Metabolites

19 pages, 11064 KiB

Open AccessArticle

Metabolomic Variability of Different Genotypes of Cashew by LC-Ms and Correlation with Near-Infrared Spectroscopy as a Tool for Fast Phenotyping

by Elenilson Alves Filho, Lorena Mara Silva, Ynayara Lima, Paulo Ribeiro, Ebenézer Silva, Guilherme Zocolo, Kirley Canuto, Selene Morais, Ana Cecília Castro and Edy de Brito

Metabolites 2019, 9(6), 121; https://doi.org/10.3390/metabo9060121 - 25 Jun 2019

Cited by 15 | Viewed by 3831

Abstract

The objective of the present work was to develop an advanced fast phenotyping tool to explore the cashew apple compositions from different genotypes, based on a portable near-infrared (MicroNIR) spectroscopy. This will be in addition to associating the variability of the respective cashew [...] Read more.

The objective of the present work was to develop an advanced fast phenotyping tool to explore the cashew apple compositions from different genotypes, based on a portable near-infrared (MicroNIR) spectroscopy. This will be in addition to associating the variability of the respective cashew apple pulps with the genotypes by ultra-performance liquid chromatography (UPLC), coupled with high-resolution mass spectrometry (HRMS). The NIR analysis is a non-destructive, low-cost procedure that provides prompt results, while considering the morphology of different cashew apples (shape, size, and color). The UPLC-HRMS analysis is characterized by specific bioactive compounds, such as the derivatives of hydroxybutanoic acid, galloyl, and flavonoids. Furthermore, both techniques allowed the identification of a group of accessions, which presented similarities among the chemical profiling. However, to improve the understanding of cashew chemical and physical variability, further variables related to the cashew apple composition, such as edaphoclimatic conditions, should be considered for future studies. These approaches lead to the conclusion that these two tools are useful for the maintenance of BAG-Caju (Cashew Germplasm Bank) and for the cashew-breeding program. Full article

(This article belongs to the Special Issue Fruit Metabolism and Metabolomics)

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21 pages, 716 KiB

Open AccessArticle

Identifying Metabolomic Profiles of Insulinemic Dietary Patterns

by Fred K. Tabung, Raji Balasubramanian, Liming Liang, Steven K. Clinton, Elizabeth M. Cespedes Feliciano, JoAnn E. Manson, Linda Van Horn, Jean Wactawski-Wende, Clary B. Clish, Edward L. Giovannucci and Kathryn M. Rexrode

Metabolites 2019, 9(6), 120; https://doi.org/10.3390/metabo9060120 - 24 Jun 2019

Cited by 13 | Viewed by 3629

Abstract

The food-based empirical dietary index for hyperinsulinemia (EDIH) score assesses the insulinemic potential of diet. This cross-sectional study evaluated associations between EDIH scores from food frequency questionnaires with c-peptide concentrations and with 448 metabolites, from fasting plasma samples, in multivariable linear regression analyses. [...] Read more.

The food-based empirical dietary index for hyperinsulinemia (EDIH) score assesses the insulinemic potential of diet. This cross-sectional study evaluated associations between EDIH scores from food frequency questionnaires with c-peptide concentrations and with 448 metabolites, from fasting plasma samples, in multivariable linear regression analyses. Metabolites were measured with liquid chromatography tandem mass spectroscopy. Using a robust two-stage study design, discovery of metabolite associations was conducted among 1109 Women’s Health Initiative (WHI) Hormone Therapy (HT) trial participants and results replicated in an independent dataset of 810 WHI Observational Study (OS) participants. In both discovery and replication datasets, statistical significance was based on the false-discovery rate adjusted P < 0.05. In the multivariable-adjusted analyses, EDIH was significantly associated with c-peptide concentrations among 919 women (HT & OS) with c-peptide data. On average, c-peptide concentrations were 18% higher (95% CI, 6%, 32%; P-trend < 0.0001) in EDIH quintile 5 compared to quintile 1. Twenty-six metabolites were significantly associated with EDIH in the discovery dataset, and 19 of these were replicated in the validation dataset. Nine metabolites were found to decrease in abundance with increasing EDIH scores and included: C14:0 CE, C16:1 CE, C18:1 CE, C18:3 CE, C20:3 CE, C20:5 CE, C36:1 PS plasmalogen, trigonelline, and eicosapentanoate, whereas the 10 metabolites observed to increase with increasing EDIH scores were: C18:2 SM, C36:3 DAG, C36:4 DAG-A, C51:3 TAG, C52:3 TAG, C52:4, TAG, C54:3 TAG, C54:4 TAG, C54:6 TAG, and C10:2 carnitine. Cholesteryl esters, phospholipids, acylglycerols, and acylcarnitines may constitute circulating metabolites that are associated with insulinemic dietary patterns. Full article

