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Tamaru Y, Nakanishi S, Tanaka K, Umetsu M, Nakazawa H, Sugiyama A, Ito T, Shimokawa N, Takagi M. Recent research advances on non-linear phenomena in various biosystems. J Biosci Bioeng 2023:S1389-1723(23)00107-X. [PMID: 37246137 DOI: 10.1016/j.jbiosc.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 05/30/2023]
Abstract
All biological phenomena can be classified as open, dissipative and non-linear. Moreover, the most typical phenomena are associated with non-linearity, dissipation and openness in biological systems. In this review article, four research topics on non-linear biosystems are described to show the examples from various biological systems. First, membrane dynamics of a lipid bilayer for the cell membrane is described. Since the cell membrane separates the inside of the cell from the outside, self-organizing systems that form spatial patterns on membranes often depend on non-linear dynamics. Second, various data banks based on recent genomics analysis supply the data including vast functional proteins from many organisms and their variable species. Since the proteins existing in nature are only a very small part of the space represented by amino acid sequence, success of mutagenesis-based molecular evolution approach crucially depends on preparing a library with high enrichment of functional proteins. Third, photosynthetic organisms depend on ambient light, the regular and irregular changes of which have a significant impact on photosynthetic processes. The light-driven process proceeds through many redox couples in the cyanobacteria constituting chain of redox reactions. Forth topics focuses on a vertebrate model, the zebrafish, which can help to understand, predict and control the chaos of complex biological systems. In particular, during early developmental stages, developmental differentiation occurs dynamically from a fertilized egg to divided and mature cells. These exciting fields of complexity, chaos, and non-linear science have experienced impressive growth in recent decades. Finally, future directions for non-liner biosystems are presented.
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Affiliation(s)
- Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan.
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Yang Z, Fu L, Cao M, Li F, Li J, Chen Z, Guo A, Zhong H, Li W, Liang Y, Luo Q. PFAS-induced lipidomic dysregulations and their associations with developmental toxicity in zebrafish embryos. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160691. [PMID: 36473658 DOI: 10.1016/j.scitotenv.2022.160691] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are persistent environmental contaminants, posing developmental toxicity to fish and human. PFAS-induced lipid metabolism disorders were demonstrated using the zebrafish (Danio rerio) embryo model, but the detailed changes of lipid compositions and the influence of these changes on the biological development are still unclear. Herein, lipidomics analysis was performed to reveal the dysregulations of lipid metabolism in zebrafish embryos exposed to perfluorooctanoic acid (PFOA) or perfluorooctane sulfonate (PFOS) through microinjection. Various abnormal phenotypes were observed, including heart bleeding, pericardium edema, spinal curvature and increased heart rate at 72 h after fertilization, especially in the PFOS exposure groups. Lipidomic profiling found downregulated phosphatidylethanolamines in the PFAS-exposed embryos, especially those containing a docosahexaenoyl (DHA) chain, indicating an excessive oxidative damage to the embryos. Glycerolipids were mainly upregulated in the PFOA groups but downregulated in the PFOS groups. These aberrations may reflect oxidative stress, energy metabolism malfunction and proinflammatory signals induced by PFASs. However, supplement of DHA may not be effective in recovering the lipidomic dysregulations and protecting from the developmental toxicity induced by PFASs, showing the complexity of the toxicological mechanisms. This work has revealed the associations between the abnormal phenotypes and dysregulations of lipid metabolism in zebrafish embryos induced by PFASs from the aspect of lipidomics, and discovered the underlying molecular mechanisms of the developmental toxicity of PFASs.
