (2013)

Tomoya Fujita Hieu D. Nguyen Takashi Ito Shengmin Zhou Lisa Osada

10.1007/s00253-013-5078-4

Cite

Citations (55)

Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis

Proceedings of the National Academy of Sciences (2018)

Yukio Kurihara Yuko Makita Mika Kawashima Tomoya Fujita Shintaro Iwasaki

Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in Arabidopsis seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in HY5 and HYH, major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including HY5, accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes.

Transcription

10.1073/pnas.1804971115

Cite

Citations (102)

High‐pressure transformation of pyrope (Mg₃Al₂Si₃O₁₂) in a sintered diamond cubic anvil assembly

Geophysical Research Letters (1998)

Etsuro Ito Atsushi Kubo Tomoo Katsura Masaki Akaogi Tomoya Fujita

Transformation of pyrope garnet was investigated at 1600°C and at pressures higher than 35 GPa using a sintered diamond cubic anvil assembly in a double‐staged split‐sphere apparatus. Pyrope transformed into orthorhombic perovskite at ca. 37 GPa, whereas a small amount of corundum coexisted with perovskite at lower pressures. The unit cell dimensions of perovskite were determined to be a = 4.771(2) Å, b = 4.947(2) Å, c = 6.950(3) Å, and V = 164.0(2) Å³. A trace of stishovite observed in the run products may be evidence of nonstoichiometry in the perovskite. These results support the view that perovskite is the major host phase of Al 2 O 3 in the lower mantle.

Pyrope

Stishovite

Orthorhombic crystal system

Diamond anvil cell

Corundum

Chromite

10.1029/98gl00519

Cite

Citations (76)

Intercalation of cationic azobenzene derivatives in a synthetic mica and their photoresponse

Applied Clay Science (2001)

Nobuo Iyi Tomoya Fujita C. V. Yelamaggad F. López Arbeloa

Azobenzene

Cationic polymerization

Moiety

Ultraviolet

10.1016/s0169-1317(00)00037-5

Cite

Citations (22)

Smectites in the montmorillonite-beidellite series

Clay Minerals (1991)

Hirohisa Yamada H. Nakazawa Katsuaki Yoshioka Tomoya Fujita

Abstract Smectites in the montmorillonite-beidellite pseudo-binary system were synthesized from glass at the hydrothermal conditions 100 MPa and 250–500°C. Products were analysed by X-ray powder diffraction for randomly oriented and glycolated samples, and also according to the Greene-Kelly test. A new mixed-layer mineral consisting of regularly interstratified montmorillonite-beidellite was found below 400°C for M 50 B 50 composition, where M and B denote the compositions of ideal Na-montmorillonite and Na-beidellite, respectively. Montmorillonite was obtained as a single phase below 375°C in the composition range from M 100 B 0 to M 78 B 22 . Above 375°C, montmorillonite decomposed into an assemblage of beidellite, saponite and a silica mineral. Beidellite as a single phase was synthesized below 400°C for M 0 B 100 composition. Above 450°C, Na-rectorite (regularly interstratified paragonite-beidellite), Mg-free dioctahedral smectite and/or Mg-rich trioctahedral smectite appeared together with silica minerals. These smectites showed the same swelling behaviour as that of montmorillonite. Phase relations in the montmorillonite-beidellite pseudo-binary system indicate no complete solid-solution series.

Saponite

10.1180/claymin.1991.026.3.05

Cite

Citations (50)

The aggregation of methylene blue in montmorillonite dispersions

Clay Minerals (2002)

Juraj Bujdák Nobuo Iyi Tomoya Fujita

Abstract Theories concerning the optical properties of cationic dyes adsorbed on clay surfaces are analysed in detail. An investigation of the aggregation of methylene blue (MB) in montmorillonite dispersions is conducted using visible (VIS) spectroscopy. The effects of the dye/ clay ratio and of the swelling properties of the montmorillonite substrate on dye aggregation are compared in terms of the effect of clay layer charge. The observed influence on dye aggregation was almost negligible for both swelling and dye loading. The layer charge of the silicate determines the extent and the type of dye aggregation in freshly prepared MB/montmorillonite dispersions. Observed spectral changes with time indicate a rearrangement and redistribution of dye H-aggregates (band close to 570 nm) to monomers (660 nm), dimers (605 nm) and J-aggregates (760 nm). Dye aggregates are probably already formed during dye cation migration in the vicinity of clay colloid particles. The extent and the type of initially formed species are probably affected by the electric double layer of clay layers. After reaching the clay surface, dye cation assemblies are rearranged and decompose as described above. Reaching chemical equilibrium, dye cations adjust the distribution of the layer charge, in order that each cation could balance the charge due to one unequivalent substitution.

Redistribution

Methylene blue

Cationic polymerization

10.1180/0009855023710022

Cite

Citations (110)