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Sun K, Li Z, Li W, Chi C, Wang M, Xu R, Gao Y, Li B, Sun Y, Liu R. Investigating the anti-atherosclerotic effects and potential mechanism of Dalbergia odorifera in ApoE-deficient mice using network pharmacology combined with metabolomics. J Pharm Biomed Anal 2024; 242:116017. [PMID: 38387125 DOI: 10.1016/j.jpba.2024.116017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024]
Abstract
Dalbergia odorifera (DO) is a precious rosewood species in Southern Asia, and its heartwood is used in China as an official plant for invigorating blood circulation and eliminating stasis. This study aims to evaluate the efficacy of DO on atherosclerosis (AS), and further explore its active components and potential mechanisms. The apolipoprotein-E (ApoE)-deficient mice fed a high-fat diet were used as model animals, and the pathological changes in mice with or without DO treatment were compared to evaluate the pharmacodynamics of DO on AS. The mechanisms were preliminarily expounded by combining with metabolomics and network pharmacology. Moreover, the bioactive components and targets were assessed by cell experiments and molecular docking, respectively. Our findings suggested that DO significantly modulated blood lipid levels and alleviated intimal hyperplasia in atherosclerotic-lesioned mice, and the mechanisms may involve the regulation of 18 metabolites that changed during the progression of AS, thus affecting 3 major metabolic pathways and 3 major signaling pathways. Moreover, the interactions between 16 compounds with anti-proliferative effect and hub targets in the 3 signaling pathways were verified using molecular docking. Collectively, our findings preliminarily support the therapeutic effect of DO in atherosclerosis, meanwhile explore the active constituents and potential pharmacological mechanisms, which is conducive to its reasonable exploitation and utilization.
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Affiliation(s)
- Kang Sun
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Zongchao Li
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Wenjing Li
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Chenglin Chi
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Minjun Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Ruoxuan Xu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Yan Gao
- Shandong International Biotechnology Park Development Co., Ltd, Yantai, China
| | - Bing Li
- Shandong International Biotechnology Park Development Co., Ltd, Yantai, China
| | - Yiying Sun
- Shandong International Biotechnology Park Development Co., Ltd, Yantai, China
| | - Rongxia Liu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
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Shahar O, Botvinnik A, Shwartz A, Lerer E, Golding P, Buko A, Hamid E, Kahn D, Guralnick M, Blakolmer K, Wolf G, Lotan A, Lerer L, Lerer B, Lifschytz T. Effect of chemically synthesized psilocybin and psychedelic mushroom extract on molecular and metabolic profiles in mouse brain. Mol Psychiatry 2024:10.1038/s41380-024-02477-w. [PMID: 38378926 DOI: 10.1038/s41380-024-02477-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024]
Abstract
Psilocybin, a naturally occurring, tryptamine alkaloid prodrug, is currently being investigated for the treatment of a range of psychiatric disorders. Preclinical reports suggest that the biological effects of psilocybin-containing mushroom extract or "full spectrum" (psychedelic) mushroom extract (PME), may differ from those of chemically synthesized psilocybin (PSIL). We compared the effects of PME to those of PSIL on the head twitch response (HTR), neuroplasticity-related synaptic proteins and frontal cortex metabolomic profiles in male C57Bl/6j mice. HTR measurement showed similar effects of PSIL and PME over 20 min. Brain specimens (frontal cortex, hippocampus, amygdala, striatum) were assayed for the synaptic proteins, GAP43, PSD95, synaptophysin and SV2A, using western blots. These proteins may serve as indicators of synaptic plasticity. Three days after treatment, there was minimal increase in synaptic proteins. After 11 days, PSIL and PME significantly increased GAP43 in the frontal cortex (p = 0.019; p = 0.039 respectively) and hippocampus (p = 0.015; p = 0.027) and synaptophysin in the hippocampus (p = 0.041; p = 0.05) and amygdala (p = 0.035; p = 0.004). PSIL increased SV2A in the amygdala (p = 0.036) and PME did so in the hippocampus (p = 0.014). In the striatum, synaptophysin was increased by PME only (p = 0.023). There were no significant effects of PSIL or PME on PSD95 in any brain area when these were analyzed separately. Nested analysis of variance (ANOVA) showed a significant increase in each of the 4 proteins over all brain areas for PME versus vehicle control, while significant PSIL effects were observed only in the hippocampus and amygdala and were limited to PSD95 and SV2A. Metabolomic analyses of the pre-frontal cortex were performed by untargeted polar metabolomics utilizing capillary electrophoresis - Fourier transform mass spectrometry (CE-FTMS) and showed a differential metabolic separation between PME and vehicle groups. The purines guanosine, hypoxanthine and inosine, associated with oxidative stress and energy production pathways, showed a progressive decline from VEH to PSIL to PME. In conclusion, our synaptic protein findings suggest that PME has a more potent and prolonged effect on synaptic plasticity than PSIL. Our metabolomics data support a gradient of effects from inert vehicle via chemical psilocybin to PME further supporting differential effects. Further studies are needed to confirm and extend these findings and to identify the molecules that may be responsible for the enhanced effects of PME as compared to psilocybin alone.
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Affiliation(s)
- Orr Shahar
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Alexander Botvinnik
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Amit Shwartz
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Elad Lerer
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
- Israel Institute for Biology, Nes Ziona, Israel
| | - Peretz Golding
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Alex Buko
- Human Metabolome Technologies, Boston, MA, USA
| | - Ethan Hamid
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Dani Kahn
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Miles Guralnick
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | | | - Gilly Wolf
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
- Achva Academic College, Beer Tuvia, Israel
| | - Amit Lotan
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Leonard Lerer
- Parow Entheobiosciences (ParowBio), Chicago, IL, USA
- Back of the Yards Algae Sciences (BYAS), Chicago, IL, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel.
| | - Tzuri Lifschytz
- Biological Psychiatry Laboratory and Hadassah BrainLabs Center for Psychedelic Research, Hadassah Medical Center, Hebrew University, Jerusalem, Israel.
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Quintieri L, Fanelli F, Monaci L, Fusco V. Milk and Its Derivatives as Sources of Components and Microorganisms with Health-Promoting Properties: Probiotics and Bioactive Peptides. Foods 2024; 13:601. [PMID: 38397577 PMCID: PMC10888271 DOI: 10.3390/foods13040601] [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: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Milk is a source of many valuable nutrients, including minerals, vitamins and proteins, with an important role in adult health. Milk and dairy products naturally containing or with added probiotics have healthy functional food properties. Indeed, probiotic microorganisms, which beneficially affect the host by improving the intestinal microbial balance, are recognized to affect the immune response and other important biological functions. In addition to macronutrients and micronutrients, biologically active peptides (BPAs) have been identified within the amino acid sequences of native milk proteins; hydrolytic reactions, such as those catalyzed by digestive enzymes, result in their release. BPAs directly influence numerous biological pathways evoking behavioral, gastrointestinal, hormonal, immunological, neurological, and nutritional responses. The addition of BPAs to food products or application in drug development could improve consumer health and provide therapeutic strategies for the treatment or prevention of diseases. Herein, we review the scientific literature on probiotics, BPAs in milk and dairy products, with special attention to milk from minor species (buffalo, sheep, camel, yak, donkey, etc.); safety assessment will be also taken into consideration. Finally, recent advances in foodomics to unveil the probiotic role in human health and discover novel active peptide sequences will also be provided.
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Affiliation(s)
| | - Francesca Fanelli
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), 70126 Bari, Italy; (L.Q.); (L.M.); (V.F.)
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Shu S, Jing R, Li L, Wang W, Zhang J, Luo Z, Shan Y, Liu Z. Effects of Different Heat Treatments on Yak Milk Proteins on Intestinal Microbiota and Metabolism. Foods 2024; 13:192. [PMID: 38254494 PMCID: PMC10814013 DOI: 10.3390/foods13020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Dairy products are susceptible to modifications in protein oxidation during heat processing, which can lead to changes in protein function, subsequently affecting intestinal health. Despite being a unique nutritional source, yak milk has not been thoroughly examined for the effects of its oxidized proteins on intestinal microbiota and metabolism. Hence, this study employed different heat treatment methods (low-temperature pasteurization, high-temperature pasteurization, and high-temperature sterilization) to induce oxidation in yak milk proteins. The study then assessed the degree of oxidation in these proteins and utilized mice as research subjects. Using metagenomics and metabolomics methods, this study examined the structure of intestinal microbial communities and metabolic products in mice consuming oxidized yak milk. The results showed a decrease in carbonyl and total thiol contents of yak milk proteins after different heat treatments, indicating that heat treatment causes oxidation in yak milk proteins. Metagenomic analysis of mouse intestinal microbiota revealed significant changes in 66 genera. In the high-temperature sterilization group (H), key differential genera included Verrucomicrobiales, Verrucomicrobiae, Akkermansiaceae, and 28 others. The high-temperature pasteurization group (M) mainly consisted of Latilactobacillus, Bacillus, and Romboutsia. The low-temperature pasteurization group (L) primarily comprised of Faecalibacterium, Chaetomium, Paenibacillaceae, Eggerthella, Sordariales, and 33 others. Functionally, compared to the control group (C), the H group upregulated translation and energy metabolism functions, the L group the M group significantly upregulated metabolism of other amino acids, translation, and cell replication and repair functions. Based on metabolomic analysis, differential changes in mouse metabolites could affect multiple metabolic pathways in the body. The most significantly affected metabolic pathways were phenylalanine metabolism, vitamin B6 metabolism, steroid hormone biosynthesis, and pantothenate and CoA biosynthesis. The changes were similar to the functional pathway analysis of mouse metagenomics, affecting amino acid and energy metabolism in mice. In summary, moderate oxidation of yak milk proteins exhibits a positive effect on mouse intestinal microbiota and metabolism. In conclusion, yak milk has a positive effect on mouse intestinal microflora and metabolism, and this study provides a scientific basis for optimizing dairy processing technology and further developing and applying yak milk.
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Affiliation(s)
- Senbiao Shu
- Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China; (S.S.); (R.J.); (L.L.); (J.Z.); (Z.L.)
| | - Rong Jing
- Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China; (S.S.); (R.J.); (L.L.); (J.Z.); (Z.L.)
| | - Liang Li
- Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China; (S.S.); (R.J.); (L.L.); (J.Z.); (Z.L.)
| | - Wenhan Wang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
| | - Jinchao Zhang
- Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China; (S.S.); (R.J.); (L.L.); (J.Z.); (Z.L.)
| | - Zhang Luo
- Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China; (S.S.); (R.J.); (L.L.); (J.Z.); (Z.L.)
| | - Yuanyuan Shan
- School of Food Science and Engineering, Northwest A & F University, Xianyang 712199, China
| | - Zhendong Liu
- Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China; (S.S.); (R.J.); (L.L.); (J.Z.); (Z.L.)
