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6. BCR, not TCR, repertoire diversity is associated with favorable COVID-19 prognosis

Author

Paran, Faith Jessica, primary, Oyama, Rieko, additional, Khasawneh, Abdullah, additional, Ai, Tomohiko, additional, Ismanto, Hendra Saputra, additional, Sherif, Aalaa Alrahman, additional, Saputri, Dianita Susilo, additional, Ono, Chikako, additional, Saita, Mizue, additional, Takei, Satomi, additional, Horiuchi, Yuki, additional, Yagi, Ken, additional, Matsuura, Yoshiharu, additional, Okazaki, Yasushi, additional, Takahashi, Kazuhisa, additional, Standley, Daron M, additional, Tabe, Yoko, additional, and Naito, Toshio, additional

Published
2024
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7. Activation of SARS-CoV-2 neutralizing antibody is slower than elevation of spike-specific IgG, IgM, and nucleocapsid-specific IgG antibodies

Author

Takahashi, Maika, Ai, Tomohiko, Sinozuka, Konomi, Baba, Yuna, Igawa, Gene, Nojiri, Shuko, Yamamoto, Takamasa, Yuri, Maiko, Takei, Satomi, Saito, Kaori, Horiuchi, Yuki, Kanno, Takayuki, Tobiume, Minoru, Khasawneh, Abdullah, Paran, Faith Jessica, Hiki, Makoto, Wakita, Mitsuru, Miida, Takashi, Suzuki, Tadaki, Okuzawa, Atsushi, Takahashi, Kazuhisa, Naito, Toshio, and Tabe, Yoko

Published
2022
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8. BCR, not TCR, repertoire diversity is associated with favorable COVID-19 prognosis.

Author

Paran, Faith Jessica, Oyama, Rieko, Khasawneh, Abdullah, Ai, Tomohiko, Ismanto, Hendra Saputra, Sherif, Aalaa Alrahman, Saputri, Dianita Susilo, Ono, Chikako, Saita, Mizue, Takei, Satomi, Horiuchi, Yuki, Yagi, Ken, Matsuura, Yoshiharu, Okazaki, Yasushi, Takahashi, Kazuhisa, Standley, Daron M., Tabe, Yoko, and Naito, Toshio

Subjects
B cell receptors, COVID-19 pandemic, T cell receptors, GENE expression, COVID-19
Abstract

Introduction: The SARS-CoV-2 pandemic has had a widespread and severe impact on society, yet there have also been instances of remarkable recovery, even in critically ill patients. Materials and methods: In this study, we used single-cell RNA sequencing to analyze the immune responses in recovered and deceased COVID-19 patients during moderate and critical stages. Results: Expanded T cell receptor (TCR) clones were predominantly SARS-CoV-2-specific, but represented only a small fraction of the total repertoire in all patients. In contrast, while deceased patients exhibited monoclonal B cell receptor (BCR) expansions without COVID-19 specificity, survivors demonstrated diverse and specific BCR clones. These findings suggest that neither TCR diversity nor BCR monoclonal expansions are sufficient for viral clearance and subsequent recovery. Differential gene expression analysis revealed that protein biosynthetic processes were enriched in survivors, but that potentially damaging mitochondrial ATP metabolism was activated in the deceased. Conclusion: This study underscores that BCR repertoire diversity, but not TCR diversity, correlates with favorable outcomes in COVID-19. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Isolation and identification of Wickerhamiella tropicalis from blood culture by MALDI-MS

Author

Takei, Satomi, primary, Teramoto, Kanae, additional, Fujimura, Junya, additional, Fujiwara, Megumi, additional, Suzuki, Mai, additional, Fukui, Yukiko, additional, Sekiguchi, Yuji, additional, Kawakami, Takaaki, additional, Chonan, Masayoshi, additional, Wakita, Mitsuru, additional, Horiuchi, Yuki, additional, Miida, Takashi, additional, Naito, Toshio, additional, Kirikae, Teruo, additional, Tada, Tatsuya, additional, and Tabe, Yoko, additional