(This article belongs to the Special Issue Metabolomics in Epidemiological Studies)

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15 pages, 2531 KiB

Open AccessArticle

Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics

by Hiroshi Tsugawa, Aya Satoh, Haruki Uchino, Tomas Cajka, Makoto Arita and Masanori Arita

Metabolites 2019, 9(6), 119; https://doi.org/10.3390/metabo9060119 - 24 Jun 2019

Cited by 33 | Viewed by 7036

Abstract

Mass spectrometry raw data repositories, including Metabolomics Workbench and MetaboLights, have contributed to increased transparency in metabolomics studies and the discovery of novel insights in biology by reanalysis with updated computational metabolomics tools. Herein, we reanalyzed the previously published lipidomics data from nine [...] Read more.

Mass spectrometry raw data repositories, including Metabolomics Workbench and MetaboLights, have contributed to increased transparency in metabolomics studies and the discovery of novel insights in biology by reanalysis with updated computational metabolomics tools. Herein, we reanalyzed the previously published lipidomics data from nine algal species, resulting in the annotation of 1437 lipids achieving a 40% increase in annotation compared to the previous results. Specifically, diacylglyceryl-carboxyhydroxy-methylcholine (DGCC) in Pavlova lutheri and Pleurochrysis carterae, glucuronosyldiacylglycerol (GlcADG) in Euglena gracilis, and P. carterae, phosphatidylmethanol (PMeOH) in E. gracilis, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in Chlorella variabilis were newly characterized with the enriched lipid spectral databases. Moreover, we integrated the data from untargeted and targeted analyses from data independent tandem mass spectrometry (DIA-MS/MS) acquisition, specifically the sequential window acquisition of all theoretical fragment-ion MS/MS (SWATH-MS/MS) spectra, to increase the lipidomic annotation coverage. After the creation of a global library of precursor and diagnostic ions of lipids by the MS-DIAL untargeted analysis, the co-eluted DIA-MS/MS spectra were resolved in MRMPROBS targeted analysis by tracing the specific product ions involved in acyl chain compositions. Our results indicated that the metabolite quantifications based on DIA-MS/MS chromatograms were somewhat inferior to the MS¹-centric quantifications, while the annotation coverage outperformed those of the untargeted analysis of the data dependent and DIA-MS/MS data. Consequently, integrated analyses of untargeted and targeted approaches are necessary to extract the maximum amount of metabolome information, and our results showcase the value of data repositories for the discovery of novel insights in lipid biology. Full article

(This article belongs to the Special Issue Metabolomics Data Processing and Data Analysis—Current Best Practices)

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14 pages, 3635 KiB

Open AccessArticle

A Quantitative HILIC–MS/MS Assay of the Metabolic Response of Huh-7 Cells Exposed to 2,3,7,8-Tetrachlorodibenzo-p-Dioxin

by Qing Liu, Jingwei Cai, Robert G. Nichols, Yuan Tian, Jintao Zhang, Philip B. Smith, Yan Wang, Chao Yan and Andrew D. Patterson

Metabolites 2019, 9(6), 118; https://doi.org/10.3390/metabo9060118 - 20 Jun 2019

Cited by 10 | Viewed by 4903

Abstract

A hydrophilic interaction liquid chromatography (HILIC)–ultra high-pressure liquid chromatography (UHPLC) coupled with tandem mass spectrometry (MS/MS) method was developed and applied to profile metabolite changes in human Huh-7 cells exposed to the potent aryl hydrocarbon receptor (AHR) ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Comparisons [...] Read more.