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Nakatani K, Izumi Y, Umakoshi H, Yokomoto-Umakoshi M, Nakaji T, Kaneko H, Nakao H, Ogawa Y, Ikeda K, Bamba T. Wide-scope targeted analysis of bioactive lipids in human plasma by LC/MS/MS. J Lipid Res 2024; 65:100492. [PMID: 38135255 PMCID: PMC10821590 DOI: 10.1016/j.jlr.2023.100492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/14/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Quantitative information on blood metabolites can be used in developing advanced medical strategies such as early detection and prevention of disease. Monitoring bioactive lipids such as steroids, bile acids, and PUFA metabolites could be a valuable indicator of health status. However, a method for simultaneously measuring these bioactive lipids has not yet been developed. Here, we report a LC/MS/MS method that can simultaneously measure 144 bioactive lipids, including steroids, bile acids, and PUFA metabolites, from human plasma, and a sample preparation method for these targets. Protein removal by methanol precipitation and purification of bioactive lipids by solid-phase extraction improved the recovery of the targeted compounds in human plasma samples, demonstrating the importance of sample preparation methods for a wide range of bioactive lipid analyses. Using the developed method, we studied the plasma from healthy human volunteers and confirmed the presence of bioactive lipid molecules associated with sex differences and circadian rhythms. The developed method of bioactive lipid analysis can be applied to health monitoring and disease biomarker discovery in precision medicine.
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Affiliation(s)
- Kohta Nakatani
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoko Nakaji
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Nakao
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazutaka Ikeda
- Laboratory of Biomolecule Analysis, Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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6
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Li S, Huang X, Li Y, Ding R, Wu X, Li L, Li C, Gu R. Spectrum-Effect Relationship in Chinese Herbal Medicine: Current Status and Future Perspectives. Crit Rev Anal Chem 2023:1-22. [PMID: 38127670 DOI: 10.1080/10408347.2023.2290056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The quality of Chinese herbal medicine (CHM) directly impacts clinical efficacy and safety. Fingerprint technology is an internationally recognized method for evaluating the quality of CHM. However, the existing quality evaluation models based on fingerprint technology have blocked the ability to assess the internal quality of CHM and cannot comprehensively reflect the correlation between pharmacodynamic information and active constituents. Through mathematical methods, a connection between the "Spectrum" (fingerprint) and the "Effect" (pharmacodynamic data) was established to conduct a spectrum-effect relationship (SER) of CHM to unravel the active component information associated with the pharmacodynamic activity. Consequently, SER can efficiently address the limitations of the segmentation of chemical components and pharmacodynamic effect in CHM and further improve the quality evaluation of CHM. This review focuses on the recent research progress of SER in the field of CHM, including the establishment of fingerprint, the selection of data analysis methods, and their recent applications in the field of CHM. Various advanced fingerprint techniques are introduced, followed by the data analysis methods used in recent years are summarized. Finally, the applications of SER based on different research subjects are described in detail. In addition, the advantages of combining SER with other data are discussed through practical applications, and the research on SER is summarized and prospected. This review proves the validity and development potential of the SER and provides a reference for the development and application of quality evaluation methods for CHM.
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Affiliation(s)
- Si Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xi Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong Ding
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xuemei Wu
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ling Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Canlin Li
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rui Gu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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7
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Li M, Pang X, Guo Z, Yang Y, Gu Z, Zhang L. Integrated metabolomics and network pharmacology to reveal the mechanism of areca nut addiction. Addict Biol 2023; 28:e13352. [PMID: 38017647 DOI: 10.1111/adb.13352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/09/2023] [Accepted: 10/16/2023] [Indexed: 11/30/2023]
Abstract
As a chewing hobby, areca nut (Areca catechu L.) has become the most common psychoactive substance in the world, besides tobacco, alcohol and caffeinated beverages. Moreover, as a first-class carcinogen designated by International Agency for Research on Cancer, long-term chewing areca nut can result in oral mucosal diseases and even oral cancer. To clarify the potential mechanism of areca nut addiction, an integrated strategy of metabolomics and network pharmacology was adopted in this study. Network pharmacology study indicated that all the key targets related to areca nut addiction could be regulated by arecoline and pointed out the importance of G-protein coupled receptor signalling pathway. Analysis results of mice plasma metabolome and faeces metabolome intervened by arecoline suggested that the component may affect the dopamine system and 5-HT system by regulating phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, primary bile acid biosynthesis, glycerophospholipid metabolism and intestinal flora structure. Moreover, the potential importance of bile acids in formation of addictive behaviour of chewing areca nut was investigated by integrative analysis of the relationships between metabolites and intestinal flora. The study can provide scientific basis for the addiction intervention and treatment of areca nut chewers.
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Affiliation(s)
- Moying Li
- School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu, China
| | - Xin Pang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
| | - Zitao Guo
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
| | - Yuliang Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhenghua Gu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
| | - Liang Zhang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu, China
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Kerth CR, Wall KR, Hicks ZM, Miller RK. Using untargeted metabolomics and volatile aroma compounds to predict expert sensory descriptors and consumer liking of beef loin steaks varying in quality grade, aging time, and degree of doneness. Meat Sci 2023; 204:109255. [PMID: 37343480 DOI: 10.1016/j.meatsci.2023.109255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/19/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Precursors to flavor are important to its development, yet little is known about the intrinsic products of metabolism that influence flavor. Our objective was to use untargeted metabolomics and volatile aroma compounds to predict expert and consumer sensory traits. USDA Select and upper 2/3 Choice beef strip loins were wet aged for 10 or 20 d and then cut into steaks, vacuum-packaged, and frozen. Steaks were cooked to 63 °C, 71 °C, or 80 °C end-point internal steak temperature. USDA Choice steaks had more intense beef flavor identity, brown, roasted, fat-like, salty, sweet, sour, umami, buttery, and overall sweet flavors compared to USDA Select steaks (P < 0.05). Steaks cooked to 80 °C had more intense beef identity, brown, roasted, and umami flavors than steaks cooked to a lower degree of doneness. Steaks cooked to either 63 °C or 71 °C had more intense bloody, metallic, and sour flavors and were juicier, more tender, and had less connective tissue than steaks cooked to a higher degree of doneness. Volatile aroma compounds increased (P < 0.05) in Choice steaks aged for 20 d, while cooking steaks to 80 increased aldehydes, ketones, and pyrazines. Raw steaks had 69 small-molecule metabolomic compounds shared across all four quality grade x aging combinations, and discriminant analysis correctly categorized (P < 0.05) these metabolites. Metabolites and volatiles can be used to predict (r2 > 0.85) expert and consumer sensory panel descriptors and liking.
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Affiliation(s)
- Chris R Kerth
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
| | | | - Zena M Hicks
- Department of Animal Science, University of Nebraska, Lincoln, NE 68182, USA
| | - Rhonda K Miller
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
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Jin Y, Chi J, LoMonaco K, Boon A, Gu H. Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome. Trends Analyt Chem 2023; 166:117155. [PMID: 37484879 PMCID: PMC10361410 DOI: 10.1016/j.trac.2023.117155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.
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Affiliation(s)
- Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jinhua Chi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Kaelene LoMonaco
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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Yamakawa PE, Fonseca AR, Guerreiro da Silva IDC, Gonçalves MV, Marchioni DM, Carioca AAF, Michonneau D, Arrais-Rodrigues C. Biochemical phenotyping of paroxysmal nocturnal hemoglobinuria reveals solute carriers and β-oxidation deficiencies. PLoS One 2023; 18:e0289285. [PMID: 37527257 PMCID: PMC10393180 DOI: 10.1371/journal.pone.0289285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
INTRODUCTION Paroxysmal nocturnal hemoglobinuria (PNH) is a clonal disease of hematopoietic cells with a variable clinical spectrum characterized by intravascular hemolysis, high risk of thrombosis, and cytopenias. To understand the biochemical shifts underlying PNH, this study aimed to search for the dysfunctional pathways involved in PNH physiopathology by comparing the systemic metabolic profiles of affected patients to healthy controls and the metabolomic profiles before and after the administration of eculizumab in PNH patients undergoing treatment. METHODS Plasma metabolic profiles, comprising 186 specific annotated metabolites, were quantified using targeted quantitative electrospray ionization tandem mass spectrometry in 23 PNH patients and 166 population-based controls. In addition, samples from 12 PNH patients on regular eculizumab maintenance therapy collected before and 24 hours after eculizumab infusion were also analyzed. RESULTS In the PNH group, levels of the long-chain acylcarnitines metabolites were significantly higher as compared to the controls, while levels of histidine, taurine, glutamate, glutamine, aspartate and phosphatidylcholines were significantly lower in the PNH group. These differences suggest altered acylcarnitine balance, reduction in the amino acids participating in the glycogenesis pathway and impaired glutaminolysis. In 12 PNH patients who were receiving regular eculizumab therapy, the concentrations of acylcarnitine C6:1, the C14:1/C6 ratio (reflecting the impaired action of the medium-chain acyl-Co A dehydrogenase), and the C4/C6 ratio (reflecting the impaired action of short-chain acyl-Co A dehydrogenase) were significantly reduced immediately before eculizumab infusion, revealing impairments in the Acyl CoA metabolism, and reached levels similar to those in the healthy controls 24 hours after infusion. CONCLUSIONS We demonstrated significant differences in the metabolomes of the PNH patients compared to healthy controls. Eculizumab infusion seemed to improve deficiencies in the acyl CoA metabolism and may have a role in the mitochondrial oxidative process of long and medium-chain fatty acids, reducing oxidative stress, and inflammation.
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Affiliation(s)
| | - Ana Rita Fonseca
- Hematology Division, Universidade Federal de São Paulo, São Paulo, Brazil
- Oncology Department, Hospital Sírio Libanês, São Paulo, Brazil
| | | | | | - Dirce Maria Marchioni
- Nutrition Department, School of Public Health, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - David Michonneau
- Hematology and Bone Marrow Transplant Department of the Saint-Louis Hospital, Paris, France
| | - Celso Arrais-Rodrigues
- Hematology Division, Universidade Federal de São Paulo, São Paulo, Brazil
- Hematology Department, Hospital Nove de Julho, DASA, São Paulo, Brazil
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11
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Castaño-Ortiz JM, Courant F, Gomez E, García-Pimentel MM, León VM, Campillo JA, Santos LHMLM, Barceló D, Rodríguez-Mozaz S. Combined exposure of the bivalve Mytilus galloprovincialis to polyethylene microplastics and two pharmaceuticals (citalopram and bezafibrate): Bioaccumulation and metabolomic studies. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131904. [PMID: 37356174 DOI: 10.1016/j.jhazmat.2023.131904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
Pharmaceuticals and microplastics constitute potential hazards in aquatic systems, but their combined effects and underlying toxicity mechanisms remain largely unknown. In this study, a simultaneous characterization of bioaccumulation, associated metabolomic alterations and potential recovery mechanisms was performed. Specifically, a bioassay on Mediterranean mussels (Mytilus galloprovincialis) was carried out with polyethylene microplastics (PE-MPLs, 1 mg/L) and citalopram or bezafibrate (500 ng/L). Single and co-exposure scenarios lasted 21 days, followed by a 7-day depuration period to assess their potential recovery. PE-MPLs delayed the bioaccumulation of citalopram (lower mean at 10 d: 447 compared to 770 ng/g dw under single exposure), although reaching similar tissue concentrations after 21 d. A more limited accumulation of bezafibrate was observed overall, regardless of PE-MPLs co-exposure (<MQL-3.2 ng/g dw). Metabolic profiles showed a strong effect of pharmaceuticals, generally independent of PE-MPLs co-exposure. Alterations of the citrate cycle (bezafibrate exposure) and steroid and prostaglandin metabolism (citalopram and bezafibrate exposures) were highlighted. PE-MPLs alone also impacted metabolic pathways, such as neurotransmitters or purine metabolism. After depuration, relevant latent or long-lasting effects were demonstrated as, for instance, the effect of citalopram on neurotransmitters metabolism. Altogether, the observed molecular-level responses to pharmaceuticals and/or PE-MPLs may lead to a dysregulation of mussels' reproduction, energy metabolism, and/or immunity.