Published
2024
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10. Multidrug-resistant Klebsiella pneumoniaeclinical isolates producing NDM- and OXA-type carbapenemase in Nepal

Author

Takei, Satomi, Tabe, Yoko, Miida, Takashi, Hishinuma, Tomomi, Khasawneh, Abdullah, Kirikae, Teruo, Sherchand, Jeevan B., and Tada, Tatsuya

Abstract

•Molecular epidemiology analysis was conducted using 46 MDR K. pneumoniaein two hospitals, Nepal.•All the isolates produced carbapenemases, and some of them produced 16S rRNA methytransferase.•Majority of the isolates were high-risk clones in hospitals in Nepal.•IncFII and ColKP3 plasmids carrying carbapenemase genes are spreading in K. pneumoniaein Nepal.

Published
2024
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12. Assessment of antibody dynamics and neutralizing activity using serological assay after SARS-CoV-2 infection and vaccination

Author

Takahashi, Toshihiro, primary, Ai, Tomohiko, additional, Saito, Kaori, additional, Nojiri, Shuko, additional, Takahashi, Maika, additional, Igawa, Gene, additional, Yamamoto, Takamasa, additional, Khasawneh, Abdullah, additional, Paran, Faith Jessica, additional, Takei, Satomi, additional, Horiuchi, Yuki, additional, Kanno, Takayuki, additional, Tobiume, Minoru, additional, Hiki, Makoto, additional, Wakita, Mitsuru, additional, Miida, Takashi, additional, Okuzawa, Atsushi, additional, Suzuki, Tadaki, additional, Takahashi, Kazuhisa, additional, Naito, Toshio, additional, and Tabe, Yoko, additional

Published
2023
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13. Investigation of the individual genetic evolution of SARS-CoV-2 in a small cluster during the rapid spread of the BF.5 lineage in Tokyo, Japan

Author

Jin, Bo, primary, Oyama, Rieko, additional, Tabe, Yoko, additional, Tsuchiya, Koji, additional, Hando, Tetsuya, additional, Wakita, Mitsuru, additional, Yan, Yan, additional, Saita, Mizue, additional, Takei, Satomi, additional, Horiuchi, Yuki, additional, Miida, Takashi, additional, Naito, Toshio, additional, Takahashi, Kazuhisa, additional, and Ogawa, Hideoki, additional

Published
2023
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16. Performance evaluation of the Ortho VITROS SARS-CoV-2 Spike-Specific Quantitative IgG test by comparison with the surrogate virus neutralizing antibody test and clinical assessment

Author

Takahashi, Maika, primary, Saito, Kaori, additional, Ai, Tomohiko, additional, Nojiri, Shuko, additional, Khasawneh, Abdullah, additional, Paran, Faith Jessica, additional, Horiuchi, Yuki, additional, Takei, Satomi, additional, Yamamoto, Takamasa, additional, Wakita, Mitsuru, additional, Hiki, Makoto, additional, Miida, Takashi, additional, Naito, Toshio, additional, Takahashi, Kazuhisa, additional, and Tabe, Yoko, additional

Published
2023
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18. The Synergetic Effect of Sitafloxacin-Arbekacin Combination in the Mycobacterium abscessus Species

Author

Watanabe, Junko, primary, Ihara, Hiroaki, additional, Takei, Satomi, additional, Nakamura, Ayako, additional, Fujimoto, Yuichi, additional, Handoh, Tetsuya, additional, Kurokawa, Kana, additional, Arai, Yuta, additional, Shibayama, Kohei, additional, Sumiyoshi, Issei, additional, Ochi, Yusuke, additional, Okabe, Takahiro, additional, Misawa, Shigeki, additional, Togo, Shinsaku, additional, Naito, Toshio, additional, Tabe, Yoko, additional, Miida, Takashi, additional, and Takahashi, Kazuhisa, additional

