Special Issue "Metabolomics and Biotechnology"

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

Deadline for manuscript submissions: closed (30 April 2014)

Special Issue Editors

Guest Editor
Dr. Fumio Matsuda (Website)

Graduate School of Information Science and Technologies, Osaka University and the RIKEN Center for Sustainable Resource Science, Japan
Interests: metabolic engineering; metabolomics; metabolic flux analysis; metabolic simulation; phytochemistry
Guest Editor
Dr. Kazuki Saito (Website)

Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, and the Graduate School of Pharmaceutical Sciences, Chiba University, Japan
Interests: metabolomics; functional genomics; phytochemistry; plant biotechnology; primary and secondary metabolism

Special Issue Information

Dear Colleagues,

Based on the technological development of the last decade, including progress with respect to sample preparations, analytical techniques, and informatics for data processing, metabolomics has become an essential tool for exploring the frontiers of emerging biotechnological fields. There are many metabolomics-driven studies; such studies range from the fundamental to the applied sciences (in the fields of plant, agriculture, food, microbes, pharmaceutics, and medicine). These studies cover many topics: e.g., the quality control of foods, traditional medicines, microbial metabolism for bio-refineries, the identification of novel metabolic functions for crop improvement, and marker discovery for disease diagnosis and pharmaceutical development.

This special issue of Metabolites, "Metabolomics and Biotechnology," will be dedicated not only to in-depth applications of metabolomics techniques to the biotechnology field, but also to a cutting-edge technology development for detailed "metabolotyping," both from a fundamental as well as an applied point of view. The topics that will be covered by this special issue include (not exclusively): the functional genomics that identify novel metabolites and gene functions, the biotechnological application of metabolomic methods, metabolic flux analysis using stable isotopes, single cell analysis requiring a sensitive quantification of diverse metabolites in tiny samples, empirical and computational methods of annotating metabolites, metabolite imaging, the mathematical modeling of metabolism, and applications in quality control, process engineering, and regulatory science. Manuscripts dealing with other challenging issues are also highly desired.

Dr. Kazuki Saito
Dr.Fumio Matsuda
Guest Editors

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (i.e., on a rolling basis once they are accepted) and will be listed together on the special issue website. Research articles, review articles, as well as communications, are all invited. For planned papers, a title and short abstract (of about 100 words) can be sent to the Editorial Office for announcement on the website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for the submission of manuscripts are available on the “Instructions for Authors” page. Metabolites is an international, peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the “Instructions for Authors” page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 500 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • metabolomics
  • metabolomics-driven biotechnology
  • marker discovery
  • quality control
  • single cell analysis
  • metabolic flux analysis
  • metabolite identification
  • gene identification
  • imaging
  • metabolic modeling

Published Papers (13 papers)