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Affiliation(s)
- J M Castaño-Ortiz
- University of Girona, Girona, Spain; Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain.
| | - F Courant
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - E Gomez
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - M M García-Pimentel
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de Murcia, C/Varadero 1, San Pedro del Pinatar, Murcia, Spain
| | - V M León
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de Murcia, C/Varadero 1, San Pedro del Pinatar, Murcia, Spain
| | - J A Campillo
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de Murcia, C/Varadero 1, San Pedro del Pinatar, Murcia, Spain
| | - L H M L M Santos
- University of Girona, Girona, Spain; Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain
| | - D Barceló
- University of Girona, Girona, Spain; Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain; Institute of Environmental Assessment and Water Research (IDAEA-CSIC) Severo Ochoa Excellence Centre, Department of Environmental Chemistry, C/ Jordi Girona 18-26, 08034 Barcelona, Spain
| | - S Rodríguez-Mozaz
- University of Girona, Girona, Spain; Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain
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12
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Abd Rahman MR, Hassan Z, Hassan MS, Hashim R, Wong LS, Leong WY, Syd Jaafar SH, Salvamani S. Enhanced Goat Milk MUFA Quality via Date Pit Supplementation: A Time-Based Pattern Recognition Analysis Utilizing Agricultural Waste Byproduct. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2023; 2023:1797017. [PMID: 37350796 PMCID: PMC10284659 DOI: 10.1155/2023/1797017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Date pits are agricultural waste byproducts and are available in tons yearly. Milk MUFAs are lipids beneficial for health and sorted out for food product development. This work is aimed at researching the effect of supplementing dairy goats with date pit powder (DPP) as a source of fatty acids (FA), an alternative to enhancing the unsaturated FA in milk and analysed via chemometrics in a 3-month supplementation-based study. Saanen-Boer crossed dairy goats were divided into six groups comprising of control, 10 g and 20 g both for Ajwa DPP (high-quality dates) and Mariami DPP (agricultural waste byproduct), and another 30 g for Mariami DPP only. The supplementation exercise was done daily on each dairy goat. The DPP and milk samples were analysed for its FA profile applying GC-FID and followed by chemometric techniques, namely, PCA and PLS. Results indicated that the n-6/n-3 ratio was the highest for the unsupplemented group compared to the DPP-treated goats with lower n-6/n-3 ratios. The M30 group showcased the most promising health-related class of FAs viewed by 3D PCA and PLS model clustering patterns, in particular monounsaturated FA (MUFA) (C18:1n9c or oleic acid). These results suggest that Mariami DPP supplementation at higher doses and time to lactating Saanen-Boer cross goats can be a means to milk FA quantity and quality enhancement and that chemometrics via pattern recognition can be useful statistical tools when dealing with overwhelming data.
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Affiliation(s)
- M. R. Abd Rahman
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana Bandar Baru Nilai, Putra Nilai, 71800 Nilai, N. Sembilan, Malaysia
- Department of Food Biotechnology, Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - Z. Hassan
- Department of Food Biotechnology, Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - M. S. Hassan
- Department of Industrial Chemistry, Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - R. Hashim
- Department of Food Biotechnology, Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - L. S. Wong
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana Bandar Baru Nilai, Putra Nilai, 71800 Nilai, N. Sembilan, Malaysia
| | - W. Y. Leong
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana Bandar Baru Nilai, Putra Nilai, 71800 Nilai, N. Sembilan, Malaysia
| | - S. H. Syd Jaafar
- Department of Food Biotechnology, Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - S. Salvamani
- School of Health Sciences, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
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3-Methoxytyrosine as an indicator of dopaminergic manipulation in equine plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1220:123652. [PMID: 36933516 DOI: 10.1016/j.jchromb.2023.123652] [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: 11/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
The use of catechol-O-methyltransferase inhibitors may mask doping agents, primarily levodopa, administered to racehorses and prolong the stimulating effects of dopaminergic compounds such as dopamine. It is known that 3-methoxytyramine is a metabolite of dopamine and 3-methoxytyrosine is a metabolite of levodopa thus these compounds are proposed to be potential biomarkers of interest. Previous research established a urinary threshold of 4,000 ng/mL for 3-methoxytyramine to monitor misuse of dopaminergic agents. However, there is no equivalent biomarker in plasma. To address this deficiency a rapid protein precipitation method was developed and validated to isolate target compounds from 100 µL equine plasma. A liquid chromatography-high resolution accurate mass (LC-HRAM) method using an IMTAKT Intrada amino acid column provided quantitative analysis of 3-methoxytyrosine (3-MTyr) with lower limit of quantification of 5 ng/mL. Reference population profiling (n = 1129) investigated the expected basal concentrations for raceday samples from equine athletes and showed a right-skewed distribution (skewness = 2.39, kurtosis = 10.65) which resulted from large variation (RSD = 71%) within the data. Logarithmic transformation of the data provided a normal distribution (skewness = 0.26, kurtosis = 3.23) resulting in the proposal of a conservative threshold for plasma 3-MTyr of 1,000 ng/mL at a 99.995% confidence level. A 12-horse administration study of Stalevo® (800 mg L-DOPA, 200 mg carbidopa, 1600 mg entacapone) revealed elevated 3-MTyr concentrations for 24-hours post-administration.
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14
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Adobor S, Banniza S, Vandenberg A, Purves RW. Untargeted profiling of secondary metabolites and phytotoxins associated with stemphylium blight of lentil. PLANTA 2023; 257:73. [PMID: 36864322 DOI: 10.1007/s00425-023-04105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Stemphylium botryosum alters lentil secondary metabolism and differentially affects resistant and susceptible genotypes. Untargeted metabolomics identifies metabolites and their potential biosynthetic pathways that play a crucial role in resistance to S. botryosum. The molecular and metabolic processes that mediate resistance to stemphylium blight caused by Stemphylium botryosum Wallr. in lentil are largely unknown. Identifying metabolites and pathways associated with Stemphylium infection may provide valuable insights and novel targets to breed for enhanced resistance. The metabolic changes following infection of four lentil genotypes by S. botryosum were investigated by comprehensive untargeted metabolic profiling employing reversed-phase or hydrophilic interaction liquid chromatography (HILIC) coupled to a Q-Exactive mass spectrometer. At the pre-flowering stage, plants were inoculated with S. botryosum isolate SB19 spore suspension and leaf samples were collected at 24, 96 and 144 h post-inoculation (hpi). Mock-inoculated plants were used as negative controls. After analyte separation, high-resolution mass spectrometry data was acquired in positive and negative ionization modes. Multivariate modeling revealed significant treatment, genotype and hpi effects on metabolic profile changes that reflect lentil response to Stemphylium infection. In addition, univariate analyses highlighted numerous differentially accumulated metabolites. By contrasting the metabolic profiles of SB19-inoculated and mock-inoculated plants and among lentil genotypes, 840 pathogenesis-related metabolites were detected including seven S. botryosum phytotoxins. These metabolites included amino acids, sugars, fatty acids and flavonoids in primary and secondary metabolism. Metabolic pathway analysis revealed 11 significant pathways including flavonoid and phenylpropanoid biosynthesis, which were affected upon S. botryosum infection. This research contributes to ongoing efforts toward a comprehensive understanding of the regulation and reprogramming of lentil metabolism under biotic stress, which will provide targets for potential applications in breeding for enhanced disease resistance.
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Affiliation(s)
- Stanley Adobor
- Pulse Crop Breeding and Genetics, Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Sabine Banniza
- Pulse Crop Breeding and Genetics, Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Albert Vandenberg
- Pulse Crop Breeding and Genetics, Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Randy W Purves
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada.
- Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, Saskatoon, SK, Canada.
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15
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Santos LHMLM, Maulvault AL, Jaén-Gil A, Marques A, Barceló D, Rodríguez-Mozaz S. Linking chemical exposure and fish metabolome: Discovering new biomarkers of environmental exposure of Argyrosomus regius to the antidepressant venlafaxine. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 98:104063. [PMID: 36623700 DOI: 10.1016/j.etap.2023.104063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/16/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
In this study, a non-target metabolomic approach was used to investigate changes in the metabolome of juvenile meagre (Argyrosomus regius) exposed to venlafaxine (20 µg/L). A total of 24, 22 and 8 endogenous metabolites tentatively identified in liver, brain and plasma, respectively, were significantly changed in venlafaxine exposed meagre, showing tissue-dependent variations in the metabolic profile. The amino acids tryptophan, tyrosine and phenylalanine, which are related to the synthesis, availability, and expression of neurotransmitters (e.g., serotonin, dopamine, epinephrine), showed to be dysregulated by venlafaxine exposure. A high impact was observed in fish brain metabolome that showed a trend of up-regulation for most of the tentatively identified metabolites. In conclusion, the identification of possible biomarkers of exposure in fish metabolome to environmental stressors such as venlafaxine is crucial to assess early signal changes at molecular level, enabling the prevention of deleterious effects at the organism and population levels.
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Affiliation(s)
- Lúcia H M L M Santos
- Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain; University of Girona, Girona, Spain.
| | - Ana Luísa Maulvault
- Division of Aquaculture and Seafood Upgrading, Portuguese Institute for the Sea and Atmosphere, I.P. (IPMA), Rua Alfredo Magalhães Ramalho, 6, 1495-006 Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, UCIBIO - Unit on Applied Molecular Biosciences, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Adrián Jaén-Gil
- NORCE Norwegian Research Centre, Climate & Environment Division, Mekjarvik 12, 4072 Randaberg, Norway
| | - António Marques
- Division of Aquaculture and Seafood Upgrading, Portuguese Institute for the Sea and Atmosphere, I.P. (IPMA), Rua Alfredo Magalhães Ramalho, 6, 1495-006 Lisboa, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain; University of Girona, Girona, Spain; IDAEA-CSIC, Department of Environmental Chemistry, C/ Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA-CERCA), C/ Emili Grahit 101, 17003 Girona, Spain; University of Girona, Girona, Spain
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16
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James L, Gomez E, Ramirez G, Dumas T, Courant F. Liquid chromatography-mass spectrometry based metabolomics investigation of different tissues of Mytilus galloprovincialis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101051. [PMID: 36527760 DOI: 10.1016/j.cbd.2022.101051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/24/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
The Mediterranean mussel (Mytilus galloprovincialis) is widely used in monitoring programs and in ecotoxicological studies to examine the biological effects of physicochemical parameter changes and the impact of chemical pollutants. Metabolomics has recently demonstrated high potential to gain further insight into the molecular effects of chemical exposure and the success of its application is dependent on the extent of prior metabolomics knowledge available on the target organism. Therefore, the purpose of this study was the investigation of the metabolites of five different functional tissues of male and female Mediterranean mussels (digestive gland, foot, gill and gonad tissues and in the remaining soft tissues) accessible to the analysis using the most common sample preparation recommended for tissue analysis (i.e. Bligh & Dyer). Metabolic fingerprints were acquired via liquid chromatography high-resolution mass spectrometry and the identification was based on an internal database developed in the laboratory. It led to the identification of 110 metabolites, among which amino acids, carboxylic acids, purine and pyrimidine metabolites were often the most abundant. The metabolic contents of the five tissues quantitatively and qualitatively differed, with a clear distinction between male and female contents observed in the gonads and digestive glands. These results underline the importance of selecting the most suitable tissue and sex to study the impact of contamination on metabolism and the need for further research to deeper characterize the metabolome of this organism.
