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Volume 8
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Metabolites, Volume 8, Issue 4 (December 2018) – 42 articles

Cover Story (view full-size image): The human plasma metabolome contains vast amounts of information on the health status of the individual. However, the factors that impact the variation in the human metabolome remain poorly characterized. In this paper, plasma metabolite profiles were associated with a range of clinical parameters in an extensively phenotyped cross-sectional population. The results revealed clear metabolic signatures related to, for example, liver and kidney function, as well as insulin resistance. Moreover, several metabolite factors were associated with the same phenotypic trait, indicating independent mechanisms. Since the results in this paper reflected findings from studies on severe clinical conditions, they may indicate early signs of disease in a largely healthy population. View this paper.
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13 pages, 3983 KiB  
Article
Dynamic Metabolic Response to Adriamycin-Induced Senescence in Breast Cancer Cells
by Rong You, Jin Dai, Ping Zhang, Gregory A. Barding, Jr. and Daniel Raftery
Metabolites 2018, 8(4), 95; https://doi.org/10.3390/metabo8040095 - 15 Dec 2018
Cited by 19 | Viewed by 3833
Abstract
Cellular senescence displays a heterogeneous set of phenotypes linked to tumor suppression; however, after drug treatment, senescence may also be involved in stable or recurrent cancer. Metabolic changes during senescence can provide detailed information on cellular status and may also have implications for [...] Read more.
Cellular senescence displays a heterogeneous set of phenotypes linked to tumor suppression; however, after drug treatment, senescence may also be involved in stable or recurrent cancer. Metabolic changes during senescence can provide detailed information on cellular status and may also have implications for the development of effective treatment strategies. The metabolic response to Adriamycin (ADR) treatment, which causes senescence as well as cell death, was obtained with the aid of metabolic profiling and isotope tracing in two human breast cancer cell lines, MCF7 and MDA-MB-231. After 5 days of ADR treatment, more than 60% of remaining, intact cells entered into a senescent state, characterized by enlarged and flattened morphology and positive blue staining using SA-β-gal. Metabolic trajectory analysis showed that the two cell lines’ responses were significantly different and were divided into two distinct stages. The metabolic shift from the first stage to the second was reflected by a partial recovery of the TCA cycle, as well as amino acid and lipid metabolisms. Isotope tracing analysis indicated that the higher level of glutamine metabolism helped maintain senescence. The results suggest that the dynamic changes during senescence indicate a multi-step process involving important metabolic pathways which might allow breast cancer cells to adapt to persistent ADR treatment, while the higher level of anapleurosis may be important for maintaining the senescent state. Ultimately, a better understanding of metabolic changes during senescence might provide targets for cancer therapy and tumor eradication. Full article
(This article belongs to the Special Issue Cancer Metabolomics 2018)
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15 pages, 2307 KiB  
Article
Characterization of Plant Volatiles Reveals Distinct Metabolic Profiles and Pathways among 12 Brassicaceae Vegetables
by Yu Liu, Hui Zhang, Shivshankar Umashankar, Xu Liang, Hui Wen Lee, Sanjay Swarup and Choon Nam Ong
Metabolites 2018, 8(4), 94; https://doi.org/10.3390/metabo8040094 - 14 Dec 2018
Cited by 27 | Viewed by 6049
Abstract
Plants emit characteristic organic volatile compounds (VOCs) with diverse biological/ecological functions. However, the links between plant species/varieties and their phytochemical emission profiles remain elusive. Here, we developed a direct headspace solid-phase microextraction (HS-SPME) technique and combined with non-targeted gas chromatography‒high-resolution mass spectrometry (GC-HRMS) [...] Read more.
