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Metabolites, Volume 4, Issue 1 (March 2014), Pages 1-141

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Editorial

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Open AccessEditorial Acknowledgement to Reviewers of Metabolites in 2013
Metabolites 2014, 4(1), 129-130; doi:10.3390/metabo4010129
Received: 26 February 2014 / Accepted: 26 February 2014 / Published: 26 February 2014
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Abstract The editors of Metabolites would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013. [...] Full article

Research

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Open AccessArticle Cellulose Digestion and Metabolism Induced Biocatalytic Transitions in Anaerobic Microbial Ecosystems
Metabolites 2014, 4(1), 36-52; doi:10.3390/metabo4010036
Received: 13 September 2013 / Revised: 18 December 2013 / Accepted: 20 December 2013 / Published: 31 December 2013
Cited by 7 | PDF Full-text (935 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Anaerobic digestion of highly polymerized biomass by microbial communities present in diverse microbial ecosystems is an indispensable metabolic process for biogeochemical cycling in nature and for industrial activities required to maintain a sustainable society. Therefore, the evaluation of the complicated microbial metabolomics [...] Read more.
Anaerobic digestion of highly polymerized biomass by microbial communities present in diverse microbial ecosystems is an indispensable metabolic process for biogeochemical cycling in nature and for industrial activities required to maintain a sustainable society. Therefore, the evaluation of the complicated microbial metabolomics presents a significant challenge. We here describe a comprehensive strategy for characterizing the degradation of highly crystallized bacterial cellulose (BC) that is accompanied by metabolite production for identifying the responsible biocatalysts, including microorganisms and their metabolic functions. To this end, we employed two-dimensional solid- and one-dimensional solution-state nuclear magnetic resonance (NMR) profiling combined with a metagenomic approach using stable isotope labeling. The key components of biocatalytic reactions determined using a metagenomic approach were correlated with cellulose degradation and metabolic products. The results indicate that BC degradation was mediated by cellulases that contain carbohydrate-binding modules and that belong to structural type A. The degradation reactions induced the metabolic dynamics of the microbial community and produced organic compounds, such as acetic acid and propionic acid, mainly metabolized by clostridial species. This combinatorial, functional and structural metagenomic approach is useful for the comprehensive characterization of biomass degradation, metabolic dynamics and their key components in diverse ecosystems. Full article
(This article belongs to the Special Issue Microbial Metabolomics)
Figures