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Affiliation(s)
- Lea James
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Elena Gomez
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Gaelle Ramirez
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Thibaut Dumas
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Frédérique Courant
- HydroSciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France.
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Wildman E, Mickiewicz B, Vogel HJ, Thompson GC. Metabolomics in pediatric lower respiratory tract infections and sepsis: a literature review. Pediatr Res 2023; 93:492-502. [PMID: 35778499 PMCID: PMC9247944 DOI: 10.1038/s41390-022-02162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 11/09/2022]
Abstract
Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality in children. The ability of healthcare providers to diagnose and prognose LRTIs in the pediatric population remains a challenge, as children can present with similar clinical features regardless of the underlying pathogen or ultimate severity. Metabolomics, the large-scale analysis of metabolites and metabolic pathways offers new tools and insights that may aid in diagnosing and predicting the outcomes of LRTIs in children. This review highlights the latest literature on the clinical utility of metabolomics in providing care for children with bronchiolitis, pneumonia, COVID-19, and sepsis. IMPACT: This article summarizes current metabolomics approaches to diagnosing and predicting the course of pediatric lower respiratory infections. This article highlights the limitations to current metabolomics research and highlights future directions for the field.
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Affiliation(s)
- Emily Wildman
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Beata Mickiewicz
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Hans J Vogel
- Bio-NMR Centre, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Graham C Thompson
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Department of Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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18
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Chandran M, S S, Abhirami, Chandran A, Jaleel A, Plakkal Ayyappan J. Defining atherosclerotic plaque biology by mass spectrometry-based omics approaches. Mol Omics 2023; 19:6-26. [PMID: 36426765 DOI: 10.1039/d2mo00260d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Atherosclerosis is the principal cause of vascular diseases and one of the leading causes of worldwide death. Even though several insights into its natural course, risk factors and interventions have been identified, it is still an ongoing global pandemic. Since the structure and biochemical composition of the plaques show high heterogeneity, a comprehensive understanding of the intraplaque composition, its microenvironment, and the mechanisms of the progression and instability across different vascular beds at their progression stages is crucial for better risk stratification and treatment modalities. Even though several cell-based studies, animal studies, and extensive multicentric population studies have been conducted concerning cardiovascular diseases for assessing the risk factors and plaque biology, the studies on human clinical samples are very limited. New novel approaches utilize samples from percutaneous coronary interventions, which could possibly gain more access to clinical samples at different stages of the diseases without complex invasive resections. As an emerging technological platform in disease discovery research, mass spectrometry-based omics technologies offer capabilities for a comprehensive understanding of the mechanisms linked to several vascular diseases. Here, we discuss the cellular and molecular processes of atherosclerosis, different mass spectrometry-based omics approaches, and the studies mostly done on clinical samples of atheroma plaque using mass spectrometry-based proteomics, metabolomics and lipidomics approaches.
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Affiliation(s)
- Mahesh Chandran
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Sudhina S
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Abhirami
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India.
| | - Akash Chandran
- Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India
| | - Abdul Jaleel
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695012, India
| | - Janeesh Plakkal Ayyappan
- Translational Nanomedicine and Lifestyle Disease Research Laboratory, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India. .,Department of Biotechnology, University of Kerala, Thiruvananthapuram 695034, Kerala, India.,Department of Nanoscience and Nanotechnology, University of Kerala, Kariavattom, Thiruvananthapuram-695581, Kerala, India.,Centre for Advanced Cancer Research, Department of Biochemistry, University of Kerala, Thiruvananthapuram 695034, Kerala, India
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Tou K, Cawley A, Bowen C, Bishop DP, Fu S. Towards Non-Targeted Screening of Lipid Biomarkers for Improved Equine Anti-Doping. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010312. [PMID: 36615506 PMCID: PMC9822433 DOI: 10.3390/molecules28010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023]
Abstract
The current approach to equine anti-doping is focused on the targeted detection of prohibited substances. However, as new substances are rapidly being developed, the need for complimentary methods for monitoring is crucial to ensure the integrity of the racing industry is upheld. Lipidomics is a growing field involved in the characterisation of lipids, their function and metabolism in a biological system. Different lipids have various biological effects throughout the equine system including platelet aggregation and inflammation. A certain class of lipids that are being reviewed are the eicosanoids (inflammatory markers). The use of eicosanoids as a complementary method for monitoring has become increasingly popular with various studies completed to highlight their potential. Studies including various corticosteroids, non-steroidal anti-inflammatories and cannabidiol have been reviewed to highlight the progress lipidomics has had in contributing to the equine anti-doping industry. This review has explored the techniques used to prepare and analyse samples for lipidomic investigations in addition to the statistical analysis and potential for lipidomics to be used for a longitudinal assessment in the equine anti-doping industry.
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Affiliation(s)
- Kathy Tou
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Correspondence:
| | - Adam Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW 2000, Australia
| | - Christopher Bowen
- Mass Spectrometry Business Unit, Shimadzu Scientific Instruments (Australasia), Sydney, NSW 2116, Australia
| | - David P. Bishop
- Hyphenated Mass Spectrometry Laboratory (HyMAS), University of Technology, Sydney, NSW 2007, Australia
| | - Shanlin Fu
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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20
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Rabelo IB, Chiba AK, Moritz E, D'Amora P, Silva IDCG, Rodrigues CA, Barros MMO, Bordin JO. Metabolomic profile in patients with primary warm autoimmune haemolytic anaemia. Br J Haematol 2022; 201:140-149. [PMID: 36484101 DOI: 10.1111/bjh.18584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 12/13/2022]
Abstract
Autoimmune haemolytic anaemia (AIHA) is a rare clinical condition with immunoglobulin fixation on the surface of erythrocytes, with or without complement activation. The pathophysiology of AIHA is complex and multifactorial, presenting functional abnormalities of T and B lymphocytes that generate an imbalance between lymphocyte activation, immunotolerance and cytokine production that culminates in autoimmune haemolysis. In AIHA, further laboratory data are needed to predict relapse and refractoriness of therapy, and thus, prevent adverse side-effects and treatment-induced toxicity. The metabolomic profile of AIHA has not yet been described. Our group developed a cross-sectional study with follow-up to assess the metabolomic profile in these patients, as well as to compare the metabolites found depending on the activity and intensity of haemolysis. We analysed the plasma of 26 patients with primary warm AIHA compared to 150 healthy individuals by mass spectrometry. Of the 95 metabolites found in the patients with AIHA, four acylcarnitines, two phosphatidylcholines (PC), asymmetric dimethylarginine (ADMA) and three sphingomyelins were significantly increased. There was an increase in PC, spermine and spermidine in the AIHA group with haemolytic activity. The PC ae 34:3/PC ae 40:2 ratio, seen only in the 12-month relapse group, was a predictor of relapse with 81% specificity and 100% sensitivity. Increased sphingomyelin, ADMA, PC and polyamines in patients with warm AIHA can interfere in autoantigen and autoimmune recognition mechanisms in a number of ways (deficient action of regulatory T lymphocytes on erythrocyte recognition as self, negative regulation of macrophage nuclear factor kappa beta activity, perpetuation of effector T lymphocyte and antibody production against erythrocyte antigens). The presence of PC ae 34:3/PC ae 40:2 ratio as a relapse predictor can help in identifying cases that require more frequent follow-up or early second-line therapies.
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Affiliation(s)
- Iara B. Rabelo
- Clinical and Experimental Oncology Department, Haematology and Hemotherapy Division College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - Akemi K. Chiba
- Clinical and Experimental Oncology Department, Haematology and Hemotherapy Division College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - Elyse Moritz
- Clinical and Experimental Oncology Department, Haematology and Hemotherapy Division College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - Paulo D'Amora
- Gynecology Department College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - Ismael Dale C. G. Silva
- Gynecology Department College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - Celso A. Rodrigues
- Clinical and Experimental Oncology Department, Haematology and Hemotherapy Division College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - Melca M. O. Barros
- Clinical and Experimental Oncology Department, Haematology and Hemotherapy Division College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
| | - José O. Bordin
- Clinical and Experimental Oncology Department, Haematology and Hemotherapy Division College of Medicine of the Federal University of São Paulo (EPM‐UNIFESP) São Paulo Brazil
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21
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Raj A, Kumar A. Recent advances in assessment methods and mechanism of microbe-mediated chlorpyrifos remediation. ENVIRONMENTAL RESEARCH 2022; 214:114011. [PMID: 35985484 DOI: 10.1016/j.envres.2022.114011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Chlorpyrifos (CP) is one of the Organophosphorus pesticides (OPs) primarily used in agriculture to safeguard crops from pests and diseases. The pervasive use of chlorpyrifos is hazardous to humans and the environment as it inhibits the receptor for acetylcholinesterase activity, leading to abnormalities linked to the central nervous system. Hence, there is an ardent need to develop an effective and sustainable approach to the on-site degradation of chlorpyrifos. The role of microbes in the remediation of pesticides is considered the most effective and eco-friendly approach, as they have strong degradative potential due to their gene and enzymes naturally adapted to these sites. Several reports have previously been published on exploring the role of microbes in the degradation of CP. However, detection of CP as an environmental contaminant is an essential prerequisite for developing an efficient microbial-mediated biodegradation method with less harmful intermediates. Most of the articles published to date discuss the fate and impact of CP in the environment along with its degradation mechanism but still fail to discuss the analytical portion. This review is focused on the latest developments in the field of bioremediation of CP along with its physicochemical properties, toxicity, fate, and conventional (UV-Visible spectrophotometer, FTIR, NMR, GC-MS, etc) and advanced detection methods (Biosensors and immunochromatography-based methods) from different environmental samples. Apart from it, this review explores the role of metagenomics, system biology, in-silico tools, and genetic engineering in facilitating the bioremediation of CP. One of the objectives of this review is to educate policymakers with scientific data that will enable the development of appropriate strategies to reduce pesticide exposure and the harmful health impacts on both Human and other environmental components. Moreover, this review provides up-to-date developments related to the sustainable remediation of CP.
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Affiliation(s)
- Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, MP, India.
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22
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Metabology: Analysis of metabolomics data using community ecology tools. Anal Chim Acta 2022; 1232:340469. [DOI: 10.1016/j.aca.2022.340469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/15/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022]
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23
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Ncube E, Mohale K, Nogemane N. Metabolomics as a Prospective Tool for Soybean ( Glycine max) Crop Improvement. Curr Issues Mol Biol 2022; 44:4181-4196. [PMID: 36135199 PMCID: PMC9497771 DOI: 10.3390/cimb44090287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 12/03/2022] Open
Abstract
Global demand for soybean and its products has stimulated research into the production of novel genotypes with higher yields, greater drought and disease tolerance, and shorter growth times. Genetic research may be the most effective way to continue developing high-performing cultivars with desirable agronomic features and improved nutritional content and seed performance. Metabolomics, which predicts the metabolic marker for plant performance under stressful conditions, is rapidly gaining interest in plant breeding and has emerged as a powerful tool for driving crop improvement. The development of increasingly sensitive, automated, and high-throughput analytical technologies, paired with improved bioinformatics and other omics techniques, has paved the way for wide characterization of genetic characteristics for crop improvement. The combination of chromatography (liquid and gas-based) with mass spectrometry has also proven to be an indisputable efficient platform for metabolomic studies, notably plant metabolic fingerprinting investigations. Nevertheless, there has been significant progress in the use of nuclear magnetic resonance (NMR), capillary electrophoresis, and Fourier-transform infrared spectroscopy (FTIR), each with its own set of benefits and drawbacks. Furthermore, utilizing multivariate analysis, principal components analysis (PCA), discriminant analysis, and projection to latent structures (PLS), it is possible to identify and differentiate various groups. The researched soybean varieties may be correctly classified by using the PCA and PLS multivariate analyses. As metabolomics is an effective method for evaluating and selecting wild specimens with desirable features for the breeding of improved new cultivars, plant breeders can benefit from the identification of metabolite biomarkers and key metabolic pathways to develop new genotypes with value-added features.