Plants emit characteristic organic volatile compounds (VOCs) with diverse biological/ecological functions. However, the links between plant species/varieties and their phytochemical emission profiles remain elusive. Here, we developed a direct headspace solid-phase microextraction (HS-SPME) technique and combined with non-targeted gas chromatography‒high-resolution mass spectrometry (GC-HRMS) platform to investigate the VOCs profiles of 12 common Brassicaceae vegetables (watercress, rocket, Brussels sprouts, broccoli, kai lan, choy sum, pak choi, cabbage, Chinese cabbage, cauliflower, radish and cherry radish). The direct HS-SPME sampling approach enabled reproducible capture of the rapid-emitting VOCs upon plant tissue disruption. The results revealed extensive variation in VOCs profiles among the 12 Brassicaceae vegetables. Furthermore, principal component analysis (PCA) showed that the VOC profiles could clearly distinguish the 12 Brassicaceae vegetables, and that these profiles well reflected the classical morphological classification. After multivariate statistical analysis, 44 VOCs with significant differences among the Brassicaceae vegetables were identified. Pathway analysis showed that three secondary metabolism pathways, including the fatty acid pathway, methylerythritol phosphate (MEP) pathway and glucosinolate (GLS) pathway, behave distinctively in these vegetables. These three pathways are responsible for the generation and emission of green leaf volatiles (GLVs), terpenes and isothiocyanates (ITCs), respectively. Correlation analysis further showed that volatile metabolites formed via the common pathway had significantly positive correlations, whereas metabolites from different pathways had either non-significant or significantly negative correlations. Genetic influences on these metabolites across various vegetable types were also evaluated. These findings extend our phytochemical knowledge of the 12 edible Brassicaceae vegetables and provide useful information on their secondary metabolism. Full article
(This article belongs to the Special Issue Plant, Food and Nutritional Metabolomics for Health Enhancement)
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15 pages, 2109 KiB  
Article
Rapid, Reproducible, Quantifiable NMR Metabolomics: Methanol and Methanol: Chloroform Precipitation for Removal of Macromolecules in Serum and Whole Blood
by Cora E. McHugh, Thomas L. Flott, Casey R. Schooff, Zyad Smiley, Michael A. Puskarich, Daniel D. Myers, John G. Younger, Alan E. Jones and Kathleen A. Stringer
Metabolites 2018, 8(4), 93; https://doi.org/10.3390/metabo8040093 - 14 Dec 2018
Cited by 23 | Viewed by 4608
Abstract
Background: Though blood is an excellent biofluid for metabolomics, proteins and lipids present in blood can interfere with 1d-1H NMR spectra and disrupt quantification of metabolites. Here, we present effective macromolecule removal strategies for serum and whole blood (WB) [...] Read more.
Background: Though blood is an excellent biofluid for metabolomics, proteins and lipids present in blood can interfere with 1d-1H NMR spectra and disrupt quantification of metabolites. Here, we present effective macromolecule removal strategies for serum and whole blood (WB) samples. Methods: A variety of macromolecule removal strategies were compared in both WB and serum, along with tests of ultrafiltration alone and in combination with precipitation methods. Results: In healthy human serum, methanol:chloroform:water extraction with ultrafiltration was compared to methanol precipitation with and without ultrafiltration. Methods were tested in healthy pooled human serum, and in serum from patients with sepsis. Effects of long-term storage at −80 °C were tested to explore the impact of macromolecule removal strategy on serum from different conditions. In WB a variety of extraction strategies were tested in two types of WB (from pigs and baboons) to examine the impact of macromolecule removal strategies on different samples. Conclusions: In healthy human serum methanol precipitation of serum with ultrafiltration was superior, but was similar in recovery and variance to methanol:chloroform:water extraction with ultrafiltration in pooled serum from patients with sepsis. In WB, high quality, quantifiable spectra were obtained with the use of a methanol: chloroform precipitation. Full article
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19 pages, 755 KiB  
Review
The Metabolome and Osteoarthritis: Possible Contributions to Symptoms and Pathology
by Jason S. Rockel and Mohit Kapoor
Metabolites 2018, 8(4), 92; https://doi.org/10.3390/metabo8040092 - 13 Dec 2018
Cited by 28 | Viewed by 4222
Abstract
Osteoarthritis (OA) is a progressive, deteriorative disease of articular joints. Although traditionally viewed as a local pathology, biomarker exploration has shown that systemic changes can be observed. These include changes to cytokines, microRNAs, and more recently, metabolites. The metabolome is the set of [...] Read more.
Osteoarthritis (OA) is a progressive, deteriorative disease of articular joints. Although traditionally viewed as a local pathology, biomarker exploration has shown that systemic changes can be observed. These include changes to cytokines, microRNAs, and more recently, metabolites. The metabolome is the set of metabolites within a biological sample and includes circulating amino acids, lipids, and sugar moieties. Recent studies suggest that metabolites in the synovial fluid and blood could be used as biomarkers for OA incidence, prognosis, and response to therapy. However, based on clinical, demographic, and anthropometric factors, the local synovial joint and circulating metabolomes may be patient specific, with select subsets of metabolites contributing to OA disease. This review explores the contribution of the local and systemic metabolite changes to OA, and their potential impact on OA symptoms and disease pathogenesis. Full article
(This article belongs to the Special Issue Metabolomics of Complex Traits)
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8 pages, 917 KiB  
Article
Reduced Plasma Levels of Very-Long-Chain Dicarboxylic Acid 28:4 in Italian and Brazilian Colorectal Cancer Patient Cohorts
by Paul L. Wood, Michelle M. Donohue, John E. Cebak, Taylor G. Beckmann, Márcia Cristina Fernandes Messias, Laura Credidio, Cláudio Saddy Rodrigues Coy, Patrícia de Oliveira Carvalho, Sara Crotti, Sara D’Aronco, Emanuele D.L. Urso and Marco Agostini
Metabolites 2018, 8(4), 91; https://doi.org/10.3390/metabo8040091 - 06 Dec 2018
Cited by 10 | Viewed by 2622
Abstract
Background: There are currently no blood-based biomarkers for early diagnosis of colorectal cancer. Previous research has suggested that very-long-chain dicarboxylic acid (VLCDCA) 28:4 might be such a biomarker. Methods: Using high-resolution mass spectrometry, we analyzed VLCDCA 28:4 in the plasma of colorectal cancer [...] Read more.
