Details of the Researcher

PHOTO

Yuki Onishi
Section
Research Center for Accelerator and Radioisotope Science
Job title
Assistant Professor
Degree

Research Interests 9

  • RI製造

  • メタボロミクス

  • NMR

  • 有機合成

  • タンパク質結晶化

  • ペプチド合成

  • 固体NMR

  • 中性子構造解析

  • J-PARC

Research Areas 2

  • Life sciences / Bioorganic chemistry /

  • Nanotechnology/Materials / Structural/physical organic chemistry /

Papers 15

  1. A Basic Study of the Effects of Mulberry Leaf Administration to Healthy C57BL/6 Mice on Gut Microbiota and Metabolites Peer-reviewed

    Li Gan, Yuga Inamura, Yu Shimizu, Yuki Yokoi, Yuki Ohnishi, Zihao Song, Yasuhiro Kumaki, Takashi Kikukawa, Makoto Demura, Masaaki Ito, Tokiyoshi Ayabe, Kiminori Nakamura, Tomoyasu Aizawa

    Metabolites　13　(9)　1003-1003　2023/09/10

    Publisher: MDPI AG

    DOI： 10.3390/metabo13091003 　

    eISSN： 2218-1989

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    Mulberry leaves contain α-glucosidase inhibitors, which have hypoglycemic effects and are considered functional foods. However, few reports have covered the effects of mulberry leaf components on normal gut microbiota and gut metabolites. Herein, gut microbiota analysis and NMR-based metabolomics were performed on the feces of mulberry leaf powder (MLP)-treated mice to determine the effects of long-term MLP consumption. Gut microbiota in the mouse were analyzed using 16S-rRNA gene sequencing, and no significant differences were revealed in the diversity and community structure of the gut microbiota in the C57BL/6 mice with or without MLP supplementation. Thirty-nine metabolites were identified via 1H-NMR analysis, and carbohydrates and amino acids were significantly (p < 0.01–0.05) altered upon MLP treatment. In the MLP-treated group, there was a marked increase and decrease in maltose and glucose concentrations, respectively, possibly due to the degradation inhibitory activity of oligosaccharides. After 5 weeks, all amino acid concentrations decreased. Furthermore, despite clear fluctuations in fecal saccharide concentrations, short-chain fatty acid production via intestinal bacterial metabolism was not strongly affected. This study provides the knowledge that MLP administration can alter the gut metabolites without affecting the normal gut microbiota, which is useful for considering MLP as a healthy food source.

  2. Metabolomics of Duodenal Juice for Biliary Tract Cancer Diagnosis Peer-reviewed

    Kazuma Kishi, Masaki Kuwatani, Yuki Ohnishi, Yasuhiro Kumaki, Hiroyuki Kumeta, Hajime Hirata, Yunosuke Takishin, Ryutaro Furukawa, Kosuke Nagai, Hiroki Yonemura, Shunichiro Nozawa, Ryo Sugiura, Kazumichi Kawakubo, Tomoyasu Aizawa, Naoya Sakamoto

    Cancers　15　(17)　4370-4370　2023/09/01

    Publisher: MDPI AG

    DOI： 10.3390/cancers15174370 　

    eISSN： 2072-6694

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    The poor prognosis of malignant biliary diseases is partially caused by their difficult early diagnosis. Therefore, many patients are only diagnosed at advanced stages. This study aimed to improve diagnosis by clarifying the differences in the duodenal juice metabolomes of benign and malignant biliary diseases. From October 2021 to January 2023, duodenal juice was obtained from 67 patients with suspected biliary diseases who required endoscopic ultrasonography and endoscopic retrograde cholangiography for diagnosis/treatment. The samples metabolomes were analyzed via nuclear magnet resonance spectroscopy using an 800-MHz spectrometer. Metabolomes of malignant and benign diseases were then compared, and multivariate analysis was performed to determine the relevant factors for malignancy/benignancy. For benignancy, no significant predictors were observed. For malignancy, acetone was a significant predictor, with higher concentrations in the malignant group than in the benign group. Regarding the receiver operating characteristic curve analysis for biliary tract carcinoma diagnosis, the predictive value of acetone in duodenal juice was comparable with serum CA19-9 levels (area under the curve: 0.7330 vs. 0.691, p = 0.697). In conclusion, duodenal juice metabolomics is a feasible method that is available for differential diagnosis in the biliary disease field.

