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Metabolites
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Feature Papers
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Feature Papers

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

Deadline for manuscript submissions: closed (15 May 2012) | Viewed by 48346

Special Issue Editor

Dr. Clare A. Daykin

E-Mail Website
Guest Editor
MetaboConsult, Heanor, Derbyshire DE75 7UY, UK
Interests: metabolomics; metabonomics; metabolite-protein interactions; biological sample handling; NMR spectroscopy; chromatography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I am delighted to present this special issue of “Feature Papers” in the newly launched Metabolites journal.  Metabolites is a new, international, open-access and peer-reviewed Journal that publishes original research and scholarship contributing to the expanding field of metabolomics and our understanding of metabolism.  Metabolites intends to inform and to stimulate interest and debate in advancing the scientific basis of the discipline.

In recognition of this new beginning Metabolites will publish a “Feature Papers” Special Issue. The scope will fall within the range of the mission of the Journal, but is not limited to any particular themes. The following general topics indicate the possible scope of this special issue, but these are not intended to be all inclusive. They are: novel approaches and technology in metabolomics; advances in data processing and analysis; metabolomics and biomarker discovery; nutritional metabolomics; and plant and environmental metabolomics.

The deadline for submission is May 15th 2012. We look forward with enthusiasm to hearing from you and thank you for supporting the Journal.

Dr. Clare A. Daykin
Guest Editor

Keywords

  • metabolomics
  • metabonomics
  • metabolic profiling
  • metabolic fingerprints
  • global profiling of metabolites
  • metabolic phenotype
  • biomarkers
  • biofluids
  • clinical metabolomics
  • nuclear magnetic resonance (NMR) spectroscopy
  • mass spectrometry
  • multivariate data analysis

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Published Papers (4 papers)

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Research

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769 KiB  
Article
1H Nuclear Magnetic Resonance (NMR) Metabolomic Study of Chronic Organophosphate Exposure in Rats
by Todd M. Alam, Muniasamy Neerathilingam, M. Kathleen Alam, David E. Volk, G. A. Shakeel Ansari, Swapna Sarkar and Bruce A. Luxon
Metabolites 2012, 2(3), 479-495; https://doi.org/10.3390/metabo2030479 - 24 Jul 2012
Cited by 15 | Viewed by 10638
Abstract
1H NMR spectroscopy and chemometric analysis were used to characterize rat urine obtained after chronic exposure to either tributyl phosphate (TBP) or triphenyl phosphate (TPP). In this study, the daily dose exposure was 1.5 mg/kg body weight for TBP, or 2.0 mg/kg [...] Read more.
1H NMR spectroscopy and chemometric analysis were used to characterize rat urine obtained after chronic exposure to either tributyl phosphate (TBP) or triphenyl phosphate (TPP). In this study, the daily dose exposure was 1.5 mg/kg body weight for TBP, or 2.0 mg/kg body weight for TPP, administered over a 15-week period. Orthogonal signal correction (OSC) -filtered partial least square discriminant analysis (OSC-PLSDA) was used to predict and classify exposure to these organophosphates. During the development of the model, the classification error was evaluated as a function of the number of latent variables. NMR spectral regions and corresponding metabolites important for determination of exposure type were identified using variable importance in projection (VIP) coefficients obtained from the OSC-PLSDA analysis. As expected, the model for classification of chronic (1.5–2.0 mg/kg body weight daily) TBP or TPP exposure was not as strong as the previously reported model developed for identifying acute (15–20 mg/kg body weight) exposure. The set of majorly impacted metabolites identified for chronic TBP or TPP exposure was slightly different than those metabolites previously identified for acute exposure. These metabolites were then mapped to different metabolite pathways and ranked, allowing the metabolic response to chronic organophosphate exposure to be addressed. Full article
(This article belongs to the Special Issue Feature Papers)
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437 KiB  
Article
The Effect of LC-MS Data Preprocessing Methods on the Selection of Plasma Biomarkers in Fed vs. Fasted Rats
by Gözde Gürdeniz, Mette Kristensen, Thomas Skov and Lars O. Dragsted
Metabolites 2012, 2(1), 77-99; https://doi.org/10.3390/metabo2010077 - 18 Jan 2012
Cited by 55 | Viewed by 10935
Abstract
The metabolic composition of plasma is affected by time passed since the last meal and by individual variation in metabolite clearance rates. Rat plasma in fed and fasted states was analyzed with liquid chromatography quadrupole-time-of-flight mass spectrometry (LC-QTOF) for an untargeted investigation of [...] Read more.
The metabolic composition of plasma is affected by time passed since the last meal and by individual variation in metabolite clearance rates. Rat plasma in fed and fasted states was analyzed with liquid chromatography quadrupole-time-of-flight mass spectrometry (LC-QTOF) for an untargeted investigation of these metabolite patterns. The dataset was used to investigate the effect of data preprocessing on biomarker selection using three different softwares, MarkerLynxTM, MZmine, XCMS along with a customized preprocessing method that performs binning of m/z channels followed by summation through retention time. Direct comparison of selected features representing the fed or fasted state showed large differences between the softwares. Many false positive markers were obtained from custom data preprocessing compared with dedicated softwares while MarkerLynxTM provided better coverage of markers. However, marker selection was more reliable with the gap filling (or peak finding) algorithms present in MZmine and XCMS. Further identification of the putative markers revealed that many of the differences between the markers selected were due to variations in features representing adducts or daughter ions of the same metabolites or of compounds from the same chemical subclasses, e.g., lyso-phosphatidylcholines (LPCs) and lyso-phosphatidylethanolamines (LPEs). We conclude that despite considerable differences in the performance of the preprocessing tools we could extract the same biological information by any of them. Carnitine, branched-chain amino acids, LPCs and LPEs were identified by all methods as markers of the fed state whereas acetylcarnitine was abundant during fasting in rats. Full article
(This article belongs to the Special Issue Feature Papers)
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Review

