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Lu H, Zheng S, Ma C, Gao X, Ji J, Luo J, Hua H, Cui J. Integrated Omics Analysis Reveals Key Pathways in Cotton Defense against Mirid Bug ( Adelphocoris suturalis Jakovlev) Feeding. INSECTS 2024; 15:254. [PMID: 38667384 PMCID: PMC11049813 DOI: 10.3390/insects15040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024]
Abstract
The recent dominance of Adelphocoris suturalis Jakovlev as the primary cotton field pest in Bt-cotton-cultivated areas has generated significant interest in cotton pest control research. This study addresses the limited understanding of cotton defense mechanisms triggered by A. suturalis feeding. Utilizing LC-QTOF-MS, we analyzed cotton metabolomic changes induced by A. suturalis, and identified 496 differential positive ions (374 upregulated, 122 downregulated) across 11 categories, such as terpenoids, alkaloids, phenylpropanoids, flavonoids, isoflavones, etc. Subsequent iTRAQ-LC-MS/MS analysis of the cotton proteome revealed 1569 differential proteins enriched in 35 metabolic pathways. Integrated metabolome and proteome analysis highlighted significant upregulation of 17 (89%) proteases in the α-linolenic acid (ALA) metabolism pathway, concomitant with a significant increase in 14 (88%) associated metabolites. Conversely, 19 (73%) proteases in the fructose and mannose biosynthesis pathway were downregulated, with 7 (27%) upregulated proteases corresponding to the downregulation of 8 pathway-associated metabolites. Expression analysis of key regulators in the ALA pathway, including allene oxidase synthase (AOS), phospholipase A (PLA), allene oxidative cyclase (AOC), and 12-oxophytodienoate reductase3 (OPR3), demonstrated significant responses to A. suturalis feeding. Finally, this study pioneers the exploration of molecular mechanisms in the plant-insect relationship, thereby offering insights into potential novel control strategies against this cotton pest.
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Affiliation(s)
- Hui Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Green Agricultural Products Safety and Warning Laboratory, Research Center of Soil Resource Comprehensive Utilization and Ecological Environment in Western Inner Mongolia, Hetao College, Bayannur 015000, China
| | - Shuaichao Zheng
- Henan Institute of Science and Technology, College of Life Science, Hualan St. 90, Xinxiang 453003, China;
| | - Chao Ma
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China;
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
| | - Hongxia Hua
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant, Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Chinese Academy of Agricultural Sciences, No. 38, Huanghe Road, Anyang 455000, China; (H.L.); (J.J.); (J.L.)
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Chai L, Cao Q, Liu K, Zhu R, Li H, Yu Y, Wang J, Niu R, Zhang D, Yang B, Ommati MM, Sun Z. Exercise Alleviates Fluoride-Induced Learning and Memory Impairment in Mice: Role of miR-206-3p and PREG. Biol Trace Elem Res 2024:10.1007/s12011-024-04068-w. [PMID: 38244175 DOI: 10.1007/s12011-024-04068-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
Fluorosis decreases the learning and memory ability in humans and animals, while exercise can reduce the risk of cognitive decline. However, the effect of exercise on learning and memory in fluoride-exposed mice is unclear. For this purpose, in this study, mice were randomly allotted into four groups (16 mice per group, half male and half female): control group (group C), fluoride group (group F, 100 mg/L sodium fluoride (NaF)), exercise group (group E, treadmill exercise), and E plus F group (group EF, treadmill exercise, and 100 mg/L NaF). During 6 months of exposure, exercise alleviated the NaF-induced decline in memory and learning. In addition, NaF induced injuries in mitochondria and myelin sheath ultrastructure and reduced the neurons number, while exercise restored them. Metabolomics results showed that phosphatidylethanolamine, pregnenolone (PREG), and lysophosphatidic acid (LysoPA) were altered among groups C, F, and EF. Combined with previous studies, it can be suggested that PREG might be a biomarker in response to exercise-relieving fluorine neurotoxicity. The miRNA sequencing results indicated that in the differently expressed miRNAs (DEmiRNAs), miR-206-3p, miR-96-5p, and miR-144-3p were shared in groups C, F, and EF. After the QRT-PCR validation and in vitro experiments, it was proved that miR-206-3p could reduce cell death and regulate AP-1 transcription factor subunit (JunD) and histone deacetylase 4 (HDAC4) to alleviate fluoride neurotoxicity. To sum up, the current study reveals that exercise could alleviate NaF-induced neurotoxicity by targeting miR-206-3p or PREG, which will contribute to revealing the pathogenesis and therapeutic method of fluoride neurotoxicity.
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Affiliation(s)
- Lei Chai
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Qiqi Cao
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Ke Liu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Run Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Hao Li
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Yanghuan Yu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Jixiang Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Ruiyan Niu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Ding Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Bo Yang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China
| | - Mohammad Mehdi Ommati
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China.
- Henan Key Laboratory of Environmental and Animal Product Safety, Henan University of Science and Technology, Luoyang, 471000, Henan, China.
| | - Zilong Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, Shanxi, China.
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Sajid MI, Nunez FJ, Amirrad F, Roosan MR, Vojtko T, McCulloch S, Alachkar A, Nauli SM. Untargeted metabolomics analysis on kidney tissues from mice reveals potential hypoxia biomarkers. Sci Rep 2023; 13:17516. [PMID: 37845304 PMCID: PMC10579359 DOI: 10.1038/s41598-023-44629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023] Open
Abstract
Chronic hypoxia may have a huge impact on the cardiovascular and renal systems. Advancements in microscopy, metabolomics, and bioinformatics provide opportunities to identify new biomarkers. In this study, we aimed at elucidating the metabolic alterations in kidney tissues induced by chronic hypoxia using untargeted metabolomic analyses. Reverse phase ultrahigh performance liquid chromatography-mass spectroscopy/mass spectroscopy (RP-UPLC-MS/MS) and hydrophilic interaction liquid chromatography (HILIC)-UPLC-MS/MS methods with positive and negative ion mode electrospray ionization were used for metabolic profiling. The metabolomic profiling revealed an increase in metabolites related to carnitine synthesis and purine metabolism. Additionally, there was a notable increase in bilirubin. Heme, N-acetyl-L-aspartic acid, thyroxine, and 3-beta-Hydroxy-5-cholestenoate were found to be significantly downregulated. 3-beta-Hydroxy-5-cholestenoate was downregulated more significantly in male than female kidneys. Trichome Staining also showed remarkable kidney fibrosis in mice subjected to chronic hypoxia. Our study offers potential intracellular metabolite signatures for hypoxic kidneys.