Background: There are currently no blood-based biomarkers for early diagnosis of colorectal cancer. Previous research has suggested that very-long-chain dicarboxylic acid (VLCDCA) 28:4 might be such a biomarker. Methods: Using high-resolution mass spectrometry, we analyzed VLCDCA 28:4 in the plasma of colorectal cancer patients in Italian [n = 62] and Brazilian [n = 52] cohorts. Additionally, we investigated individuals diagnosed with familial adenomatous polyposis (FAP; n = 27), one of the most important clinical forms of inherited susceptibility to colorectal cancer. Results: Decrements in plasma levels of VLCDCA 28:4 were monitored in colorectal cancer patients. These decreases were independent of the stage of tumor development and the individual’s age. However, no decrements in VLCDCA 28:4 were monitored in FAP patients. Conclusions: The plasma levels of VLCDCA 28:4 represent a potential biomarker of sporadic colorectal cancer. In addition, it is possible that resupply of this anti-inflammatory lipid may represent a new therapeutic strategy for CRC and inflammatory disorders. Full article
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17 pages, 1251 KiB  
Article
Prospective Biomarkers from Plasma Metabolomics of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Implicate Redox Imbalance in Disease Symptomatology
by Arnaud Germain, David Ruppert, Susan M. Levine and Maureen R. Hanson
Metabolites 2018, 8(4), 90; https://doi.org/10.3390/metabo8040090 - 06 Dec 2018
Cited by 36 | Viewed by 18684
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disease of enigmatic origin with no established cure. Its constellation of symptoms has silently ruined the lives of millions of people around the world. A plethora of hypotheses have been vainly investigated over the past few [...] Read more.
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a disease of enigmatic origin with no established cure. Its constellation of symptoms has silently ruined the lives of millions of people around the world. A plethora of hypotheses have been vainly investigated over the past few decades, so that the biological basis of this debilitating condition remains a mystery. In this study, we investigate whether there is a disturbance in homeostasis of metabolic networks in the plasma of a female 32-patient cohort compared to 19 healthy female controls. Extensive analysis of the 832-metabolite dataset generated by Metabolon®, covering eight biological classes, generated important insight into metabolic disruptions that occur in ME/CFS. We report on 14 metabolites with differences in abundance, allowing us to develop a theory of broad redox imbalance in ME/CFS patients, which is consistent with findings of prior work in the ME/CFS field. Moreover, exploration of enrichment analysis using www.MetaboAnalyst.ca provides information concerning similarities between metabolite disruptions in ME/CFS and those that occur in other diseases, while its biomarker analysis unit yielded prospective plasma biomarkers for ME/CFS. This work contributes key elements to the development of ME/CFS diagnostics, a crucial step required for discovering a therapy for any disease of unknown origin. Full article
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15 pages, 3286 KiB  
Article
Effects of Early Intervention with Maternal Fecal Microbiota and Antibiotics on the Gut Microbiota and Metabolite Profiles of Piglets
by Chunhui Lin, Jiajia Wan, Yong Su and Weiyun Zhu
Metabolites 2018, 8(4), 89; https://doi.org/10.3390/metabo8040089 - 06 Dec 2018
Cited by 25 | Viewed by 4342
Abstract
We investigated the effects of early intervention with maternal fecal microbiota and antibiotics on gut microbiota and the metabolites. Five litters of healthy neonatal piglets (Duroc × Landrace × Yorkshire, nine piglets in each litter) were used. Piglets in each litter were orally [...] Read more.