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Research

Jump to: Review

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; doi:10.3390/metabo4041018
Received: 28 April 2014 / Revised: 10 September 2014 / Accepted: 5 November 2014 / Published: 13 November 2014
Cited by 5 | 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 [...] 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)
Open AccessArticle An Efficient High Throughput Metabotyping Platform for Screening of Biomass Willows
Metabolites 2014, 4(4), 946-976; doi:10.3390/metabo4040946
Received: 4 September 2014 / Revised: 15 October 2014 / Accepted: 22 October 2014 / Published: 28 October 2014
Cited by 2 | 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 [...] 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 Novel Strategy for Non-Targeted Isotope-Assisted Metabolomics by Means of Metabolic Turnover and Multivariate Analysis
Metabolites 2014, 4(3), 722-739; doi:10.3390/metabo4030722
Received: 21 April 2014 / Revised: 5 August 2014 / Accepted: 12 August 2014 / Published: 25 August 2014
Cited by 1 | PDF Full-text (438 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Isotope-labeling is a useful technique for understanding cellular metabolism. Recent advances in metabolomics have extended the capability of isotope-assisted studies to reveal global metabolism. For instance, isotope-assisted metabolomics technology has enabled the mapping of a global metabolic network, estimation of flux at [...] Read more.
Isotope-labeling is a useful technique for understanding cellular metabolism. Recent advances in metabolomics have extended the capability of isotope-assisted studies to reveal global metabolism. For instance, isotope-assisted metabolomics technology has enabled the mapping of a global metabolic network, estimation of flux at branch points of metabolic pathways, and assignment of elemental formulas to unknown metabolites. Furthermore, some data processing tools have been developed to apply these techniques to a non-targeted approach, which plays an important role in revealing unknown or unexpected metabolism. However, data collection and integration strategies for non-targeted isotope-assisted metabolomics have not been established. Therefore, a systematic approach is proposed to elucidate metabolic dynamics without targeting pathways by means of time-resolved isotope tracking, i.e., “metabolic turnover analysis”, as well as multivariate analysis. We applied this approach to study the metabolic dynamics in amino acid perturbation of Saccharomyces cerevisiae. In metabolic turnover analysis, 69 peaks including 35 unidentified peaks were investigated. Multivariate analysis of metabolic turnover successfully detected a pathway known to be inhibited by amino acid perturbation. In addition, our strategy enabled identification of unknown peaks putatively related to the perturbation. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Open AccessArticle Metabolite Profiling of Root Exudates of Common Bean under Phosphorus Deficiency
Metabolites 2014, 4(3), 599-611; doi:10.3390/metabo4030599
Received: 24 April 2014 / Revised: 29 June 2014 / Accepted: 3 July 2014 / Published: 16 July 2014
Cited by 5 | PDF Full-text (250 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Root exudates improve the nutrient acquisition of plants and affect rhizosphere microbial communities. The plant nutrient status affects the composition of root exudates. The purpose of this study was to examine common bean (Phaseolus vulgaris L.) root exudates under phosphorus (P) [...] Read more.
Root exudates improve the nutrient acquisition of plants and affect rhizosphere microbial communities. The plant nutrient status affects the composition of root exudates. The purpose of this study was to examine common bean (Phaseolus vulgaris L.) root exudates under phosphorus (P) deficiency using a metabolite profiling technique. Common bean plants were grown in a culture solution at P concentrations of 0 (P0), 1 (P1) and 8 (P8) mg P L−1 for 1, 10 and 20 days after transplanting (DAT). Root exudates were collected, and their metabolites were determined by capillary electrophoresis time-of-flight mass spectrometry (CE-TOF MS). The shoot P concentration and dry weight of common bean plants grown at P0 were lower than those grown at P8. One hundred and fifty-nine, 203 and 212 metabolites were identified in the root exudates, and 16% (26/159), 13% (26/203) and 9% (20/212) of metabolites showed a P0/P8 ratio higher than 2.0 at 1, 10 and 20 DAT, respectively. The relative peak areas of several metabolites, including organic acids and amino acids, in root exudates were higher at P0 than at P8. These results suggest that more than 10% of primary and secondary metabolites are induced to exude from roots of common bean by P deficiency. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