A hydrophilic interaction liquid chromatography (HILIC)–ultra high-pressure liquid chromatography (UHPLC) coupled with tandem mass spectrometry (MS/MS) method was developed and applied to profile metabolite changes in human Huh-7 cells exposed to the potent aryl hydrocarbon receptor (AHR) ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Comparisons of sensitivity (limit of detection as low as 0.01 µM) and reproducibility (84% of compounds had an interday relative standard deviation (RSD) less than 10.0%; 83% of compounds had an intraday RSD less than 15.0%) were assessed for all the metabolites. The exposure of Huh-7 cells to the hepatotoxic carcinogen TCDD at low doses (1 nM and 10 nM for 4 h and 24 h, respectively) was reflected by the disturbance of amino acid metabolism, energy metabolism (glycolysis, TCA cycle), and nucleic acid metabolism. TCDD caused a significant decrease in amino acids such as serine, alanine, and proline while promoting an increase in arginine levels with 24 h treatment. Energy metabolism intermediates such as phosphoenolpyruvate and acetyl–CoA and nucleosides such as UMP, XMP, and CMP were also markedly decreased. These results support the application of HILIC–UHPLC–MS/MS for robust and reliable analysis of the cellular response to environmentally relevant toxicants at lower doses. Full article

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27 pages, 1681 KiB

Open AccessReview

Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective

by Su H. Chu, Mengna Huang, Rachel S. Kelly, Elisa Benedetti, Jalal K. Siddiqui, Oana A. Zeleznik, Alexandre Pereira, David Herrington, Craig E. Wheelock, Jan Krumsiek, Michael McGeachie, Steven C. Moore, Peter Kraft, Ewy Mathé, Jessica Lasky-Su and on behalf of the Consortium of Metabolomics Studies Statistics Working Group

Metabolites 2019, 9(6), 117; https://doi.org/10.3390/metabo9060117 - 18 Jun 2019

Cited by 44 | Viewed by 7175

Abstract

It is not controversial that study design considerations and challenges must be addressed when investigating the linkage between single omic measurements and human phenotypes. It follows that such considerations are just as critical, if not more so, in the context of multi-omic studies. [...] Read more.

It is not controversial that study design considerations and challenges must be addressed when investigating the linkage between single omic measurements and human phenotypes. It follows that such considerations are just as critical, if not more so, in the context of multi-omic studies. In this review, we discuss (1) epidemiologic principles of study design, including selection of biospecimen source(s) and the implications of the timing of sample collection, in the context of a multi-omic investigation, and (2) the strengths and limitations of various techniques of data integration across multi-omic data types that may arise in population-based studies utilizing metabolomic data. Full article

(This article belongs to the Special Issue Metabolomics in Epidemiological Studies)

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17 pages, 3352 KiB

Open AccessArticle

Comparison of the Serum Metabolic Fingerprint of Different Exercise Modes in Men with and without Metabolic Syndrome

by Aikaterina Siopi, Olga Deda, Vasiliki Manou, Ioannis Kosmidis, Despina Komninou, Nikolaos Raikos, Georgios A. Theodoridis and Vassilis Mougios

Metabolites 2019, 9(6), 116; https://doi.org/10.3390/metabo9060116 - 15 Jun 2019

Cited by 17 | Viewed by 3420

Abstract

Exercise plays a beneficial role in the treatment of metabolic syndrome (MetS). Metabolomics can provide new insights and facilitate the optimization of exercise prescription. This study aimed to investigate whether the response of the human serum metabolic fingerprint to exercise depends on exercise [...] Read more.