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312 KiB  
Review
Polyamines under Abiotic Stress: Metabolic Crossroads and Hormonal Crosstalks in Plants
by Marta Bitrián, Xavier Zarza, Teresa Altabella, Antonio F. Tiburcio and Rubén Alcázar
Metabolites 2012, 2(3), 516-528; https://doi.org/10.3390/metabo2030516 - 20 Aug 2012
Cited by 132 | Viewed by 13417
Abstract
Polyamines are essential compounds for cell survival and have key roles in plant stress protection. Current evidence points to the occurrence of intricate cross-talks between polyamines, stress hormones and other metabolic pathways required for their function. In this review we integrate the polyamine [...] Read more.
Polyamines are essential compounds for cell survival and have key roles in plant stress protection. Current evidence points to the occurrence of intricate cross-talks between polyamines, stress hormones and other metabolic pathways required for their function. In this review we integrate the polyamine metabolic pathway in the context of its immediate metabolic network which is required to understand the multiple ways by which polyamines can maintain their homeostasis and participate in plant stress responses. Full article
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298 KiB  
Review
5-Aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-Monophosphate (AICAR), a Highly Conserved Purine Intermediate with Multiple Effects
by Bertrand Daignan-Fornier and Benoît Pinson
Metabolites 2012, 2(2), 292-302; https://doi.org/10.3390/metabo2020292 - 23 Mar 2012
Cited by 49 | Viewed by 12749
Abstract
AICAR (5-Aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate) is a natural metabolic intermediate of purine biosynthesis that is present in all organisms. In yeast, AICAR plays important regulatory roles under physiological conditions, notably through its direct interactions with transcription factors. In humans, AICAR accumulates in several metabolic diseases, [...] Read more.
AICAR (5-Aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate) is a natural metabolic intermediate of purine biosynthesis that is present in all organisms. In yeast, AICAR plays important regulatory roles under physiological conditions, notably through its direct interactions with transcription factors. In humans, AICAR accumulates in several metabolic diseases, but its contribution to the symptoms has not yet been elucidated. Further, AICAR has highly promising properties which have been recently revealed. Indeed, it enhances endurance of sedentary mice. In addition, it has antiproliferative effects notably by specifically inducing apoptosis of aneuploid cells. Some of the effects of AICAR are due to its ability to stimulate the AMP-activated protein kinase but some others are not. It is consequently clear that AICAR affects multiple targets although only few of them have been identified so far. This review proposes an overview of the field and suggests future directions. Full article
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