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49 results on '"Oda, Naoko"'

1. Dietary phosphate disturbs of gut microbiome in mice

Author

Oda, Naoko, primary, Sugihara, Kohei, additional, Uebanso, Takashi, additional, Ohminami, Hirokazu, additional, Ohnishi, Kohta, additional, Masuda, Masashi, additional, Yamanaka-Okumura, Hisami, additional, and Taketani, Yutaka, additional

Published
2023
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2. Crystal Structures of Tropomyosin: Flexible Coiled-Coil

Author

Nitanai, Yasushi, Minakata, Shiho, Maeda, Kayo, Oda, Naoko, Maéda, Yuichiro, Back, Nathan, editor, Cohen, Irun R., editor, Kritchevsky, David, editor, Lajtha, Abel, editor, Paoletti, Rodolfo, editor, Ebashi, Setsuro, editor, and Ohtsuki, Iwao, editor

Published
2007
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6. Altered Fecal Microbiotas and Organic Acid Concentrations Indicate Possible Gut Dysbiosis in University Rugby Players: An Observational Study

Author

Morishima, So, primary, Oda, Naoko, additional, Ikeda, Hiromi, additional, Segawa, Tomohiro, additional, Oda, Machi, additional, Tsukahara, Takamitsu, additional, Kawase, Yasuharu, additional, Takagi, Tomohisa, additional, Naito, Yuji, additional, Fujibayashi, Mami, additional, and Inoue, Ryo, additional

Published
2021
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7. 食餌性リンは大腸炎モデル動物の病態を悪化させる

Author

Sugihara, Kohei, Masuda, Masashi, Nakao, Mari, Abuduli, Maerjianghan, Imi, Yukiko, Oda, Naoko, Okahisa, Toshiya, Yamamoto, Hironori, Takeda, Eiji, and Taketani, Yutaka

Subjects
Dietary Pi, proinflammatory cytokine, ROS, DSS-induced colitis, NF-κB
Abstract

The recent widespread consumption of Western diets and food additives worldwide is associated with excessive inorganic phosphate intake. However, researchers have known little about the impact of dietary phosphate intake on the development of inflammatory bowel disease to date. In this study, we investigated the effects of dietary phosphate on intestinal inflammation in experimental colitis. Sprague-Dawley rats were fed different phosphate diets (0.5%, 1.0% and 1.5% phosphate) with or without dextran sulfate sodium. For in vitro study, the effects of phosphate on proinflammatory cytokine induction and reactive oxygen species production in RAW264.7 macrophage were examined. Dietary phosphate exacerbated intestinal inflammation in experimental colitis in a dose-dependent manner, as assessed by the clinical disease activity score, colon length, and histology. Furthermore, the high phosphate diet increased myeloperoxidase activity and proinflammatory cytokine mRNA expression through the activation of nuclear factor κB in the inflamed colon. In addition, high phosphate loading in RAW264.7 cells directly enhanced reactive oxygen species production and proinflammatory cytokine gene expression. Our results demonstrated that the high phosphate diet exacerbated intestinal inflammation in experimental colitis. These findings have important therapeutic implications for inflammatory bowel disease patients.

Published
2017

23. Crystal Structures of Tropomyosin: Flexible Coiled-Coil.

Author

Back, Nathan, Cohen, Irun R., Kritchevsky, David, Lajtha, Abel, Paoletti, Rodolfo, Ebashi, Setsuro, Ohtsuki, Iwao, Nitanai, Yasushi, Minakata, Shiho, Maeda, Kayo, Oda, Naoko, and Maéda, Yuichiro

Abstract

Tropomyosin (Tm) is a 400 Å long coiled coil protein, and with troponin it regulates contraction in skeletal and cardiac muscles in a [Ca2+]-dependent manner. Tm consists of multiple domains with diverse stabilities in the coiled coil form, thus providing Tm with dynamic flexibility. This flexibility must play important roles in the actin binding and the cooperative transition between the calcium regulated states of the entire muscle thin filament. In order to understand the flexibility of Tm in its entirety, the atomic coordinates of Tm are needed. Here we report the two crystal structures of Tm segments. One is rabbit skeletal muscle α-Tm encompassing residues 176-284 with an N-terminal extension of 25 residues from the leucine zipper sequence of GCN4, which includes the region that interacts with the troponin core domain. The other is α-Tm encompassing residues 176-273 with N- and C-terminal extensions of the leucine zipper sequences. These two crystal structures imply that this molecule is a flexible coiled coil. First, Tm's are not homogeneous and smooth coiled coils, but instead they undulate, with highly fluctuating local parameters specifying the coiled coil. Independent fluctuating showed by two crystal structures is important. Second, in the first crystal, the coiled coil is bent by 9 degrees in the region centered about Y214-E218-Y221, where the inter-helical distance has its maximum. On the other hand, no bend is observed at the same region in the second crystal even if its inter-helical distance has also its maximum. E218, an unusual negatively charged residue at the a position in the heptad repeat, seems to play the key role in destabilizing the coiled coil with alanine destabilizing clusters. [ABSTRACT FROM AUTHOR]

