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Metabolites, Volume 4, Issue 4 (December 2014) , Pages 879-1118

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Open AccessArticle Towards the Fecal Metabolome Derived from Moderate Red Wine Intake
Metabolites 2014, 4(4), 1101-1118; https://doi.org/10.3390/metabo4041101
Received: 31 July 2014 / Revised: 28 November 2014 / Accepted: 15 December 2014 / Published: 19 December 2014
Cited by 10 | Viewed by 2562 | PDF Full-text (624 KB) | HTML Full-text | XML Full-text
Abstract
Dietary polyphenols, including red wine phenolic compounds, are extensively metabolized during their passage through the gastrointestinal tract; and their biological effects at the gut level (i.e., anti-inflammatory activity, microbiota modulation, interaction with cells, among others) seem to be due more to [...] Read more.
Dietary polyphenols, including red wine phenolic compounds, are extensively metabolized during their passage through the gastrointestinal tract; and their biological effects at the gut level (i.e., anti-inflammatory activity, microbiota modulation, interaction with cells, among others) seem to be due more to their microbial-derived metabolites rather than to the original forms found in food. In an effort to improve our understanding of the biological effects that phenolic compounds exert at the gut level, this paper summarizes the changes observed in the human fecal metabolome after an intervention study consisting of a daily consumption of 250 mL of wine during four weeks by healthy volunteers (n = 33). It assembles data from two analytical approaches: (1) UPLC-ESI-MS/MS analysis of phenolic metabolites in fecal solutions (targeted analysis); and (2) UHPLC-TOF MS analysis of the fecal solutions (non-targeted analysis). Both approaches revealed statistically-significant changes in the concentration of several metabolites as a consequence of the wine intake. Similarity and complementarity between targeted and non-targeted approaches in the analysis of the fecal metabolome are discussed. Both strategies allowed the definition of a complex metabolic profile derived from wine intake. Likewise, the identification of endogenous markers could lead to new hypotheses to unravel the relationship between moderate wine consumption and the metabolic functionality of gut microbiota. Full article
(This article belongs to the Special Issue Metabolomic Studies of the Human Gut Microbiome)
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Open AccessArticle Distribution of Heparan Sulfate Oligosaccharides in Murine Mucopolysaccharidosis Type IIIA
Metabolites 2014, 4(4), 1088-1100; https://doi.org/10.3390/metabo4041088
Received: 22 September 2014 / Revised: 27 November 2014 / Accepted: 3 December 2014 / Published: 11 December 2014
Cited by 2 | Viewed by 2401 | PDF Full-text (373 KB) | HTML Full-text | XML Full-text
Abstract
Heparan sulfate (HS) catabolism begins with endo-degradation of the polysaccharide to smaller HS oligosaccharides, followed by the sequential action of exo-enzymes to reduce these oligosaccharides to monosaccharides and inorganic sulfate. In mucopolysaccharidosis type IIIA (MPS IIIA) the exo-enzyme, N-sulfoglucosamine sulfohydrolase, is deficient resulting [...] Read more.
Heparan sulfate (HS) catabolism begins with endo-degradation of the polysaccharide to smaller HS oligosaccharides, followed by the sequential action of exo-enzymes to reduce these oligosaccharides to monosaccharides and inorganic sulfate. In mucopolysaccharidosis type IIIA (MPS IIIA) the exo-enzyme, N-sulfoglucosamine sulfohydrolase, is deficient resulting in an inability to hydrolyze non-reducing end glucosamine N-sulfate esters. Consequently, partially degraded HS oligosaccharides with non-reducing end glucosamine sulfate esters accumulate. We investigated the distribution of these HS oligosaccharides in tissues of a mouse model of MPS IIIA using high performance liquid chromatography electrospray ionization-tandem mass spectrometry. Oligosaccharide levels were compared to total uronic acid (UA), which was used as a measure of total glycosaminoglycan. Ten oligosaccharides, ranging in size from di- to hexasaccharides, were present in all the tissues examined including brain, spleen, lung, heart, liver, kidney and urine. However, the relative levels varied up to 10-fold, suggesting different levels of HS turnover and storage. The relationship between the di- and tetrasaccharides and total UA was tissue specific with spleen and kidney showing a different disaccharide:total UA ratio than the other tissues. The hexasaccharides showed a stronger correlation with total UA in all tissue types suggesting that hexasaccharides may more accurately reflect the storage burden in these tissues. Full article
(This article belongs to the Special Issue Inborn Errors of Metabolism)
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Open AccessReview Computational Strategies for a System-Level Understanding of Metabolism
Metabolites 2014, 4(4), 1034-1087; https://doi.org/10.3390/metabo4041034
Received: 1 August 2014 / Revised: 5 November 2014 / Accepted: 12 November 2014 / Published: 24 November 2014
Cited by 10 | Viewed by 4459 | PDF Full-text (1300 KB) | HTML Full-text | XML Full-text
Abstract
Cell metabolism is the biochemical machinery that provides energy and building blocks to sustain life. Understanding its fine regulation is of pivotal relevance in several fields, from metabolic engineering applications to the treatment of metabolic disorders and cancer. Sophisticated computational approaches are needed [...] Read more.