Open AccessArticle Fluxomics of the Eastern Oyster for Environmental Stress Studies
Metabolites 2014, 4(1), 53-70; doi:10.3390/metabo4010053
Received: 21 August 2013 / Revised: 27 November 2013 / Accepted: 19 December 2013 / Published: 7 January 2014
Cited by 5 | PDF Full-text (1347 KB) | HTML Full-text | XML Full-text
Abstract
The metabolism of 2-13C/15N-glycine and U-13C-glucose was determined in four tissue blocks (adductor muscle, stomach and digestive gland, mantle, and gills) of the Eastern oyster (Crassostrea virginica) using proton (1H) and carbon-13 [...] Read more.
The metabolism of 2-13C/15N-glycine and U-13C-glucose was determined in four tissue blocks (adductor muscle, stomach and digestive gland, mantle, and gills) of the Eastern oyster (Crassostrea virginica) using proton (1H) and carbon-13 (13C) nuclear magnetic resonance (NMR) spectroscopy. The oysters were treated in aerated seawater with three treatments (5.5 mM U-13C-glucose, 2.7 mM 2-13C/15N-glycine, and 5.5 mM U-13C-glucose plus 2.7 mM 2-13C/15N-glycine) and the relative mass balance and 13C fractional enrichments were determined in the four tissue blocks. In all tissues, glycine was metabolized by the glycine cycle forming serine exclusively in the mitochondria by the glycine cleavage system forming 2,3-13C-serine. In muscle, a minor amount of serine-derived pyruvate entered the Krebs cycle as substantiated by detection of a trace of 2,3-13C-aspartate. In all tissues, U-13C-glucose formed glycogen by glycogen synthesis, alanine by glycolysis, and glutamate and aspartate through the Krebs cycle. Alanine was formed exclusively from glucose via alanine transaminase and not glycine via alanine-glyoxylate transaminase. Based on isotopomer analysis, pyruvate carboxylase and pyruvate dehydrogenase appeared to be equal points for pyruvate entry into the Krebs cycle. In the 5.5 mM U-13C-glucose plus 2.7 mM 2-13C/15N-glycine emergence treatment used to simulate 12 h of “low tide”, oysters accumulated more 13C-labeled metabolites, including both anaerobic glycolytic and aerobic Krebs cycle intermediates. The aerobic metabolites could be the biochemical result of the gaping behavior of mollusks during emergence. The change in tissue distribution and mass balance of 13C-labeled nutrients (U-13C-glucose and 2-13C/15N-glycine) provides the basis for a new quantitative fluxomic method for elucidating sub-lethal environmental effects in marine organisms called whole body mass balance phenotyping (WoMBaP). Full article
(This article belongs to the Special Issue Response to Environment and Stress Metabolism)
Open AccessArticle Comparative Analysis of Biological Sphingolipids with Glycerophospholipids and Diacylglycerol by LC-MS/MS
Metabolites 2014, 4(1), 98-114; doi:10.3390/metabo4010098
Received: 4 December 2013 / Revised: 8 January 2014 / Accepted: 20 January 2014 / Published: 27 January 2014
Cited by 12 | PDF Full-text (978 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Liquid chromatography-electrospray ionization mass spectrometry (LC-MS) is an effective and popular technique used in lipid metabolomic studies. Although many LC-MS methods enabling the determination of sphingolipid molecular species have been reported, they do not cover a broad range of sphingolipid metabolites with [...] Read more.
Liquid chromatography-electrospray ionization mass spectrometry (LC-MS) is an effective and popular technique used in lipid metabolomic studies. Although many LC-MS methods enabling the determination of sphingolipid molecular species have been reported, they do not cover a broad range of sphingolipid metabolites with expanding glycerophospholipids (GPLs) and diacylglycerol (DAG). In this study, we developed an approach for the comprehensive analysis of sphingolipids, GPLs and DAG molecular species in a biological sample, without alkaline hydrolysis. After validating the reliability of this approach, we analyzed tissue lipids of sphingomyelin synthase 2-knockout mice and found that changes in sphingolipid metabolism in the liver affect the level of docosahexaenoic acid-containing GPLs. Our method analyzes GPLs and DAG, as well as sphingolipids within biological samples and, thus, will facilitate more comprehensive studies of sphingolipid metabolism in pathology and diagnostics. Full article
(This article belongs to the Special Issue Cell and Tissue Metabolomics)
Open AccessArticle 1H NMR Analysis of Cerebrospinal Fluid from Alzheimer’s Disease Patients: An Example of a Possible Misinterpretation Due to Non-Adjustment of pH
Metabolites 2014, 4(1), 115-128; doi:10.3390/metabo4010115
Received: 2 December 2013 / Revised: 10 January 2014 / Accepted: 7 February 2014 / Published: 19 February 2014
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Abstract
Two publications from the same research group reporting on the detection of new possible biomarkers for the early diagnosis of Alzheimer’s disease (AD), based on the analysis of cerebrospinal fluid samples (CSF) with 1H Nuclear Magnetic Resonance (NMR), are at the [...] Read more.
Two publications from the same research group reporting on the detection of new possible biomarkers for the early diagnosis of Alzheimer’s disease (AD), based on the analysis of cerebrospinal fluid samples (CSF) with 1H Nuclear Magnetic Resonance (NMR), are at the origin of the present study. The authors observed significant differences in 1H NMR spectra of CSF from AD patients and healthy controls and, thus, proposed some NMR signals (without attribution) as possible biomarkers. However, this work was carried out in non-standardized pH conditions. Our study aims at warning about a possible misinterpretation that can arise from 1H NMR analyses of CSF samples if pH adjustment is not done before NMR analysis. Indeed, CSF pH increases rapidly after removal and is subject to changes over conservation time. We first identify the NMR signals described by the authors as biomarkers. We then focus on the chemical shift variations of their NMR signals as a function of pH in both standard solutions and CSF samples. Finally, a principal component analysis of 1H NMR data demonstrates that the same CSF samples recorded at pH 8.1 and 10.0 are statistically differentiated. Full article
(This article belongs to the Special Issue Sample Preparation for Metabolite Analysis)