Exercise plays a beneficial role in the treatment of metabolic syndrome (MetS). Metabolomics can provide new insights and facilitate the optimization of exercise prescription. This study aimed to investigate whether the response of the human serum metabolic fingerprint to exercise depends on exercise mode or the presence of MetS. Twenty-three sedentary men (nine with MetS and fourteen healthy) completed four trials: Resting, high-intensity interval exercise (HIIE), continuous moderate-intensity exercise (CME), and resistance exercise (RE). Blood samples were collected pre-exercise, immediately after exercise, and 1 h post-exercise for targeted metabolomic analysis in serum by liquid chromatography–mass spectrometry. Time exerted the strongest differentiating effect, followed by exercise mode. The largest changes from baseline were found in the immediate post-exercise samples. RE caused the strongest responses overall, followed by HIIE, while CME had minimal effect. Unlike previous results in urine, no valid model could separate the two groups in serum. Exercise exerted a beneficial effect on prominent serum biomarkers of metabolic risks, such as branched-chain amino acids, alanine, acetylcarnitine, choline, and betaine. These findings contribute to the ongoing research efforts to map the molecular responses to exercise and to optimize exercise guidelines for individuals at cardiometabolic risk. Full article

(This article belongs to the Special Issue Exercise Metabonomics)

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24 pages, 1601 KiB

Open AccessArticle

Euglena Central Metabolic Pathways and Their Subcellular Locations

by Sahutchai Inwongwan, Nicholas J. Kruger, R. George Ratcliffe and Ellis C. O’Neill

Metabolites 2019, 9(6), 115; https://doi.org/10.3390/metabo9060115 - 14 Jun 2019

Cited by 15 | Viewed by 5582

Abstract

Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know where the component enzymes are in the cell, but despite a long history of research [...] Read more.

Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know where the component enzymes are in the cell, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. We analysed bioinformatic, biochemical, and proteomic information from a variety of sources to assess the subcellular location of the enzymes of the central metabolic pathways, and we use these assignments to propose a model of the metabolic network of Euglena. Other than photosynthesis, all major pathways present in the chloroplast are also present elsewhere in the cell. Our model demonstrates how Euglena can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts. Full article

(This article belongs to the Special Issue Metabolites from Phototrophic Prokaryotes and Algae Volume 2)

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19 pages, 3847 KiB

Open AccessArticle

Comparative Metabolomics of Early Development of the Parasitic Plants Phelipanche aegyptiaca and Triphysaria versicolor

by Kristen Clermont, Yaxin Wang, Siming Liu, Zhenzhen Yang, Claude W. dePamphilis, John I. Yoder, Eva Collakova and James H. Westwood

Metabolites 2019, 9(6), 114; https://doi.org/10.3390/metabo9060114 - 13 Jun 2019

Cited by 9 | Viewed by 3745

Abstract

Parasitic weeds of the family Orobanchaceae attach to the roots of host plants via haustoria capable of drawing nutrients from host vascular tissue. The connection of the haustorium to the host marks a shift in parasite metabolism from autotrophy to at least partial [...] Read more.

Parasitic weeds of the family Orobanchaceae attach to the roots of host plants via haustoria capable of drawing nutrients from host vascular tissue. The connection of the haustorium to the host marks a shift in parasite metabolism from autotrophy to at least partial heterotrophy, depending on the level of parasite dependence. Species within the family Orobanchaceae span the spectrum of host nutrient dependency, yet the diversity of parasitic plant metabolism remains poorly understood, particularly during the key metabolic shift surrounding haustorial attachment. Comparative profiling of major metabolites in the obligate holoparasite Phelipanche aegyptiaca and the facultative hemiparasite Triphysaria versicolor before and after attachment to the hosts revealed several metabolic shifts implicating remodeling of energy and amino acid metabolism. After attachment, both parasites showed metabolite profiles that were different from their respective hosts. In P. aegyptiaca, prominent changes in metabolite profiles were also associated with transitioning between different tissue types before and after attachment, with aspartate levels increasing significantly after the attachment. Based on the results from ¹⁵N labeling experiments, asparagine and/or aspartate-rich proteins were enriched in host-derived nitrogen in T. versicolor. These results point to the importance of aspartate and/or asparagine in the early stages of attachment in these plant parasites and provide a rationale for targeting aspartate-family amino acid biosynthesis for disrupting the growth of parasitic weeds. Full article

