Special Issue "NMR-based Metabolomics and Its Application"

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A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (31 January 2013)

Special Issue Editor

Guest Editor
Dr. Horst Schirra

School for Chemistry & Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
Website | E-Mail
Interests: NMR-based metabonomics; structural systems biology

Special Issue Information

Submission

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Published Papers (7 papers)

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Research

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Open AccessArticle Studies of Secondary Melanoma on C57BL/6J Mouse Liver Using 1H NMR Metabolomics
Metabolites 2013, 3(4), 1011-1035; doi:10.3390/metabo3041011
Received: 23 August 2013 / Revised: 24 September 2013 / Accepted: 10 October 2013 / Published: 31 October 2013
Cited by 6 | PDF Full-text (722 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
NMR metabolomics, consisting of solid state high resolution magic angle spinning (HR-MAS) 1H-NMR, liquid state high resolution 1H-NMR, and principal components analysis (PCA) has been used to study secondary metastatic B16-F10 melanoma in C57BL/6J mouse liver. The melanoma group can be
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NMR metabolomics, consisting of solid state high resolution magic angle spinning (HR-MAS) 1H-NMR, liquid state high resolution 1H-NMR, and principal components analysis (PCA) has been used to study secondary metastatic B16-F10 melanoma in C57BL/6J mouse liver. The melanoma group can be differentiated from its control group by PCA analysis of the estimates of absolute concentrations from liquid state 1H-NMR spectra on liver tissue extracts or by the estimates of absolute peak intensities of metabolites from 1H HR-MAS-NMR data on intact liver tissues. In particular, we found that the estimates of absolute concentrations of glutamate, creatine, fumarate and cholesterol are elevated in the melanoma group as compared to controls, while the estimates of absolute concentrations of succinate, glycine, glucose, and the family of linear lipids including long chain fatty acids, total choline and acyl glycerol are decreased. The ratio of glycerophosphocholine (GPC) to phosphocholine (PCho) is increased by about 1.5 fold in the melanoma group, while the estimate of absolute concentration of total choline is actually lower in melanoma mice. These results suggest the following picture in secondary melanoma metastasis: Linear lipid levels are decreased by beta oxidation in the melanoma group, which contributes to an increase in the synthesis of cholesterol, and also provides an energy source input for TCA cycle. These findings suggest a link between lipid oxidation, the TCA cycle and the hypoxia-inducible factors (HIF) signal pathway in tumor metastases. Thus, this study indicates that the metabolic profile derived from NMR analysis can provide a valuable bio-signature of malignancy and cell hypoxia in metastatic melanoma. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)
Open AccessArticle Influence of Freezing and Storage Procedure on Human Urine Samples in NMR-Based Metabolomics
Metabolites 2013, 3(2), 243-258; doi:10.3390/metabo3020243
Received: 19 February 2013 / Revised: 28 March 2013 / Accepted: 1 April 2013 / Published: 9 April 2013
Cited by 8 | PDF Full-text (3471 KB) | HTML Full-text | XML Full-text
Abstract
It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to
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It is consensus in the metabolomics community that standardized protocols should be followed for sample handling, storage and analysis, as it is of utmost importance to maintain constant measurement conditions to identify subtle biological differences. The aim of this work, therefore, was to systematically investigate the influence of freezing procedures and storage temperatures and their effect on NMR spectra as a potentially disturbing aspect for NMR-based metabolomics studies. Urine samples were collected from two healthy volunteers, centrifuged and divided into aliquots. Urine aliquots were frozen either at −20 °C, on dry ice, at −80 °C or in liquid nitrogen and then stored at −20 °C, −80 °C or in liquid nitrogen vapor phase for 1–5 weeks before NMR analysis. Results show spectral changes depending on the freezing procedure, with samples frozen on dry ice showing the largest deviations. The effect was found to be based on pH differences, which were caused by variations in CO2 concentrations introduced by the freezing procedure. Thus, we recommend that urine samples should be frozen at −20 °C and transferred to lower storage temperatures within one week and that freezing procedures should be part of the publication protocol. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)
Open AccessArticle Metabonomic Response to Milk Proteins after a Single Bout of Heavy Resistance Exercise Elucidated by 1H Nuclear Magnetic Resonance Spectroscopy
Metabolites 2013, 3(1), 33-46; doi:10.3390/metabo3010033
Received: 13 November 2012 / Revised: 18 December 2012 / Accepted: 21 January 2013 / Published: 30 January 2013
Cited by 5 | PDF Full-text (1054 KB) | HTML Full-text | XML Full-text
Abstract
In the present study, proton NMR-based metabonomics was applied on femoral arterial plasma samples collected from young male subjects (milk protein n = 12 in a crossover design; non-caloric control n = 8) at different time intervals (70, 220, 370 min) after heavy
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In the present study, proton NMR-based metabonomics was applied on femoral arterial plasma samples collected from young male subjects (milk protein n = 12 in a crossover design; non-caloric control n = 8) at different time intervals (70, 220, 370 min) after heavy resistance training and intake of either a whey or calcium caseinate protein drink in order to elucidate the impact of the protein source on post-exercise metabolism, which is important for muscle hypertrophy. Dynamic changes in the post-exercise plasma metabolite profile consisted of fluctuations in alanine, beta-hydroxybutyrate, branched amino acids, creatine, glucose, glutamine, glutamate, histidine, lipids and tyrosine. In comparison with the intake of a non-caloric drink, the same pattern of changes in low-molecular weight plasma metabolites was found for both whey and caseinate intake. However, the study indicated that whey and caseinate protein intake had a different impact on low-density and very-low-density lipoproteins present in the blood, which may be ascribed to different effects of the two protein sources on the mobilization of lipid resources during energy deficiency. In conclusion, no difference in the effects on low-molecular weight metabolites as measured by proton NMR-based metabonomics was found between the two protein sources. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)