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Affiliation(s)
- Muhammad Imran Sajid
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, 9401 Jeronimo Road, Irvine, CA, 92618-1908, USA
- Faculty of Pharmaceutical Sciences, University of Central Punjab, Lahore, 54000, Pakistan
| | - Francisco J Nunez
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, 9401 Jeronimo Road, Irvine, CA, 92618-1908, USA
| | - Farideh Amirrad
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, 9401 Jeronimo Road, Irvine, CA, 92618-1908, USA
| | - Moom Rahman Roosan
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, 9401 Jeronimo Road, Irvine, CA, 92618-1908, USA
| | - Tom Vojtko
- Metabolon Inc, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Scott McCulloch
- Metabolon Inc, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Amal Alachkar
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-4625, USA.
| | - Surya M Nauli
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, 9401 Jeronimo Road, Irvine, CA, 92618-1908, USA.
- Department of Medicine, University of California Irvine, Orange, CA, 92868, USA.
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Balashova E, Trifonova O, Maslov D, Lichtenberg S, Lokhov P, Archakov A. Metabolome profiling in the study of aging processes. BIOMEDITSINSKAYA KHIMIYA 2022; 68:321-338. [DOI: 10.18097/pbmc20226805321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aging of a living organism is closely related to systemic metabolic changes. But due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, this problem is solved using one of the main approaches of metabolomics — untargeted metabolome profiling. The purpose of this publication is to systematize the results of metabolomic studies based on such profiling, both in animal models and in humans.
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Affiliation(s)
| | | | - D.L. Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
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Balashova EE, Maslov DL, Trifonova OP, Lokhov PG, Archakov AI. Metabolome Profiling in Aging Studies. BIOLOGY 2022; 11:1570. [PMID: 36358271 PMCID: PMC9687709 DOI: 10.3390/biology11111570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/07/2024]
Abstract
Organism aging is closely related to systemic metabolic changes. However, due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, scientists are trying to solve this problem using one of the main approaches of metabolomics-untargeted metabolome profiling. The purpose of this publication is to review metabolomic studies based on such profiling, both in animal models and in humans. This review describes metabolites that vary significantly across age groups and include carbohydrates, amino acids, carnitines, biogenic amines, and lipids. Metabolic pathways associated with the aging process are also shown, including those associated with amino acid, lipid, and energy metabolism. The presented data reveal the mechanisms of aging and can be used as a basis for monitoring biological age and predicting age-related diseases in the early stages of their development.
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Affiliation(s)
- Elena E. Balashova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, 119121 Moscow, Russia
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Zhang Z, Wu X, Zhou M, Qi J, Zhang R, Li X, Wang C, Ruan C, Han Y. Plasma Metabolomics Identifies the Dysregulated Metabolic Profile of Primary Immune Thrombocytopenia (ITP) Based on GC-MS. Front Pharmacol 2022; 13:845275. [PMID: 35685646 PMCID: PMC9170960 DOI: 10.3389/fphar.2022.845275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/06/2022] [Indexed: 12/04/2022] Open
Abstract
ITP is a common autoimmune bleeding disorder with elusive pathogenesis. Our study was implemented to profile the plasma metabolic alterations of patients diagnosed with ITP, aiming at exploring the potential novel biomarkers and partial mechanism of ITP. The metabolomic analysis of plasma samples was conducted using GC-MS on 98 ITP patients and 30 healthy controls (HCs). Age and gender matched samples were selected to enter the training set or test set respectively. OPLS-DA, t-test with FDR correction and ROC analyses were employed to screen out and evaluate the differential metabolites. Possible pathways were enriched based on metabolomics pathway analysis (MetPA). A total of 85 metabolites were investigated in our study and 17 differential metabolites with diagnostic potential were identified between ITP patients and HCs. MetPA showed that the metabolic disorders of ITP patients were mainly related to phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism and glyoxylate and dicarboxylate metabolism. Additionally, we discriminated 6 differential metabolites and 5 enriched pathways in predicting the resistance to glucocorticoids in chronic ITP patients. The distinct metabolites discovered in our study could become novel biomarkers for the auxiliary diagnosis and prognosis prediction of ITP. Besides, the dysregulated pathways might contribute to the development of ITP.
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Affiliation(s)
- Ziyan Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Xiaojin Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Meng Zhou
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jiaqian Qi
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Rui Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Xueqian Li
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Chang Wang
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Changgeng Ruan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Yue Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
- *Correspondence: Yue Han,
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Cui P, Li X, Huang C, Li Q, Lin D. Metabolomics and its Applications in Cancer Cachexia. Front Mol Biosci 2022; 9:789889. [PMID: 35198602 PMCID: PMC8860494 DOI: 10.3389/fmolb.2022.789889] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer cachexia (CC) is a complicated metabolic derangement and muscle wasting syndrome, affecting 50–80% cancer patients. So far, molecular mechanisms underlying CC remain elusive. Metabolomics techniques have been used to study metabolic shifts including changes of metabolite concentrations and disturbed metabolic pathways in the progression of CC, and expand further fundamental understanding of muscle loss. In this article, we aim to review the research progress and applications of metabolomics on CC in the past decade, and provide a theoretical basis for the study of prediction, early diagnosis, and therapy of CC.