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Affiliation(s)
- Efficient Ncube
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Private Bag x 6, Florida, Johannesburg 1710, South Africa
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24
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Metabolomic and transcriptomic analysis of roots of tobacco varieties resistant and susceptible to bacterial wilt. Genomics 2022; 114:110471. [DOI: 10.1016/j.ygeno.2022.110471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/10/2022] [Accepted: 08/27/2022] [Indexed: 12/21/2022]
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25
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Keen B, Cawley A, Reedy B, Fu S. Metabolomics in clinical and forensic toxicology, sports anti-doping and veterinary residues. Drug Test Anal 2022; 14:794-807. [PMID: 35194967 PMCID: PMC9544538 DOI: 10.1002/dta.3245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Abstract
Metabolomics is a multidisciplinary field providing workflows for complementary approaches to conventional analytical determinations. It allows for the study of metabolically related groups of compounds or even the study of novel pathways within the biological system. The procedural stages of metabolomics; experimental design, sample preparation, analytical determinations, data processing and statistical analysis, compound identification and validation strategies are explored in this review. The selected approach will depend on the type of study being conducted. Experimental design influences the whole metabolomics workflow and thus needs to be properly assessed to ensure sufficient sample size, minimal introduced and biological variation and appropriate statistical power. Sample preparation needs to be simple, yet potentially global in order to detect as many compounds as possible. Analytical determinations need to be optimised either for the list of targeted compounds or a universal approach. Data processing and statistical analysis approaches vary widely and need to be better harmonised for review and interpretation. This includes validation strategies that are currently deficient in many presented workflows. Common compound identification approaches have been explored in this review. Metabolomics applications are discussed for clinical and forensic toxicology, human and equine sports anti-doping and veterinary residues.
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Affiliation(s)
- Bethany Keen
- Centre for Forensic ScienceUniversity of Technology SydneyBroadwayNew South WalesAustralia
| | - Adam Cawley
- Australian Racing Forensic LaboratoryRacing NSWSydneyNew South WalesAustralia
| | - Brian Reedy
- School of Mathematical and Physical SciencesUniversity of Technology SydneyBroadwayNew South WalesAustralia
| | - Shanlin Fu
- Centre for Forensic ScienceUniversity of Technology SydneyBroadwayNew South WalesAustralia
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26
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Klingberg J, Keen B, Cawley A, Pasin D, Fu S. Developments in high-resolution mass spectrometric analyses of new psychoactive substances. Arch Toxicol 2022; 96:949-967. [PMID: 35141767 PMCID: PMC8921034 DOI: 10.1007/s00204-022-03224-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
The proliferation of new psychoactive substances (NPS) has necessitated the development and improvement of current practices for the detection and identification of known NPS and newly emerging derivatives. High-resolution mass spectrometry (HRMS) is quickly becoming the industry standard for these analyses due to its ability to be operated in data-independent acquisition (DIA) modes, allowing for the collection of large amounts of data and enabling retrospective data interrogation as new information becomes available. The increasing popularity of HRMS has also prompted the exploration of new ways to screen for NPS, including broad-spectrum wastewater analysis to identify usage trends in the community and metabolomic-based approaches to examine the effects of drugs of abuse on endogenous compounds. In this paper, the novel applications of HRMS techniques to the analysis of NPS is reviewed. In particular, the development of innovative data analysis and interpretation approaches is discussed, including the application of machine learning and molecular networking to toxicological analyses.
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Affiliation(s)
- Joshua Klingberg
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW, 2000, Australia.
| | - Bethany Keen
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Adam Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW, 2000, Australia
| | - Daniel Pasin
- Section of Forensic Chemistry, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Fu
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, 2007, Australia
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27
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Guo J, Shen S, Huan T. Paramounter: Direct Measurement of Universal Parameters To Process Metabolomics Data in a "White Box". Anal Chem 2022; 94:4260-4268. [PMID: 35245044 DOI: 10.1021/acs.analchem.1c04758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Choosing appropriate data processing parameters is critical in processing liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics data. The conventional design of experiments (DOE) approach is time-consuming and provides no intuitive explanation why the selected parameters generate the best results. After studying commonly used metabolomics data processing software, this work summarized a set of universal parameters, including mass tolerance, peak height, peak width, and instrumental shift. These universal parameters are shared among different feature extraction programs and are critical to metabolic feature extraction. We then developed Paramounter, an R program that automatically measures these universal parameters from raw LC-MS-based metabolomics data prior to metabolic feature extraction. This is made possible through novel concepts of rank-based intensity sorting, zone of interest, and many others. Paramounter also translates universal parameters to software-specific parameters for data processing in different programs. Applying Paramounter is demonstrated to provide a threefold increase in the extracted metabolites compared to using default parameters in MS-DIAL-based feature extraction. Furthermore, the comparison between Paramounter, AutoTuner, and IPO showed that Paramounter generates 3.7- and 1.6-fold more true positive features than AutoTuner and IPO, respectively. Further validation of Paramounter on 11 datasets covering different sample types, data acquisition modes, and MS vendors proved that Paramounter is a convenient and robust program. Overall, the proposed universal parameters and the development of Paramounter address a critical need in metabolomics data processing, transforming metabolomics feature extraction from a "black box" to a "white box." Paramounter is freely available on GitHub (https://github.com/HuanLab/Paramounter).
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Affiliation(s)
- Jian Guo
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Sam Shen
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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28
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Dumas T, Courant F, Fenet H, Gomez E. Environmental Metabolomics Promises and Achievements in the Field of Aquatic Ecotoxicology: Viewed through the Pharmaceutical Lens. Metabolites 2022; 12:186. [PMID: 35208259 PMCID: PMC8880617 DOI: 10.3390/metabo12020186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
Scientists often set ambitious targets using environmental metabolomics to address challenging ecotoxicological issues. This promising approach has a high potential to elucidate the mechanisms of action (MeOAs) of contaminants (in hazard assessments) and to develop biomarkers (in environmental biomonitoring). However, metabolomics fingerprints often involve a complex mixture of molecular effects that are hard to link to a specific MeOA (if detected in the analytical conditions used). Given these promises and limitations, here we propose an updated review on the achievements of this approach. Metabolomics-based studies conducted on the effects of pharmaceutical active compounds in aquatic organisms provide a relevant means to review the achievements of this approach, as prior knowledge about the MeOA of these molecules could help overcome some shortcomings. This review highlighted that current metabolomics advances have enabled more accurate MeOA assessment, especially when combined with other omics approaches. The combination of metabolomics with other measured biological endpoints has also turned out to be an efficient way to link molecular effects to (sub)-individual adverse outcomes, thereby paving the way to the construction of adverse outcome pathways (AOPs). Here, we also discuss the importance of determining MeOA as a key strategy in the identification of MeOA-specific biomarkers for biomonitoring. We have put forward some recommendations to take full advantage of environmental metabolomics and thus help fulfil these promises.
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Affiliation(s)
| | - Frédérique Courant
- HydroSciences Montpellier, IRD, CNRS, University of Montpellier, Montpellier, France; (T.D.); (H.F.); (E.G.)
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29
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Othibeng K, Nephali L, Myoli A, Buthelezi N, Jonker W, Huyser J, Tugizimana F. Metabolic Circuits in Sap Extracts Reflect the Effects of a Microbial Biostimulant on Maize Metabolism under Drought Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040510. [PMID: 35214843 PMCID: PMC8877938 DOI: 10.3390/plants11040510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 05/17/2023]
Abstract
The use of microbial biostimulants in the agricultural sector is increasingly gaining momentum and drawing scientific attention to decode the molecular interactions between the biostimulants and plants. Although these biostimulants have been shown to improve plant health and development, the underlying molecular phenomenology remains enigmatic. Thus, this study is a metabolomics work to unravel metabolic circuits in sap extracts from maize plants treated with a microbial biostimulant, under normal and drought conditions. The biostimulant, which was a consortium of different Bacilli strains, was applied at the planting stage, followed by drought stress application. The maize sap extracts were collected at 5 weeks after emergence, and the extracted metabolites were analyzed on liquid chromatography-mass spectrometry platforms. The acquired data were mined using chemometrics and bioinformatics tools. The results showed that under both well-watered and drought stress conditions, the application of the biostimulant led to differential changes in the profiles of amino acids, hormones, TCA intermediates, phenolics, steviol glycosides and oxylipins. These metabolic changes spanned several biological pathways and involved a high correlation of the biochemical as well as structural metabolic relationships that coordinate the maize metabolism. The hypothetical model, postulated from this study, describes metabolic events induced by the microbial biostimulant for growth promotion and enhanced defences. Such understanding of biostimulant-induced changes in maize sap pinpoints to the biochemistry and molecular mechanisms that govern the biostimulant-plant interactions, which contribute to ongoing efforts to generate actionable knowledge of the molecular and physiological mechanisms that define modes of action of biostimulants.
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Affiliation(s)
- Kgalaletso Othibeng
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Akhona Myoli
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Nombuso Buthelezi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
| | - Willem Jonker
- International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa; (W.J.); (J.H.)
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa; (W.J.); (J.H.)
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.O.); (L.N.); (A.M.); (N.B.)
- International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa; (W.J.); (J.H.)
- Correspondence: or ; Tel.: +27-011-559-7784
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30
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Colás-Ruiz NR, Ramirez G, Courant F, Gomez E, Hampel M, Lara-Martín PA. Multi-omic approach to evaluate the response of gilt-head sea bream (Sparus aurata) exposed to the UV filter sulisobenzone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:150080. [PMID: 34525742 DOI: 10.1016/j.scitotenv.2021.150080] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Sulisobenzone (BP-4) is one of the benzophenone type UV filters most frequently detected in aquatic ecosystems. As a suspected endocrine disrupting compound, scarce information is available yet about other molecular effects and its mechanism of action. Here, we used an integrated transcriptomic and metabolomic approach to improve the current understanding on the toxicity of BP-4 towards aquatic species. Gilt-head sea bream individuals were exposed at environmentally relevant concentrations (10 μg L-1) for 22 days. Transcriptomic analysis revealed 371 differentially expressed genes in liver while metabolomic analysis identified 123 differentially modulated features in plasma and 118 in liver. Integration of transcriptomic and metabolomic data showed disruption of the energy metabolism (>10 pathways related to the metabolism of amino acids and carbohydrates were impacted) and lipid metabolism (5 glycerophospholipids and the expression of 3 enzymes were affected), suggesting oxidative stress. We also observed, for the first time in vivo and at environmental relevant concentrations, the disruption of several enzymes involved in the steroid and thyroid hormones biosynthesis. DNA and RNA synthesis was also impacted by changes in the purine and pyrimidine metabolisms. Overall, the multiomic workflow presented here increases the evidence on suspected effects of BP-4 exposure and identifies additional modes of action of the compounds that could have been overlooked by using single omic approaches.