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Affiliation(s)
- Zhiyi Yang
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lei Fu
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mengxi Cao
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Fang Li
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jingguang Li
- The Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center of Food Safety and Risk Assessment, Beijing 100021, China
| | - Zhiyu Chen
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ang Guo
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huifang Zhong
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wenbo Li
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yong Liang
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Qian Luo
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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MacRae CA, Peterson RT. Zebrafish as a Mainstream Model for In Vivo Systems Pharmacology and Toxicology. Annu Rev Pharmacol Toxicol 2023; 63:43-64. [PMID: 36151053 DOI: 10.1146/annurev-pharmtox-051421-105617] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pharmacology and toxicology are part of a much broader effort to understand the relationship between chemistry and biology. While biomedicine has necessarily focused on specific cases, typically of direct human relevance, there are real advantages in pursuing more systematic approaches to characterizing how health and disease are influenced by small molecules and other interventions. In this context, the zebrafish is now established as the representative screenable vertebrate and, through ongoing advances in the available scale of genome editing and automated phenotyping, is beginning to address systems-level solutions to some biomedical problems. The addition of broader efforts to integrate information content across preclinical model organisms and the incorporation of rigorous analytics, including closed-loop deep learning, will facilitate efforts to create systems pharmacology and toxicology with the ability to continuously optimize chemical biological interactions around societal needs. In this review, we outline progress toward this goal.
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Affiliation(s)
- Calum A MacRae
- Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA;
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4
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Liu H, Cui H, Huang Y, Gao S, Tao S, Hu J, Wan Y. Xenobiotics Targeting Cardiolipin Metabolism to Promote Thrombosis in Zebrafish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3855-3866. [PMID: 33629855 DOI: 10.1021/acs.est.0c08068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Exposure to environmental pollutants is an important factor contributing to the development and severity of thrombosis. However, the important physiological molecules in the thrombotic processes affected by environmental exposures remain unknown. In this study, we show that exposure to environmental chemicals disrupts the equilibrium of cardiolipins (CLs), and directing CL synthesis promotes thrombosis. Using an untargeted metabolomics approach, approximately 3030 molecules were detected in zebrafish embryos exposed to 11 environmental chemicals and automatically clustered into a network. Interconnectivity among CLs and linoleates or isoxanthopterin was discovered through the highly consistent variations in the coregulated metabolites in the network. The chemical exposure resulted in significant upregulation of CLs through influencing the enzymatic activities of phospholipase A2, cardiolipin synthase, and lysocardiolipin acyltransferase. Consequently, metabolic disorders of CLs affected the levels of anticardiolipin antibodies, disrupted the homeostasis between platelet thromboxane A2 and endothelial prostacyclin, and promoted thrombotic events including heart ischemia and tachycardia. Our study thus reveals the common molecular mechanisms underlying the CL-induced thrombosis targeted by environmental exposures.
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Affiliation(s)
- Hang Liu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hongyang Cui
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yixuan Huang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shixiong Gao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shu Tao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jianying Hu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi Wan
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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A novel lung alveolar cell model for exploring volatile biomarkers of particle-induced lung injury. Sci Rep 2020; 10:15700. [PMID: 32973288 PMCID: PMC7515894 DOI: 10.1038/s41598-020-72825-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/03/2020] [Indexed: 11/08/2022] Open
Abstract
Quartz can increase oxidative stress, lipid peroxidation, and inflammation. The objective of this study was to explore the volatile biomarkers of quartz-induced lung injury using a lung alveolar cell model. We exposed the human alveolar A549 cell line to 0, 200, and 500 μg/mL quartz particles for 24 h and used gas chromatography-mass spectrometry to measure the volatile metabolites in the headspace air of cells. We identified ten volatile metabolites that had concentration-response relationships with particles exposure, including 1,2,4-oxadiazole, 5-(4-nitrophenyl)-3-phenyl- (CAS: 28825-12-9), 2,6-dimethyl-6-trifluoroacetoxyoctane (CAS: 61986-67-2), 3-buten-1-amine, N,N-dimethyl- (CAS: 55831-89-5), 2-propanol, 2-methyl- (CAS: 75-65-0), glycolaldehyde dimethyl acetal (CAS: 30934-97-5), propanoic acid, 2-oxo-, ethyl ester (CAS: 617-35-6), octane (CAS: 111-65-9), octane, 3,3-dimethyl- (CAS: 4110-44-5), heptane, 2,3-dimethyl- (CAS: 3074-71-3) and ethanedioic acid, bis(trimethylsilyl) ester (CAS: 18294-04-7). The volatile biomarkers are generated through the pathways of propanoate and nitrogen metabolism. The volatile biomarkers of the alkanes and methylated alkanes are related to oxidative and lipid peroxidation of the cell membrane. The lung alveolar cell model has the potential to explore the volatile biomarkers of particulate-induced lung injury.