Review

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Open AccessReview Regulation Systems of Bacteria such as Escherichia coli in Response to Nutrient Limitation and Environmental Stresses
Metabolites 2014, 4(1), 1-35; doi:10.3390/metabo4010001
Received: 9 September 2013 / Revised: 18 November 2013 / Accepted: 6 December 2013 / Published: 30 December 2013
Cited by 17 | PDF Full-text (1828 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
An overview was made to understand the regulation system of a bacterial cell such as Escherichia coli in response to nutrient limitation such as carbon, nitrogen, phosphate, sulfur, ion sources, and environmental stresses such as oxidative stress, acid shock, heat shock, and [...] Read more.
An overview was made to understand the regulation system of a bacterial cell such as Escherichia coli in response to nutrient limitation such as carbon, nitrogen, phosphate, sulfur, ion sources, and environmental stresses such as oxidative stress, acid shock, heat shock, and solvent stresses. It is quite important to understand how the cell detects environmental signals, integrate such information, and how the cell system is regulated. As for catabolite regulation, F1,6B P (FDP), PEP, and PYR play important roles in enzyme level regulation together with transcriptional regulation by such transcription factors as Cra, Fis, CsrA, and cAMP-Crp. αKG plays an important role in the coordinated control between carbon (C)- and nitrogen (N)-limitations, where αKG inhibits enzyme I (EI) of phosphotransferase system (PTS), thus regulating the glucose uptake rate in accordance with N level. As such, multiple regulation systems are co-ordinated for the cell synthesis and energy generation against nutrient limitations and environmental stresses. As for oxidative stress, the TCA cycle both generates and scavenges the reactive oxygen species (ROSs), where NADPH produced at ICDH and the oxidative pentose phosphate pathways play an important role in coping with oxidative stress. Solvent resistant mechanism was also considered for the stresses caused by biofuels and biochemicals production in the cell. Full article
(This article belongs to the Special Issue Response to Environment and Stress Metabolism)
Open AccessReview Microextraction by Packed Sorbent (MEPS) and Solid-Phase Microextraction (SPME) as Sample Preparation Procedures for the Metabolomic Profiling of Urine
Metabolites 2014, 4(1), 71-97; doi:10.3390/metabo4010071
Received: 13 December 2013 / Revised: 14 January 2014 / Accepted: 21 January 2014 / Published: 27 January 2014
Cited by 11 | PDF Full-text (1053 KB) | HTML Full-text | XML Full-text
Abstract
For a long time, sample preparation was unrecognized as a critical issue in the analytical methodology, thus limiting the performance that could be achieved. However, the improvement of microextraction techniques, particularly microextraction by packed sorbent (MEPS) and solid-phase microextraction (SPME), completely modified [...] Read more.
For a long time, sample preparation was unrecognized as a critical issue in the analytical methodology, thus limiting the performance that could be achieved. However, the improvement of microextraction techniques, particularly microextraction by packed sorbent (MEPS) and solid-phase microextraction (SPME), completely modified this scenario by introducing unprecedented control over this process. Urine is a biological fluid that is very interesting for metabolomics studies, allowing human health and disease characterization in a minimally invasive form. In this manuscript, we will critically review the most relevant and promising works in this field, highlighting how the metabolomic profiling of urine can be an extremely valuable tool for the early diagnosis of highly prevalent diseases, such as cardiovascular, oncologic and neurodegenerative ones. Full article
(This article belongs to the Special Issue Sample Preparation for Metabolite Analysis)
Figures

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 [...] Read more.
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)

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