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Takaragawa H, Wakayama M. Responses of leaf gas exchange and metabolites to drought stress in different organs of sugarcane and its closely related species Erianthus arundinaceus. PLANTA 2024; 260:90. [PMID: 39256219 PMCID: PMC11387454 DOI: 10.1007/s00425-024-04508-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/09/2024] [Indexed: 09/12/2024]
Abstract
MAIN CONCLUSION The high intrinsic water-use efficiency of Erianthus may be due to the low abaxial stomatal density and the accumulation of leaf metabolites such as betaine and gamma-aminobutyric acid. Sugarcane is an important crop that is widely cultivated in tropical and subtropical regions of the world. Because drought is among the main impediments limiting sugarcane production in these regions, breeding of drought-tolerant sugarcane varieties is important for sustainable production. Erianthus arundinaceus, a species closely related to sugarcane, exhibits high intrinsic water-use efficiency (iWUE), the underlying mechanisms for which remain unknown. To improve the genetic base for conferring drought tolerance in sugarcane, in the present study, we performed a comprehensive comparative analysis of leaf gas exchange and metabolites in different organs of sugarcane and Erianthus under wet and dry soil-moisture conditions. Erianthus exhibited lower stomatal conductance under both conditions, which resulted in a higher iWUE than in sugarcane. Organ-specific metabolites showed gradations between continuous parts and organs, suggesting linkages between them. Cluster analysis of organ-specific metabolites revealed the effects of the species and treatments in the leaves. Principal component analysis of leaf metabolites confirmed a rough ordering of the factors affecting their accumulations. Compared to sugarcane leaf, Erianthus leaf accumulated more raffinose, betaine, glutamine, gamma-aminobutyric acid, and S-adenosylmethionine, which function as osmolytes and stress-response compounds, under both the conditions. Our extensive analyses reveal that the high iWUE of Erianthus may be due to the specific accumulation of such metabolites in the leaves, in addition to the low stomatal density on the abaxial side of leaves. The identification of drought-tolerance traits of Erianthus will benefit the generation of sugarcane varieties capable of withstanding drought stress.
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Affiliation(s)
- Hiroo Takaragawa
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Maezato Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan.
| | - Masataka Wakayama
- Integrated Medical and Agricultural School for Public Health, Ehime University, Tōon, Ehime, 791-0295, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan.
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Sun ML, Yang Y, Hu R, Li JL, Liu SH, Chen YZ, Wang DY, Wang L, Li YZ, Zhong Y, Yao J, Li XN. Simple and field-adapted species identification of biological specimens combining multiplex multienzyme isothermal rapid amplification, lateral flow dipsticks, and universal primers for initial rapid screening without standard PCR laboratory. Int J Legal Med 2024; 138:561-570. [PMID: 37801116 DOI: 10.1007/s00414-023-03101-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Species identification of biological specimens can provide the valuable clues and accelerate the speed of prosecution material processing for forensic investigation, especially when the case scene is inaccessible and the physical evidence is cumbersome. Thus, establishing a rapid, simple, and field-adapted species identification method is crucial for forensic scientists, particularly as first-line technology at the crime scene for initial rapid screening. In this study, we established a new field-adapted species identification method by combining multiplex multienzyme isothermal rapid amplification (MIRA), lateral flow dipstick (LFD) system, and universal primers. Universal primers targeting COX I and COX II genes were used in multiplex MIRA-LFD system for seven species identification, and a dedicated MIRA-LFD system primer targeting CYT B gene was used to detect the human material. DNA extraction was performed by collecting DNA directly from the centrifuged supernatant. Our study found that the entire amplification process took only 15 min at 37 °C and the results of LFDs could be visually observed after 10 min. The detection sensitivity of human material could reach 10 pg, which is equivalent to the detection of single cell. Different common animal samples mixed at the ratio of 1 ng:1 ng, 10 ng:1 ng, and 1 ng:10 ng could be detected successfully. Furthermore, the damaged and degraded samples could also be detected. Therefore, the convenient, feasible, and rapid approach for species identification is suitable for popularization as first-line technology at the crime scene for initial rapid screening and provides a great convenient for forensic application.
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Affiliation(s)
- Mao-Ling Sun
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Ying Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ran Hu
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jia-Lun Li
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Shu-Han Liu
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Dong-Yi Wang
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Lan Wang
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Yang Zhong
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China.