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Affiliation(s)
- Pengfei Cui
- College of Food and Pharmacy, Xuchang University, Xuchang, China
| | - Xiaoyi Li
- Xuchang Central Hospital, Xuchang, China
| | - Caihua Huang
- Department of Physical Education, Xiamen University of Technology, Xiamen, China
| | - Qinxi Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Donghai Lin
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Donghai Lin,
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Terroir Effect on the Phenolic Composition and Chromatic Characteristics of Mencía/Jaen Monovarietal Wines: Bierzo D.O. (Spain) and Dão D.O. (Portugal). Molecules 2020; 25:molecules25246008. [PMID: 33353130 PMCID: PMC7766348 DOI: 10.3390/molecules25246008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 11/17/2022] Open
Abstract
‘Mencía’/‘Jaen’ it’s an important red grape variety, exclusive of the Iberian Peninsula, used in wine production namely in Bierzo D.O. and Dão D.O., respectively. This work evaluates the effect of the two different “terroirs” on the phenolic composition and chromatic characteristics of ‘Mencía’/‘Jaen’ monovarietal wines produced at an industrial scale in the same vintage. Using Principal Component Analysis (PCA), Partial Least Squares-Discrimination Analysis (PLS-DA), and Orthogonal PLS-DA (OPLS-DA) it was found that peonidin-3-coumaroylglucoside, petunidin-3-glucoside, malvidin-3-coumaroylglucoside, peonidin-3-glucoside, malvidin-3-acetylglucoside, malvidin-3-glucoside, and ferulic acid were the phenolic compounds with the highest differences between the two regions. PLS regression allowed to correlate the differences in lightness (L*) and redness (a*) of wines from ‘Jaen’ and ‘Mencía’ to differences in colored anthocyanins, polymeric pigments, total pigments, total anthocyanins, cyanidin-3-acetylglucoside, delphinidin-3-acetylglucoside, delphinidin-3-glucoside, peonidin-3-coumaroylglucoside, petunidin-3-glucoside and malvidin-3-glucoside in wines, and the colorless ferulic, caffeic, and coutaric acids, and ethyl caffeate. The wines a* values were more affected by colored anthocyanins, ferulic acid, total anthocyanins, delphinidin-3-acetylglucoside, delphinidin-3-glucoside and petunidin-3-acetylglucoside, and catechin. The positive influence of ferulic acid in the a* values and ferulic, caffeic, coutaric acids, and ethyl caffeate on the L* values can be due to the co-pigmentation phenomena. The higher dryness and lower temperatures during the September nights in this vintage might explain the differences observed in the anthocyanin content and chromatic characteristics of the wines.
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Yue B, Zhang X, Li W, Wang J, Sun Z, Niu R. Fluoride exposure altered metabolomic profile in rat serum. CHEMOSPHERE 2020; 258:127387. [PMID: 32947680 DOI: 10.1016/j.chemosphere.2020.127387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
It is well known that serum is an ideal and potential choice to reflect the toxicity of fluoride. However, the effects of fluoride on serum metabolome have not been reported until now. In this study, the models of 3-week-old rats exposed fluoride by breast milk and 11-week-old rats exposed fluoride via breast milk and drinking water containing sodium fluoride (100 mg/L) were established. Using Ultra Performance Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (UPLC-MS/MS), as compared with control group, 28 negative (NEG) and 52 positive (POS) metabolites were significantly up-regulated, meanwhile 30 NEG and 21 POS significantly down-regulated metabolites were found in serum of 3-week-old rats exposed to fluoride. For 11-week-old fluorosis rats, there were 119 NEG and 65 POS metabolites significantly increased, and 7 NEG, 5 POS metabolites were obviously decreased. Importantly, nicotinamide, adenosine, 1-Oleoyl-sn-glycero-3-phosphocholine (OGPC), and 1-Stearoyl-sn-glycerol 3-phosphocholine (SGPC) were shared by two models. The metabolites of urea cycle, such as urea and N2-Acetyl-l-ornithine, betaine as a methyl donor, were regarded to reflect the fluorosis degree. These metabolites could be the potential markers of fluorosis, contributing to the prevention and treatment of fluorosis.
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Affiliation(s)
- Baijuan Yue
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Xuhua Zhang
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Wanpan Li
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jundong Wang
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zilong Sun
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Ruiyan Niu
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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Seyler L, Kujawinski EB, Azua-Bustos A, Lee MD, Marlow J, Perl SM, Cleaves II HJ. Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. ASTROBIOLOGY 2020; 20:1251-1261. [PMID: 32551936 PMCID: PMC7116171 DOI: 10.1089/ast.2019.2135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It is now routinely possible to sequence and recover microbial genomes from environmental samples. To the degree it is feasible to assign transcriptional and translational functions to these genomes, it should be possible, in principle, to largely understand the complete molecular inputs and outputs of a microbial community. However, gene-based tools alone are presently insufficient to describe the full suite of chemical reactions and small molecules that compose a living cell. Metabolomic tools have developed quickly and now enable rapid detection and identification of small molecules within biological and environmental samples. The convergence of these technologies will soon facilitate the detection of novel enzymatic activities, novel organisms, and potentially extraterrestrial life-forms on solar system bodies. This review explores the methodological problems and scientific opportunities facing researchers who hope to apply metabolomic methods in astrobiology-related fields, and how present challenges might be overcome.
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Affiliation(s)
- Lauren Seyler
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Address correspondence to: Lauren Seyler, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 86 Water Street, Woods Hole, MA 02543, USA
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Armando Azua-Bustos
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Michael D. Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - Jeffrey Marlow
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Scott M. Perl
- Geological and Planetary Sciences, California Institute of Technology/NASA Jet Propulsion Laboratory, Pasadena, California, USA
- Mineral Sciences, Los Angeles Natural History Museum, Los Angeles, California, USA
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Natural Sciences, Institute for Advanced Study, Princeton, New Jersey, USA
- Geographical Research Laboratory, Carnegie Institution of Washington
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Lokhov PG, Balashova EE, Trifonova OP, Maslov DL, Archakov AI. [Ten years of the Russian metabolomics: history of development and achievements]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:279-293. [PMID: 32893819 DOI: 10.18097/pbmc20206604279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Metabolomics is one of the omics sciences, the technologies of which are widely used today in many life sciences. Its application influenced the discovery of new biomarkers of diseases, the description of biochemical processes occurring in many organisms, laid the basis for a new generation of clinical laboratory diagnostics. The purpose of this review is to show how metabolomics is represented in the studies of Russian scientists, to demonstrate the main directions and achievements of the Russian science in this field. The review also highlights the history of metabolomics, existing problems and the place of Russian metabolomics in their solution.