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6
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Yan SC, Chen ZF, Zhang H, Chen Y, Qi Z, Liu G, Cai Z. Evaluation and optimization of sample pretreatment for GC/MS-based metabolomics in embryonic zebrafish. Talanta 2019; 207:120260. [PMID: 31594598 DOI: 10.1016/j.talanta.2019.120260] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/10/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022]
Abstract
Metabolomics tactics have been applied in the research associated with embryonic zebrafish. However, the report regarding the evaluation of impacts of sample pretreatment on metabolomics results from zebrafish embryos is limited. In the present study, different data normalization approaches, extraction solvents, and extraction strategies for off-line derivatization gas chromatography coupled with mass spectrometry-based metabolomics analysis of zebrafish eleutheroembryos were evaluated and optimized. The results showed that, when 4-chlorophenylalanine normalization, sample homogenization and pure methanol combined with ultrasonic extraction were conducted, better repeatabilities, higher signals and broader coverages of detected metabolites can be achieved. The recovery and standard deviation of most standards were in the range of 82%-121% and 6.6%-12%, respectively, while the relative standard deviation of major detected metabolites ranged from 5.4% to 19%, indicating good extraction efficiencies and method precision. Under the developed method, 87 important endogenous metabolites such as citric acid and hypoxanthine were identified by universal databases or standards among 270 extracted metabolites, which consisted of sugars, amines, amino acids, nucleotides, fatty acids, and sterols. Therefore, the results could provide a proper pretreatment protocol for the analysis of wide-coverage metabolome in embryonic zebrafish. In addition, this study highlights the impact of normalization and extraction methods on the data quality of metabolomics analysis.
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Affiliation(s)
- Shi-Chao Yan
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zhi-Feng Chen
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Hui Zhang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yanyan Chen
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zenghua Qi
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Guoguang Liu
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zongwei Cai
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China.
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7
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Dhillon SS, Torell F, Donten M, Lundstedt-Enkel K, Bennett K, Rännar S, Trygg J, Lundstedt T. Metabolic profiling of zebrafish embryo development from blastula period to early larval stages. PLoS One 2019; 14:e0213661. [PMID: 31086370 PMCID: PMC6516655 DOI: 10.1371/journal.pone.0213661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/15/2019] [Indexed: 11/18/2022] Open
Abstract
The zebrafish embryo is a popular model for drug screening, disease modelling and molecular genetics. In this study, samples were obtained from zebrafish at different developmental stages. The stages that were chosen were 3/4, 4/5, 24, 48, 72 and 96 hours post fertilization (hpf). Each sample included fifty embryos. The samples were analysed using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). Principle component analysis (PCA) was applied to get an overview of the data and orthogonal projection to latent structure discriminant analysis (OPLS-DA) was utilised to discriminate between the developmental stages. In this way, changes in metabolite profiles during vertebrate development could be identified. Using a GC-TOF-MS metabolomics approach it was found that nucleotides and metabolic fuel (glucose) were elevated at early stages of embryogenesis, whereas at later stages amino acids and intermediates in the Krebs cycle were abundant. This agrees with zebrafish developmental biology, as organs such as the liver and pancreas develop at later stages. Thus, metabolomics of zebrafish embryos offers a unique opportunity to investigate large scale changes in metabolic processes during important developmental stages in vertebrate development. In terms of stability of the metabolic profile and viability of the embryos, it was concluded at 72 hpf was a suitable time point for the use of zebrafish as a model system in numerous scientific applications.