Cell metabolism is the biochemical machinery that provides energy and building blocks to sustain life. Understanding its fine regulation is of pivotal relevance in several fields, from metabolic engineering applications to the treatment of metabolic disorders and cancer. Sophisticated computational approaches are needed to unravel the complexity of metabolism. To this aim, a plethora of methods have been developed, yet it is generally hard to identify which computational strategy is most suited for the investigation of a specific aspect of metabolism. This review provides an up-to-date description of the computational methods available for the analysis of metabolic pathways, discussing their main advantages and drawbacks. In particular, attention is devoted to the identification of the appropriate scale and level of accuracy in the reconstruction of metabolic networks, and to the inference of model structure and parameters, especially when dealing with a shortage of experimental measurements. The choice of the proper computational methods to derive in silico data is then addressed, including topological analyses, constraint-based modeling and simulation of the system dynamics. A description of some computational approaches to gain new biological knowledge or to formulate hypotheses is finally provided. Full article
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Open AccessArticle Multi-Spectroscopic Analysis of Seed Quality and 13C-Stable-Iotopologue Monitoring in Initial Growth Metabolism of Jatropha curcas L.
Metabolites 2014, 4(4), 1018-1033; https://doi.org/10.3390/metabo4041018
Received: 28 April 2014 / Revised: 10 September 2014 / Accepted: 5 November 2014 / Published: 13 November 2014
Cited by 7 | Viewed by 2382 | PDF Full-text (1399 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In the present study, we applied nuclear magnetic resonance (NMR), as well as near-infrared (NIR) spectroscopy, to Jatropha curcas to fulfill two objectives: (1) to qualitatively examine the seeds stored at different conditions, and (2) to monitor the metabolism of J. curcas during [...] Read more.
In the present study, we applied nuclear magnetic resonance (NMR), as well as near-infrared (NIR) spectroscopy, to Jatropha curcas to fulfill two objectives: (1) to qualitatively examine the seeds stored at different conditions, and (2) to monitor the metabolism of J. curcas during its initial growth stage under stable-isotope-labeling condition (until 15 days after seeding). NIR spectra could non-invasively distinguish differences in storage conditions. NMR metabolic analysis of water-soluble metabolites identified sucrose and raffinose family oligosaccharides as positive markers and gluconic acid as a negative marker of seed germination. Isotopic labeling patteren of metabolites in germinated seedlings cultured in agar-plate containg 13C-glucose and 15N-nitrate was analyzed by zero-quantum-filtered-total correlation spectroscopy (ZQF-TOCSY) and 13C-detected 1H-13C heteronuclear correlation spectroscopy (HETCOR). 13C-detected HETOCR with 13C-optimized cryogenic probe provided high-resolution 13C-NMR spectra of each metabolite in molecular crowd. The 13C-13C/12C bondmer estimated from 1H-13C HETCOR spectra indicated that glutamine and arginine were the major organic compounds for nitrogen and carbon transfer from roots to leaves. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Open AccessReview New Strategies for the Treatment of Phenylketonuria (PKU)
Metabolites 2014, 4(4), 1007-1017; https://doi.org/10.3390/metabo4041007
Received: 21 May 2014 / Revised: 27 October 2014 / Accepted: 30 October 2014 / Published: 4 November 2014
Cited by 20 | Viewed by 6671 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
Phenylketonuria (PKU) was the first inherited metabolic disease in which dietary treatment was found to prevent the disease’s clinical features. Treatment of phenylketonuria remains difficult due to progressive decrease in adherence to diet and the presence of neurocognitive defects despite therapy. This review [...] Read more.