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Affiliation(s)
- P G Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - D L Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Park YH, Kong T, Roede JR, Jones DP, Lee K. A biplot correlation range for group-wise metabolite selection in mass spectrometry. BioData Min 2019; 12:4. [PMID: 30740145 PMCID: PMC6360680 DOI: 10.1186/s13040-019-0191-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/10/2019] [Indexed: 02/08/2023] Open
Abstract
Background Analytic methods are available to acquire extensive metabolic information in a cost-effective manner for personalized medicine, yet disease risk and diagnosis mostly rely upon individual biomarkers based on statistical principles of false discovery rate and correlation. Due to functional redundancies and multiple layers of regulation in complex biologic systems, individual biomarkers, while useful, are inherently limited in disease characterization. Data reduction and discriminant analysis tools such as principal component analysis (PCA), partial least squares (PLS), or orthogonal PLS (O-PLS) provide approaches to separate the metabolic phenotypes, but do not offer a statistical basis for selection of group-wise metabolites as contributors to metabolic phenotypes. Methods We present a dimensionality-reduction based approach termed ‘biplot correlation range (BCR)’ that uses biplot correlation analysis with direct orthogonal signal correction and PLS to provide the group-wise selection of metabolic markers contributing to metabolic phenotypes. Results Using a simulated multiple-layer system that often arises in complex biologic systems, we show the feasibility and superiority of the proposed approach in comparison of existing approaches based on false discovery rate and correlation. To demonstrate the proposed method in a real-life dataset, we used LC-MS based metabolomics to determine spectrum of metabolites present in liver mitochondria from wild-type (WT) mice and thioredoxin-2 transgenic (TG) mice. We select discriminatory variables in terms of increased score in the direction of class identity using BCR. The results show that BCR provides means to identify metabolites contributing to class separation in a manner that a statistical method by false discovery rate or statistical total correlation spectroscopy can hardly find in complex data analysis for predictive health and personalized medicine. Electronic supplementary material The online version of this article (10.1186/s13040-019-0191-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youngja H Park
- 1College of Pharmacy, Korea University, Sejong, 30019 South Korea
| | - Taewoon Kong
- 2Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - James R Roede
- 3Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Denver, CO 80045 USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy and Critical Care Medicine, Atlanta, GA 30322 USA.,5Department of Medicine, Emory University, Atlanta, GA 30322 USA
| | - Kichun Lee
- 6Department of Industrial Engineering, Hanyang University, Seoul, 04763 South Korea
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Sousa PFM, de Waard A, Åberg KM. Elucidation of chromatographic peak shifts in complex samples using a chemometrical approach. Anal Bioanal Chem 2018; 410:5229-5235. [PMID: 29947907 PMCID: PMC6061714 DOI: 10.1007/s00216-018-1173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/04/2018] [Accepted: 05/29/2018] [Indexed: 11/08/2022]
Abstract
Chromatographic retention time peak shifts between consecutive analyses is a well-known fact yet not fully understood. Algorithms have been developed to align peaks between runs, but with no specific studies considering the causes of peak shifts. Here, designed experiments reveal chromatographic shift patterns for a complex peptide mixture that are attributable to the temperature and pH of the mobile phase. These results demonstrate that peak shifts are highly structured and are to a high degree explained by underlying differences in physico-chemical parameters of the chromatographic system and also provide experimental support for the alignment algorithm called the generalized fuzzy Hough transform which exploits this fact. It can be expected that the development of alignment algorithms enters a new phase resulting in increasingly accurate alignment by considering the latent structure of the peak shifts.
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Affiliation(s)
- Pedro F M Sousa
- Unit for Analytical Chemistry, Department of Environmental and Analytical Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Angela de Waard
- Unit for Analytical Chemistry, Department of Environmental and Analytical Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden
| | - K Magnus Åberg
- Unit for Analytical Chemistry, Department of Environmental and Analytical Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden
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14
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Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. Current Challenges in Plant Eco-Metabolomics. Int J Mol Sci 2018; 19:E1385. [PMID: 29734799 PMCID: PMC5983679 DOI: 10.3390/ijms19051385] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
- UFZ-Helmholtz-Centre for Environmental Research, Department Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
| | - Oliver Alka
- Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
| | - Gerd Balcke
- Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany.
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany.
| | - Onno W Calf
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Sophie Dietz
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Kai Dührkop
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany.
| | - Uwe Heinig
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Marlen Kücklich
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Mirka Macel
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany.
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Christian Ristok
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Victor Manuel Rodríguez
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Meredith Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany.
| | - Rabea Schweiger
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Nir Shahaf
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Christoph Steinbeck
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Maria Tortosa
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Brigitte M Weiß
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Anja Widdig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
- Research Group of Primate Kin Selection, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
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Li SY, Zhu BQ, Reeves MJ, Duan CQ. Phenolic Analysis and Theoretic Design for Chinese Commercial Wines’ Authentication. J Food Sci 2017; 83:30-38. [DOI: 10.1111/1750-3841.13961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 09/04/2017] [Accepted: 09/27/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Si-Yu Li
- Center for Viticulture & Enology, College of Food Science and Nutritional Engineering; China Agricultural Univ.; Beijing 100083 China
- Key Laboratory of Viticulture and Enology; Ministry of Agriculture; Beijing 100083 China
| | - Bao-Qing Zhu
- College of Biological Sciences and Technology; Beijing Forestry Univ.; Beijing 100083 China
| | - Malcolm J. Reeves
- Center for Viticulture & Enology, College of Food Science and Nutritional Engineering; China Agricultural Univ.; Beijing 100083 China
- Inst. of Food, Nutrition and Human Health; Massey Univ.; Palmerston North 4442 New Zealand
| | - Chang-Qing Duan
- Center for Viticulture & Enology, College of Food Science and Nutritional Engineering; China Agricultural Univ.; Beijing 100083 China
- Key Laboratory of Viticulture and Enology; Ministry of Agriculture; Beijing 100083 China
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16
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Božičević A, Dobrzyński M, De Bie H, Gafner F, Garo E, Hamburger M. Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust. Anal Chem 2017; 89:12682-12689. [PMID: 29087694 DOI: 10.1021/acs.analchem.7b02221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.