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China.
| | - Xiao-Na Li
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China.
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China.
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Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Ajayi FF, Alnuaimi A, Hamdi M, Mostafa H, Wakayama M, Mudgil P, Maqsood S. Metabolomics approach for the identification of bioactive compounds released from young and mature soybean upon in vitro gastrointestinal digestion and their effect on health-related bioactive properties. Food Chem 2023; 420:136050. [PMID: 37098305 DOI: 10.1016/j.foodchem.2023.136050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023]
Abstract
The aim of the present study was to comparatively investigate the relative phytochemical profiles (phenolic content, organic and amino acids, free sugars, and other metabolites using metabolomics approach), and bioactive potentials of young (YS) and mature soybean (MS) upon in vitro simulated gastrointestinal digestion (SGID). Cumulatively, a total of 198 metabolites were identified in MS and YS, 119 metabolites in undigested YS, and a total of 136 metabolites in undigested MS, which further increased to 156 and 152 in YS and MS upon SGID, respectively. Gastric digesta of both YS and MS exhibited higher inhibitory properties towards α-amylase and DPP-IV enzymes than their intestinal digesta. Furthermore, the intestinal digesta of MS showed higher antioxidant and anti-inflammatory activities compared to the YS intestinal digesta. Overall, the results suggested that the gastrointestinal digestion of YS and MS displayed distinctive metabolic profiles together with varied bioactive potentials.
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Raza A. Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants. PLANT CELL REPORTS 2022; 41:741-763. [PMID: 33251564 DOI: 10.1007/s00299-020-02635-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 05/22/2023]
Abstract
Comprehensive metabolomic investigations provide a large set of stress-related metabolites and metabolic pathways, advancing crops under heat stress conditions. Metabolomics-assisted breeding, including mQTL and mGWAS boosted our understanding of improving numerous quantitative traits under heat stress. During the past decade, metabolomics has emerged as a fascinating scientific field that includes documentation, evaluation of metabolites, and chemical methods for cell monitoring programs in numerous plant species. A comprehensive metabolome profiling allowed the investigator to handle the comprehensive data groups of metabolites and the equivalent metabolic pathways in an extraordinary manner. Metabolomics, together with transcriptomics, plays an influential role in discovering connections between stress and genes/metabolite, phenotyping, and biomarkers documentation. Further, it helps to decode several metabolic systems connected with heat stress (HS) tolerance in plants. Heat stress is a critical environmental factor that is globally affecting the growth and productivity of plants. Thus, there is an urgent need to exploit modern breeding and biotechnological tools like metabolomics to develop cultivars with improved HS tolerance. Several studies have reported that amino acids, carbohydrates, nitrogen metabolisms, etc. and metabolites involved in the biosynthesis and catalyzing actions play a game-changing role in HS response and help plants to cope with the HS. The use of metabolomics-assisted breeding (MAB) allows a well-organized transmission of higher yield and HS tolerance at the metabolome level with specific properties. Progressive metabolomics systematic techniques have accelerated metabolic profiling. Nonetheless, continuous developments in bioinformatics, statistical tools, and databases are allowing us to produce ever-progressing, comprehensive insights into the biochemical configuration of plants and by what means this is inclined by genetic and environmental cues. Currently, assimilating metabolomics with post-genomic platforms has allowed a significant division of genetic-phenotypic connotation in several plant species. This review highlights the potential of a state-of-the-art plant metabolomics approach for the improvement of crops under HS. The development of plants with specific properties using integrated omics (metabolomics and transcriptomics) and MAB can provide new directions for future research to enhance HS tolerance in plants to achieve a goal of "zero hunger".