We investigated the effects of early intervention with maternal fecal microbiota and antibiotics on gut microbiota and the metabolites. Five litters of healthy neonatal piglets (Duroc × Landrace × Yorkshire, nine piglets in each litter) were used. Piglets in each litter were orally treated with saline (CO), amoxicillin treatment (AM), or maternal fecal microbiota transplantation (MFMT) on days 1–6, with three piglets in each treatment. Results were compared to the CO group. MFMT decreased the relative abundances of Clostridium sensu stricto and Parabacteroides in the colon on day 7, whereas the abundance of Blautia increased, and the abundance of Corynebacterium in the stomach reduced on day 21. AM reduced the abundance of Arcanobacterium in the stomach on day 7 and reduced the abundances of Streptococcus and Lachnoclostridium in the ileum and colon on day 21, respectively. The metabolite profile indicated that MFMT markedly influenced carbohydrate metabolism and amino acid (AA) metabolism on day 7. On day 21, carbohydrate metabolism and AA metabolism were affected by AM. The results suggest that MFMT and AM discriminatively modulate gastrointestinal microflora and alter the colonic metabolic profiles of piglets and show different effects in the long-term. MFMT showed a location-specific influence on the gastrointestinal microbiota. Full article
(This article belongs to the Special Issue Gut Metabolism of Natural Products)
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15 pages, 1733 KiB  
Article
Impact of Blood Collection Tubes and Sample Handling Time on Serum and Plasma Metabolome and Lipidome
by Charmion Cruickshank-Quinn, Laura K. Zheng, Kevin Quinn, Russell Bowler, Richard Reisdorph and Nichole Reisdorph
Metabolites 2018, 8(4), 88; https://doi.org/10.3390/metabo8040088 - 04 Dec 2018
Cited by 35 | Viewed by 5041
Abstract
Background: Metabolomics is emerging as a valuable tool in clinical science. However, one major challenge in clinical metabolomics is the limited use of standardized guidelines for sample collection and handling. In this study, we conducted a pilot analysis of serum and plasma [...] Read more.
Background: Metabolomics is emerging as a valuable tool in clinical science. However, one major challenge in clinical metabolomics is the limited use of standardized guidelines for sample collection and handling. In this study, we conducted a pilot analysis of serum and plasma to determine the effects of processing time and collection tube on the metabolome. Methods: Blood was collected in 3 tubes: Vacutainer serum separator tube (SST, serum), EDTA (plasma) and P100 (plasma) and stored at 4 degrees for 0, 0.5, 1, 2, 4 and 24 h prior to centrifugation. Compounds were extracted using liquid-liquid extraction to obtain a hydrophilic and a hydrophobic fraction and analyzed using liquid chromatography mass spectrometry. Differences among the blood collection tubes and sample processing time were evaluated (ANOVA, Bonferroni FWER ≤ 0.05 and ANOVA, Benjamini Hochberg FDR ≤ 0.1, respectively). Results: Among the serum and plasma tubes 93.5% of compounds overlapped, 382 compounds were unique to serum and one compound was unique to plasma. There were 46, 50 and 86 compounds affected by processing time in SST, EDTA and P100 tubes, respectively, including many lipids. In contrast, 496 hydrophilic and 242 hydrophobic compounds differed by collection tube. Forty-five different chemical classes including alcohols, sugars, amino acids and prenol lipids were affected by the choice of blood collection tube. Conclusion: Our results suggest that the choice of blood collection tube has a significant effect on detected metabolites and their overall abundances. Perhaps surprisingly, variation in sample processing time has less of an effect compared to collection tube; however, a larger sample size is needed to confirm this. Full article
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20 pages, 4070 KiB  
Article
Untargeted Metabolic Profiling Cell-Based Approach of Pulmonary Artery Smooth Muscle Cells in Response to High Glucose and the Effect of the Antioxidant Vitamins D and E
by Abdulwahab Alamri, Abdulhadi S. Burzangi, Paul Coats and David G. Watson
Metabolites 2018, 8(4), 87; https://doi.org/10.3390/metabo8040087 - 30 Nov 2018
Cited by 13 | Viewed by 3700
Abstract
Pulmonary arterial hypertension (PAH) is a multi-factorial disease characterized by the hyperproliferation of pulmonary artery smooth muscle cells (PASMCs). Excessive reactive oxygen species (ROS) formation resulted in alterations of the structure and function of pulmonary arterial walls, leading to right ventricular failure and [...] Read more.