Published
2022
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19. Performance evaluation of the Roche Elecsys® Anti-SARS-CoV-2 immunoassays by comparison with neutralizing antibodies and clinical assessment

Author

Takei, Satomi, primary, Ai, Tomohiko, additional, Yamamoto, Takamasa, additional, Igawa, Gene, additional, Kanno, Takayuki, additional, Tobiume, Minoru, additional, Hiki, Makoto, additional, Saito, Kaori, additional, Khasawneh, Abdullah, additional, Wakita, Mitsuru, additional, Misawa, Shigeki, additional, Miida, Takashi, additional, Okuzawa, Atsushi, additional, Suzuki, Tadaki, additional, Takahashi, Kazuhisa, additional, Naito, Toshio, additional, and Tabe, Yoko, additional

Published
2022
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21. The Synergetic Effect of Sitafloxacin-Arbekacin Combination in the Mycobacteroides abscessus Complex

Author

Watanabe, Junko, primary, Ihara, Hiroaki, additional, Takei, Satomi, additional, Nakamura, Ayako, additional, Fujimoto, Yuichi, additional, Handoh, Tetsuya, additional, Kurokawa, Kana, additional, Arai, Yuta, additional, Shibayama, Kohei, additional, Sumiyoshi, Issei, additional, Ochi, Yusuke, additional, Okabe, Takahiro, additional, Misawa, Shigeki, additional, Togo, Shinsaku, additional, Miida, Takashi, additional, and Takahashi, Kazuhisa, additional

Published
2021
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22. m 6 A‐mediated alternative splicing coupled with nonsense‐mediated mRNA decay regulates SAM synthetase homeostasis

Author

Watabe, Eichi, primary, Togo‐Ohno, Marina, additional, Ishigami, Yuma, additional, Wani, Shotaro, additional, Hirota, Keiko, additional, Kimura‐Asami, Mariko, additional, Hasan, Sharmin, additional, Takei, Satomi, additional, Fukamizu, Akiyoshi, additional, Suzuki, Yutaka, additional, Suzuki, Tsutomu, additional, and Kuroyanagi, Hidehito, additional

Published
2021
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23. The Synergetic Effect of Imipenem-Clarithromycin Combination in the Mycobacteroides abscessus Complex

Author

Takei, Satomi, primary, Ihara, Hiroaki, additional, Togo, Shinsaku, additional, Nakamura, Ayako, additional, Fujimoto, Yuichi, additional, Watanabe, Junko, additional, Kurokawa, Kana, additional, Shibayama, Kohei, additional, Sumiyoshi, Issei, additional, Ochi, Yusuke, additional, Iwai, Moe, additional, Okabe, Takahiro, additional, Chonan, Masayoshi, additional, Misawa, Shigeki, additional, Ohsaka, Akimichi, additional, and Takahashi, Kazuhisa, additional

Published
2020
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24. Antimicrobial Susceptibility in the Mycobacteroides abscessus Complex is Restored by an Imipenem-Clarithromycin Combination

Author

Ihara, Hiroaki, primary, Takei, Satomi, additional, Togo, Shinsaku, additional, Nakamura, Ayako, additional, Fujimoto, Yuichi, additional, Watanabe, Junko, additional, Kurokawa, Kana, additional, Kohei, Shibayama, additional, Sumiyoshi, Issei, additional, Ochi, Yusuke, additional, Iwai, Moe, additional, Okabe, Takahiro, additional, Chonan, Masayoshi, additional, Misawa, Shigeki, additional, Ohsaka, Akimichi, additional, and Takahashi, Kazuhisa, additional

Published
2020
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25. m6A‐mediated alternative splicing coupled with nonsense‐mediated mRNA decay regulates SAM synthetase homeostasis.