(This article belongs to the Special Issue Metabolomics in Agriculture)

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21 pages, 2636 KiB

Open AccessArticle

Cerebral Vitamin B5 (D-Pantothenic Acid) Deficiency as a Potential Cause of Metabolic Perturbation and Neurodegeneration in Huntington’s Disease

by Stefano Patassini, Paul Begley, Jingshu Xu, Stephanie J. Church, Nina Kureishy, Suzanne J. Reid, Henry J. Waldvogel, Richard L. M. Faull, Russell G. Snell, Richard D. Unwin and Garth J. S. Cooper

Metabolites 2019, 9(6), 113; https://doi.org/10.3390/metabo9060113 - 11 Jun 2019

Cited by 44 | Viewed by 6982

Abstract

Huntington’s disease (HD) is a neurodegenerative disorder caused by an expanded CAG repeat in exon 1 of the HTT gene. HD usually manifests in mid-life with loss of GABAergic projection neurons from the striatum accompanied by progressive atrophy of the putamen followed by [...] Read more.

Huntington’s disease (HD) is a neurodegenerative disorder caused by an expanded CAG repeat in exon 1 of the HTT gene. HD usually manifests in mid-life with loss of GABAergic projection neurons from the striatum accompanied by progressive atrophy of the putamen followed by other brain regions, but linkages between the genetics and neurodegeneration are not understood. We measured metabolic perturbations in HD-human brain in a case-control study, identifying pervasive lowering of vitamin B5, the obligatory precursor of coenzyme A (CoA) that is essential for normal intermediary metabolism. Cerebral pantothenate deficiency is a newly-identified metabolic defect in human HD that could potentially: (i) impair neuronal CoA biosynthesis; (ii) stimulate polyol-pathway activity; (iii) impair glycolysis and tricarboxylic acid cycle activity; and (iv) modify brain-urea metabolism. Pantothenate deficiency could lead to neurodegeneration/dementia in HD that might be preventable by treatment with vitamin B5. Full article

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13 pages, 2923 KiB

Open AccessArticle

Dynamic Changes of Plasma Metabolome in Response to Severe Feed Restriction in Pregnant Ewes

by Changzheng Guo, Yanfeng Xue, Hossam-eldin Seddik, Yuyang Yin, Fan Hu and Shengyong Mao

Metabolites 2019, 9(6), 112; https://doi.org/10.3390/metabo9060112 - 10 Jun 2019

Cited by 18 | Viewed by 3614

Abstract

Maternal metabolic disorders in ewes induced by energy deficiency have a detrimental effect on the maternal health and lambs. However, the dynamic processes of metabolic disorders are unknown. Therefore, this study attempted to explore the dynamic changes of maternal metabolism based on metabolomics [...] Read more.

Maternal metabolic disorders in ewes induced by energy deficiency have a detrimental effect on the maternal health and lambs. However, the dynamic processes of metabolic disorders are unknown. Therefore, this study attempted to explore the dynamic changes of maternal metabolism based on metabolomics approach during energy deficiency in pregnant ewes. Twenty pregnant Hu sheep were fed a basic diet or a 70% restricted basic diet. The HPLC-MS platform was applied to identify blood metabolites. Principal component analysis of blood samples based on their metabolic profile showed that blood samples of feed restriction group differed after the treatment. In particular, when comparing both groups, there were 120, 129, and 114 differential metabolites at day 5, day 10, and day 114 between the two groups, respectively. Enrichment analysis results showed that four metabolic pathways (glycerophospholipid metabolism, linoleic acid metabolism, arginine and proline metabolism, and aminoacyl-tRNA biosynthesis) at day 5, four metabolic pathways (aminoacyl-tRNA biosynthesis, aminoacyl-tRNA biosynthesis, glycerophospholipid metabolism, and citrate cycle) at day 10, and nine metabolic pathways (aminoacyl-tRNA biosynthesis, synthesis and degradation of ketone bodies, glycerophospholipid metabolism, butanoate metabolism, linoleic acid metabolism, citrate cycle, alanine, aspartate and glutamate metabolism, valine, leucine and isoleucine biosynthesis, and arginine and proline metabolism) at day 15 were significantly enriched between the two groups. These findings revealed temporal changes of metabolic disorders in pregnant ewes caused by severe feed restriction, which may provide insights into mitigation measures. Full article