  3. Enzymatic characterization of a mannuronan C5-epimerase from the subtropical brown alga Cladosiphon okamuranus Peer-reviewed

    Fisheries Science　2023/09

    DOI： 10.1007/s12562-023-01720-7 　

  4. Antimicrobial Properties and Mode of Action of Cryptdin-4, a Mouse α-Defensin Regulated by Peptide Redox Structures and Bacterial Cultivation Conditions Peer-reviewed

    Yi Wang, Yuchi Song, Shaonan Yan, Rina Hiramine, Yuki Ohnishi, Yuki Yokoi, Kiminori Nakamura, Takashi Kikukawa, Tokiyoshi Ayabe, Tomoyasu Aizawa

    Antibiotics　12　(6)　1047-1047　2023/06/14

    Publisher: MDPI AG

    DOI： 10.3390/antibiotics12061047 　

    eISSN： 2079-6382

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    Cryptdin-4 (crp4) is an enteric α-defensin derived from mice, and is a main mediator of immunity to oral infections and a determinant of the composition of the intestinal microbiota. Structurally, crp4 exists in two states: the oxidized form (crp4oxi), constrained by three invariant disulfide bonds, and the reduced form (crp4red) with six free thiol groups, both of which exist in the intestinal tract. In this study, the antibacterial mechanisms of crp4 in both forms under aerobic and anaerobic conditions were investigated using Escherichia coli (E. coli), an anaerobic facultative bacterium, as a model. Fluorescent dye studies revealed that both crp4oxi and crp4red exhibited antimicrobial activity against cells cultured under aerobic conditions via rapid membrane depolarization. Furthermore, the antioxidant treatment experiments suggested that only crp4oxi exhibited antimicrobial activity by the induction and accumulation of reactive oxygen species (ROS). However, under anaerobic culture conditions, the ability of both forms to disrupt the function of bacterial membranes decreased and activity was greatly reduced, but crp4red maintained some antimicrobial activity. This activity may be due to the inhibition of intracellular functions by DNA binding. Altogether, these data indicate that, according to its redox structure and the environmental redox conditions, crp4 could perform different antimicrobial activities via different mechanisms.

  5. Application of Benchtop NMR for Metabolomics Study Using Feces of Mice with DSS-Induced Colitis Peer-reviewed

    Zihao Song, Yuki Ohnishi, Seiji Osada, Li Gan, Jiaxi Jiang, Zhiyan Hu, Hiroyuki Kumeta, Yasuhiro Kumaki, Yuki Yokoi, Kiminori Nakamura, Tokiyoshi Ayabe, Kazuo Yamauchi, Tomoyasu Aizawa

    Metabolites　13　(5)　611-611　2023/04/28

    Publisher: MDPI AG

    DOI： 10.3390/metabo13050611 　

    eISSN： 2218-1989

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    Nuclear magnetic resonance (NMR)-based metabolomics, which comprehensively measures metabolites in biological systems and investigates their response to various perturbations, is widely used in research to identify biomarkers and investigate the pathogenesis of underlying diseases. However, further applications of high-field superconducting NMR for medical purposes and field research are restricted by its high cost and low accessibility. In this study, we applied a low-field, benchtop NMR spectrometer (60 MHz) employing a permanent magnet to characterize the alterations in the metabolic profile of fecal extracts obtained from dextran sodium sulfate (DSS)-induced ulcerative colitis model mice and compared them with the data acquired from high-field NMR (800 MHz). Nineteen metabolites were assigned to the 60 MHz 1H NMR spectra. Non-targeted multivariate analysis successfully discriminated the DSS-induced group from the healthy control group and showed high comparability with high-field NMR. In addition, the concentration of acetate, identified as a metabolite with characteristic behavior, could be accurately quantified using a generalized Lorentzian curve fitting method based on the 60 MHz NMR spectra.