Open AccessArticle Metabolic Profiling of Retrograde Pathway Transcription Factors Rtg1 and Rtg3 Knockout Yeast
Metabolites 2014, 4(3), 580-598; doi:10.3390/metabo4030580
Received: 22 April 2014 / Revised: 12 June 2014 / Accepted: 24 June 2014 / Published: 8 July 2014
Cited by 3 | PDF Full-text (675 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rtg1 and Rtg3 are two basic helix-loop-helix (bHLH) transcription factors found in yeast Saccharomyces cerevisiae that are involved in the regulation of the mitochondrial retrograde (RTG) pathway. Under RTG response, anaplerotic synthesis of citrate is activated, consequently maintaining the supply of important [...] Read more.
Rtg1 and Rtg3 are two basic helix-loop-helix (bHLH) transcription factors found in yeast Saccharomyces cerevisiae that are involved in the regulation of the mitochondrial retrograde (RTG) pathway. Under RTG response, anaplerotic synthesis of citrate is activated, consequently maintaining the supply of important precursors necessary for amino acid and nucleotide synthesis. Although the roles of Rtg1 and Rtg3 in TCA and glyoxylate cycles have been extensively reported, the investigation of other metabolic pathways has been lacking. Characteristic dimer formation in bHLH proteins, which allows for combinatorial gene expression, and the link between RTG and other regulatory pathways suggest more complex metabolic signaling involved in Rtg1/Rtg3 regulation. In this study, using a metabolomics approach, we examined metabolic alteration following RTG1 and RTG3 deletion. We found that apart from TCA and glyoxylate cycles, which have been previously reported, polyamine biosynthesis and other amino acid metabolism were significantly altered in RTG-deficient strains. We revealed that metabolic alterations occurred at various metabolic sites and that these changes relate to different growth phases, but the difference can be detected even at the mid-exponential phase, when mitochondrial function is repressed. Moreover, the effect of metabolic rearrangements can be seen through the chronological lifespan (CLS) measurement, where we confirmed the role of the RTG pathway in extending the yeast lifespan. Through a comprehensive metabolic profiling, we were able to explore metabolic phenotypes previously unidentified by other means and illustrate the possible correlations of Rtg1 and Rtg3 in different pathways. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
Open AccessArticle Insect-Induced Daidzein, Formononetin and Their Conjugates in Soybean Leaves
Metabolites 2014, 4(3), 532-546; doi:10.3390/metabo4030532
Received: 29 April 2014 / Revised: 23 June 2014 / Accepted: 24 June 2014 / Published: 4 July 2014
Cited by 4 | PDF Full-text (752 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In response to attack by bacterial pathogens, soybean (Gylcine max) leaves accumulate isoflavone aglucones, isoflavone glucosides, and glyceollins. In contrast to pathogens, the dynamics of related insect-inducible metabolites in soybean leaves remain poorly understood. In this study, we analyzed the [...] Read more.
In response to attack by bacterial pathogens, soybean (Gylcine max) leaves accumulate isoflavone aglucones, isoflavone glucosides, and glyceollins. In contrast to pathogens, the dynamics of related insect-inducible metabolites in soybean leaves remain poorly understood. In this study, we analyzed the biochemical responses of soybean leaves to Spodoptera litura (Lepidoptera: Noctuidae) herbivory and also S. litura gut contents, which contain oral secretion elicitors. Following S. litura herbivory, soybean leaves displayed an induced accumulation of the flavone and isoflavone aglycones 4’,7-dihyroxyflavone, daidzein, and formononetin, and also the isoflavone glucoside daidzin. Interestingly, foliar application of S. litura oral secretions also elicited the accumulation of isoflavone aglycones (daidzein and formononetin), isoflavone 7-O-glucosides (daidzin, ononin), and isoflavone 7-O-(6’-O-malonyl-β-glucosides) (malonyldaidzin, malonylononin). Consistent with the up-regulation of the isoflavonoid biosynthetic pathway, folair phenylalanine levels also increased following oral secretion treatment. To establish that these metabolitic changes were the result of de novo biosynthesis, we demonstrated that labeled (13C9) phenylalanine was incorporated into the isoflavone aglucones. These results are consistent with the presence of soybean defense elicitors in S. litura oral secretions. We demonstrate that isoflavone aglycones and isoflavone conjugates are induced in soybean leaves, not only by pathogens as previously demonstrated, but also by foliar insect herbivory. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Open AccessArticle Molar-Based Targeted Metabolic Profiling of Cyanobacterial Strains with Potential for Biological Production