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Affiliation(s)
- Alen Božičević
- Division of Pharmaceutical Biology, University of Basel , Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Maciej Dobrzyński
- Institute of Cell Biology, University of Bern , Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Hans De Bie
- Advanced Chemistry Development, Inc. , 8 King Street East Suite 107, Toronto, Ontario M5C, Canada
| | - Frank Gafner
- Mibelle Biochemistry, Mibelle AG , Bolimattstrasse 1, 5033 Buchs, Switzerland
| | - Eliane Garo
- Division of Pharmaceutical Biology, University of Basel , Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Matthias Hamburger
- Division of Pharmaceutical Biology, University of Basel , Klingelbergstrasse 50, 4056 Basel, Switzerland
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17
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Orbitofrontal Neuroadaptations and Cross-Species Synaptic Biomarkers in Heavy-Drinking Macaques. J Neurosci 2017; 37:3646-3660. [PMID: 28270566 DOI: 10.1523/jneurosci.0133-17.2017] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/17/2017] [Accepted: 02/28/2017] [Indexed: 02/08/2023] Open
Abstract
Cognitive impairments, uncontrolled drinking, and neuropathological cortical changes characterize alcohol use disorder. Dysfunction of the orbitofrontal cortex (OFC), a critical cortical subregion that controls learning, decision-making, and prediction of reward outcomes, contributes to executive cognitive function deficits in alcoholic individuals. Electrophysiological and quantitative synaptomics techniques were used to test the hypothesis that heavy drinking produces neuroadaptations in the macaque OFC. Integrative bioinformatics and reverse genetic approaches were used to identify and validate synaptic proteins with novel links to heavy drinking in BXD mice. In drinking monkeys, evoked firing of OFC pyramidal neurons was reduced, whereas the amplitude and frequency of postsynaptic currents were enhanced compared with controls. Bath application of alcohol reduced evoked firing in neurons from control monkeys, but not drinking monkeys. Profiling of the OFC synaptome identified alcohol-sensitive proteins that control glutamate release (e.g., SV2A, synaptogyrin-1) and postsynaptic signaling (e.g., GluA1, PRRT2) with no changes in synaptic GABAergic proteins. Western blot analysis confirmed the increase in GluA1 expression in drinking monkeys. An exploratory analysis of the OFC synaptome found cross-species genetic links to alcohol intake in discrete proteins (e.g., C2CD2L, DIRAS2) that discriminated between low- and heavy-drinking monkeys. Validation studies revealed that BXD mouse strains with the D allele at the C2cd2l interval drank less alcohol than B allele strains. Thus, by profiling of the OFC synaptome, we identified changes in proteins controlling glutamate release and postsynaptic signaling and discovered several proteins related to heavy drinking that have potential as novel targets for treating alcohol use disorder.SIGNIFICANCE STATEMENT Clinical research identified cognitive deficits in alcoholic individuals as a risk factor for relapse, and alcoholic individuals display deficits on cognitive tasks that are dependent upon the orbitofrontal cortex (OFC). To identify neurobiological mechanisms that underpin OFC dysfunction, this study used electrophysiology and integrative synaptomics in a translational nonhuman primate model of heavy alcohol consumption. We found adaptations in synaptic proteins that control glutamatergic signaling in chronically drinking monkeys. Our functional genomic exploratory analyses identified proteins with genetic links to alcohol and cocaine intake across mice, monkeys, and humans. Future work is necessary to determine whether targeting these novel targets reduces excessive and harmful levels of alcohol drinking.
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18
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Djekic D, Pinto R, Vorkas PA, Henein MY. Replication of LC–MS untargeted lipidomics results in patients with calcific coronary disease: An interlaboratory reproducibility study. Int J Cardiol 2016; 222:1042-1048. [DOI: 10.1016/j.ijcard.2016.07.214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/28/2016] [Indexed: 01/29/2023]
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19
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Dong X, Liu G, Wu X, Lu X, Yan L, Muhammad R, Shah A, Wu L, Jiang C. Different metabolite profile and metabolic pathway with leaves and roots in response to boron deficiency at the initial stage of citrus rootstock growth. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:121-131. [PMID: 27428366 DOI: 10.1016/j.plaphy.2016.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/08/2016] [Accepted: 07/09/2016] [Indexed: 05/02/2023]
Abstract
Boron (B) is a microelement required for higher plants, and B deficiency has serious negative effect on metabolic processes. We concentrated on the changes in metabolite profiles of trifoliate orange leaves and roots as a consequence of B deficiency at the initial stage of growth by gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Enlargement and browning of root tips were observed in B-deficient plants, while any obvious symptom was not recorded in the leaves after 30 days of B deprivation. The distinct patterns of alterations in metabolites observed in leaves and roots due to B deficiency suggest the presence of specific organ responses to B starvation. The accumulation of soluble sugars was occurred in leaves, which may be attributed to down-regulated pentose phosphate pathway (PPP) and amino acid biosynthesis under B deficiency, while the amount of most amino acids in roots was increased, indicating that the effects of B deficiency on amino acids metabolism in trifoliate orange may be a consequence of disruptions in root tissues and decreased protein biosynthesis. Several important products of shikimate pathway were also significantly affected by B deficiency, which may be related to abnormal growth of roots induced by B deficiency. Conclusively, our results revealed a global perspective of the discriminative metabolism responses appearing between B-deprived leaves and roots and provided new insight into the relationship between B deficiency symptom in roots and the altered amino acids profiling and shikimate pathway induced by B deficiency during seedling establishment.