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Affiliation(s)
- Sundeep S. Dhillon
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Frida Torell
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
- Accelerator Lab (ACL), Karlsruhe Institute of Technology, Karlsruhe, Germany
- AcureOmics, Umeå, Sweden
| | | | - Katrin Lundstedt-Enkel
- AcureOmics, Umeå, Sweden
- Environmental toxicology, Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Stefan Rännar
- AcureOmics, Umeå, Sweden
- Corporate Research, Sartorius AG, Göttingen, Germany
| | - Johan Trygg
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
- Corporate Research, Sartorius AG, Göttingen, Germany
- * E-mail:
| | - Torbjörn Lundstedt
- AcureOmics, Umeå, Sweden
- Deparment of Pharmaceutical Bioscience, BMC, Uppsala University, Uppsala, Sweden
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Ming M, Wang X, Lian L, Zhang H, Gao W, Zhu B, Lou D. Metabolic responses ofSaccharomyces cerevisiaeto ethanol stress using gas chromatography-mass spectrometry. Mol Omics 2019; 15:216-221. [DOI: 10.1039/c9mo00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Metabolic responses ofSaccharomyces cerevisiaeunder ethanol stress by a metabolomics method based on GC-MS.
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Affiliation(s)
- Ming Ming
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Xiyue Wang
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Lili Lian
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Hao Zhang
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Wenxiu Gao
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Bo Zhu
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
| | - Dawei Lou
- Department of Analytical Chemistry
- Jilin Institute of Chemical Technology
- Jilin
- P. R. China
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Fernandez O, Urrutia M, Bernillon S, Giauffret C, Tardieu F, Le Gouis J, Langlade N, Charcosset A, Moing A, Gibon Y. Fortune telling: metabolic markers of plant performance. Metabolomics 2016; 12:158. [PMID: 27729832 PMCID: PMC5025497 DOI: 10.1007/s11306-016-1099-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/16/2016] [Indexed: 02/01/2023]
Abstract
BACKGROUND In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC-MS, LC-MS, 1H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory evaluation and crop yield have been obtained. AIM OF REVIEW (i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding. KEY MESSAGE Using examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance.
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Affiliation(s)
- Olivier Fernandez
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Maria Urrutia
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
| | - Stéphane Bernillon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | | | | | | | - Nicolas Langlade
- UMR LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Alain Charcosset
- UMR GQE, INRA, CNRS, Université Paris Sud, AgroParisTech, Ferme du Moulon, 91190 Gif-Sur-Yvette, France
| | - Annick Moing
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d’Ornon, France
- Plateforme Métabolome Bordeaux, CGFB, MetaboHUB-PHENOME, 33140 Villenave d’Ornon, France
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10
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Teoh ST, Putri S, Mukai Y, Bamba T, Fukusaki E. A metabolomics-based strategy for identification of gene targets for phenotype improvement and its application to 1-butanol tolerance in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:144. [PMID: 26379776 PMCID: PMC4570087 DOI: 10.1186/s13068-015-0330-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/28/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Traditional approaches to phenotype improvement include rational selection of genes for modification, and probability-driven processes such as laboratory evolution or random mutagenesis. A promising middle-ground approach is semi-rational engineering, where genetic modification targets are inferred from system-wide comparison of strains. Here, we have applied a metabolomics-based, semi-rational strategy of phenotype improvement to 1-butanol tolerance in Saccharomyces cerevisiae. RESULTS Nineteen yeast single-deletion mutant strains with varying growth rates under 1-butanol stress were subjected to non-targeted metabolome analysis by GC/MS, and a regression model was constructed using metabolite peak intensities as predictors and stress growth rates as the response. From this model, metabolites positively and negatively correlated with growth rate were identified including threonine and citric acid. Based on the assumption that these metabolites were linked to 1-butanol tolerance, new deletion strains accumulating higher threonine or lower citric acid were selected and subjected to tolerance measurement and metabolome analysis. The new strains exhibiting the predicted changes in metabolite levels also displayed significantly higher growth rate under stress over the control strain, thus validating the link between these metabolites and 1-butanol tolerance. CONCLUSIONS A strategy for semi-rational phenotype improvement using metabolomics was proposed and applied to the 1-butanol tolerance of S. cerevisiae. Metabolites correlated with growth rate under 1-butanol stress were identified, and new mutant strains showing higher growth rate under stress could be selected based on these metabolites. The results demonstrate the potential of metabolomics in semi-rational strain engineering.