Published
2007
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24. Regional evolution of venom-gland phospholipase A2 isoenzymes of Trimeresurus flavoviridis snakes in the southwestern islands of Japan

Author

CHIJIWA, Takahito, primary, DESHIMARU, Masanobu, additional, NOBUHISA, Ikuo, additional, NAKAI, Makoto, additional, OGAWA, Tomohisa, additional, ODA, Naoko, additional, NAKASHIMA, Kin-ichi, additional, FUKUMAKI, Yasuyuki, additional, SHIMOHIGASHI, Yasuyuki, additional, HATTORI, Shosaku, additional, and OHNO, Motonori, additional

Published
2000
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42. Glutathione-independent Formaldehyde Dehydrogenase from Pseudomons putida: Survey of Functional Groups with Special Regard for Cysteine Residues

Author

Tsuru, Daisuke, Oda, Naoko, Matsuo, Yo, Ishikawa, Sara, Ito, Kiyoshi, and Yoshimoto, Tadashi

Abstract

The role of cysteine residues for structure and function of formaldehyde dehydrogenase from Pseudomonas putidawas analysed by amino acid sequence comparison, homology-based structure modeling, site-directed mutagenesis, and chemical modification. Five out of seven cysteine residues found in the enzyme were concluded to coordinate with an active site zinc (Cys-46) and structural zinc atoms (Cys-97, -100, -103, and -111) from the sequence comparison with other Zn-containing medium-chain alcohol dehydrogenase homologues. The three-dimensional structure model based on the known structure of the horse liver E-type alcohol dehydrogenase (ADH) indicated that Cys-257 is located very far from the active site Zn and NAD+binding region, suggesting that Cys-257 does not participate in the enzyme reaction. The structure also suggested that Cys-166 does not coordinate to active site Zn, but Asp-169 functions as a Zn-ligand, instead.

Published
1997
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43. Refolding of Trimeresurus flavoviridisPhospholipases A2

Author

Tsuno, Shinji, Ogawa, Tomohisa, Nakashima, Kin-ichi, Oda, Naoko, Lee, Sannumu, Shimohigashi, Yasuyuki, Aoyagi, Haruhiko, and Ohno, Motonori

Abstract

Trimeresurus flavoviridis(Habu snake) venom contains phospholipase A2(PLA2) isozymes which are rich in disulfide bond and show diverse activities in spite of their highly homologous structures. When reduced form of Tyr(NO2)-67-PLA2, which is a mimic of Asp-49-PLA2mutant, was oxidized at pH 8.0 in the presence of 5 mM L-cysteine and 5 mM Ca2+, native form of Tyr(NO2)-67-PLA2was produced as being judged from both activity regeneration and adequate HPLC profile. Reduced forms of two Lys-49-PLA2isozymes with extremely low lipolytic activity, which are called basic proteins I and II, also generated native forms of proteins when oxidized under the same conditions as above. Protein disulfide isomerase accelerated proper folding of reduced Tyr(NO2)-67-PLA2at an initial phase of oxidation and was effective for rearrangement of incorrectly paired disulfide bonds of Asp-49-PLA2to native construction. However, this isomerase failed to convert reduced form of partially active L-fragment, Asp-49-PLA2lacking N-terminal octapeptide, to the native form, indicating that the entire sequence of protein in a nascent state is primarily required for proper folding. The present data together with the fact that reduced Asp-49-PLA2folded properly (S. Tanaka et al. J. Biochem., 96, 1443 (1984)) afforded a strong basis for the structure and function study of T. flavoviridisPLA2s by means of in vitro mutagenesis technique.

Published
1992
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46. Nucleotide Sequence of the Gene Encoding the Precursor Protein of Pepstatin insensitive Acid Protease B, Scytalidopepsin B, from Scytalidium lignicolum

Author

ODA, Naoko, GOTOH, Yoshikazu, OYAMA, Hiroshi, MURAO, Sawao, ODA, Kohei, and TSURU, Daisuke

Abstract

A chromosomal DNA of Scytalidium lignicolumwas digested with Sau3AI. The digest was self-ligated and amplified by inverse PCR procedure using primers designed based on the nucleotide sequences of up- and down-stream regions of an intron present in the scytalidopepsin B gene. Analysis of the nucleotide sequence of PCR product (700 bp) showed that the enzyme is synthesized as a precursor protein consisting of the prepro- and mature enzyme regions. The deduced amino acid sequence was highly similar to those of aspergillopepsin A and recently reported endothiapepsins B and C, but quite different from those of pepstatin-insensitive bacterial acid proteases and the pepstatin-sensitive aspartic protease family.

Published
1998
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