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19 pages, 1629 KiB

Open AccessReview

An Updated Overview of Metabolomic Profile Changes in Chronic Obstructive Pulmonary Disease

by Nan Ran, Zhiqiang Pang, Yinuo Gu, He Pan, Xu Zuo, Xuewa Guan, Yuze Yuan, Ziyan Wang, Yingqiao Guo, Zixu Cui and Fang Wang

Metabolites 2019, 9(6), 111; https://doi.org/10.3390/metabo9060111 - 10 Jun 2019

Cited by 31 | Viewed by 5418

Abstract

Chronic obstructive pulmonary disease (COPD), a common and heterogeneous respiratory disease, is characterized by persistent and incompletely reversible airflow limitation. Metabolomics is applied to analyze the difference of metabolic profile based on the low-molecular-weight metabolites (<1 kDa). Emerging metabolomic analysis may provide insights [...] Read more.

Chronic obstructive pulmonary disease (COPD), a common and heterogeneous respiratory disease, is characterized by persistent and incompletely reversible airflow limitation. Metabolomics is applied to analyze the difference of metabolic profile based on the low-molecular-weight metabolites (<1 kDa). Emerging metabolomic analysis may provide insights into the pathogenesis and diagnosis of COPD. This review aims to summarize the alteration of metabolites in blood/serum/plasma, urine, exhaled breath condensate, lung tissue samples, etc. from COPD individuals, thereby uncovering the potential pathogenesis of COPD according to the perturbed metabolic pathways. Metabolomic researches have indicated that the dysfunctions of amino acid metabolism, lipid metabolism, energy production pathways, and the imbalance of oxidations and antioxidations might lead to local and systematic inflammation by activating the Nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway and releasing inflammatory cytokines, like interleutin-6 (IL-6), tumor necrosis factor-α, and IL-8. In addition, they might cause protein malnutrition and oxidative stress and contribute to the development and exacerbation of COPD. Full article

(This article belongs to the Special Issue Metabolomics and Chronic Obstructive Lung Diseases)

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8 pages, 569 KiB

Open AccessArticle

Secondary Metabolites of Aeromonas veronii Strain A134 Isolated from a Microcystis aeruginosa Bloom

by Gad Weiss, Dimitry Kovalerchick, Omer Murik, Assaf Sukenik, Aaron Kaplan and Shmuel Carmeli

Metabolites 2019, 9(6), 110; https://doi.org/10.3390/metabo9060110 - 09 Jun 2019

Cited by 9 | Viewed by 3279

Abstract

Aeromonas veronii strain A134 was isolated from Microcystis aeruginosa colonies collected from Lake Kinneret (Sea of Galilee), Israel. The Aeromonas culture media inhibited the growth of M. aeruginosa (strain MGK). The crude extract of a large-scale culture of A. veronii A134 was separated [...] Read more.

Aeromonas veronii strain A134 was isolated from Microcystis aeruginosa colonies collected from Lake Kinneret (Sea of Galilee), Israel. The Aeromonas culture media inhibited the growth of M. aeruginosa (strain MGK). The crude extract of a large-scale culture of A. veronii A134 was separated in a few chromatographic steps to yield three new secondary metabolites, 9-chlorolumichrome (1), veronimide (2) and veronipyrazine (3), along with a known lumichrome and several known diketopiperazines. The structures of the new compounds were established by analyses of the data from 1D and 2D NMR experiments and HRMS data of the compounds, as well as a single-crystal X-ray analysis of synthetic 1. The structure elucidation and proposed biogenesis of the new compounds are described below. Full article