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Affiliation(s)
- Xiaochang Dong
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Guidong Liu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China
| | - Xiuwen Wu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Xiaopei Lu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Lei Yan
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Riaz Muhammad
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Asad Shah
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Lishu Wu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
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Fu HY, Guo JW, Yu YJ, Li HD, Cui HP, Liu PP, Wang B, Wang S, Lu P. A simple multi-scale Gaussian smoothing-based strategy for automatic chromatographic peak extraction. J Chromatogr A 2016; 1452:1-9. [PMID: 27207578 DOI: 10.1016/j.chroma.2016.05.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/23/2022]
Abstract
Peak detection is a critical step in chromatographic data analysis. In the present work, we developed a multi-scale Gaussian smoothing-based strategy for accurate peak extraction. The strategy consisted of three stages: background drift correction, peak detection, and peak filtration. Background drift correction was implemented using a moving window strategy. The new peak detection method is a variant of the system used by the well-known MassSpecWavelet, i.e., chromatographic peaks are found at local maximum values under various smoothing window scales. Therefore, peaks can be detected through the ridge lines of maximum values under these window scales, and signals that are monotonously increased/decreased around the peak position could be treated as part of the peak. Instrumental noise was estimated after peak elimination, and a peak filtration strategy was performed to remove peaks with signal-to-noise ratios smaller than 3. The performance of our method was evaluated using two complex datasets. These datasets include essential oil samples for quality control obtained from gas chromatography and tobacco plant samples for metabolic profiling analysis obtained from gas chromatography coupled with mass spectrometry. Results confirmed the reasonability of the developed method.
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Affiliation(s)
- Hai-Yan Fu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China.
| | - Jun-Wei Guo
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Yong-Jie Yu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China; School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Key Laboratory of Hui Medicine Modernization, Ministry of Education, Yinchuan 750004, China.
| | - He-Dong Li
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Hua-Peng Cui
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Ping-Ping Liu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Bing Wang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Sheng Wang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peng Lu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
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Tebani A, Schmitz-Afonso I, Rutledge DN, Gonzalez BJ, Bekri S, Afonso C. Optimization of a liquid chromatography ion mobility-mass spectrometry method for untargeted metabolomics using experimental design and multivariate data analysis. Anal Chim Acta 2016; 913:55-62. [DOI: 10.1016/j.aca.2016.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 01/10/2023]
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22
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Liu G, Dong X, Liu L, Wu L, Peng S, Jiang C. Metabolic profiling reveals altered pattern of central metabolism in navel orange plants as a result of boron deficiency. PHYSIOLOGIA PLANTARUM 2015; 153:513-24. [PMID: 25212059 DOI: 10.1111/ppl.12279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/28/2014] [Accepted: 08/08/2014] [Indexed: 05/02/2023]
Abstract
We focused on the changes of metabolite profiles in navel orange plants under long-term boron (B) deficiency using a gas chromatography-mass spectrometry (GC-MS) approach. Curling of the leaves and leaf chlorosis were observed only in the upper leaves (present before start of the treatment) of B-deficient plants, while the lower leaves (grown during treatment) did not show any visible symptoms. The metabolites with up-accumulation in B-deficient leaves were mainly proline, l-ornithine, lysine, glucoheptonic acid, fucose, fumarate, oxalate, quinate, myo-inositol and allo-inositol, while the metabolites with down-accumulation in B-deficient leaves were mainly serine, asparagine, saccharic acid, citrate, succinate, shikimate and phytol. The levels of glucose and fructose were increased only in the upper leaves by B deficiency, while starch content was increased in all the leaves and in roots. The increased levels of malate, ribitol, gluconic acid and glyceric acid occurred only in the lower leaves of B-deficient plants. The increased levels of phenols only in the upper leaves indicated that the effects of B on phenol metabolism in citrus plants may be a consequence of disruptions in leaf structure. Metabolites with opposite reactions in upper and lower leaves were mainly glutamine, glycine and pyrrole-2-carboxylic acid. To our knowledge, the phenomena of allo-inositol even higher than myo-inositol occurred characterized for the first time in this species. These results suggested that the altered pattern of central metabolism may be either specific or adaptive responses of navel orange plants to B deficiency.
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Affiliation(s)
- Guidong Liu
- Key Laboratory of Horticulture Plant Biology (HZU) MOE, Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China
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Mehl F, Marti G, Merle P, Delort E, Baroux L, Sommer H, Wolfender JL, Rudaz S, Boccard J. Integrating metabolomic data from multiple analytical platforms for a comprehensive characterisation of lemon essential oils. FLAVOUR FRAG J 2014. [DOI: 10.1002/ffj.3230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Florence Mehl
- School of Pharmaceutical Sciences, EPGL; University of Geneva, University of Lausanne; 20, Bd d'Yvoy 1211 Geneva 4 Switzerland
| | - Guillaume Marti
- School of Pharmaceutical Sciences, EPGL; University of Geneva, University of Lausanne; 20, Bd d'Yvoy 1211 Geneva 4 Switzerland
| | | | | | - Lucie Baroux
- Firmenich, Corporate Research; Geneva Switzerland
| | - Horst Sommer
- Firmenich, Corporate Research; Geneva Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL; University of Geneva, University of Lausanne; 20, Bd d'Yvoy 1211 Geneva 4 Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, EPGL; University of Geneva, University of Lausanne; 20, Bd d'Yvoy 1211 Geneva 4 Switzerland
| | - Julien Boccard
- School of Pharmaceutical Sciences, EPGL; University of Geneva, University of Lausanne; 20, Bd d'Yvoy 1211 Geneva 4 Switzerland
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Wang H, Lian K, Han B, Wang Y, Kuo SH, Geng Y, Qiang J, Sun M, Wang M. Age-related alterations in the metabolic profile in the hippocampus of the senescence-accelerated mouse prone 8: a spontaneous Alzheimer's disease mouse model. J Alzheimers Dis 2014; 39:841-8. [PMID: 24284365 DOI: 10.3233/jad-131463] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD), the most common age-dependent neurodegenerative disorder, produces a progressive decline in cognitive function. The metabolic mechanism of AD has emerged in recent years. In this study, we used multivariate analyses of gas chromatography-mass spectrometry measurements to determine that learning and retention-related metabolic profiles are altered during aging in the hippocampus of the senescence-accelerated mouse prone 8 (SAMP8). Alterations in 17 metabolites were detected in mature and aged mice compared to young mice (13 decreased and 4 increased metabolites), including metabolites related to dysfunctional lipid metabolism (significantly increased cholesterol, oleic acid, and phosphoglyceride levels), decreased amino acid (alanine, serine, glycine, aspartic acid, glutamate, and gamma-aminobutyric acid), and energy-related metabolite levels (malic acid, butanedioic acid, fumaric acid, and citric acid), and other altered metabolites (increased N-acetyl-aspartic acid and decreased pyroglutamic acid, urea, and lactic acid) in the hippocampus. All of these alterations indicated that the metabolic mechanisms of age-related cognitive impairment in SAMP8 mice were related to multiple pathways and networks. Lipid metabolism, especially cholesterol metabolism, appears to play a distinct role in the hippocampus in AD.