Phenylketonuria (PKU) was the first inherited metabolic disease in which dietary treatment was found to prevent the disease’s clinical features. Treatment of phenylketonuria remains difficult due to progressive decrease in adherence to diet and the presence of neurocognitive defects despite therapy. This review aims to summarize the current literature on new treatment strategies. Additions to treatment include new, more palatable foods based on glycomacropeptide that contains very limited amount of aromatic amino acids, the administration of large neutral amino acids to prevent phenylalanine entry into the brain or tetrahydropterina cofactor capable of increasing residual activity of phenylalanine hydroxylase. Moreover, human trials have recently been performed with subcutaneous administration of phenylalanine ammonia-lyase, and further efforts are underway to develop an oral therapy containing phenylanine ammonia-lyase. Gene therapy also seems to be a promising approach in the near future. Full article
(This article belongs to the Special Issue Inborn Errors of Metabolism)
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Open AccessReview Clinically Important Features of Porphyrin and Heme Metabolism and the Porphyrias
Metabolites 2014, 4(4), 977-1006; https://doi.org/10.3390/metabo4040977
Received: 31 May 2014 / Revised: 14 October 2014 / Accepted: 16 October 2014 / Published: 3 November 2014
Cited by 32 | Viewed by 4373 | PDF Full-text (337 KB) | HTML Full-text | XML Full-text
Abstract
Heme, like chlorophyll, is a primordial molecule and is one of the fundamental pigments of life. Disorders of normal heme synthesis may cause human diseases, including certain anemias (X-linked sideroblastic anemias) and porphyrias. Porphyrias are classified as hepatic and erythropoietic porphyrias based on [...] Read more.
Heme, like chlorophyll, is a primordial molecule and is one of the fundamental pigments of life. Disorders of normal heme synthesis may cause human diseases, including certain anemias (X-linked sideroblastic anemias) and porphyrias. Porphyrias are classified as hepatic and erythropoietic porphyrias based on the organ system in which heme precursors (5-aminolevulinic acid (ALA), porphobilinogen and porphyrins) are chiefly overproduced. The hepatic porphyrias are further subdivided into acute porphyrias and chronic hepatic porphyrias. The acute porphyrias include acute intermittent, hereditary copro-, variegate and ALA dehydratase deficiency porphyria. Chronic hepatic porphyrias include porphyria cutanea tarda and hepatoerythropoietic porphyria. The erythropoietic porphyrias include congenital erythropoietic porphyria (Gűnther’s disease) and erythropoietic protoporphyria. In this review, we summarize the key features of normal heme synthesis and its differing regulation in liver versus bone marrow. In both organs, principal regulation is exerted at the level of the first and rate-controlling enzyme, but by different molecules (heme in the liver and iron in the bone marrow). We also describe salient clinical, laboratory and genetic features of the eight types of porphyria. Full article
(This article belongs to the Special Issue Inborn Errors of Metabolism)
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Open AccessArticle An Efficient High Throughput Metabotyping Platform for Screening of Biomass Willows
Metabolites 2014, 4(4), 946-976; https://doi.org/10.3390/metabo4040946
Received: 4 September 2014 / Revised: 15 October 2014 / Accepted: 22 October 2014 / Published: 28 October 2014
Cited by 8 | Viewed by 2754 | PDF Full-text (2402 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Future improvement of woody biomass crops such as willow and poplar relies on our ability to select for metabolic traits that sequester more atmospheric carbon into biomass, or into useful products to replace petrochemical streams. We describe the development of metabotyping screens for [...] Read more.
