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Kim J, Woo HK, Vimalajeewa D, Vidakovic B. Analysis and classification of 1H-NMR spectra by multifractal analysis. PLoS One 2023; 18:e0286205. [PMID: 37289702 PMCID: PMC10249796 DOI: 10.1371/journal.pone.0286205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/11/2023] [Indexed: 06/10/2023] Open
Abstract
The objective of this research focuses on the development of a statistical methodology able to answer the question of whether variation in the intake of sulfur amino acids (SAA) affects the metabolic process. Traditional approaches, which evaluate specific biomarkers after a series of preprocessing procedures, have been criticized as not being fully informative, as well as inappropriate for translation of methodology. Rather than focusing on particular biomarkers, our proposed methodology involves the multifractal analysis that measures the inhomogeneity of regularity of the proton nuclear magnetic resonance (1H-NMR) spectrum by wavelet-based multifractal spectrum. With two different statistical models (Model-I and Model-II), three different geometric features of the multifractal spectrum of each 1H-NMR spectrum (spectral mode, left slope, and broadness) are employed to evaluate the effect of SAA and discriminate 1H-NMR spectra associated with different treatments. The investigated effects of SAA include group effect (high and low doses of SAA), depletion/repletion effect, and time over data effect. The 1H-NMR spectra analysis outcomes show that group effect is significant for both models. The hourly variation in time and depletion/repletion effects does not show noticeable differences for the three features in Model-I. However, these two effects are significant for the spectral mode feature in Model-II. The 1H-NMR spectra of the SAA low groups exhibit highly regular patterns with more variability than that of the SAA high groups for both models. Moreover, the discriminatory analysis conducted using the support vector machine and the principal components analysis shows that the 1H-NMR spectra of SAA high and low groups can be easily discriminatory for both models, while the spectra of depletion and repletion within these groups are discriminatory for Model-I and Model-II. Therefore, the study outcomes imply that the amount of SAA is important and that SAA intake affects mostly the hourly variation of the metabolic process and the difference between depletion and repletion each day. In conclusion, the proposed multifractal analysis of 1H-NMR spectra provides a novel tool to investigate metabolic processes.
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Affiliation(s)
- Jongphil Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States of America
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America
| | - Hin Kyeol Woo
- Snapchat Inc., New York, NY, United States of America
| | - Dixon Vimalajeewa
- Department of Statistics, Texas A&M University, College Station, TX, United States of America
| | - Brani Vidakovic
- Department of Statistics, Texas A&M University, College Station, TX, United States of America
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Nagaoka S. Nutrition and Food Science Studies of Cholesterol Metabolism Regulation. ACTA ACUST UNITED AC 2018. [DOI: 10.4327/jsnfs.71.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Satoshi Nagaoka
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University
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DeRatt BN, Ralat MA, Gregory JF. Short-Term Vitamin B-6 Restriction Does Not Affect Plasma Concentrations of Hydrogen Sulfide Biomarkers Lanthionine and Homolanthionine in Healthy Men and Women. J Nutr 2016; 146:714-719. [PMID: 26962179 PMCID: PMC4807651 DOI: 10.3945/jn.115.227819] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/11/2016] [Accepted: 02/11/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Suboptimal vitamin B-6 status is associated with increased cardiovascular disease risk, although the mechanism is unknown. The synthesis of the vasodilator hydrogen sulfide occurs through side reactions of the transsulfuration enzymes cystathionine β-synthase and cystathionine γ-lyase, with pyridoxal 5'-phosphate as a coenzyme. Two proposed hydrogen sulfide biomarkers, lanthionine and homolanthionine, are produced concurrently. OBJECTIVE To determine whether hydrogen sulfide production is reduced by vitamin B-6 deficiency, we examined the relations between plasma concentrations of lanthionine and homolanthionine, along with other components of the transsulfuration pathway (homocysteine, cystathionine, and Cys), in a secondary analysis of samples from 2 vitamin B-6 restriction studies in healthy men and women. METHODS Metabolite concentrations were measured in plasma from 23 healthy adults (12 men and 11 women) before and after 28-d controlled dietary vitamin B-6 restriction (0.37 ± 0.04 mg/d). Vitamin B-6 restriction effects on lanthionine and homolanthionine concentrations were assessed. Associations between hydrogen sulfide biomarkers, transsulfuration metabolites, and functional indicators of vitamin B-6 deficiency were analyzed by linear regression. RESULTS Preprandial plasma lanthionine and homolanthionine concentrations ranged from 89.0 to 372 nmol/L and 5.75 to 32.3 nmol/L, respectively, in healthy adults. Mean lanthionine and homolanthionine concentrations were not affected by vitamin B-6 restriction (P < 0.66), with marked heterogeneity of individual responses. After restriction, homolanthionine was positively associated with functional indicators of vitamin B-6 deficiency, which differed from hypothesized negative associations. Plasma lanthionine was positively correlated with the concentration of its precursor, Cys, before (R2 = 0.36; P = 0.002) and after (R2 = 0.37; P = 0.002) restriction. Likewise, homolanthionine concentration was positively correlated with its precursor homocysteine, but only in vitamin B-6 adequacy (R2 = 0.41; P < 0.001). CONCLUSIONS The resiliency of plasma lanthionine and homolanthionine concentrations after short-term vitamin B-6 restriction suggests a minimal effect of moderate vitamin B-6 deficiency on hydrogen sulfide production. Additional research is needed to better understand the metabolism and disposal of these biomarkers in humans. This study was registered at clinicaltrials.gov as NCT00877812.