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Affiliation(s)
- Shao Thing Teoh
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Sastia Putri
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Yukio Mukai
- />Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829 Japan
| | - Takeshi Bamba
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Eiichiro Fukusaki
- />Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
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11
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Fukusaki E. Application of Metabolomics for High Resolution Phenotype Analysis. ACTA ACUST UNITED AC 2015; 3:S0045. [PMID: 26819889 DOI: 10.5702/massspectrometry.s0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/27/2014] [Indexed: 12/30/2022]
Abstract
Metabolome, a total profile of whole metabolites, is placed on downstream of proteome. Metabolome is thought to be results of implementation of genomic information. In other words, metabolome can be called as high resolution phenotype. The easiest operation of metabolomics is the integration to the upstream ome information including transcriptome and/or proteome. Those trials have been reported at a certain scientific level. In addition, metabolomics can be operated in stand-alone mode without any other ome information. Among metabolomics tactics, the author's group is particularly focusing on metabolic fingerprinting, in which metabolome information is employed as explanatory variant to evaluate response variant. Metabolic fingerprinting technique is expected not only for analyzing slight difference depending on genotype difference but also for expressing dynamic variation of living organisms. The author introduces several good examples which he performed. Those are useful for easy understanding of the power of metabolomics. In addition, the author mentions the latest technology for analysis of metabolic dynamism. The author's group developed a facile analytical method for semi-quantitative metabolic dynamism. The author introduces the novel method that uses time dependent variation of isotope distribution based on stable isotope dilution.
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Affiliation(s)
- Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University
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12
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Santoro MM. Zebrafish as a model to explore cell metabolism. Trends Endocrinol Metab 2014; 25:546-54. [PMID: 24997878 DOI: 10.1016/j.tem.2014.06.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/04/2014] [Accepted: 06/10/2014] [Indexed: 12/20/2022]
Abstract
Cell metabolism plays a key role in many essential biological processes. The recent availability of novel technologies and organisms to model cell metabolism in vivo is expanding current knowledge of cell metabolism. In this context, the zebrafish (Danio rerio) is emerging as a valuable model system to learn about the metabolic routes critical for cellular homeostasis. Here, the most recent methods and studies on cell metabolism are summarized, which support the overall value for the zebrafish model system not only to study metabolism but also metabolic disease states. It is envisioned that this small vertebrate system will help in the understanding of pathogenesis for numerous metabolic-related disorders in humans and in the identification of their therapeutic treatments.
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Affiliation(s)
- Massimo M Santoro
- Laboratory of Endothelial Molecular Biology, Vesalius Research Center, Department of Oncology, University of Leuven, Leuven, B-3000, Belgium; Laboratory of Endothelial Molecular Biology, Vesalius Research Center, VIB, Leuven, B-3000, Belgium.
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An PNT, Yamaguchi M, Bamba T, Fukusaki E. Metabolome analysis of Drosophila melanogaster during embryogenesis. PLoS One 2014; 9:e99519. [PMID: 25121768 PMCID: PMC4133167 DOI: 10.1371/journal.pone.0099519] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 05/15/2014] [Indexed: 02/02/2023] Open
Abstract
The Drosophila melanogaster embryo has been widely utilized as a model for genetics and developmental biology due to its small size, short generation time, and large brood size. Information on embryonic metabolism during developmental progression is important for further understanding the mechanisms of Drosophila embryogenesis. Therefore, the aim of this study is to assess the changes in embryos’ metabolome that occur at different stages of the Drosophila embryonic development. Time course samples of Drosophila embryos were subjected to GC/MS-based metabolome analysis for profiling of low molecular weight hydrophilic metabolites, including sugars, amino acids, and organic acids. The results showed that the metabolic profiles of Drosophila embryo varied during the course of development and there was a strong correlation between the metabolome and different embryonic stages. Using the metabolome information, we were able to establish a prediction model for developmental stages of embryos starting from their high-resolution quantitative metabolite composition. Among the important metabolites revealed from our model, we suggest that different amino acids appear to play distinct roles in different developmental stages and an appropriate balance in trehalose-glucose ratio is crucial to supply the carbohydrate source for the development of Drosophila embryo.