Pulmonary arterial hypertension (PAH) is a multi-factorial disease characterized by the hyperproliferation of pulmonary artery smooth muscle cells (PASMCs). Excessive reactive oxygen species (ROS) formation resulted in alterations of the structure and function of pulmonary arterial walls, leading to right ventricular failure and death. Diabetes mellitus has not yet been implicated in pulmonary hypertension. However, recently, variable studies have shown that diabetes is correlated with pulmonary hypertension pathobiology, which could participate in the modification of pulmonary artery muscles. The metabolomic changes in PASMCs were studied in response to 25 mM of D-glucose (high glucose, or HG) in order to establish a diabetic-like condition in an in vitro setting, and compared to five mM of D-glucose (normal glucose, or LG). The effect of co-culturing these cells with an ideal blood serum concentration of cholecalciferol-D3 and tocopherol was also examined. The current study aimed to examine the role of hyperglycemia in pulmonary arterial hypertension by the quantification and detection of the metabolomic alteration of smooth muscle cells in high-glucose conditions. Untargeted metabolomics was carried out using hydrophilic interaction liquid chromatography and high-resolution mass spectrometry. Cell proliferation was assessed by cell viability and the [3H] thymidine incorporation assay, and the redox state within the cells was examined by measuring reactive oxygen species (ROS) generation. The results demonstrated that PASMCs in high glucose (HG) grew, proliferated faster, and generated higher levels of superoxide anion (O2·−) and hydrogen peroxide (H2O2). The metabolomics of cells cultured in HG showed that the carbohydrate pathway, especially that of the upper glycolytic pathway metabolites, was influenced by the activation of the oxidation pathway: the pentose phosphate pathway (PPP). The amount of amino acids such as aspartate and glutathione reduced via HG, while glutathione disulfide, N6-Acetyl-L-lysine, glutamate, and 5-aminopentanoate increased. Lipids either as fatty acids or glycerophospholipids were downregulated in most of the metabolites, with the exception of docosatetraenoic acid and PG (16:0/16:1(9Z)). Purine and pyrimidine were influenced by hyperglycaemia following PPP oxidation. The results in addition showed that cells exposed to 25 mM of glucose were oxidatively stressed comparing to those cultured in five mM of glucose. Cholecalciferol (D3, or vitamin D) and tocopherol (vitamin E) were shown to restore the redox status of many metabolic pathways. Full article
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18 pages, 5355 KiB  
Article
Urolithin A Is a Dietary Microbiota-Derived Human Aryl Hydrocarbon Receptor Antagonist
by Gulsum E. Muku, Iain A. Murray, Juan C. Espín and Gary H. Perdew
Metabolites 2018, 8(4), 86; https://doi.org/10.3390/metabo8040086 - 29 Nov 2018
Cited by 60 | Viewed by 6901
Abstract
Urolithins (e.g., UroA and B) are gut microbiota-derived metabolites of the natural polyphenol ellagic acid. Urolithins are associated with various health benefits, including attenuation of inflammatory signaling, anti-cancer effects and repression of lipid accumulation. The molecular mechanisms underlying the beneficial effects of urolithins [...] Read more.
Urolithins (e.g., UroA and B) are gut microbiota-derived metabolites of the natural polyphenol ellagic acid. Urolithins are associated with various health benefits, including attenuation of inflammatory signaling, anti-cancer effects and repression of lipid accumulation. The molecular mechanisms underlying the beneficial effects of urolithins remain unclear. We hypothesize that some of the human health benefits of urolithins are mediated through the aryl hydrocarbon receptor (AHR). Utilizing a cell-based reporter system, we tested urolithins for the capacity to modulate AHR activity. Cytochrome P450 1A1 (CYP1A1) mRNA levels were assessed by real-time quantitative polymerase chain reaction. Competitive ligand binding assays were performed to determine whether UroA is a direct ligand for the AHR. Subcellular AHR protein levels were examined utilizing immunoblotting analysis. AHR expression was repressed in Caco-2 cells by siRNA transfection to investigate AHR-dependency. UroA and B were able to antagonize 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced AHR-mediated transcriptional activity. Furthermore, UroA and B attenuated TCDD-mediated stimulation of CYP1A1 mRNA levels. In addition, competitive ligand binding assays characterized UroA as a direct AHR ligand. Consistent with other AHR antagonists, UroA failed to induce AHR retention in the nucleus. AHR is necessary for UroA-mediated attenuation of cytokine-induced interleukin 6 (IL6) and prostaglandin-endoperoxide synthase 2 (PTGS2) expression in Caco-2 cells. Here we identified UroA as the first dietary-derived human selective AHR antagonist produced by the gut microbiota through multi-step metabolism. Furthermore, previously reported anti-inflammatory activity of UroA may at least in part be mediated through AHR. Full article
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16 pages, 3036 KiB  
Article
Hepatic Metabolic Profile Reveals the Adaptive Mechanisms of Ewes to Severe Undernutrition during Late Gestation
by Yanfeng Xue, Changzheng Guo, Fan Hu, Junhua Liu and Shengyong Mao
Metabolites 2018, 8(4), 85; https://doi.org/10.3390/metabo8040085 - 27 Nov 2018
Cited by 17 | Viewed by 3172
Abstract
The mechanisms underlying the adaption of liver metabolism to the undernutrition in ewes during late gestation remain unclear. This research aimed to explore the adaptive mechanisms of liver metabolism by hepatic metabolome analysis in pregnant ewes to the negative energy balance induced by [...] Read more.