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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Ogura T, Wakayama M, Ashino Y, Kadowaki R, Sato M, Soga T, Tomita M. Effects of feed crops and boiling on chicken egg yolk and white determined by a metabolome analysis. Food Chem 2020; 327:127077. [DOI: 10.1016/j.foodchem.2020.127077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
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Difference in pyruvic acid metabolism between neonatal and adult mouse lungs exposed to hyperoxia. PLoS One 2020; 15:e0238604. [PMID: 32881962 PMCID: PMC7470327 DOI: 10.1371/journal.pone.0238604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/19/2020] [Indexed: 11/19/2022] Open
Abstract
Objective Neonatal lungs are more tolerant to hyperoxic injury than are adult lungs. This study investigated differences in the response to hyperoxic exposure between neonatal and adult mouse lungs using metabolomics analysis with capillary electrophoresis time-of-flight mass spectrometry (CE- TOFMS). Methods Neonatal and adult mice were exposed to 21% or 95% O2 for four days. Subsequently, lung tissue samples were collected and analyzed by CE-TOFMS. Pyruvate dehydrogenase (PDH) enzyme activity was determined using a microplate assay kit. PDH kinase (Pdk) 1, Pdk2, Pdk3, and Pdk4 mRNA expression levels were determined using quantitative reverse transcription-polymerase chain reaction. Pdk4 protein expression was quantified by Western blotting and Pdk4 protein localization was evaluated by immunohistochemistry. Results Levels of 3-phosphoglyceric acid, 2-phosphoglyceric acid, phosphoenolpyruvic acid, and lactic acid were significantly elevated in the lungs of hyperoxia-exposed versus normoxia-exposed adult mice, whereas no significant differences were observed with hyperoxia exposure in neonatal mice. PDH activity was reduced in the lungs of adult mice only. Pdk4 mRNA expression levels after hyperoxic exposure were significantly elevated in adult mice compared with that in neonatal mice. Conversely, gene expression levels of Pdk1, Pdk2, and Pdk3 did not differ after hyperoxic exposure in either neonatal or adult mice. Pdk4 protein levels were also significantly increased in adult mouse lungs exposed to hyperoxia and were localized mainly to the epithelium of terminal bronchiole. Conclusions Specific metabolites associated with glycolysis and gluconeogenesis were altered after hyperoxia exposure in the lungs of adult mice, but not in neonates, which was likely a result of reduced PDH activity due to Pdk4 mRNA upregulation under hyperoxia.
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Hamid SS, Wakayama M, Ashino Y, Kadowaki R, Soga T, Tomita M. Effect of blanching on the concentration of metabolites in two parts of Undaria pinnatifida, Wakame (leaf) and Mekabu (sporophyll). ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Sugawara T, Wakayama M, Hattori M. Metabolomic Profiling of Melon (<i>Cucumis melo </i>L.) Cultivated in Shonai, Yamagata Prefecture and Development of Effective Utilization of Residues from Fruit Processing. J JPN SOC FOOD SCI 2020. [DOI: 10.3136/nskkk.67.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Tetsuya Sugawara
- Yamagata Research Institute of Technology, Shonai Testing Facility
| | - Masataka Wakayama
- Institute for Advanced Biosciences Keio University Tsuruoka Metabolome Campus
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Subedi A, Muroi M, Futamura Y, Kawamura T, Aono H, Nishi M, Ryo A, Watanabe N, Osada H. A novel inhibitor of tumorspheres reveals the activation of the serine biosynthetic pathway upon mitochondrial inhibition. FEBS Lett 2019; 593:763-776. [PMID: 30874300 DOI: 10.1002/1873-3468.13361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
Differences in the metabolism of cancer cells or cancer stem cells (CSCs) as compared to normal cells have provided avenues to safely target cancers. To discover metabolic inhibitors of CSCs, we performed alkaline phosphatase- and tumoursphere-based drug screening using induced cancer stem cell-like cells. From the screening of a RIKEN NPDepo chemical library, we discovered NPD2381 as a novel and selective cancer-stemness inhibitor that targets mitochondrial metabolism. Using our ChemProteoBase profiling, we found that NPD2381 increases the expression of enzymes within the serine biosynthesis pathway. We also found a role for serine in protecting cancer cells from mitochondrial inhibitors. Our results suggest the existence of a compensatory mechanism to increase the level of intracellular serine in response to mitochondrial inhibitors.