Future improvement of woody biomass crops such as willow and poplar relies on our ability to select for metabolic traits that sequester more atmospheric carbon into biomass, or into useful products to replace petrochemical streams. We describe the development of metabotyping screens for willow, using combined 1D 1H-NMR-MS. A protocol was developed to overcome 1D 1H-NMR spectral alignment problems caused by variable pH and peak broadening arising from high organic acid levels and metal cations. The outcome was a robust method to allow direct statistical comparison of profiles arising from source (leaf) and sink (stem) tissues allowing data to be normalised to a constant weight of the soluble metabolome. We also describe the analysis of two willow biomass varieties, demonstrating how fingerprints from 1D 1H-NMR-MS vary from the top to the bottom of the plant. Automated extraction of quantitative data of 56 primary and secondary metabolites from 1D 1H-NMR spectra was realised by the construction and application of a Salix metabolite spectral library using the Chenomx software suite. The optimised metabotyping screen in conjunction with automated quantitation will enable high-throughput screening of genetic collections. It also provides genotype and tissue specific data for future modelling of carbon flow in metabolic networks. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Open AccessArticle Volatile Metabolite Profiling of Durum Wheat Kernels Contaminated by Fusarium poae
Metabolites 2014, 4(4), 932-945; https://doi.org/10.3390/metabo4040932
Received: 1 August 2014 / Revised: 29 September 2014 / Accepted: 10 October 2014 / Published: 17 October 2014
Cited by 5 | Viewed by 2327 | PDF Full-text (325 KB) | HTML Full-text | XML Full-text
Abstract
Volatile metabolites from mold contamination have been proposed for the early identification of toxigenic fungi to prevent toxicological risks, but there are no such data available for Fusarium poae. F. poae is one of the species complexes involved in Fusarium head blight, a [...] Read more.
Volatile metabolites from mold contamination have been proposed for the early identification of toxigenic fungi to prevent toxicological risks, but there are no such data available for Fusarium poae. F. poae is one of the species complexes involved in Fusarium head blight, a cereal disease that results in significant yield losses and quality reductions. The identification of volatile organic compounds associated with F. poae metabolism could provide good markers to indicate early fungal contamination. To this aim, we evaluated the volatile profile of healthy and F. poae-infected durum wheat kernels by SPME-GC/MS analysis. The production of volatile metabolites was monitored for seven days, and the time course analysis of key volatiles was determined. A total of 29 volatile markers were selected among the detected compounds, and multivariate analysis was applied to establish the relationship between potential volatile markers and fungal contamination. A range of volatile compounds, including alcohols, ketones, esters, furans and aromatics, were identified, both in contaminated and in healthy kernels. However, the overall volatile profile of infected samples and controls differed, indicating that the whole volatile profile, rather than individual volatile compounds, could be used to identify F. poae contamination of durum wheat grains. Full article
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Open AccessArticle Micropreconcentrator in LTCC Technology with Mass Spectrometry for the Detection of Acetone in Healthy and Type-1 Diabetes Mellitus Patient Breath
Metabolites 2014, 4(4), 921-931; https://doi.org/10.3390/metabo4040921
Received: 22 July 2014 / Revised: 11 September 2014 / Accepted: 15 September 2014 / Published: 10 October 2014
Cited by 11 | Viewed by 2833 | PDF Full-text (552 KB) | HTML Full-text | XML Full-text
Abstract
Breath analysis has long been recognized as a potentially attractive method for the diagnosis of several diseases. The main advantage over other diagnostic methods such as blood or urine analysis is that breath analysis is fully non-invasive, comfortable for patients and breath samples [...] Read more.