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Kashima Y, Kanematsu S, Asai S, Kusada M, Watanabe S, Kawashima T, Nakamura T, Shimada M, Goto T, Nagaoka S. Identification of a novel hypocholesterolemic protein, major royal jelly protein 1, derived from royal jelly. PLoS One 2014; 9:e105073. [PMID: 25144734 PMCID: PMC4140749 DOI: 10.1371/journal.pone.0105073] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/20/2014] [Indexed: 11/19/2022] Open
Abstract
Royal jelly (RJ) intake lowers serum cholesterol levels in animals and humans, but the active component in RJ that lowers serum cholesterol level and its molecular mechanism are unclear. In this study, we set out to identify the bile acid-binding protein contained in RJ, because dietary bile acid-binding proteins including soybean protein and its peptide are effective in ameliorating hypercholesterolemia. Using a cholic acid-conjugated column, we separated some bile acid-binding proteins from RJ and identified the major RJ protein 1 (MRJP1), MRJP2, and MRJP3 as novel bile acid-binding proteins from RJ, based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Purified MRJP1, which is the most abundant protein of the bile acid-binding proteins in RJ, exhibited taurocholate-binding activity in vitro. The micellar solubility of cholesterol was significantly decreased in the presence of MRJP1 compared with casein in vitro. Liver bile acids levels were significantly increased, and cholesterol 7α-hydroxylase (CYP7A1) mRNA and protein tended to increase by MRJP1 feeding compared with the control. CYP7A1 mRNA and protein levels were significantly increased by MRJP1 tryptic hydrolysate treatment compared with that of casein tryptic hydrolysate in hepatocytes. MRJP1 hypocholesterolemic effect has been investigated in rats. The cholesterol-lowering action induced by MRJP1 occurs because MRJP1 interacts with bile acids induces a significant increase in fecal bile acids excretion and a tendency to increase in fecal cholesterol excretion and also enhances the hepatic cholesterol catabolism. We have identified, for the first time, a novel hypocholesterolemic protein, MRJP1, in RJ. Interestingly, MRJP1 exhibits greater hypocholesterolemic activity than the medicine β-sitosterol in rats.
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Affiliation(s)
| | | | - Saori Asai
- Akitaya Honten Co., Ltd., Kano, Gifu, Japan
| | - Mio Kusada
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | | | | | | | - Masaya Shimada
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Tsuyoshi Goto
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Satoshi Nagaoka
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
- * E-mail:
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Fitzpatrick AM, Park Y, Brown LAS, Jones DP. Children with severe asthma have unique oxidative stress-associated metabolomic profiles. J Allergy Clin Immunol 2014; 133:258-61.e1-8. [PMID: 24369802 DOI: 10.1016/j.jaci.2013.10.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 10/25/2022]
Affiliation(s)
- Anne M Fitzpatrick
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga; Children's Healthcare of Atlanta Center for Developmental Lung Biology, Atlanta, Ga.