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Affiliation(s)
- Nieves R Colás-Ruiz
- Faculty of Marine and Environmental Sciences (CASEM), University of Cadiz, 11510 Puerto Real, Cádiz, Spain
| | - Gaëlle Ramirez
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Frédérique Courant
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Elena Gomez
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Miriam Hampel
- Faculty of Marine and Environmental Sciences (CASEM), University of Cadiz, 11510 Puerto Real, Cádiz, Spain
| | - Pablo A Lara-Martín
- Faculty of Marine and Environmental Sciences (CASEM), University of Cadiz, 11510 Puerto Real, Cádiz, Spain.
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31
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Nephali L, Steenkamp P, Burgess K, Huyser J, Brand M, van der Hooft JJJ, Tugizimana F. Mass Spectral Molecular Networking to Profile the Metabolome of Biostimulant Bacillus Strains. FRONTIERS IN PLANT SCIENCE 2022; 13:920963. [PMID: 35755693 PMCID: PMC9218640 DOI: 10.3389/fpls.2022.920963] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/18/2022] [Indexed: 05/17/2023]
Abstract
Beneficial soil microbes like plant growth-promoting rhizobacteria (PGPR) significantly contribute to plant growth and development through various mechanisms activated by plant-PGPR interactions. However, a complete understanding of the biochemistry of the PGPR and microbial intraspecific interactions within the consortia is still enigmatic. Such complexities constrain the design and use of PGPR formulations for sustainable agriculture. Therefore, we report the application of mass spectrometry (MS)-based untargeted metabolomics and molecular networking (MN) to interrogate and profile the intracellular chemical space of PGPR Bacillus strains: B. laterosporus, B. amyloliquefaciens, B. licheniformis 1001, and B. licheniformis M017 and their consortium. The results revealed differential and diverse chemistries in the four Bacillus strains when grown separately, and also differing from when grown as a consortium. MolNetEnhancer networks revealed 11 differential molecular families that are comprised of lipids and lipid-like molecules, benzenoids, nucleotide-like molecules, and organic acids and derivatives. Consortium and B. amyloliquefaciens metabolite profiles were characterized by the high abundance of surfactins, whereas B. licheniformis strains were characterized by the unique presence of lichenysins. Thus, this work, applying metabolome mining tools, maps the microbial chemical space of isolates and their consortium, thus providing valuable insights into molecular information of microbial systems. Such fundamental knowledge is essential for the innovative design and use of PGPR-based biostimulants.
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Affiliation(s)
- Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Paul Steenkamp
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Karl Burgess
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Margaretha Brand
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Justin J. J. van der Hooft
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
- *Correspondence: Justin J. J. van der Hooft,
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
- Fidele Tugizimana,
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32
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Culberson AL, Chilmonczyk MA, Kottke PA, Bowles-Welch AC, Ghoshal D, Fedorov AG. Sample-to-analysis platform for rapid intracellular mass spectrometry from small numbers of cells. LAB ON A CHIP 2021; 21:4696-4706. [PMID: 34751694 PMCID: PMC8721559 DOI: 10.1039/d1lc00884f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Real-time, advanced diagnostics of the biochemical state within cells remains a significant challenge for research and development, production, and application of cell-based therapies. The fundamental biochemical processes and mechanisms of action of such advanced therapies are still largely unknown, including the critical quality attributes that correlate to therapeutic function, performance, and potency and the critical process parameters that impact quality throughout cell therapy manufacturing. An integrated microfluidic platform has been developed for in-line analysis of a small number of cells via direct infusion nano-electrospray ionization mass spectrometry. Central to this platform is a microfabricated cell processing device that prepares cells from limited sample volumes removed directly from cell culture systems. The sample-to-analysis workflow overcomes the labor intensive, time-consuming, and destructive nature of existing mass spectrometry approaches for analysis of cells. By providing rapid, high-throughput analyses of the intracellular state, this platform enables untargeted discovery of critical quality attributes and their real-time, in-process monitoring.
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Affiliation(s)
- Austin L Culberson
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Mason A Chilmonczyk
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Peter A Kottke
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Annie C Bowles-Welch
- Marcus Center for Therapeutic Cell Characterization and Manufacturing, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Delta Ghoshal
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Andrei G Fedorov
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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Zhang C, Shi C, Zhang H, Yu K, Wang Y, Jiang J, Kan G. Metabolomics reveals the mechanism of Antarctic yeast Rhodotorula mucliaginosa AN5 to cope with cadmium stress. Biometals 2021; 35:53-65. [PMID: 34731410 DOI: 10.1007/s10534-021-00350-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/25/2021] [Indexed: 01/02/2023]
Abstract
Heavy metal pollution in Antarctica has far exceeded expectations. Antarctic yeast is widely present in polar marine environment. The mechanisms of metabolomics effect of heavy metal on polar yeast have not been reported previously. In this study, gas chromatography-mass spectrometry (GC-MS) wascarried out to performed the metabolite profiling analysis of Antarctic sea-ice yeast Rhodotorula mucilaginosa AN5 exposed to different cadmium (Cd) stresses of 5 mM (HM5), 10 mM (HM10) and 20 mM (HM20), respectively. Metabolic profile analysis showed that the composition and contents of cellular metabolites have been altered by cadmium. 93 different metabolites were identified altogether, among which 23, 58 and 81 different metabolites were found in HM5, HM10 and HM20 group respectively. MetaboAnalyst analysis showed that in HM5, HM10 and HM20 groups, 12, 24 and 31 metabolic pathways were involved in the stress of cadmium to R. mucilaginosa, respectively. By contrasting with Kyoto Encyclopedia of Genes and Genomes database, we discovered that exposure of yeast AN5 to Cd stress resulted in profound biochemical changes including amino acids, organic acids and saccharides. These results will supply a nonnegligible basis of studying the adaptive resistance mechanism of Antarctic yeast Rhodotorula mucilaginosa to heavy metal.
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Affiliation(s)
- Chuanzhou Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Huancui District, Weihai, 264209, Shandong, China
| | - Cuijuan Shi
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Huancui District, Weihai, 264209, Shandong, China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Huancui District, Weihai, 264209, Shandong, China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Huancui District, Weihai, 264209, Shandong, China
| | - Yingying Wang
- School of Science, Harbin Institute of Technology (Weihai), Weihai, 264209, Shandong, China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Huancui District, Weihai, 264209, Shandong, China.,School of Environment, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Huancui District, Weihai, 264209, Shandong, China.
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Surendran A, Atefi N, Zhang H, Aliani M, Ravandi A. Defining Acute Coronary Syndrome through Metabolomics. Metabolites 2021; 11:685. [PMID: 34677400 PMCID: PMC8540033 DOI: 10.3390/metabo11100685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/19/2021] [Accepted: 09/25/2021] [Indexed: 02/06/2023] Open
Abstract
As an emerging platform technology, metabolomics offers new insights into the pathomechanisms associated with complex disease conditions, including cardiovascular diseases. It also facilitates assessing the risk of developing the disease before its clinical manifestation. For this reason, metabolomics is of growing interest for understanding the pathogenesis of acute coronary syndromes (ACS), finding new biomarkers of ACS, and its associated risk management. Metabolomics-based studies in ACS have already demonstrated immense potential for biomarker discovery and mechanistic insights by identifying metabolomic signatures (e.g., branched-chain amino acids, acylcarnitines, lysophosphatidylcholines) associated with disease progression. Herein, we discuss the various metabolomics approaches and the challenges involved in metabolic profiling, focusing on ACS. Special attention has been paid to the clinical studies of metabolomics and lipidomics in ACS, with an emphasis on ischemia/reperfusion injury.
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Affiliation(s)
- Arun Surendran
- Cardiovascular Lipidomics Laboratory, St. Boniface Hospital, Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (A.S.); (N.A.); (H.Z.)
- Mass Spectrometry and Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
| | - Negar Atefi
- Cardiovascular Lipidomics Laboratory, St. Boniface Hospital, Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (A.S.); (N.A.); (H.Z.)
| | - Hannah Zhang
- Cardiovascular Lipidomics Laboratory, St. Boniface Hospital, Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (A.S.); (N.A.); (H.Z.)
| | - Michel Aliani
- Faculty of Agricultural and Food Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R2H 2A6, Canada;
| | - Amir Ravandi
- Cardiovascular Lipidomics Laboratory, St. Boniface Hospital, Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada; (A.S.); (N.A.); (H.Z.)
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
- Section of Cardiology, Department of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
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35
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Bjerrum JT, Wang YL, Seidelin JB, Nielsen OH. IBD metabonomics predicts phenotype, disease course, and treatment response. EBioMedicine 2021; 71:103551. [PMID: 34419930 PMCID: PMC8379620 DOI: 10.1016/j.ebiom.2021.103551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023] Open
Abstract
Metabonomics in inflammatory bowel disease (IBD) characterizes the effector molecules of biological systems and thus aims to describe the molecular phenotype, generate insight into the pathology, and predict disease course and response to treatment. Nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and integrated NMR and MS platforms coupled with multivariate analyses have been applied to create such metabolic profiles. Recent advances have identified quiescent ulcerative colitis as a distinct molecular phenotype and demonstrated metabonomics as a promising clinical tool for predicting relapse and response to treatment with biologics as well as fecal microbiome transplantation, thus facilitating much needed precision medicine. However, understanding this complex research field and how it translates into clinical settings is a challenge. This review aims to describe the current workflow, analytical strategies, and associated bioinformatics, and translate current IBD metabonomic knowledge into new potential clinically applicable treatment strategies, and outline future key translational perspectives.
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Affiliation(s)
- Jacob T Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1 DK-2730, Denmark.
| | - Yulan L Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Jakob B Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1 DK-2730, Denmark
| | - Ole H Nielsen
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, Denmark
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36
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Omics applications in the fight against abuse of anabolic substances in cattle: challenges, perspectives and opportunities. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Ariza-Castro N, Courant F, Dumas T, Marion B, Fenet H, Gomez E. Elucidating venlafaxine metabolism in the Mediterranean mussel (Mytilus galloprovincialis) through combined targeted and non-targeted approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146387. [PMID: 34030260 DOI: 10.1016/j.scitotenv.2021.146387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
Exposure of aquatic organisms to antidepressants is currently well documented, while little information is available on how wild organisms cope with exposure to these pharmaceutical products. Studies on antidepressant metabolism in exposed organisms could generate information on their detoxification pathways and pharmacokinetics. The goal of this study was to enhance knowledge on the metabolism of venlafaxine (VEN)-an antidepressant frequently found in aquatic ecosystems-in Mytilus galloprovincialis, a bivalve that is present worldwide. An original tissue extraction technique based on the cationic properties of VEN was developed for further analysis of VEN and its metabolites using targeted and non-targeted approaches. This extraction method was assessed in terms of recovery and matrix effects for VEN metabolites. Commercial analytical standards were applied to characterize metabolites found in mussels exposed to 10 μg/L VEN for 3 and 7 days. Targeted and non-targeted approaches using liquid chromatography (LC) combined with high-resolution mass spectrometry (HRMS) were implemented to screen for expected metabolites based on the literature on aquatic species, and for metabolites not previously documented. Four venlafaxine metabolites were identified, namely N-desmethylvenlafaxine and O-desmethylvenlafaxine, which were clearly identified using analytical standards, and two other metabolites revealed by non-target analysis. According to the signal intensity, hydroxy-venlafaxine (OH-VEN) was the predominant metabolite detected in mussels exposed for 3 and 7 days.