Author

Watabe, Eichi, Togo‐Ohno, Marina, Ishigami, Yuma, Wani, Shotaro, Hirota, Keiko, Kimura‐Asami, Mariko, Hasan, Sharmin, Takei, Satomi, Fukamizu, Akiyoshi, Suzuki, Yutaka, Suzuki, Tsutomu, and Kuroyanagi, Hidehito

Subjects
HOMEOSTASIS, GENETIC regulation, RNA sequencing, MESSENGER RNA, METHYLTRANSFERASES
Abstract

Alternative splicing of pre‐mRNAs can regulate gene expression levels by coupling with nonsense‐mediated mRNA decay (NMD). In order to elucidate a repertoire of mRNAs regulated by alternative splicing coupled with NMD (AS‐NMD) in an organism, we performed long‐read RNA sequencing of poly(A)+ RNAs from an NMD‐deficient mutant strain of Caenorhabditis elegans, and obtained full‐length sequences for mRNA isoforms from 259 high‐confidence AS‐NMD genes. Among them are the S‐adenosyl‐L‐methionine (SAM) synthetase (sams) genes sams‐3 and sams‐4. SAM synthetase activity autoregulates sams gene expression through AS‐NMD in a negative feedback loop. We furthermore find that METT‐10, the orthologue of human U6 snRNA methyltransferase METTL16, is required for the splicing regulation in␣vivo, and specifically methylates the invariant AG dinucleotide at the distal 3′ splice site (3′SS) in␣vitro. Direct RNA sequencing coupled with machine learning confirms m6A modification of endogenous sams mRNAs. Overall, these results indicate that homeostasis of SAM synthetase in C. elegans is maintained by alternative splicing regulation through m6A modification at the 3′SS of the sams genes. SYNOPSIS: Alternative splicing (AS) of pre‐mRNAs can regulate gene expression levels by coupling with nonsense‐mediated mRNA decay (NMD). Here, assessment of the organismal substrate repertoire of this process reveals SAM synthetase (sams) gene expression regulation via m6A modification in C. elegans. Long‐read sequencing of poly(A)+ RNAs from an NMD‐deficient mutant strain reveals 259 high‐confidence AS‐NMD genes, including the SAM synthetase (sams) genes.SAMS activity negatively autoregulates AS‐NMD of the sams genes in␣vivo.Direct RNA sequencing coupled with machine learning reveals m6A modification of endogenous sams mRNAs at the distal 3′ splice sites.Methyltransferase METT‐10 catalyzes m6A modification specifically at the distal 3′ splice site of sams pre‐mRNA in␣vitro.METT‐10 regulates alternative splicing of the sams genes in␣vivo. [ABSTRACT FROM AUTHOR]

Published
2021
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26. A rice gene that confers broad-spectrum resistance to β-triketone herbicides

Author

Maeda, Hideo, primary, Murata, Kazumasa, additional, Sakuma, Nozomi, additional, Takei, Satomi, additional, Yamazaki, Akihiko, additional, Karim, Md. Rezaul, additional, Kawata, Motoshige, additional, Hirose, Sakiko, additional, Kawagishi-Kobayashi, Makiko, additional, Taniguchi, Yojiro, additional, Suzuki, Satoru, additional, Sekino, Keisuke, additional, Ohshima, Masahiro, additional, Kato, Hiroshi, additional, Yoshida, Hitoshi, additional, and Tozawa, Yuzuru, additional

Published
2019
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31. Comprehensive analysis of mutually exclusive alternative splicing in C. elegans.

Author

Kuroyanagi H, Takei S, and Suzuki Y

Abstract

Mutually exclusive selection of one exon in a cluster of exons is a rare form of alternative pre-mRNA splicing, yet suggests strict regulation. However, the repertoires of regulation mechanisms for the mutually exclusive (ME) splicing in vivo are still unknown. Here, we experimentally explore putative ME exons in C. elegans to demonstrate that 29 ME exon clusters in 27 genes are actually selected in a mutually exclusive manner. Twenty-two of the clusters consist of homologous ME exons. Five clusters have too short intervening introns to be excised between the ME exons. Fidelity of ME splicing relies at least in part on nonsense-mediated mRNA decay for 14 clusters. These results thus characterize all the repertoires of ME splicing in this organism.

Published
2014
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