Review

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Open AccessReview Applications of NMR in Dairy Research
Metabolites 2014, 4(1), 131-141; doi:10.3390/metabo4010131
Received: 14 November 2013 / Revised: 28 January 2014 / Accepted: 18 February 2014 / Published: 4 March 2014
Cited by 2 | PDF Full-text (185 KB) | HTML Full-text | XML Full-text
Abstract
NMR is a robust analytical technique that has been employed to investigate the properties of many substances of agricultural relevance. NMR was first used to investigate the properties of milk in the 1950s and has since been employed in a wide range of
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NMR is a robust analytical technique that has been employed to investigate the properties of many substances of agricultural relevance. NMR was first used to investigate the properties of milk in the 1950s and has since been employed in a wide range of studies; including properties analysis of specific milk proteins to metabolomics techniques used to monitor the health of dairy cows. In this brief review, we highlight the different uses of NMR in the dairy industry. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)
Open AccessReview The Future of NMR Metabolomics in Cancer Therapy: Towards Personalizing Treatment and Developing Targeted Drugs?
Metabolites 2013, 3(2), 373-396; doi:10.3390/metabo3020373
Received: 8 February 2013 / Revised: 7 May 2013 / Accepted: 10 May 2013 / Published: 17 May 2013
Cited by 8 | PDF Full-text (803 KB) | HTML Full-text | XML Full-text
Abstract
There has been a recent shift in how cancers are defined, where tumors are no longer simply classified by their tissue origin, but also by their molecular characteristics. Furthermore, personalized medicine has become a popular term and it could start to play an
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There has been a recent shift in how cancers are defined, where tumors are no longer simply classified by their tissue origin, but also by their molecular characteristics. Furthermore, personalized medicine has become a popular term and it could start to play an important role in future medical care. However, today, a “one size fits all” approach is still the most common form of cancer treatment. In this mini-review paper, we report on the role of nuclear magnetic resonance (NMR) metabolomics in drug development and in personalized medicine. NMR spectroscopy has successfully been used to evaluate current and potential therapies, both single-agents and combination therapies, to analyze toxicology, optimal dose, resistance, sensitivity, and biological mechanisms. It can also provide biological insight on tumor subtypes and their different responses to drugs, and indicate which patients are most likely to experience off-target effects and predict characteristics for treatment efficacy. Identifying pre-treatment metabolic profiles that correlate to these events could significantly improve how we view and treat tumors. We also briefly discuss several targeted cancer drugs that have been studied by metabolomics. We conclude that NMR technology provides a key platform in metabolomics that is well-positioned to play a crucial role in realizing the ultimate goal of better tailored cancer medicine. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)
Open AccessReview Getting Your Peaks in Line: A Review of Alignment Methods for NMR Spectral Data
Metabolites 2013, 3(2), 259-276; doi:10.3390/metabo3020259
Received: 1 February 2013 / Revised: 29 March 2013 / Accepted: 2 April 2013 / Published: 15 April 2013
Cited by 10 | PDF Full-text (1122 KB) | HTML Full-text | XML Full-text
Abstract
One of the most significant challenges in the comparative analysis of Nuclear Magnetic Resonance (NMR) metabolome profiles is the occurrence of shifts between peaks across different spectra, for example caused by fluctuations in pH, temperature, instrument factors and ion content. Proper alignment of
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One of the most significant challenges in the comparative analysis of Nuclear Magnetic Resonance (NMR) metabolome profiles is the occurrence of shifts between peaks across different spectra, for example caused by fluctuations in pH, temperature, instrument factors and ion content. Proper alignment of spectral peaks is therefore often a crucial preprocessing step prior to downstream quantitative analysis. Various alignment methods have been developed specifically for this purpose. Other methods were originally developed to align other data types (GC, LC, SELDI-MS, etc.), but can also be applied to NMR data. This review discusses the available methods, as well as related problems such as reference determination or the evaluation of alignment quality. We present a generic alignment framework that allows for comparison and classification of different alignment approaches according to their algorithmic principles, and we discuss their performance. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)
Open AccessReview NMR-Based Milk Metabolomics
Metabolites 2013, 3(2), 204-222; doi:10.3390/metabo3020204
Received: 1 February 2013 / Revised: 22 March 2013 / Accepted: 25 March 2013 / Published: 2 April 2013
Cited by 18 | PDF Full-text (305 KB) | HTML Full-text | XML Full-text
Abstract
Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and
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Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining a better understanding of how milk composition is linked to nutritional or quality traits. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)

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