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Affiliation(s)
- Amit Subedi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Makoto Muroi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Tatsuro Kawamura
- RIKEN-Max Planck Joint Research Division for Systems Chemical Biology, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Harumi Aono
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Mayuko Nishi
- Department of Microbiology, Yokohama City University School of Medicine, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Japan
| | - Nobumoto Watanabe
- RIKEN-Max Planck Joint Research Division for Systems Chemical Biology, RIKEN Center for Sustainable Resource Science, Wako, Japan.,Bio-Active Compounds Discovery Research Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Japan.,RIKEN-Max Planck Joint Research Division for Systems Chemical Biology, RIKEN Center for Sustainable Resource Science, Wako, Japan
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Ramautar R, Somsen GW, de Jong GJ. CE-MS for metabolomics: Developments and applications in the period 2016-2018. Electrophoresis 2018; 40:165-179. [PMID: 30232802 PMCID: PMC6586046 DOI: 10.1002/elps.201800323] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 12/16/2022]
Abstract
In the field of metabolomics, CE-MS is now recognized as a strong analytical technique for the analysis of (highly) polar and charged metabolites in a wide range of biological samples. Over the past few years, significant attention has been paid to the design and improvement of CE-MS approaches for (large-scale) metabolic profiling studies and for establishing protocols in order to further expand the role of CE-MS in metabolomics. In this paper, which is a follow-up of a previous review paper covering the years 2014-2016 (Electrophoresis 2017, 38, 190-202), main advances in CE-MS approaches for metabolomics studies are outlined covering the literature from July 2016 to June 2018. Aspects like developments in interfacing designs and data analysis tools for improving the performance of CE-MS for metabolomics are discussed. Representative examples highlight the utility of CE-MS in the fields of biomedical, clinical, microbial, and plant metabolomics. A complete overview of recent CE-MS-based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings and MS detection mode. Finally, some general conclusions and perspectives are given.
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Affiliation(s)
- Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerhardus J de Jong
- Biomolecular Analysis, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Gender-related metabolomics and lipidomics: From experimental animal models to clinical evidence. J Proteomics 2018; 178:82-91. [DOI: 10.1016/j.jprot.2017.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/16/2017] [Accepted: 11/01/2017] [Indexed: 02/06/2023]
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Next-generation capillary electrophoresis–mass spectrometry approaches in metabolomics. Curr Opin Biotechnol 2017; 43:1-7. [DOI: 10.1016/j.copbio.2016.07.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/28/2016] [Accepted: 07/04/2016] [Indexed: 12/14/2022]
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Rodrigues KT, Cieslarová Z, Tavares MFM, Simionato AVC. Strategies Involving Mass Spectrometry Combined with Capillary Electrophoresis in Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:99-141. [DOI: 10.1007/978-3-319-47656-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Barnes S, Benton HP, Casazza K, Cooper SJ, Cui X, Du X, Engler J, Kabarowski JH, Li S, Pathmasiri W, Prasain JK, Renfrow MB, Tiwari HK. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:461-75. [PMID: 27434804 PMCID: PMC4964969 DOI: 10.1002/jms.3782] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/07/2016] [Accepted: 04/24/2016] [Indexed: 05/16/2023]
Abstract
The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program's goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. The complete set of training materials including slide sets and videos can be viewed at http://www.uab.edu/proteomics/metabolomics/workshop/workshop_june_2015.php. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Stephen Barnes
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Pharmacology and Toxicology, School of Medicine University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | | | - Krista Casazza
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | | | - Xiangqin Cui
- Section on Statistical Genetics, School of Public Health University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jeffrey Engler
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Janusz H. Kabarowski
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Shuzhao Li
- Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Wimal Pathmasiri
- RTI International, Research Triangle Park, Durham, NC, 27709, USA
| | - Jeevan K. Prasain
- Department of Pharmacology and Toxicology, School of Medicine University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Hemant K. Tiwari
- Section on Statistical Genetics, School of Public Health University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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Abstract
In clinical metabolomics, capillary electrophoresis-mass spectrometry (CE-MS) has become a very useful technique for the analysis of highly polar and charged metabolites in complex biologic samples. A comprehensive overview of recent developments in CE-MS for metabolic profiling studies is presented. This review covers theory, CE separation modes, capillary coatings, and practical aspects of CE-MS coupling. Attention is also given to sample pretreatment and data analysis strategies used for metabolomics. The applicability of CE-MS for clinical metabolomics is illustrated using samples ranging from plasma and urine to cells and tissues. CE-MS application to large-scale and quantitative clinical metabolomics is addressed. Conclusions and perspectives on this unique analytic strategy are presented.
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