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Mizuno-Iijima S, Kawamoto S, Asano M, Mashimo T, Wakana S, Nakamura K, Nishijima KI, Okamoto H, Saito K, Yoshina S, Miwa Y, Nakamura Y, Ohkuma M, Yoshiki A. Mammalian genome research resources available from the National BioResource Project in Japan. Mamm Genome 2024:10.1007/s00335-024-10063-2. [PMID: 39261329 DOI: 10.1007/s00335-024-10063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 08/08/2024] [Indexed: 09/13/2024]
Abstract
Mammalian genome research has conventionally involved mice and rats as model organisms for humans. Given the recent advances in life science research, to understand complex and higher-order biological phenomena and to elucidate pathologies and develop therapies to promote human health and overcome diseases, it is necessary to utilize not only mice and rats but also other bioresources such as standardized genetic materials and appropriate cell lines in order to gain deeper molecular and cellular insights. The Japanese bioresource infrastructure program called the National BioResource Project (NBRP) systematically collects, preserves, controls the quality, and provides bioresources for use in life science research worldwide. In this review, based on information from a database of papers related to NBRP bioresources, we present the bioresources that have proved useful for mammalian genome research, including mice, rats, other animal resources; DNA-related materials; and human/animal cells and microbes.
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Affiliation(s)
- Saori Mizuno-Iijima
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Shoko Kawamoto
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Shigeharu Wakana
- Department of Animal Experimentation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, 650-0047, Japan
| | - Katsuki Nakamura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Ken-Ichi Nishijima
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Hitoshi Okamoto
- RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Yoshihiro Miwa
- Gene Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan.
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Zhou X, Wang Z, Li S, Rong X, Bu J, Liu Q, Ouyang Z. Differentiating enantiomers by directional rotation of ions in a mass spectrometer. Science 2024; 383:612-618. [PMID: 38330101 DOI: 10.1126/science.adj8342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
Conventional mass spectrometry does not distinguish between enantiomers, or mirror-image isomers. Here we report a technique to break the chiral symmetry and to differentiate enantiomers by inducing directional rotation of chiral gas-phase ions. Dual alternating current excitations were applied to manipulate the motions of trapped ions, including the rotation around the center of mass and macro movement around the center of the trap. Differences in collision cross section were induced, which could be measured by ion cloud profiling at high resolutions above 10,000. High-field ion mobility and tandem mass spectrometry analyses of the enantiomers were combined and implemented by using a miniature ion trap mass spectrometer. The effectiveness of the developed method was demonstrated with a variety of organic compounds including amino acids, sugars, and several drug molecules, as well as a proof-of-principle ligand optimization study for asymmetric hydrogenation.
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Affiliation(s)
- Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Zhuofan Wang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Shuai Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xianle Rong
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiexun Bu
- PURSPEC Technology (Beijing) Ltd., Beijing 100084, China
| | - Qiang Liu
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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Liu C, Wu Y, Li M, Liu F, Kong P, Yang H, Liu X. Enantiomer-Specific Colorimetric Tandem Assays for Salivary d-Alanine Associated with Gastric Cancer. Anal Chem 2024; 96:1906-1912. [PMID: 38251936 DOI: 10.1021/acs.analchem.3c04017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Salivary d-alanine (d-Ala) and d-proline (d-Pro) are of concern for their potential in the noninvasive diagnosis of gastric cancer (GC). Most reports have succeeded in determining the total concentration of d-Ala and d-Pro. However, for personalized diagnosis and better elucidation of the underlying specific correlation of d-Ala (or d-Pro) with GC, it is desirable to determine the specific concentration of d-Ala or d-Pro. Herein, we propose an enantiomer-specific tandem assay of d-Ala based on the colorimetric reaction between 2,4-dinitrophenylhydrazine and pyruvic acid generated from the deamination of d-Ala catalyzed by d-amino acid oxidase, which is easily distinguished from l-form amino acids, d-Pro, and many other species. A linear concentration range is established from 20 to 400 μmol/L with a limit of detection of 1.01 μmol/L. Real saliva sample tests reveal that the levels of d-Ala in GC cases are remarkably higher than those in healthy individuals, which offers a simple and low-cost strategy for GC diagnosis. Simultaneously, the total concentrations of d-Ala and d-Pro in saliva are determined. Hence, the concentration of d-Pro and the proportion of d-Ala could be calculated, which further provides more molecule- and individual-specific information. This research may offer a convenient method for noninvasive diagnosis of GC and pave a new route to explore the potentials of rare d-form amino acids in disease diagnosis and treatment.
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Affiliation(s)
- Chang Liu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Yanan Wu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Mengying Li
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Fang Liu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Pengfei Kong
- Department of Gastric Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Haifeng Yang
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Xinling Liu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
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Li G, Jeon CK, Ma M, Jia Y, Zheng Z, Delafield DG, Lu G, Romanova EV, Sweedler JV, Ruotolo BT, Li L. Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chem Sci 2023; 14:5936-5944. [PMID: 37293657 PMCID: PMC10246695 DOI: 10.1039/d3sc00678f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/06/2023] [Indexed: 06/10/2023] Open
Abstract
Growing evidence supports the confident association between distinct amyloid beta (Aβ) isoforms and Alzheimer's Disease (AD) pathogenesis. As such, critical investigations seeking to uncover the translational factors contributing to Aβ toxicity represent a venture of significant value. Herein, we comprehensively assess full-length Aβ42 stereochemistry, with a specific focus on models that consider naturally-occurring isomerization of Asp and Ser residues. We customize various forms of d-isomerized Aβ as natural mimics, ranging from fragments containing a single d residue to full length Aβ42 that includes multiple isomerized residues, systematically evaluating their cytotoxicity against a neuronal cell line. Combining multidimensional ion mobility-mass spectrometry experimental data with replica exchange molecular dynamics simulations, we confirm that co-d-epimerization at Asp and Ser residues within Aβ42 in both N-terminal and core regions effectively reduces its cytotoxicity. We provide evidence that this rescuing effect is associated with the differential and domain-specific compaction and remodeling of Aβ42 secondary structure.
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Affiliation(s)
- Gongyu Li
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
- Haihe Laboratory of Sustainable Chemical Transformations Tianjin 300192 China
| | - Chae Kyung Jeon
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Min Ma
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Yifei Jia
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University Tianjin 300070 China
| | - Daniel G Delafield
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Gaoyuan Lu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Elena V Romanova
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Jonathan V Sweedler
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
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