  6. An oxidative metabolic pathway of 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEHU) from alginate in an alginate-assimilating bacterium Peer-reviewed

    Ryuji Nishiyama, Takao Ojima, Yuki Ohnishi, Yasuhiro Kumaki, Tomoyasu Aizawa, Akira Inoue

    Communications Biology　4　(1)　2021/12

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s42003-021-02786-8 　

    eISSN： 2399-3642

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    <title>Abstract</title>Alginate-assimilating bacteria degrade alginate into an unsaturated monosaccharide, which is converted into 4-deoxy-L-<italic>erythro</italic>-5-hexoseulose uronic acid (DEHU). DEHU is reduced to 2-keto-3-deoxy-D-gluconate by a DEHU-specific reductase using NAD(P)H. This is followed by pyruvate production via the Entner-Doudoroff pathway. Previously, we identified FlRed as a DEHU reductase in an alginate-assimilating bacterium, <italic>Flavobacterium</italic> sp. strain UMI-01. Here, we showed that FlRed can also catalyze the oxidation of DEHU with NAD+, producing 2-keto-3-deoxy-D-glucarate (KDGR). FlRed showed a predilection for NADH and NAD+ over NADPH and NADP+, respectively, and the <italic>K</italic>m value for NADH was approximately 2.6-fold less than that for NAD+. Furthermore, we identified two key enzymes, FlDet and FlDeg, for KDGR catabolism. FlDet was identified as an enzyme of the ribonuclease activity regulator A family, which converts KDGR to α-ketoglutaric semialdehyde (α-KGSA). FlDeg, a type II α-KGSA dehydrogenase, generated α-ketoglutaric acid by oxidizing the aldehyde group of α-KGSA using NAD(P)+. Consequently, unlike the conventional DEHU reduction pathway, DEHU can be directly converted to α-ketoglutaric acid without consuming NAD(P)H. Alginate upregulated the expression of not only FlRed and two enzymes of the DEHU-reduction pathway, but also FlDet and FlDeg. These results revealed dual pathways of DEHU metabolism involving reduction or oxidation by FlRed.

  7. Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother-Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses. International-journal Peer-reviewed

    Yosuke Komatsu, Daiki Kumakura, Namiko Seto, Hirohisa Izumi, Yasuhiro Takeda, Yuki Ohnishi, Shinji Nakaoka, Tomoyasu Aizawa

    Frontiers in nutrition　8　813690-813690　2021

    DOI： 10.3389/fnut.2021.813690 　

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    Background: The gut microbiome and fecal metabolites of breastfed infants changes during lactation, and are influenced by breast milk components. This study aimed to investigate dynamic associations of milk components with the infant gut microbiome and fecal metabolites throughout the lactation period in a mother-infant model. Methods: One month after delivery, breast milk and subsequent infant feces were collected in a pair for 5 months from a mother and an exclusively breastfed infant. Composition of the fecal microbiome was determined with 16S rRNA sequencing. Low-molecular-weight metabolites, including human milk oligosaccharides (HMOs), and antibacterial proteins were measured in feces and milk using 1H NMR metabolomics and enzyme-linked immunosorbent assays. The association of milk bioactive components with the infant gut microbiome and fecal metabolites was determined with Python clustering and correlation analyses. Results: The HMOs in milk did not fluctuate throughout the lactation period. However, they began to disappear in infant feces at the beginning of month 4. Notably, at this time-point, a bifidobacterium species switching (from B. breve to B. longum subsp. infantis) occurred, accompanied by fluctuations in several metabolites including acetate and butyrate in infant feces. Conclusions: Milk bioactive components, such as HMOs, might play different roles in the exclusively breastfed infants depending on the lactation period.

  8. Cordyceps militaris Fruit Body Extract Decreases Testosterone Catabolism and Testosterone-Stimulated Prostate Hypertrophy. International-journal Peer-reviewed

    Kazuya Kusama, Mayuko Miyagawa, Koichiro Ota, Naoko Kuwabara, Kaori Saeki, Yuki Ohnishi, Yasuhiro Kumaki, Tomoyasu Aizawa, Toyokazu Nakasone, Shigemi Okamatsu, Hiroaki Miyaoka, Kazuhiro Tamura