| | - Youngja Park
- Department of Medicine, Emory University School of Medicine, Atlanta, Ga; College of Pharmacy, Korea University, Seong, Korea
| | - Lou Ann S Brown
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga; Children's Healthcare of Atlanta Center for Developmental Lung Biology, Atlanta, Ga
| | - Dean P Jones
- Department of Medicine, Emory University School of Medicine, Atlanta, Ga
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Tanaka Y, Shimada M, Nagaoka S. L-Cysteine-induced up-regulation of the low-density lipoprotein receptor is mediated via a transforming growth factor-alpha signalling pathway. Biochem Biophys Res Commun 2014; 444:401-5. [PMID: 24472543 DOI: 10.1016/j.bbrc.2014.01.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/19/2014] [Indexed: 11/16/2022]
Abstract
Sulphur-containing amino acids regulate plasma cholesterol levels in animals and humans. However, their mechanism of action remains unclear. Low-density lipoprotein receptor (LDLR) plays an important role in cholesterol metabolism. We therefore investigated the effects of sulphur-containing amino acids on the expression of LDLR in hepatocytes. HepG2 cells were cultured in Dulbecco's Modified Eagle's Medium with or without sulphur-containing amino acids and cysteine-containing compounds. We found that L-cysteine increased LDLR mRNA and enhanced LDLR gene promoter activity through the extracellular-signal-related kinase and p38 mitogen-activated protein kinase signalling pathways in HepG2 cells. Moreover, we observed that L-cysteine stimulated the release of transforming growth factor-alpha (TGF-α) and that TGF-α increased the LDLR mRNA levels. This study provides a report of the L-cysteine mediated up-regulation of the LDLR expression via TGF-α signalling pathway. Our findings provide insights into cholesterol homeostasis and amino acid signalling.
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Affiliation(s)
- Yuma Tanaka
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Masaya Shimada
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Satoshi Nagaoka
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
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Park Y, Lee K, Ziegler TR, Martin GS, Hebbar G, Vidakovic B, Jones DP. Multifractal analysis for nutritional assessment. PLoS One 2013; 8:e69000. [PMID: 23990878 PMCID: PMC3749179 DOI: 10.1371/journal.pone.0069000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 06/10/2013] [Indexed: 11/18/2022] Open
Abstract
The concept of multifractality is currently used to describe self-similar and complex scaling properties observed in numerous biological signals. Fractals are geometric objects or dynamic variations which exhibit some degree of similarity (irregularity) to the original object in a wide range of scales. This approach determines irregularity of biologic signal as an indicator of adaptability, the capability to respond to unpredictable stress, and health. In the present work, we propose the application of multifractal analysis of wavelet-transformed proton nuclear magnetic resonance (1H NMR) spectra of plasma to determine nutritional insufficiency. For validation of this method on 1H NMR signal of human plasma, standard deviation from classical statistical approach and Hurst exponent (H), left slope and partition function from multifractal analysis were extracted from 1H NMR spectra to test whether multifractal indices could discriminate healthy subjects from unhealthy, intensive care unit patients. After validation, the multifractal approach was applied to spectra of plasma from a modified crossover study of sulfur amino acid insufficiency and tested for associations with blood lipids. The results showed that standard deviation and H, but not left slope, were significantly different for sulfur amino acid sufficiency and insufficiency. Quadratic discriminant analysis of H, left slope and the partition function showed 78% overall classification accuracy according to sulfur amino acid status. Triglycerides and apolipoprotein C3 were significantly correlated with a multifractal model containing H, left slope, and standard deviation, and cholesterol and high-sensitivity C-reactive protein were significantly correlated to H. In conclusion, multifractal analysis of 1H NMR spectra provides a new approach to characterize nutritional status.