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Affiliation(s)
- N Ariza-Castro
- HydroSciences, IRD, CNRS, Université de Montpellier, Montpellier, France; Escuela de Química, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica.
| | - F Courant
- HydroSciences, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - T Dumas
- HydroSciences, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - B Marion
- Institut des Biomolecules Max Mousseron, ENSCM, CNRS, Université de Montpellier, Montpellier, France
| | - H Fenet
- HydroSciences, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - E Gomez
- HydroSciences, IRD, CNRS, Université de Montpellier, Montpellier, France
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Kim HJ, Lee YR, Lee S, Kwon S, Chun YT, Hyun SH, Sung HJ, Lee J, Kang HG. Discovery of donor age markers from bloodstain by LC-MS/MS using a metabolic approach. Int J Legal Med 2021; 136:297-308. [PMID: 34218338 DOI: 10.1007/s00414-021-02640-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/14/2021] [Indexed: 01/27/2023]
Abstract
Bloodstains are frequently encountered at crime scenes and they provide important evidence about the incident, such as information about the victim or suspect and the time of death or other events. Efforts have been made to identify the age of the bloodstain's donor through genomic approaches, but there are some limitations, such as the availability of databases and the quality dependence of DNA. There is a need for the development of a tool that can obtain information at once from a small blood sample. The aim of this study is to identify bloodstain metabolite candidates that can be used to determine donor age. We prepared bloodstain samples and analyzed metabolites using high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). Eighteen molecular features (MFs) were selected as candidates using volcano plots and multivariate analysis. Based on the MS/MS spectrum of the MFs, the following nine metabolites were identified from the METaboliteLINk database: Δ2-cis eicosenoic acid, ergothioneine, adenosine 5'-monophosphate, benzaldehyde, phenacylamine, myristic acid ethyl ester, p-coumaric acid, niacinamide, and N-arachidonoyl-L-alanine. These nine age markers at high or low abundances could be used to estimate the age of a bloodstain's donor. This study was the first to develop metabolite age markers that can be used to analyze crime scene bloodstains.
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Affiliation(s)
- Hyo-Jin Kim
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea
| | - You-Rim Lee
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea
| | - Seungyeon Lee
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea
| | - Sohyen Kwon
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea
| | - Yeon Tae Chun
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, Republic of Korea.,Integrative Research Support Center, The Catholic University of Korea, School of Medicine, 222 Banpo-daero, Seocho-gu, Seoul, 06501, Republic of Korea
| | - Sung Hee Hyun
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea.,Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Uijeongbu, 11759, Republic of Korea
| | - Ho Joong Sung
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea.,Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, Republic of Korea
| | - Jiyeong Lee
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Uijeongbu, 11759, Republic of Korea.
| | - Hee-Gyoo Kang
- Department of Senior Healthcare, Graduate School, Eulji University, 712, Dongil-ro, Uijeongbu-si, Gyeonggi-do, 11759, Republic of Korea. .,Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam, 13135, Republic of Korea.
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Murti RH, Afifah EN, Nuringtyas TR. Metabolomic Response of Tomatoes ( Solanum lycopersicum L.) against Bacterial Wilt ( Ralstonia solanacearum) Using 1H-NMR Spectroscopy. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10061143. [PMID: 34205226 PMCID: PMC8226496 DOI: 10.3390/plants10061143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 05/31/2023]
Abstract
Ralstonia solanacearum is the pathogen responsible for wilting, yield losses, and death in tomato plants. The use of resistant cultivars has been proven as the most appropriate solution to controlling this pathogen. Therefore, further study of host-plant resistance mechanisms in tomatoes is urgently needed. 1H-NMR (nuclear magnetic resonance) spectroscopy combined with multivariate data analysis has been used to identify the biochemical compounds that play a crucial role in the defense mechanisms of tomato against bacterial wilt. Eleven metabolites consisting of amino acids, sugars and organic acids were identified and presented at different concentrations in each cultivar. Leucine and valine were determined as distinguishable metabolites of resistant and susceptible cultivars. Permata and Hawaii 7996 as resistant cultivars had a significant decrease of valine after inoculation about 1.5-2 times compared to the susceptible cultivar (GM2). Meanwhile, the resistant cultivars had a higher level of leucine, about 1.3-1.5 times compared to the susceptible ones. Synthesis of leucine and valine are linked as a member of the pyruvate family. Therefore, the decrease in valine may be related to the higher need for leucine to form the leucine-rich receptor, which plays a role in the plant's immune system against the bacterial wilt.
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Affiliation(s)
- Rudi Hari Murti
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia;
| | - Enik Nurlaili Afifah
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia;
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40
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Zheng Y, Li X, Yan R, Deng S, Li M, Zhang J, Ma L, Yu H. Evaluation of Biological Mechanisms of Eucommiae Folium in Hypertensive Kidney Injury by Integration of Untargeted Metabolomics and Network Pharmacology. J Proteome Res 2021; 20:3102-3113. [PMID: 34018394 DOI: 10.1021/acs.jproteome.0c00973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hypertensive kidney injury (Hki) is one of the most common complications of hypertension. Early prevention and treatment of renal injury in patients with hypertension is great significance. The study, which used an integrated ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS) analysis, network pharmacology approach, and plasma metabolomics, aimed to discover the active ingredients and therapeutic mechanisms of Eucommiae folium (Ef) in treating Hki. The chemical components of Ef were analyzed by UPLC-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS), and the "compound-target-disease" network was constructed by screening the closely related drug targets from the drug-target database, then the signaling pathways related to Hki were analyzed. Finally, the enzyme-linked immunosorbent assay (ELISA) and real-time quantitative reverse-transcription polymerase chain reaction were used to test and verify the key targets in the common pathways of metabolomics and network pharmacology. The results indicated that Eucommiae folium might play an excellent role in treating Hki, likely through regulating the vascular endothelial growth factor signaling pathway, hypoxia inducible factor 1 (HIF-1) signaling pathway, and glycerophospholipid metabolism pathway, which were validated by increasing levels of nitric oxide, endothelial nitric oxide synthase and reducing levels of endothelin 1, angiotensin II, renin, cyclic guanosine monophosphate, blood urea nitrogen, and serum creatinine, as well as the reduced gene expression of Ache, Ddah2, Egfr, Lcat, Pla2g2a, Stat3 and Vegfa. The study systematically explored the protective mechanisms of Ef against Hki and also provided the practical treatment strategies of Hki from the Chinese herb.
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Affiliation(s)
- Yanchao Zheng
- Tianjin Ubasio Biotechnology Group Co., Ltd., Tianjin 300457, China.,School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiankuan Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Renyi Yan
- Tianjin Ubasio Biotechnology Group Co., Ltd., Tianjin 300457, China
| | - Sha Deng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Mengyuan Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jian Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin Ma
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hongjian Yu
- Tianjin Ubasio Biotechnology Group Co., Ltd., Tianjin 300457, China
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41
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Lai KP, Gong Z, Tse WKF. Zebrafish as the toxicant screening model: Transgenic and omics approaches. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 234:105813. [PMID: 33812311 DOI: 10.1016/j.aquatox.2021.105813] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The production of large amounts of synthetic industrial and biomedical compounds, together with environmental pollutants, poses a risk to our ecosystem and induces negative effects on the health of wildlife and human beings. With the emergence of the global problem of chemical contamination, the adverse biological effects of these chemicals are gaining attention among the scientific communities, industry, governments, and the public. Among these chemicals, endocrine disrupting chemicals (EDCs) are regarded as one of the major global issues that potentially affecting our health. There is an urgent need of understanding the potential hazards of such chemicals. Zebrafish have been widely used in the aquatic toxicology. In this review, we first discuss the strategy of transgenic lines that used in the toxicological studies, followed by summarizing the current omics approaches (transcriptomics, proteomics, metabolomics, and epigenomics) on toxicities of EDCs in this model. We will also discuss the possible transgenerational effects in zebrafish and future prospective of the integrated omics approaches with customized transgenic organism. To conclude, we summarize the current findings in the field, and provide our opinions on future environmental toxicity research in the zebrafish model.
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Affiliation(s)
- Keng Po Lai
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin 541004, PR China; Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, PR China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, PR China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, PR China.
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore.
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan.
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Spina R, Saliba S, Dupire F, Ptak A, Hehn A, Piutti S, Poinsignon S, Leclerc S, Bouguet-Bonnet S, Laurain-Mattar D. Molecular Identification of Endophytic Bacteria in Leucojum aestivum In Vitro Culture , NMR-Based Metabolomics Study and LC-MS Analysis Leading to Potential Amaryllidaceae Alkaloid Production. Int J Mol Sci 2021; 22:ijms22041773. [PMID: 33578992 PMCID: PMC7916811 DOI: 10.3390/ijms22041773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 12/23/2022] Open
Abstract
In this study, endophytic bacteria belonging to the Bacillus genus were isolated from in vitro bulblets of Leucojum aestivum and their ability to produce Amaryllidaceae alkaloids was studied. Proton Nuclear Magnetic Resonance (1H NMR)-based metabolomics combined with multivariate data analysis was chosen to compare the metabolism of this plant (in vivo bulbs, in vitro bulblets) with those of the endophytic bacteria community. Primary metabolites were quantified by quantitative 1H NMR (qNMR) method. The results showed that tyrosine, one precursor of the Amaryllidaceae alkaloid biosynthesis pathway, was higher in endophytic extract compared to plant extract. In total, 22 compounds were identified including five molecules common to plant and endophyte extracts (tyrosine, isoleucine, valine, fatty acids and tyramine). In addition, endophytic extracts were analyzed using Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS) for the identification of compounds in very low concentrations. Five Amaryllidaceae alkaloids were detected in the extracts of endophytic bacteria. Lycorine, previously detected by 1H NMR, was confirmed with LC-MS analysis. Tazettine, pseudolycorine, acetylpseudolycorine, 1,2-dihydro-chlidanthine were also identified by LC-MS using the positive ionization mode or by GC-MS. In addition, 11 primary metabolites were identified in the endophytic extracts such as tyramine, which was obtained by decarboxylation of tyrosine. Thus, Bacillus sp. isolated from L. aestivum bulblets synthesized some primary and specialized metabolites in common with the L.aestivum plant. These endophytic bacteria are an interesting new approach for producing the Amaryllidaceae alkaloid such as lycorine.
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Affiliation(s)
- Rosella Spina
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France; (S.S.); (F.D.)
- Correspondence: (R.S.); (D.L.-M.); Tel.: +33-3-7274-5262 (R.S.); +33-3-7274-5675 (D.L.-M.)
| | - Sahar Saliba
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France; (S.S.); (F.D.)
| | - François Dupire
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France; (S.S.); (F.D.)
| | - Agata Ptak
- Department of Plant Breeding, Physiology and Seed Science, University of Agriculture in Krakow, Łobzowska 24, 31-140 Krakow, Poland;
| | - Alain Hehn
- Université de Lorraine, INRAE, LAE, F-54000 Nancy, France; (A.H.); (S.P.)
| | - Séverine Piutti
- Université de Lorraine, INRAE, LAE, F-54000 Nancy, France; (A.H.); (S.P.)
| | - Sophie Poinsignon
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (S.P.); (S.B.-B.)
| | | | | | - Dominique Laurain-Mattar
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France; (S.S.); (F.D.)
- Correspondence: (R.S.); (D.L.-M.); Tel.: +33-3-7274-5262 (R.S.); +33-3-7274-5675 (D.L.-M.)