    Nutrients　13　(1)　2020/12/26

    DOI： 10.3390/nu13010050 　

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    The androgens testosterone and dihydrotestosterone (DHT) are essential for a variety of systemic functions in mature males. Alteration of these hormones results in late-onset hypogonadism (LOH) and benign prostate hyperplasia (BPH). The fruit bodies of fungi of the genus Cordyceps have been regarded as folk medicine or health food with tonic and antifatigue effects. The extract from the fruit body of Cordyceps militaris parasitizing Samia cynthia ricini (CM) was evaluated as a novel-candidate natural product for ameliorating male andropause symptoms. To explore the effects of CM on LOH and BPH, CM was applied to rat models and cultured testicular cells and prostate cells. The concentrations of androgens in the serum and culture media were determined by ELISA. Expression of steroidogenic enzymes and androgen-related genes was evaluated by qPCR, and prostatic cell proliferation was assessed with the cell-viability assay. CM maintained the serum levels of testosterone and DHT, but inhibited testosterone-induced prostate hypertrophy. CM also increased the secretion of testosterone and DHT by primary testicular cells, with no changes in the mRNA expression of steroidogenic enzymes, but decreased the growth of prostatic cell lines. Our data suggest that CM could improve both LOH and BPH in males.

  9. ヒト便試料の保存条件とメタボローム変動のNMR解析(Impact of sample storage conditions on NMR-based human fecal metabolomics)

    宋 子豪, 包 克非, 北田 直也, 清水 由宇, 菊池 摩仁, 熊木 康裕, 大西 裕季, 塚本 卓, 菊川 峰志, 出村 誠, 中村 公則, 綾部 時芳, 山村 凌大, 中村 幸志, 玉腰 暁子, 相沢 智康

    腸内細菌学雑誌　34　(2)　148-148　2020/04

    Publisher: (公財)腸内細菌学会

    ISSN： 1343-0882

    eISSN： 1349-8363

  10. Studies on the Quality Control of Fermented Brown Rice and Rice Bran with Aspergillus oryzae by Metabolome Analysis Using 1H-NMR Peer-reviewed

    Yukiko Horie, Hideyuki Nemoto, Jin Fujita, Shigeo Ikegawa, Yasuhiro Kumaki, Yuki Ohnishi, Hiroyuki Kumeta, Makoto Demura, Tomoyasu Aizawa

    Nippon Shokuhin Kagaku Kogaku Kaishi　66　(4)　139-146　2019/04/15

    Publisher: Japanese Society for Food Science and Technology

    DOI： 10.3136/nskkk.66.139 　

    ISSN： 1341-027X

    eISSN： 1881-6681

  11. Neutron and X-ray crystallographic analysis of the human α-thrombin-bivalirudin complex at pD 5.0: Protonation states and hydration structure of the enzyme?product complex Peer-reviewed

    YAMADA Taro, KURIHARA Kazuo, OHNISHI Yuki, TAMADA Taro, TOMOYORI Katsuaki, MASUMI Kenji, TANAKA Ichiro, KUROKI Ryota, NIIMURA Nobuo

    Biochimica et Biophysica Acta - Proteins and Proteomics　1834　(8)　1532-1538　2013/08

    DOI： 10.1016/j.bbapap.2013.05.014 　

  12. Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0: Protonation states and hydration structure in the free-form Peer-reviewed

    OHNISHI Yuki, YAMADA Taro, KURIHARA Kazuo, TANAKA Ichiro, SAKIYAMA Fumio, MASAKI Takeharu, NIIMURA Nobuo

    Biochimica et Biophysica Acta - Proteins and Proteomics　1834　(8)　1642-1647　2013/08

    DOI： 10.1016/j.bbapap.2013.05.012 　

  13. A preliminary neutron diffraction analysis of Achromobacter protease I Peer-reviewed

    Yuki Ohnishi, Takeharu Masaki, Taro Yamada, Kazuo Kurihara, Ichiro Tanaka, Nobuo Niimura

    INTERNATIONAL CONFERENCE ON NEUTRON SCATTERING 2009　251　2010

    DOI： 10.1088/1742-6596/251/1/012032 　

    ISSN： 1742-6588

  14. A neutron crystallographic analysis of T6 porcine insulin at 2.1 Å resolution Peer-reviewed

    IWAI Wakari, YAMADA Taro, KURIHARA Kazuo, OHNISHI Yuki, KOBAYASHI Yoichiro, TANAKA Ichiro, TAKAHASHI Haruyuki, KUROKI Ryota, TAMADA Taro, NIIMURA Nobuo