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Affiliation(s)
- Youngja Park
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
- College of Pharmacy, Korea University, Sejong City, Korea
| | - Kichun Lee
- Department of Industrial Engineering, Hanyang University, Seoul, Korea
- * E-mail: (KL); (DPJ)
| | - Thomas R. Ziegler
- Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Greg S. Martin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Gautam Hebbar
- Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Brani Vidakovic
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (KL); (DPJ)
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Gregory JF, Park Y, Lamers Y, Bandyopadhyay N, Chi YY, Lee K, Kim S, da Silva V, Hove N, Ranka S, Kahveci T, Muller KE, Stevens RD, Newgard CB, Stacpoole PW, Jones DP. Metabolomic analysis reveals extended metabolic consequences of marginal vitamin B-6 deficiency in healthy human subjects. PLoS One 2013; 8:e63544. [PMID: 23776431 PMCID: PMC3679127 DOI: 10.1371/journal.pone.0063544] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 04/05/2013] [Indexed: 12/31/2022] Open
Abstract
Marginal deficiency of vitamin B-6 is common among segments of the population worldwide. Because pyridoxal 5′-phosphate (PLP) serves as a coenzyme in the metabolism of amino acids, carbohydrates, organic acids, and neurotransmitters, as well as in aspects of one-carbon metabolism, vitamin B-6 deficiency could have many effects. Healthy men and women (age: 20-40 y; n = 23) were fed a 2-day controlled, nutritionally adequate diet followed by a 28-day low-vitamin B-6 diet (<0.5 mg/d) to induce marginal deficiency, as reflected by a decline of plasma PLP from 52.6±14.1 (mean ± SD) to 21.5±4.6 nmol/L (P<0.0001) and increased cystathionine from 131±65 to 199±56 nmol/L (P<0.001). Fasting plasma samples obtained before and after vitamin B6 restriction were analyzed by 1H-NMR with and without filtration and by targeted quantitative analysis by mass spectrometry (MS). Multilevel partial least squares-discriminant analysis and S-plots of NMR spectra showed that NMR is effective in classifying samples according to vitamin B-6 status and identified discriminating features. NMR spectral features of selected metabolites indicated that vitamin B-6 restriction significantly increased the ratios of glutamine/glutamate and 2-oxoglutarate/glutamate (P<0.001) and tended to increase concentrations of acetate, pyruvate, and trimethylamine-N-oxide (adjusted P<0.05). Tandem MS showed significantly greater plasma proline after vitamin B-6 restriction (adjusted P<0.05), but there were no effects on the profile of 14 other amino acids and 45 acylcarnitines. These findings demonstrate that marginal vitamin B-6 deficiency has widespread metabolic perturbations and illustrate the utility of metabolomics in evaluating complex effects of altered vitamin B-6 intake.
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Affiliation(s)
- Jesse F Gregory
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
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Abstract
Nutritional metabolomics is rapidly maturing to use small-molecule chemical profiling to support integration of diet and nutrition in complex biosystems research. These developments are critical to facilitate transition of nutritional sciences from population-based to individual-based criteria for nutritional research, assessment, and management. This review addresses progress in making these approaches manageable for nutrition research. Important concept developments concerning the exposome, predictive health, and complex pathobiology serve to emphasize the central role of diet and nutrition in integrated biosystems models of health and disease. Improved analytic tools and databases for targeted and nontargeted metabolic profiling, along with bioinformatics, pathway mapping, and computational modeling, are now used for nutrition research on diet, metabolism, microbiome, and health associations. These new developments enable metabolome-wide association studies (MWAS) and provide a foundation for nutritional metabolomics, along with genomics, epigenomics, and health phenotyping, to support the integrated models required for personalized diet and nutrition forecasting.
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Affiliation(s)
- Dean P. Jones
- Department of Medicine, Emory University, Atlanta, GA 30322 USA
| | - Youngja Park
- Department of Medicine, Emory University, Atlanta, GA 30322 USA
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Roede JR, Park Y, Li S, Strobel FH, Jones DP. Detailed mitochondrial phenotyping by high resolution metabolomics. PLoS One 2012; 7:e33020. [PMID: 22412977 PMCID: PMC3295783 DOI: 10.1371/journal.pone.0033020] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 02/04/2012] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial phenotype is complex and difficult to define at the level of individual cell types. Newer metabolic profiling methods provide information on dozens of metabolic pathways from a relatively small sample. This pilot study used “top-down” metabolic profiling to determine the spectrum of metabolites present in liver mitochondria. High resolution mass spectral analyses and multivariate statistical tests provided global metabolic information about mitochondria and showed that liver mitochondria possess a significant phenotype based on gender and genotype. The data also show that mitochondria contain a large number of unidentified chemicals.
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Affiliation(s)
- James R. Roede
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Youngja Park
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Shuzhao Li
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, Georgia, United States of America
| | - Frederick H. Strobel
- Mass Spectrometry Center, Emory University, Atlanta, Georgia, United States of America
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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