(This article belongs to the Special Issue Metabolomics in Chemical Ecology)

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18 pages, 1084 KiB

Open AccessArticle

Characterization of Bulk Phosphatidylcholine Compositions in Human Plasma Using Side-Chain Resolving Lipidomics

by Jan D. Quell, Werner Römisch-Margl, Mark Haid, Jan Krumsiek, Thomas Skurk, Anna Halama, Nisha Stephan, Jerzy Adamski, Hans Hauner, Dennis Mook-Kanamori, Robert P. Mohney, Hannelore Daniel, Karsten Suhre and Gabi Kastenmüller

Metabolites 2019, 9(6), 109; https://doi.org/10.3390/metabo9060109 - 08 Jun 2019

Cited by 13 | Viewed by 5494

Abstract

Kit-based assays, such as AbsoluteIDQ^TM p150, are widely used in large cohort studies and provide a standardized method to quantify blood concentrations of phosphatidylcholines (PCs). Many disease-relevant associations of PCs were reported using this method. However, their interpretation is hampered by [...] Read more.

Kit-based assays, such as AbsoluteIDQ^TM p150, are widely used in large cohort studies and provide a standardized method to quantify blood concentrations of phosphatidylcholines (PCs). Many disease-relevant associations of PCs were reported using this method. However, their interpretation is hampered by lack of functionally-relevant information on the detailed fatty acid side-chain compositions as only the total number of carbon atoms and double bonds is identified by the kit. To enable more substantiated interpretations, we characterized these PC sums using the side-chain resolving Lipidyzer^TM platform, analyzing 223 samples in parallel to the AbsoluteIDQ^TM. Combining these datasets, we estimated the quantitative composition of PC sums and subsequently tested their replication in an independent cohort. We identified major constituents of 28 PC sums, revealing also various unexpected compositions. As an example, PC 16:0_22:5 accounted for more than 50% of the PC sum with in total 38 carbon atoms and 5 double bonds (PC aa 38:5). For 13 PC sums, we found relatively high abundances of odd-chain fatty acids. In conclusion, our study provides insights in PC compositions in human plasma, facilitating interpretation of existing epidemiological data sets and potentially enabling imputation of PC compositions for future meta-analyses of lipidomics data. Full article

(This article belongs to the Special Issue Metabolomics in Epidemiological Studies)

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25 pages, 1348 KiB

Open AccessPerspective

Translational Metabolomics: Current Challenges and Future Opportunities

by Farhana R. Pinu, Seyed Ali Goldansaz and Jacob Jaine

Metabolites 2019, 9(6), 108; https://doi.org/10.3390/metabo9060108 - 06 Jun 2019

Cited by 136 | Viewed by 9450

Abstract

Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most [...] Read more.

Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored. Full article

(This article belongs to the Special Issue Agribio and Food Metabolomics)

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12 pages, 2720 KiB

Open AccessArticle

Simultaneous Synthesis of Vitamins D₂, D₄, D₅, D₆, and D₇ from Commercially Available Phytosterol, β-Sitosterol, and Identification of Each Vitamin D by HSQC NMR

by Shiro Komba, Eiichi Kotake-Nara and Wakako Tsuzuki

Metabolites 2019, 9(6), 107; https://doi.org/10.3390/metabo9060107 - 06 Jun 2019

Cited by 8 | Viewed by 4106

Abstract

We succeeded in simultaneously synthesizing the vitamin D family, vitamins D₂, D₄, D₅, D₆, and D₇, from β-sitosterol, which is sold as a commercially available reagent from Tokyo Chemical Industry Co., Ltd. It [...] Read more.