    Acta Crystallographica section D　65　(10)　1042-1050　2009/10

    DOI： 10.1107/S090744490902770X 　

  15. A neutron crystallographic analysis of a cubic porcine insulin at pD 6.6 Peer-reviewed

    ISHIKAWA Takuya, CHATAKE Toshiyuki, OHNISHI Yuki, TANAKA Ichiro, KURIHARA Kazuo, KUROKI Ryota, NIIMURA Nobuo

    Chemical Physics　345　(2-3)　152-158　2008/04

    DOI： 10.1016/j.chemphys.2007.06.053 　

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Misc. 5

  1. シマグワワインのNMRメタボローム解析

    稲村勇雅, 久米田博之, 久米田博之, 熊木康裕, 大西裕季, 菊川峰志, 菊川峰志, 出村誠, 出村誠, 小山朗夫, 伊東昌章, 岩波俊介, 相沢智康, 相沢智康

    日本農芸化学会大会講演要旨集(Web)　2017　ROMBUNNO.3A04p09 (WEB ONLY)　2017/03/05

    ISSN： 2186-7976

  2. Structural Study of Hydrogen and Hydration by the IBARAKI Biological Crystal Diffractometer (iBIX)/Industrial Use

    TANAKA Ichiro, KUSAKA Katsuhiro, HOSOYA Takaaki, OHHARA Takashi, KURIHARA Kazuo, NIIMURA Nobuo, YAMADA Taro, TOMOYORI Katsuaki, YOKOYAMA Takeshi, OHNISHI Yuki, OOSUMI Takashi, UCHIDA Hirohisa, SUZUKI Eiichiro, KASHIWAGI Tatsuki, MIYAMOTO Akio, FURUKAWA Yasunori, YOSHIMURA Masashi, KAWAMURA Takahiro

    Radioisotopes　60　(2)　89-97　2011/02/15

    Publisher: 日本アイソトープ協会

    DOI： 10.3769/radioisotopes.60.89 　

    ISSN： 0033-8303

  3. A neutron crystallographic analysis of a ‘phosphate-free’ ribonuclease A at 1.7A resolution.

    Daichi Yagi, Taro Yamada, Kazuo Kurihara, Yuki Ohnishi, Masahiro Yamashita, Ryota Kuroki, Ichiro Tanaka, Nobuo Niimura

    Acta Cryst　D　892-899　2009

    DOI： 10.1107/S0907444909018885 　

  4. CLOSE UP サイズフリー・良質結晶育成装置について

    大西 裕季, 伊藤 剛士, 新村 信雄

    原子力eye　50　(11)　40-43　2004/11

    Publisher: 日刊工業出版プロダクション

    ISSN： 1343-3563

  5. タンパク質・DNA等結晶成長相図作成とそれに基づいたラショナルな結晶育成技術

    大西 裕季, 新井 栄揮, 新村 信雄

    基礎科学ノ-ト　10　10-13　2003/02

    Publisher: 先端基礎研究センタ-基礎研究推進室

    ISSN： 1340-3079

Research Projects 1

  1. The next generation structural biology using a new pulsed-neutron diffractometer

    TANAKA Ichiro, TOMOYORI Katsuaki, YAMADA Taro, KUSAKA Katsuhiro, OHNISHI Yuuki, NIIMURA Nobuo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Ibaraki University

    2008 - 2010

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    A new diffractometer for protein crystallography (iBIX) at the next generation pulsed-neutron source at J-PARC, has been completed and operational since the end of 2008. After various commissionings, data collection of ribonuclease A could be done at the accelerator power of 120kW for a crystal of 5 mm3 in volume for about 10 days as the first protein sample at iBIX. As a result of structural analysis, hydrogen position and orientation of waters for a purpose could be confirmed. According to the result, it turned out that it is possible to collect a full data set of a protein in about 3 days for a crystal of 1 mm3 in volume when J-PARC accelerator power becomes 1MW and 30 detectors of iBIX are provided as a total as scheduled.