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Affiliation(s)
- Phan Nguyen Thuy An
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Insect Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- * E-mail:
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Abstract
In this review, we present an overview of the recent advances of genomic technologies applied to studies of fish species belonging to the superclass of Osteichthyes (bony fish) with a major emphasis on the infraclass of Teleostei, also called teleosts. This superclass that represents more than 50% of all known vertebrate species has gained considerable attention from genome researchers in the last decade. We discuss many examples that demonstrate that this highly deserved attention is currently leading to new opportunities for answering important biological questions on gene function and evolutionary processes. In addition to giving an overview of the technologies that have been applied for studying various fish species we put the recent advances in genome research on the model species zebrafish and medaka in the context of its impact for studies of all fish of the superclass of Osteichthyes. We thereby want to illustrate how the combined value of research on model species together with a broad angle perspective on all bony fish species will have a huge impact on research in all fields of fundamental science and will speed up applications in many societally important areas such as the development of new medicines, toxicology test systems, environmental sensing systems and sustainable aquaculture strategies.
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Abstract
Metabolism has a decisive role in many fundamental biological processes, including organism development and tissue homeostasis. Here we describe a protocol for fast and reliable (13)C-isotope-based in vivo metabolic profiling. This protocol covers the loading of isotope precursor; extraction, preparation and quantification of the labeled lipid metabolites (e.g., the prenyl lipid CoQ10) by the means of HPLC-MS; and its analysis in zebrafish embryos. This protocol can be applied to different types of experimental settings, including tissue-specific metabolic analyses or dynamic metabolic changes that occur during vertebrate embryogenesis. The protocol takes 5-7 d to complete, requiring minimal equipment and analytical expertise, and it represents a unique alternative to the existing ex vivo (e.g., cell lines) isotope-based metabolic methods. This procedure represents a valuable approach for researchers interested in studying the effect of gene manipulation on lipid metabolism in zebrafish and in understanding the genetic conditions that result in metabolism dysfunction.
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Abstract
Zebrafish offer a unique vertebrate model for research areas such as drug development, disease modeling and other biological exploration. There is significant conservation of genetics and other cellular networks among zebrafish and other vertebrate models, including humans. Here we discuss the recent work and efforts made in different fields of biology to explore the potential of zebrafish. Along with this, we also reviewed the concept of systems biology. A biological system is made up of a large number of components that interact in a huge variety of combinations. To understand completely the behavior of a system, it is important to know its components and interactions, and this can be achieved through a systems biology approach. At the end of the paper we present a concept of integrating zebrafish into the systems biology approach.
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Affiliation(s)
- Mian Yahya Mushtaq
- a Natural Products Laboratory, Institute of Biology, Leiden University , Leiden , The Netherlands
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17
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Current metabolomics: practical applications. J Biosci Bioeng 2013; 115:579-89. [PMID: 23369275 DOI: 10.1016/j.jbiosc.2012.12.007] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 10/30/2012] [Accepted: 12/05/2012] [Indexed: 12/13/2022]
Abstract
The field of metabolomics continues to grow rapidly over the last decade and has been proven to be a powerful technology in predicting and explaining complex phenotypes in diverse biological systems. Metabolomics complements other omics, such as transcriptomics and proteomics and since it is a 'downstream' result of gene expression, changes in the metabolome is considered to best reflect the activities of the cell at a functional level. Thus far, metabolomics might be the sole technology capable of detecting complex, biologically essential changes. As one of the omics technology, metabolomics has exciting applications in varied fields, including medical science, synthetic biology, medicine, and predictive modeling of plant, animal and microbial systems. In addition, integrated applications with genomics, transcriptomics, and proteomics provide greater understanding of global system biology. In this review, we discuss recent applications of metabolomics in microbiology, plant, animal, food, and medical science.