Metabolites 2014, 4(2), 499-516; doi:10.3390/metabo4020499
Received: 17 April 2014 / Revised: 5 June 2014 / Accepted: 12 June 2014 / Published: 20 June 2014
Cited by 14 | PDF Full-text (1321 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Recently, cyanobacteria have become one of the most attractive hosts for biochemical production due to its high proliferative ability and ease of genetic manipulation. Several researches aimed at biological production using modified cyanobacteria have been reported previously. However, to improve the yield [...] Read more.
Recently, cyanobacteria have become one of the most attractive hosts for biochemical production due to its high proliferative ability and ease of genetic manipulation. Several researches aimed at biological production using modified cyanobacteria have been reported previously. However, to improve the yield of bioproducts, a thorough understanding of the intercellular metabolism of cyanobacteria is necessary. Metabolic profiling techniques have proven to be powerful tools for monitoring cellular metabolism of various organisms and can be applied to elucidate the details of cyanobacterial metabolism. In this study, we constructed a metabolic profiling method for cyanobacteria using 13C-labeled cell extracts as internal standards. Using this method, absolute concentrations of 84 metabolites were successfully determined in three cyanobacterial strains which are commonly used as background strains for metabolic engineering. By comparing the differences in basic metabolic potentials of the three cyanobacterial strains, we found a well-correlated relationship between intracellular energy state and growth in cyanobacteria. By integrating our results with the previously reported biological production pathways in cyanobacteria, we found putative limiting step of carbon flux. The information obtained from this study will not only help gain insights in cyanobacterial physiology but also serve as a foundation for future metabolic engineering studies using cyanobacteria. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
Open AccessArticle Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids
Metabolites 2014, 4(2), 408-420; doi:10.3390/metabo4020408
Received: 17 March 2014 / Revised: 10 May 2014 / Accepted: 20 May 2014 / Published: 30 May 2014
Cited by 5 | PDF Full-text (434 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
13C metabolic flux analysis (MFA) is a tool of metabolic engineering for investigation of in vivo flux distribution. A direct 13C enrichment analysis of intracellular free amino acids (FAAs) is expected to reduce time for labeling experiments of the MFA. [...] Read more.
13C metabolic flux analysis (MFA) is a tool of metabolic engineering for investigation of in vivo flux distribution. A direct 13C enrichment analysis of intracellular free amino acids (FAAs) is expected to reduce time for labeling experiments of the MFA. Measurable FAAs should, however, vary among the MFA experiments since the pool sizes of intracellular free metabolites depend on cellular metabolic conditions. In this study, minimal 13C enrichment data of FAAs was investigated to perform the FAAs-based MFA. An examination of a continuous culture of Escherichia coli using 13C-labeled glucose showed that the time required to reach an isotopically steady state for FAAs is rather faster than that for conventional method using proteinogenic amino acids (PAAs). Considering 95% confidence intervals, it was found that the metabolic flux distribution estimated using FAAs has a similar reliability to that of the PAAs-based method. The comparative analysis identified glutamate, aspartate, alanine and phenylalanine as the common amino acids observed in E. coli under different culture conditions. The results of MFA also demonstrated that the 13C enrichment data of the four amino acids is required for a reliable analysis of the flux distribution. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Open AccessArticle Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae
Metabolites 2014, 4(2), 347-372; doi:10.3390/metabo4020347
Received: 27 March 2014 / Revised: 1 May 2014 / Accepted: 6 May 2014 / Published: 15 May 2014
Cited by 4 | PDF Full-text (418 KB) | HTML Full-text | XML Full-text
Abstract
Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads [...] Read more.
Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism’s physiology under dynamic conditions. We found that the biomass yield was slightly reduced (−5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments). Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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Review