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43
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Hani YMI, Prud'Homme SM, Nuzillard JM, Bonnard I, Robert C, Nott K, Ronkart S, Dedourge-Geffard O, Geffard A. 1H-NMR metabolomics profiling of zebra mussel (Dreissena polymorpha): A field-scale monitoring tool in ecotoxicological studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116048. [PMID: 33190982 DOI: 10.1016/j.envpol.2020.116048] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Biomonitoring of aquatic environments requires new tools to characterize the effects of pollutants on living organisms. Zebra mussels (Dreissena polymorpha) from the same site in north-eastern France were caged for two months, upstream and downstream of three wastewater treatment plants (WWTPs) in the international watershed of the Meuse (Charleville-Mézières "CM" in France, Namur "Nam" and Charleroi "Cr" in Belgium). The aim was to test 1H-NMR metabolomics for the assessment of water bodies' quality. The metabolomic approach was combined with a more "classical" one, i.e., the measurement of a range of energy biomarkers: lactate dehydrogenase (LDH), lipase, acid phosphatase (ACP) and amylase activities, condition index (CI), total reserves, electron transport system (ETS) activity and cellular energy allocation (CEA). Five of the eight energy biomarkers were significantly impacted (LDH, ACP, lipase, total reserves and ETS), without a clear pattern between sites (Up and Down) and stations (CM, Nam and Cr). The metabolomic approach revealed variations among the three stations, and also between the upstream and downstream of Nam and CM WWTPs. A total of 28 known metabolites was detected, among which four (lactate, glycine, maltose and glutamate) explained the observed metabolome variations between sites and stations, in accordance with chemical exposure levels. Metabolome changes suggest that zebra mussel exposure to field contamination could alter their osmoregulation and anaerobic metabolism capacities. This study reveals that lactate is a potential biomarker of interest, and 1H-NMR metabolomics can be an efficient approach to assess the health status of zebra mussels in the biomonitoring of aquatic environments.
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Affiliation(s)
- Younes Mohamed Ismail Hani
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO (Stress Environnementaux et Biosurveillance des Milieux Aquatiques), Moulin de la Housse, Reims, France; Université de Bordeaux, UMR EPOC 5805, équipe Ecotoxicologie Aquatique, Place du Dr Peyneau, 33120, Arcachon, France.
| | - Sophie Martine Prud'Homme
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO (Stress Environnementaux et Biosurveillance des Milieux Aquatiques), Moulin de la Housse, Reims, France; Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097, Reims, France
| | - Isabelle Bonnard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO (Stress Environnementaux et Biosurveillance des Milieux Aquatiques), Moulin de la Housse, Reims, France
| | | | - Katherine Nott
- La Société Wallonne des Eaux, Rue de la Concorde 41, 4800, Verviers, Belgium
| | - Sébastien Ronkart
- La Société Wallonne des Eaux, Rue de la Concorde 41, 4800, Verviers, Belgium
| | - Odile Dedourge-Geffard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO (Stress Environnementaux et Biosurveillance des Milieux Aquatiques), Moulin de la Housse, Reims, France
| | - Alain Geffard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO (Stress Environnementaux et Biosurveillance des Milieux Aquatiques), Moulin de la Housse, Reims, France
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Li Y, Niu D, Wu Y, Dong Z, Li J. Integrated analysis of transcriptomic and metabolomic data to evaluate responses to hypersalinity stress in the gill of the razor clam (Sinonovacula constricta). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100793. [PMID: 33513539 DOI: 10.1016/j.cbd.2021.100793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/01/2023]
Abstract
Salinity is an important ecological factor that affects physiological metabolism, survival, and distribution of marine organisms. Despite changes in the osmolarity and composition of the cytosol during salinity shifts, marine mollusks are able to maintain their metabolic function. The razor clam (Sinonovacula constricta) survives the wide range of salinity in the intertidal zone via changes in behavior and physiology. To explore the stress responses and mechanisms of salinity tolerance in razor clams, we collected transcriptomic and metabolomic data from a control group (salinity 20‰, S20) and a salinity-stress group (salinity 35‰, S35). The transcriptome data showed that genes related to the immune system, cytoskeleton remodeling, and signal transduction pathways dominated in the S35 group to counteract hypersalinity stress in the gill. The metabolomic analysis showed that 142 metabolites were significantly different between the S35 and S20 groups and that amino acid and carbohydrate metabolism were affected by hypersalinity stress. Levels of amino acids and energy substances, such as l-proline, isoleucine, and fructose, were higher in the gill of the S35 group. The combination of transcriptomic and metabolomic data indicated that metabolism of amino acids, carbohydrates, and lipids was enhanced in the gill during adaptation to high salinity. These results clarified the complex physiological processes involved in the response to hyperosmotic stress and maintenance of metabolism in the gill of razor clams. These findings provide a reference for further study of the biological responses of euryhaline shellfish to hyperosmotic stress and a molecular basis for the search for populations with high salinity tolerance.
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Affiliation(s)
- Yan Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Donghong Niu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Centre of Aquaculture, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Yinghan Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Zhiguo Dong
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Centre of Aquaculture, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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Miller KE, Jorgenson JW. Comparison of microcapillary column length and inner diameter investigated with gradient analysis of lipids by ultrahigh-pressure liquid chromatography-mass spectrometry. J Sep Sci 2020; 43:4094-4102. [PMID: 32946185 PMCID: PMC7727313 DOI: 10.1002/jssc.202000545] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/15/2020] [Accepted: 08/24/2020] [Indexed: 11/29/2022]
Abstract
Biological samples in lipidomic studies can consist of extremely complex mixtures due to the diverse range of species and isomerism. Herein, highly efficient, in-house packed microcapillary columns introduce the potential to better separate these complex mixtures. We compared the effects of changing column length (15, 30, and 60 cm) and inner diameter (75 and 100 μm) on lipid separation efficiency by reversed-phase gradient analysis using ultrahigh-pressure liquid chromatography coupled to mass spectrometry with operating pressures ranging from 450 to 2200 bar. Seven lipid standards composed of phosphatidylcholine and triacylglycerol species were analyzed at four different gradient rates to calculate conditional peak capacity. The longest column, 60 cm, at the shallowest gradient of 2% gave the highest peak capacity of 359 with a separation window of 2 h. The intermediate column length of 30 cm with 75 μm inner diameter provided a peak capacity of 287 with a separation window of 1 h. There was no significant difference in peak capacity between 75 and 100 μm inner diameter columns. This study showed that using highly efficient microcapillary columns increased peak capacity and resolution of lipids, and thus, this technique seems promising for enhancing lipid coverage and enabling better discovery of lipid biomarkers.
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Affiliation(s)
- Kelsey E. Miller
- Center for Environmental Measurement and ModelingU.S. Environmental Protection AgencyResearch Triangle ParkNorth Carolina27709USA
| | - James W. Jorgenson
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27599USA
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Sen C, Ray PR, Bhattacharyya M. A critical review on metabolomic analysis of milk and milk products. INT J DAIRY TECHNOL 2020. [DOI: 10.1111/1471-0307.12745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chandrakanta Sen
- Department of Dairy Chemistry West Bengal University of Animal and Fishery Sciences Mohanpur Nadia West Bengal 741252 India
| | - Pinaki Ranjan Ray
- Department of Dairy Chemistry West Bengal University of Animal and Fishery Sciences Mohanpur Nadia West Bengal 741252 India
| | - Mahasweta Bhattacharyya
- Department of Dairy Chemistry West Bengal University of Animal and Fishery Sciences Mohanpur Nadia West Bengal 741252 India
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Multifactorial Analysis of Environmental Metabolomic Data in Ecotoxicology: Wild Marine Mussel Exposed to WWTP Effluent as a Case Study. Metabolites 2020; 10:metabo10070269. [PMID: 32610679 PMCID: PMC7407289 DOI: 10.3390/metabo10070269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 01/22/2023] Open
Abstract
Environmental metabolomics is a powerful approach to investigate the response of organisms to contaminant exposure at a molecular scale. However, metabolomic responses to realistic environmental conditions can be hindered by factors intrinsic to the environment and the organism. Hence, a well-designed experimental exposure associated with adequate statistical analysis could be helpful to better characterize and relate the observed variability to its different origins. In the current study, we applied a multifactorial experiment combined to Analysis of variance Multiblock Orthogonal Partial Least Squares (AMOPLS), to assess the metabolic response of wild marine mussels, Mytilus galloprovincialis, exposed to a wastewater treatment plant effluent, considering gender as an experimental factor. First, the total observed variability was decomposed to highlight the contribution of each effect related to the experimental factors. Both the exposure and the interaction gender × exposure had a statistically significant impact on the observed metabolic alteration. Then, these metabolic patterns were further characterized by analyzing the individual variable contributions to each effect. A main change in glycerophospholipid levels was highlighted in both males and females as a common response, possibly caused by oxidative stress, which could lead to reproductive disorders, whereas metabolic alterations in some polar lipids and kynurenine pathway were rather gender-specific. This may indicate a disturbance in the energy metabolism and immune system only in males. Finally, AMOPLS is a useful tool facilitating the interpretation of complex metabolomic data and is expected to have a broad application in the field of ecotoxicology.
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Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
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Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
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Gubelit YI, Grossart HP. New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton? Front Microbiol 2020; 11:1275. [PMID: 32670226 PMCID: PMC7328189 DOI: 10.3389/fmicb.2020.01275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
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Affiliation(s)
- Yulia I. Gubelit
- Laboratory of Freshwater Hydrobiology, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Dumas T, Bonnefille B, Gomez E, Boccard J, Castro NA, Fenet H, Courant F. Metabolomics approach reveals disruption of metabolic pathways in the marine bivalve Mytilus galloprovincialis exposed to a WWTP effluent extract. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136551. [PMID: 31945539 DOI: 10.1016/j.scitotenv.2020.136551] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/20/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
Conventional wastewater treatment plants (WWTPs) discharge a highly diverse range of organic contaminants in aquatic environments, including marine waters. The health of marine ecosystems could be threatened by contaminants release. Environmental metabolomics can be helpful to assess the effects of multi-contamination on marine organisms without any a priori information since it is able to provide meaningful information on the biochemical response of organisms to a stress. The aim of the present study was to evaluate the potential of metabolomics to highlight key metabolites disrupted by a WWTP effluent extract exposure and then elucidate the biological effects of such exposure on Mediterranean mussels (Mytilus galloprovincialis). Exposed male mussels showed numerous metabolites altered in response to WWTP effluent exposure. The highlighted metabolites belong mainly to amino acids metabolism (e.g. tyrosine, phenylalanine, leucine, proline, etc.), neurohormones (dopamine and a serotonin metabolite), purine and pyrimidine metabolism (e.g. adenosine, adenine, guanine, uracil etc.), citric acid cycle intermediates (e.g. malate, fumarate), and a component involved in oxidative stress defense (oxidized glutathione). Modulation of these metabolites could reflect the alteration of several biological processes such as energy metabolism, DNA and RNA synthesis, immune system, osmoregulation, byssus formation and reproduction, which may lead to a negative impact of organism fitness. Our study provided further insight into the effects of WWTP effluents on marine organisms.
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Affiliation(s)
- Thibaut Dumas
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Bénilde Bonnefille
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Elena Gomez
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Julien Boccard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva 1211, Switzerland
| | - Nancy Ariza Castro
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France; Escuela de Química, Instituto Tecnológico de Costa Rica, Cartago, 159-7050, Costa Rica
| | - Hélène Fenet
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Frédérique Courant
- Hydrosciences Montpellier, University of Montpellier, IRD, CNRS, Montpellier, France.
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