The mechanisms underlying the adaption of liver metabolism to the undernutrition in ewes during late gestation remain unclear. This research aimed to explore the adaptive mechanisms of liver metabolism by hepatic metabolome analysis in pregnant ewes to the negative energy balance induced by severe feed restriction. Twenty ewes carrying multiple fetuses and gestating for 115 days were fed normally or restricted to a 30% feed level (10 ewes in each group) for 15 days. All ewes were sacrificed and hepatic samples were collected and analyzed by liquid chromatography-mass spectrometry. Both the principal components analysis and partial least squares of discriminant analysis of hepatic metabolites showed the clear separation between ewes in the control and severely feed-restricted groups. The metabolic profile demonstrated that the proportions of differential metabolites between the two groups in fatty acids and lipids, organic acids, and amino acids and derivatives were 61.11%, 16.67%, and 11.11%, respectively. Enriched pathways of differential metabolites were mainly involved in fatty acids and amino acids metabolism and biosynthesis. Correlation networks of differential metabolites revealed that general metabolic pattern was changed apparently and mainly based on fatty acids and lipids in the livers of feed-restricted ewes. The accumulation and oxidation of long-chain fatty acids were intensified in the livers of feed-restricted ewes, while those of medium-chain fatty acids were the opposite. In general, severe feed restriction significantly affected the levels of hepatic metabolites and altered the overall metabolic pattern. Furthermore, fatty acids oxidation as well as the utilization of amino acids and organic acids were intensified to adapt to the negative energy balance during late gestation. Full article
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17 pages, 4454 KiB  
Article
An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction
by Amornpan Klanchui, Sudarat Dulsawat, Kullapat Chaloemngam, Supapon Cheevadhanarak, Peerada Prommeenate and Asawin Meechai
Metabolites 2018, 8(4), 84; https://doi.org/10.3390/metabo8040084 - 26 Nov 2018
Cited by 14 | Viewed by 3691
Abstract
Glycogen-enriched biomass of Arthrospira platensis has increasingly gained attention as a source for bioethanol production. To study the metabolic capabilities of glycogen production in A. platensis C1, a genome-scale metabolic model (GEM) could be a useful tool for predicting cellular behavior and suggesting [...] Read more.
Glycogen-enriched biomass of Arthrospira platensis has increasingly gained attention as a source for bioethanol production. To study the metabolic capabilities of glycogen production in A. platensis C1, a genome-scale metabolic model (GEM) could be a useful tool for predicting cellular behavior and suggesting strategies for glycogen overproduction. New experimentally validated GEM of A. platensis C1 namely iAK888, which has improved metabolic coverage and functionality was employed in this research. The iAK888 is a fully functional compartmentalized GEM consisting of 888 genes, 1,096 reactions, and 994 metabolites. This model was demonstrated to reasonably predict growth and glycogen fluxes under different growth conditions. In addition, iAK888 was further employed to predict the effect of deficiencies of NO3−, PO43−, or SO42− on the growth and glycogen production in A. platensis C1. The simulation results showed that these nutrient limitations led to a decrease in growth flux and an increase in glycogen flux. The experiment of A. platensis C1 confirmed the enhancement of glycogen fluxes after the cells being transferred from normal Zarrouk’s medium to either NO3−, PO43−, or SO42−-free Zarrouk’s media. Therefore, iAK888 could be served as a predictive model for glycogen overproduction and a valuable multidisciplinary tool for further studies of this important academic and industrial organism. Full article
(This article belongs to the Special Issue Metabolites from Phototrophic Prokaryotes and Algae Volume 2)
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17 pages, 2040 KiB  
Article
Roux-en-Y Gastric Bypass Surgery Induces Distinct but Frequently Transient Effects on Acylcarnitine, Bile Acid and Phospholipid Levels
by Jarlei Fiamoncini, Carina Fernandes Barbosa, José Rubens Arnoni Junior, José Celestino Araújo Junior, Cinthia Taglieri, Tiago Szego, Barbara Gelhaus, Heraldo Possolo de Souza, Hannelore Daniel and Thais Martins de Lima
Metabolites 2018, 8(4), 83; https://doi.org/10.3390/metabo8040083 - 23 Nov 2018
Cited by 12 | Viewed by 3213
Abstract
Roux-en-Y gastric bypass (RYGB) is an effective method to achieve sustained weight loss, but the mechanisms responsible for RYGB effects have not yet been fully characterized. In this study, we profiled the concentrations of 143 lipid metabolites in dry blood spots (DBS) of [...] Read more.