Jump to: Research

Open AccessReview The Metabolic Basis of Pollen Thermo-Tolerance: Perspectives for Breeding
Metabolites 2014, 4(4), 889-920; doi:10.3390/metabo4040889
Received: 21 July 2014 / Revised: 10 September 2014 / Accepted: 22 September 2014 / Published: 30 September 2014
Cited by 5 | 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 [...] 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)
Open AccessReview Recent Advances in the Application of Metabolomics to Studies of Biogenic Volatile Organic Compounds (BVOC) Produced by Plant
Metabolites 2014, 4(3), 699-721; doi:10.3390/metabo4030699
Received: 18 May 2014 / Revised: 12 August 2014 / Accepted: 13 August 2014 / Published: 21 August 2014
Cited by 4 | PDF Full-text (475 KB) | HTML Full-text | XML Full-text
Abstract
In many plants, biogenic volatile organic compounds (BVOCs) are produced as specialized metabolites that contribute to the characteristics of each plant. The varieties and composition of BVOCs are chemically diverse by plant species and the circumstances in which the plants grow, and [...] Read more.
In many plants, biogenic volatile organic compounds (BVOCs) are produced as specialized metabolites that contribute to the characteristics of each plant. The varieties and composition of BVOCs are chemically diverse by plant species and the circumstances in which the plants grow, and also influenced by herbivory damage and pathogen infection. Plant-produced BVOCs are receptive to many organisms, from microorganisms to human, as both airborne attractants and repellants. In addition, it is known that some BVOCs act as signals to prime a plant for the defense response in plant-to-plant communications. The compositional profiles of BVOCs can, thus, have profound influences in the physiological and ecological aspects of living organisms. Apart from that, some of them are commercially valuable as aroma/flavor compounds for human. Metabolomic technologies have recently revealed new insights in biological systems through metabolic dynamics. Here, the recent advances in metabolomics technologies focusing on plant-produced BVOC analyses are overviewed. Their application markedly improves our knowledge of the role of BVOCs in chemosystematics, ecological influences, and aroma research, as well as being useful to prove the biosynthetic mechanisms of BVOCs. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
Open AccessReview Metabolomics for Biomarker Discovery in Gastroenterological Cancer
Metabolites 2014, 4(3), 547-571; doi:10.3390/metabo4030547
Received: 9 April 2014 / Revised: 11 June 2014 / Accepted: 25 June 2014 / Published: 7 July 2014
Cited by 3 | PDF Full-text (241 KB) | HTML Full-text | XML Full-text
Abstract
The study of the omics cascade, which involves comprehensive investigations based on genomics, transcriptomics, proteomics, metabolomics, etc., has developed rapidly and now plays an important role in life science research. Among such analyses, metabolome analysis, in which the concentrations of low [...] Read more.
The study of the omics cascade, which involves comprehensive investigations based on genomics, transcriptomics, proteomics, metabolomics, etc., has developed rapidly and now plays an important role in life science research. Among such analyses, metabolome analysis, in which the concentrations of low molecular weight metabolites are comprehensively analyzed, has rapidly developed along with improvements in analytical technology, and hence, has been applied to a variety of research fields including the clinical, cell biology, and plant/food science fields. The metabolome represents the endpoint of the omics cascade and is also the closest point in the cascade to the phenotype. Moreover, it is affected by variations in not only the expression but also the enzymatic activity of several proteins. Therefore, metabolome analysis can be a useful approach for finding effective diagnostic markers and examining unknown pathological conditions. The number of studies involving metabolome analysis has recently been increasing year-on-year. Here, we describe the findings of studies that used metabolome analysis to attempt to discover biomarker candidates for gastroenterological cancer and discuss metabolome analysis-based disease diagnosis. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
Open AccessReview MALDI Mass Spectrometry Imaging for Visualizing In Situ Metabolism of Endogenous Metabolites and Dietary Phytochemicals
Metabolites 2014, 4(2), 319-346; doi:10.3390/metabo4020319
Received: 26 February 2014 / Revised: 17 April 2014 / Accepted: 4 May 2014 / Published: 9 May 2014
Cited by 13 | PDF Full-text (2566 KB) | HTML Full-text | XML Full-text
Abstract
Understanding the spatial distribution of bioactive small molecules is indispensable for elucidating their biological or pharmaceutical roles. Mass spectrometry imaging (MSI) enables determination of the distribution of ionizable molecules present in tissue sections of whole-body or single heterogeneous organ samples by direct [...] Read more.
Understanding the spatial distribution of bioactive small molecules is indispensable for elucidating their biological or pharmaceutical roles. Mass spectrometry imaging (MSI) enables determination of the distribution of ionizable molecules present in tissue sections of whole-body or single heterogeneous organ samples by direct ionization and detection. This emerging technique is now widely used for in situ label-free molecular imaging of endogenous or exogenous small molecules. MSI allows the simultaneous visualization of many types of molecules including a parent molecule and its metabolites. Thus, MSI has received much attention as a potential tool for pathological analysis, understanding pharmaceutical mechanisms, and biomarker discovery. On the other hand, several issues regarding the technical limitations of MSI are as of yet still unresolved. In this review, we describe the capabilities of the latest matrix-assisted laser desorption/ionization (MALDI)-MSI technology for visualizing in situ metabolism of endogenous metabolites or dietary phytochemicals (food factors), and also discuss the technical problems and new challenges, including MALDI matrix selection and metabolite identification, that need to be addressed for effective and widespread application of MSI in the diverse fields of biological, biomedical, and nutraceutical (food functionality) research. Full article
(This article belongs to the Special Issue Metabolomics and Biotechnology)
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