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Huang SM, Xu F, Lam SH, Gong Z, Ong CN. Metabolomics of developing zebrafish embryos using gas chromatography- and liquid chromatography-mass spectrometry. MOLECULAR BIOSYSTEMS 2013; 9:1372-80. [DOI: 10.1039/c3mb25450j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Metabolite profiles correlate closely with neurobehavioral function in experimental spinal cord injury in rats. PLoS One 2012; 7:e43152. [PMID: 22912814 PMCID: PMC3418274 DOI: 10.1371/journal.pone.0043152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/16/2012] [Indexed: 12/05/2022] Open
Abstract
Traumatic spinal cord injury (SCI) results in direct physical damage and the generation of local factors contributing to secondary pathogenesis. Untargeted metabolomic profiling was used to uncover metabolic changes and to identify relationships between metabolites and neurobehavioral functions in the spinal cord after injury in rats. In the early metabolic phase, neuronal signaling, stress, and inflammation-associated metabolites were strongly altered. A dynamic inflammatory response consisting of elevated levels of prostaglandin E2 and palmitoyl ethanolamide as well as pro- and anti-inflammatory polyunsaturated fatty acids was observed. N-acetyl-aspartyl-glutamate (NAAG) and N-acetyl-aspartate (NAA) were significantly decreased possibly reflecting neuronal cell death. A second metabolic phase was also seen, consistent with membrane remodeling and antioxidant defense response. These metabolomic changes were consistent with the pathology and progression of SCI. Several metabolites, including NAA, NAAG, and the ω-3 fatty acids docosapentaenoate and docosahexaenoate correlated greatly with the established Basso, Beattie and Bresnahan locomotive score (BBB score). Our findings suggest the possibility of a biochemical basis for BBB score and illustrate that metabolites may correlate with neurobehavior. In particular the NAA level in the spinal cord might provide a meaningful biomarker that could help to determine the degree of injury severity and prognosticate neurologic recovery.
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McNiven EMS, German JB, Slupsky CM. Analytical metabolomics: nutritional opportunities for personalized health. J Nutr Biochem 2012; 22:995-1002. [PMID: 21999844 DOI: 10.1016/j.jnutbio.2011.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/31/2011] [Indexed: 02/08/2023]
Abstract
Nutrition is the cornerstone of health; survival depends on acquiring essential nutrients, and dietary components can both prevent and promote disease. Metabolomics, the study of all small molecule metabolic products in a system, has been shown to provide a detailed snapshot of the body's processes at any particular point in time, opening up the possibility of monitoring health and disease, prevention and treatment. Metabolomics has the potential to fundamentally change clinical chemistry and, by extension, the fields of nutrition, toxicology and medicine. Technological advances, combined with new knowledge of the human genome and gut microbiome, have made and will continue to make possible earlier, more accurate, less invasive diagnoses, all while enhancing our understanding of the root causes of disease and leading to a generation of dietary recommendations that enable optimal health. This article reviews the recent contributions of metabolomics to the fields of nutrition, toxicology and medicine. It is expected that these fields will eventually blend together through development of new technologies in metabolomics and genomics into a new area of clinical chemistry: personalized medicine.
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Abstract
There is a general agreement that the development of metabolomics depends not only on advances in chemical analysis techniques but also on advances in computing and data analysis methods. Metabolomics data usually requires intensive pre-processing, analysis, and mining procedures. Selecting and applying such procedures requires attention to issues including justification, traceability, and reproducibility. We describe a strategy for selecting data mining techniques which takes into consideration the goals of data mining techniques on the one hand, and the goals of metabolomics investigations and the nature of the data on the other. The strategy aims to ensure the validity and soundness of results and promote the achievement of the investigation goals.