Roux-en-Y gastric bypass (RYGB) is an effective method to achieve sustained weight loss, but the mechanisms responsible for RYGB effects have not yet been fully characterized. In this study, we profiled the concentrations of 143 lipid metabolites in dry blood spots (DBS) of RYGB patients. DBS from obese patients (BMI range 35–44 kg/m2) were collected 7 days before, 15 and 90 days after the surgery. LC-MS/MS was used to quantify acylcarnitines, phosphatidylcholines, sphingomyelins and bile acids. RYGB caused a rapid increase in acylcarnitine levels that proved to be only transient, contrasting with the sustained decrease in phosphatidylcholines and increase of sphingomyelins and bile acids. A PLS-DA analysis revealed a 3-component model (R2 = 0.9, Q2 = 0.74) with key metabolites responsible for the overall metabolite differences. These included the BCAA-derived acylcarnitines and sphingomyelins with 16 and 18 carbons. We found important correlations between the levels of BCAA-derived acylcarnitines and specific sphingomyelins with plasma cholesterol and triacylglycerol concentrations. Along with the marked weight loss and clinical improvements, RYGB induced specific alterations in plasma acylcarnitines, bile acid and phospholipid levels. This calls for more studies on RYGB effects aiming to elucidate the metabolic adaptations that follow this procedure. Full article
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18 pages, 1321 KiB  
Article
Untargeted Metabolomics of Extracts from Faecal Samples Demonstrates Distinct Differences between Paediatric Crohn’s Disease Patients and Healthy Controls but No Significant Changes Resulting from Exclusive Enteral Nutrition Treatment
by Adel Alghamdi, Konstantinos Gerasimidis, Gavin Blackburn, Didem Akinci, Christine Edwards, Richard K. Russell and David G. Watson
Metabolites 2018, 8(4), 82; https://doi.org/10.3390/metabo8040082 - 22 Nov 2018
Cited by 20 | Viewed by 4266
Abstract
Metabolomic profiling using high resolution mass spectrometry with hydrophilic interaction chromatography was applied to 11 faecal extracts from eleven healthy children and to 43 faecal extracts from eleven children undergoing exclusive enteral nutrition for the treatment of active Crohn’s disease (CD) at timepoints [...] Read more.
Metabolomic profiling using high resolution mass spectrometry with hydrophilic interaction chromatography was applied to 11 faecal extracts from eleven healthy children and to 43 faecal extracts from eleven children undergoing exclusive enteral nutrition for the treatment of active Crohn’s disease (CD) at timepoints before, during (15, 30, and 60 days), and after treatment. Differences between the control and CD samples were identified at each timepoint. An orthogonal partial least square-discriminant analysis (OPLS-DA) model identified eight metabolites that were normally distributed according to Q-Q plots. The OPLS-DA model was able to discriminate the CD samples from the controls at every timepoint, but the model was not able to differentiate the CD samples from one another at the different timepoints during treatment with exclusive enteral nutrition. The differentiated metabolites identified in the CD samples included tyrosine, an ornithine isomer, arachidonic acid, eicosatrienoic acid, docosatetraenoic acid, a sphingomyelin, a ceramide, and dimethylsphinganine. Despite successful treatment, underlying differences remained in the metabolome of the CD patients. These differences dominated the separation of the samples when multivariate methods were applied. Full article
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8 pages, 2056 KiB  
Article
Tear Film Amphiphilic and Anti-Inflammatory Lipids in Bovine Pink Eye
by Paul L. Wood, Michelle N. Donohue, John E. Cebak, Taylor G. Beckmann, MacKenzie Treece, Jason W. Johnson and Lynda M. J. Miller
Metabolites 2018, 8(4), 81; https://doi.org/10.3390/metabo8040081 - 21 Nov 2018
Cited by 8 | Viewed by 2789
Abstract
Background: Tear film fluid serves as a dynamic barrier that both lubricates the eye and protects against allergens and infectious agents. However, a detailed analysis of a bacteria-induced immune response on the tear film lipidome has not been undertaken. Methods: We [...] Read more.