We succeeded in simultaneously synthesizing the vitamin D family, vitamins D₂, D₄, D₅, D₆, and D₇, from β-sitosterol, which is sold as a commercially available reagent from Tokyo Chemical Industry Co., Ltd. It is officially sold as a mixture of four phytosterols {β-sitosterol (40–45%), campesterol (20–30%), stigmasterol, and brassicasterol}. Owing to this, we anticipated that, using this reagent, various vitamin D analogs could be synthesized simultaneously. We also synthesized vitamin D₃ from pure cholesterol and analyzed and compared all vitamin D analogs (D₂, D₃, D₄, D₅, D₆, and D₇) by HSQC NMR. We succeeded in clearly demonstrating the difference in the NMR chemical shifts for each vitamin D analog. Full article

(This article belongs to the Special Issue Compound Identification of Small Molecules)

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11 pages, 1055 KiB

Open AccessConference Report

Tackling the Complexity of the Exposome: Considerations from the Gunma University Initiative for Advanced Research (GIAR) Exposome Symposium

by Pei Zhang, Manish Arora, Romanas Chaleckis, Tomohiko Isobe, Mohit Jain, Isabel Meister, Erik Melén, Matthew Perzanowski, Federico Torta, Markus R. Wenk and Craig E. Wheelock

Metabolites 2019, 9(6), 106; https://doi.org/10.3390/metabo9060106 - 06 Jun 2019

Cited by 13 | Viewed by 4869

Abstract

The attempt to describe complex diseases by solely genetic determination has not been successful. There is increasing recognition that the development of disease is often a consequence of interactions between multiple genetic and environmental factors. To date, much of the research on environmental [...] Read more.

The attempt to describe complex diseases by solely genetic determination has not been successful. There is increasing recognition that the development of disease is often a consequence of interactions between multiple genetic and environmental factors. To date, much of the research on environmental determinants of disease has focused on single exposures generally measured at a single time point. In order to address this limitation, the concept of the exposome has been introduced as a comprehensive approach, studying the full complement of environmental exposures from conception onwards. However, exposures are vast, dynamic, and diverse, and only a small proportion can be reasonably measured due to limitations in technology and feasibility. In addition, the interplay between genes and exposure as well as between different exposures is complicated and multifaceted, which leads to difficulties in linking disease or health outcomes with exposures. The large numbers of collected samples require well-designed logistics. Furthermore, the immense data sets generated from exposome studies require a significant computational investment for both data analysis and data storage. This report summarizes discussions during an international exposome symposium held at Gunma University in Japan regarding the concept of the exposome, challenges in exposome research, and future perspectives in the field. Full article

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13 pages, 1373 KiB

Open AccessArticle

Exo-Metabolites of Phaseolus vulgaris-Nodulating Rhizobial Strains

by Diana Montes-Grajales, Nuria Esturau-Escofet, Baldomero Esquivel and Esperanza Martinez-Romero

Metabolites 2019, 9(6), 105; https://doi.org/10.3390/metabo9060105 - 30 May 2019

Cited by 8 | Viewed by 3489

Abstract

Rhizobia are able to convert dinitrogen into biologically available forms of nitrogen through their symbiotic association with leguminous plants. This results in plant growth promotion, and also in conferring host resistance to different types of stress. These bacteria can interact with other organisms [...] Read more.

Rhizobia are able to convert dinitrogen into biologically available forms of nitrogen through their symbiotic association with leguminous plants. This results in plant growth promotion, and also in conferring host resistance to different types of stress. These bacteria can interact with other organisms and survive in a wide range of environments, such as soil, rhizosphere, and inside roots. As most of these processes are molecularly mediated, the aim of this research was to identify and quantify the exo-metabolites produced by Rhizobium etli CFN42, Rhizobium leucaenae CFN299, Rhizobium tropici CIAT899, Rhizobium phaseoli Ch24-10, and Sinorhizobium americanum CFNEI156, by nuclear magnetic resonance (NMR). Bacteria were grown in free-living cultures using minimal medium containing sucrose and glutamate. Interestingly, we found that even when these bacteria belong to the same family (Rhizobiaceae) and all form nitrogen-fixing nodules on Phaseolus vulgaris roots, they exhibited different patterns and concentrations of chemical species produced by them. Full article

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Metabolites, Volume 9, Issue 6 (June 2019) – 17 articles

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