Breath analysis has long been recognized as a potentially attractive method for the diagnosis of several diseases. The main advantage over other diagnostic methods such as blood or urine analysis is that breath analysis is fully non-invasive, comfortable for patients and breath samples can be easily obtained. One possible future application of breath analysis may be the diagnosing and monitoring of diabetes. It is, therefore, essential, to firstly determine a relationship between exhaled biomarker concentration and glucose in blood as well as to compare the results with the results obtained from non-diabetic subjects. Concentrations of molecules which are biomarkers of diseases’ states, or early indicators of disease should be well documented, i.e., the variations of abnormal concentrations of breath biomarkers with age, gender and ethnic issues need to be verified. Furthermore, based on performed measurements it is rather obvious that analysis of exhaled acetone as a single biomarker of diabetes is unrealistic. In this paper, the author presents results of his research conducted on samples of breath gas from eleven healthy volunteers (HV) and fourteen type- 1 diabetic patients (T1DM) which were collected in 1-l SKC breath bags. The exhaled acetone concentration was measured using mass spectrometry (HPR-20 QIC, Hiden Analytical, Warrington, UK) coupled with a micropreconcentrator in LTCC (Low Temperature Cofired Ceramic). However, as according to recent studies the level of acetone varies to a significant extent for each blood glucose concentration of single individuals, a direct and absolute relationship between blood glucose and acetone has not been proved. Nevertheless, basing on the research results acetone in diabetic breath was found to be higher than 1.11 ppmv, while its average concentration in normal breath was lower than 0.83 ppmv. Full article
(This article belongs to the Special Issue Breath Analysis in Metabolomics)
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Open AccessReview The Metabolic Basis of Pollen Thermo-Tolerance: Perspectives for Breeding
Metabolites 2014, 4(4), 889-920; https://doi.org/10.3390/metabo4040889
Received: 21 July 2014 / Revised: 10 September 2014 / Accepted: 22 September 2014 / Published: 30 September 2014
Cited by 16 | Viewed by 3561 | PDF Full-text (656 KB) | HTML Full-text | XML Full-text
Abstract
Crop production is highly sensitive to elevated temperatures. A rise of a few degrees above the optimum growing temperature can lead to a dramatic yield loss. A predicted increase of 1–3 degrees in the twenty first century urges breeders to develop thermo-tolerant crops [...] Read more.
Crop production is highly sensitive to elevated temperatures. A rise of a few degrees above the optimum growing temperature can lead to a dramatic yield loss. A predicted increase of 1–3 degrees in the twenty first century urges breeders to develop thermo-tolerant crops which are tolerant to high temperatures. Breeding for thermo-tolerance is a challenge due to the low heritability of this trait. A better understanding of heat stress tolerance and the development of reliable methods to phenotype thermo-tolerance are key factors for a successful breeding approach. Plant reproduction is the most temperature-sensitive process in the plant life cycle. More precisely, pollen quality is strongly affected by heat stress conditions. High temperature leads to a decrease of pollen viability which is directly correlated with a loss of fruit production. The reduction in pollen viability is associated with changes in the level and composition of several (groups of) metabolites, which play an important role in pollen development, for example by contributing to pollen nutrition or by providing protection to environmental stresses. This review aims to underline the importance of maintaining metabolite homeostasis during pollen development, in order to produce mature and fertile pollen under high temperature. The review will give an overview of the current state of the art on the role of various pollen metabolites in pollen homeostasis and thermo-tolerance. Their possible use as metabolic markers to assist breeding programs for plant thermo-tolerance will be discussed. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Open AccessArticle Evaluation of Bio-VOC Sampler for Analysis of Volatile Organic Compounds in Exhaled Breath
Metabolites 2014, 4(4), 879-888; https://doi.org/10.3390/metabo4040879
Received: 16 May 2014 / Revised: 26 August 2014 / Accepted: 22 September 2014 / Published: 29 September 2014
Cited by 13 | Viewed by 3442 | PDF Full-text (273 KB) | HTML Full-text | XML Full-text
Abstract
Monitoring volatile organic compounds (VOCs) from exhaled breath has been used to determine exposures of humans to chemicals. Prior to analysis of VOCs, breath samples are often collected with canisters or bags and concentrated. The Bio-VOC breath sampler, a commercial sampling device, has [...] Read more.
Monitoring volatile organic compounds (VOCs) from exhaled breath has been used to determine exposures of humans to chemicals. Prior to analysis of VOCs, breath samples are often collected with canisters or bags and concentrated. The Bio-VOC breath sampler, a commercial sampling device, has been recently introduced to the market with growing use. The main advantage for this sampler is to collect the last portion of exhaled breath, which is more likely to represent the air deep in the lungs. However, information about the Bio-VOC sampler is somewhat limited. Therefore, we have thoroughly evaluated the sampler here. We determined the volume of the breath air collected in the sampler was approximately 88 mL. When sampling was repeated multiple times, with the succeeding exhalations applied to a single sorbent tube, we observed linear relationships between the normalized peak intensity and the number of repeated collections with the sampler in many of the breath VOCs detected. No moisture effect was observed on the Tenax sorbent tubes used. However, due to the limitation in the collection volume, the use of the Bio-VOC sampler is recommended only for detection of VOCs present at high concentrations unless repeated collections of breath samples on the sampler are conducted. Full article
(This article belongs to the Special Issue Breath Analysis in Metabolomics)
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