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Abstract
As the current paradigms of drug discovery evolve, it has become clear that a more comprehensive understanding of the interactions between small molecules and organismal biology will be vital. The zebrafish is emerging as a complement to existing in vitro technologies and established preclinical in vivo models that can be scaled for high-throughput. In this review, we highlight the current status of zebrafish toxicology studies, identify potential future niches for the model in the drug development pipeline, and define the hurdles that must be overcome as zebrafish technologies are refined for systematic toxicology.
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Affiliation(s)
- Randall T Peterson
- Harvard Medical School, Massachusetts General Hospital, and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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Soanes KH, Achenbach JC, Burton IW, Hui JPM, Penny SL, Karakach TK. Molecular Characterization of Zebrafish Embryogenesis via DNA Microarrays and Multiplatform Time Course Metabolomics Studies. J Proteome Res 2011; 10:5102-17. [DOI: 10.1021/pr2005549] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kelly H. Soanes
- National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3Z1
| | - John C. Achenbach
- National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Ian W. Burton
- National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Joseph P. M. Hui
- National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Susanne L. Penny
- National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3Z1
| | - Tobias K. Karakach
- National Research Council of Canada, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3Z1
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Yoshida R, Tamura T, Takaoka C, Harada K, Kobayashi A, Mukai Y, Fukusaki E. Metabolomics-based systematic prediction of yeast lifespan and its application for semi-rational screening of ageing-related mutants. Aging Cell 2010; 9:616-25. [PMID: 20550517 DOI: 10.1111/j.1474-9726.2010.00590.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Metabolomics - the comprehensive analysis of metabolites - was recently used to classify yeast mutants with no overt phenotype using raw data as metabolic fingerprints or footprints. In this study, we demonstrate the estimation of a complicated phenotype, longevity, and semi-rational screening for relevant mutants using metabolic profiles as strain-specific fingerprints. The fingerprints used in our experiments are profiled data consisting of individually identified and quantified metabolites rather than raw spectrum data. We chose yeast replicative lifespan as a model phenotype. Several yeast mutants that affect lifespan were selected for analysis, and they were subjected to metabolic profiling using mass spectrometry. Fingerprinting based on the profiles revealed a correlation between lifespan and metabolic profile. Amino acids and nucleotide derivatives were the main contributors to this correlation. Furthermore, we established a multivariate model to predict lifespan from a metabolic profile. The model facilitated the identification of putative longevity mutants. This work represents a novel approach to evaluate and screen complicated and quantitative phenotype by means of metabolomics.
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Affiliation(s)
- Ryo Yoshida
- Department of Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
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Sukardi H, Ung CY, Gong Z, Lam SH. Incorporating zebrafish omics into chemical biology and toxicology. Zebrafish 2010; 7:41-52. [PMID: 20384484 DOI: 10.1089/zeb.2009.0636] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In this communication, we describe the general aspects of omics approaches for analyses of transcriptome, proteome, and metabolome, and how they can be strategically incorporated into chemical screening and perturbation studies using the zebrafish system. Pharmacological efficacy and selectivity of chemicals can be evaluated based on chemical-induced phenotypic effects; however, phenotypic observation has limitations in identifying mechanistic action of chemicals. We suggest adapting gene-expression-based high-throughput screening as a complementary strategy to zebrafish-phenotype-based screening for mechanistic insights about the mode of action and toxicity of a chemical, large-scale predictive applications and comparative analysis of chemical-induced omics signatures, which are useful to identify conserved biological responses, signaling pathways, and biomarkers. The potential mechanistic, predictive, and comparative applications of omics approaches can be implemented in the zebrafish system. Examples of these using the omics approaches in zebrafish, including data of ours and others, are presented and discussed. Omics also facilitates the translatability of zebrafish studies across species through comparison of conserved chemical-induced responses. This review is intended to update interested readers with the current omics approaches that have been applied in chemical studies on zebrafish and their potential in enhancing discovery in chemical biology.
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Affiliation(s)
- Hendrian Sukardi
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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