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Affiliation(s)
- Hualong Wang
- Department of Neurology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Kaoqi Lian
- The School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Bing Han
- Department of Neurology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yanyong Wang
- Department of Neurology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Sheng-Han Kuo
- Department of Neurology, Columbia University, New York, NY, USA
| | - Yuan Geng
- Brain Aging and Cognitive Neuroscience Laboratory of Hebei Province, Shijiazhuang, Hebei, PR China
| | - Jing Qiang
- Department of Neurology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Meiyu Sun
- Department of Neurology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Mingwei Wang
- Department of Neurology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China Brain Aging and Cognitive Neuroscience Laboratory of Hebei Province, Shijiazhuang, Hebei, PR China
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David A, Abdul-Sada A, Lange A, Tyler CR, Hill EM. A new approach for plasma (xeno)metabolomics based on solid-phase extraction and nanoflow liquid chromatography-nanoelectrospray ionisation mass spectrometry. J Chromatogr A 2014; 1365:72-85. [PMID: 25260345 DOI: 10.1016/j.chroma.2014.09.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 11/30/2022]
Abstract
Current metabolite profiling methods based on liquid chromatography-mass spectrometry (LC-MS) platforms do not detect many of the components present at trace concentrations in extracts of plasma due to their low ionisation efficiency or to interference from highly abundant compounds. Nanoflow LC-nanospray MS platforms, which are commonly used in proteomics, could overcome these limitations and significantly increase analytical sensitivity and coverage of the plasma (xeno)metabolome (i.e., metabolites and xenobiotics), but require small injection volumes (<0.5μL). In this study, we developed sample preparation methods to remove ion suppressive phospholipids and concentrate remaining components of the plasma (xeno)metabolome in order to analyse sub-microliter volumes of plasma extracts for nanoflow ultra-high-performance liquid chromatography-nanoelectrospray ionisation-time-of-flight mass spectrometry (nUHPLC-nESI-TOFMS). These methods use phospholipid filtration plates in combination with polymeric or mixed mode exchange solid-phase extraction (SPE). The phospholipid filtration plates removed >94% of the predominant phospholipid/lysophospholipid species from plasma, whilst absolute recoveries of 63 selected (xeno)metabolites from spiked plasma were generally between 60 and 104%. After a further SPE step, recoveries of test compounds were between 50 and 81%. Studies revealed that both the sample preparation methodology and nUHPLC-nESI-TOFMS analyses gave acceptable repeatability. A qualitative comparison of SPE methods revealed that sample concentration by either polymer or mixed mode ion-exchange SPE gave comprehensive metabolite coverage of plasma extracts, but the use of cation exchange SPE significantly increased detection of many cationic compounds in the sample extracts. Method detection limits for steroid, eicosanoid and bile metabolites were <1.0ng/mL plasma and for pharmaceutical contaminants were between 0.01 and 30ng/mL plasma. Comparison of the phospholipid removal/cation exchange SPE and the classical protein precipitation (PPT) sample preparation methodologies revealed that both methods detected the same range of (xeno)metabolites. However, unlike PPT extracts, the SPE preparations allowed direct injection of more concentrated plasma extracts onto the nUHPLC-nESI-TOFMS platform without blockage of the nanocolumn or nanospray, thus resulting in a wider coverage of the (xeno)metabolome. This is the first work to demonstrate the significantly enhanced sensitivity arising from the use of concentrated SPE sample preparations and direct nUHPLC-nESI-TOFMS analysis for untargeted profiling of plasma samples and constitutes a step forward for identifying mixtures of chemical stressors accumulated in blood as well as the disruption of key metabolite pathways in the same sample.
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Affiliation(s)
- Arthur David
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Alaa Abdul-Sada
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Anke Lange
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Elizabeth M Hill
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK.
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Trifonova OP, Lokhov PG, Archakov AI. [Metabolic profiling of human blood]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2014; 60:281-94. [PMID: 25019391 DOI: 10.18097/pbmc20146003281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Metabolomics is a novel "omics" branch of science intended for studying a comprehensive set of low molecular weight substances (metabolites) of various biological objects. Metabolite profiles represent a molecular phenotype of biological systems and reflect information encoded at the genome level and realized at the transcriptome and proteome levels. Analysis of human blood metabolic profile is universal and promising tool for clinical applications because it is a sensitive measure of both endogenous and exogenous (environmental) factors affected on the patient's organism. Technical implementation of metabolic profiling of blood and statistic analysis of metabolite profiles for effective diagnostics and risk assessments of diseases are discussed in this review.
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Qi Y, Jiang C, Cheng J, Krausz KW, Li T, Ferrell JM, Gonzalez FJ, Chiang JYL. Bile acid signaling in lipid metabolism: metabolomic and lipidomic analysis of lipid and bile acid markers linked to anti-obesity and anti-diabetes in mice. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:19-29. [PMID: 24796972 DOI: 10.1016/j.bbalip.2014.04.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/17/2014] [Accepted: 04/28/2014] [Indexed: 12/11/2022]
Abstract
Bile acid synthesis is the major pathway for catabolism of cholesterol. Cholesterol 7α-hydroxylase (CYP7A1) is the rate-limiting enzyme in the bile acid biosynthetic pathway in the liver and plays an important role in regulating lipid, glucose and energy metabolism. Transgenic mice overexpressing CYP7A1 (CYP7A1-tg mice) were resistant to high-fat diet (HFD)-induced obesity, fatty liver, and diabetes. However the mechanism of resistance to HFD-induced obesity of CYP7A1-tg mice has not been determined. In this study, metabolomic and lipidomic profiles of CYP7A1-tg mice were analyzed to explore the metabolic alterations in CYP7A1-tg mice that govern the protection against obesity and insulin resistance by using ultra-performance liquid chromatography-coupled with electrospray ionization quadrupole time-of-flight mass spectrometry combined with multivariate analyses. Lipidomics analysis identified seven lipid markers including lysophosphatidylcholines, phosphatidylcholines, sphingomyelins and ceramides that were significantly decreased in serum of HFD-fed CYP7A1-tg mice. Metabolomics analysis identified 13 metabolites in bile acid synthesis including taurochenodeoxycholic acid, taurodeoxycholic acid, tauroursodeoxycholic acid, taurocholic acid, and tauro-β-muricholic acid (T-β-MCA) that differed between CYP7A1-tg and wild-type mice. Notably, T-β-MCA, an antagonist of the farnesoid X receptor (FXR) was significantly increased in intestine of CYP7A1-tg mice. This study suggests that reducing 12α-hydroxylated bile acids and increasing intestinal T-β-MCA may reduce high fat diet-induced increase of phospholipids, sphingomyelins and ceramides, and ameliorate diabetes and obesity. This article is part of a Special Issue entitled Linking transcription to physiology in lipodomics.
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Affiliation(s)
- Yunpeng Qi
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Changtao Jiang
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jie Cheng
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiangang Li
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Jessica M Ferrell
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Y L Chiang
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
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Repetitive transcranial magnetic stimulation applications normalized prefrontal dysfunctions and cognitive-related metabolic profiling in aged mice. PLoS One 2013; 8:e81482. [PMID: 24278445 PMCID: PMC3838337 DOI: 10.1371/journal.pone.0081482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 10/16/2013] [Indexed: 12/17/2022] Open
Abstract
Chronic high-frequency repetitive transcranial magnetic stimulation (rTMS) is a noninvasive brain stimulation technique that has recently received increasing interests as a therapeutic procedure for neurodegenerative diseases. To identify the metabolism mechanism underlying the improving effects of rTMS, we observed that high frequency (25Hz) rTMS for 14 days could reverse the decline of the performance of the passive avoidance task in aged mice. We further investigated the metabolite profiles in the prefrontal cortex (PFC) in those mice and found that rTMS could also reverse the metabolic abnormalities of gamma-aminobutyric acid, N-acetyl aspartic, and cholesterol levels to the degree similar to the young mice. These data suggested that the rTMS could ameliorate the age-related cognitive impairment and improving the metabolic profiles in PFC, and potentially can be used to improve cognitive decline in the elderly.
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Trifonova O, Lokhov P, Archakov A. Postgenomics diagnostics: metabolomics approaches to human blood profiling. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:550-9. [PMID: 24044364 DOI: 10.1089/omi.2012.0121] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We live in exciting times with the prospects of postgenomics diagnostics. Metabolomics is a novel "omics" data-intensive science that is accelerating the development of postgenomics diagnostics, particularly with use of accessible peripheral tissue compartments. Metabolomics involves the study of a comprehensive set of low molecular weight substances (metabolites) present in biological systems. The metabolite profiles represent the molecular phenotype of biological systems and reflect the information encoded at the genomic level and implemented at the transcriptomic and proteomic levels. Analysis of the human blood metabolite profile is a universal and highly promising tool for clinical postgenomics applications because it reflects both the endogenous and exogenous (environmental) factors influencing an individual organism. This article presents a critical synthesis and original analysis of both the technical implementation of metabolic profiling of blood and statistical analysis of metabolite profiles for effective disease diagnostics and risk assessment in the present postgenomics era.
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Trifonova OP, Lokhov PG, Archakov AI. Metabolic profiling of human blood. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2013. [DOI: 10.1134/s1990750813030128] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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31
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Chen K, Lynen F, Hitzel L, Hanna-Brown M, Szucs R, Sandra P. A New Strategy for Fast Chiral Screening by Combining HPLC-DAD with a Multivariate Curve Resolution–Alternating Least Squares Algorithm. Chromatographia 2013. [DOI: 10.1007/s10337-013-2520-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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A consensus orthogonal partial least squares discriminant analysis (OPLS-DA) strategy for multiblock Omics data fusion. Anal Chim Acta 2013; 769:30-9. [DOI: 10.1016/j.aca.2013.01.022] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/28/2012] [Accepted: 01/14/2013] [Indexed: 11/22/2022]
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Kuang H, Li Z, Peng C, Liu L, Xu L, Zhu Y, Wang L, Xu C. Metabonomics Approaches and the Potential Application in Foodsafety Evaluation. Crit Rev Food Sci Nutr 2012; 52:761-74. [DOI: 10.1080/10408398.2010.508345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012. [DOI: 10.1038/nrm3314 and 4394=4394-- scwx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Patti GJ, Yanes O, Siuzdak G. Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012. [DOI: 10.1038/nrm3314 order by 1#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Patti GJ, Yanes O, Siuzdak G. Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012. [DOI: 10.1038/nrm3314 and 5927=6679-- elyo] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Patti GJ, Yanes O, Siuzdak G. Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012. [DOI: 10.1038/nrm3314 and 3511=(select (case when (3511=3511) then 3511 else (select 9304 union select 4747) end))-- isaz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Patti GJ, Yanes O, Siuzdak G. Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol 2012. [DOI: 10.1038/nrm3314 rlike (select (case when (1444=9719) then 0x31302e313033382f6e726d33333134 else 0x28 end))-- dyhd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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