Background: Tear film fluid serves as a dynamic barrier that both lubricates the eye and protects against allergens and infectious agents. However, a detailed analysis of a bacteria-induced immune response on the tear film lipidome has not been undertaken. Methods: We undertook a high-resolution mass spectrometry lipidomics analysis of endogenous anti-inflammatory and structural tear film lipids in bovine pink eye. Results: Bovine pink eye resulted in dramatic elevations in tear fluid levels of the anti-inflammatory lipids resolvin E2, cyclic phosphatidic acid 16:0, and cyclic phosphatidic acid 18:0. In addition, there were elevated levels of the structural lipids (O-acyl)-ω-hydroxy-fatty acids, cholesterol sulfate, ethanolamine plasmalogens, and sphingomyelins. Lipid peroxidation also was augmented in pink eye as evidenced by the hydroperoxy derivatives of ethanolamine plasmalogens. Conclusions: Ocular infections with Moraxella bovis result in the induction of a number of endogenous anti-inflammatory lipids and augmentation of the levels of structural glycerophospholipids and sphingolipids. Increased levels of hydroperoxy glycerophospholipids also indicate that this bacterial infection results in lipid peroxidation. Full article
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9 pages, 717 KiB  
Article
A Simple and Convenient Synthesis of Unlabeled and 13C-Labeled 3-(3-Hydroxyphenyl)-3-Hydroxypropionic Acid and Its Quantification in Human Urine Samples
by Yeganeh Khaniani, Matthias Lipfert, Dipanjan Bhattacharyya, Rolando Perez Pineiro, Jiamin Zheng and David S. Wishart
Metabolites 2018, 8(4), 80; https://doi.org/10.3390/metabo8040080 - 21 Nov 2018
Cited by 8 | Viewed by 3423
Abstract
An improved method to synthesize the highly abundant and biomedically important urinary metabolite 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) is reported. The modified protocol is based on an indium-mediated sonochemical Reformatsky reaction. The synthesis is a simple two-step route as opposed to a complex four-step route [...] Read more.
An improved method to synthesize the highly abundant and biomedically important urinary metabolite 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) is reported. The modified protocol is based on an indium-mediated sonochemical Reformatsky reaction. The synthesis is a simple two-step route as opposed to a complex four-step route previously reported in the literature that requires specialized equipment, flammable materials, and high-pressure reaction vessels. The described procedure also provides an expedient route to prepare a 13C isotopically labeled HPHPA that can be used as a standard for quantitative LC-MS analysis. This report also illustrates how the synthesized metabolite standard was used to detect and accurately quantify its presence in human urine samples using both NMR and LC-MS techniques. Full article
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10 pages, 1318 KiB  
Article
Metabolomics of Breast Milk: The Importance of Phenotypes
by Angelica Dessì, Despina Briana, Sara Corbu, Stavroula Gavrili, Flaminia Cesare Marincola, Sofia Georgantzi, Roberta Pintus, Vassilios Fanos and Ariadne Malamitsi-Puchner
Metabolites 2018, 8(4), 79; https://doi.org/10.3390/metabo8040079 - 20 Nov 2018
Cited by 40 | Viewed by 4695
Abstract
Breast milk is the gold standard of nutrition for newborns. Its composition is tailored to the nutritional needs of the infant and varies between mothers. In recent years, several bioactive molecules have been discovered in addition to the main nutrients, such as multipotent [...] Read more.
Breast milk is the gold standard of nutrition for newborns. Its composition is tailored to the nutritional needs of the infant and varies between mothers. In recent years, several bioactive molecules have been discovered in addition to the main nutrients, such as multipotent stem cells, hormones, immunoglobulins, and bacteria. Furthermore, the human milk oligosaccharides (HMOs) seem to exert several important protective biological functions. According to the HMOs’ composition, breast milk can be classified as a secretory or non-secretory phenotype. In our study, we investigated the metabolome of milk collected from 58 mothers that delivered neonates at term, that were appropriate, small or large for gestational age, by performing nuclear magnetic resonance spectroscopy (1H-NMR). From the data analysis, two groups were distinguished based on their different types of oligosaccharides, and classified according the mother phenotype: secretory and non-secretory. This information is of major importance given the different biological function of the different HMOs, such as immune-modulation and protection against disease. This would allow us to predict whether the neonate would be, for instance, more prone to developing certain diseases, and to tailor her or his nutrition to fit their needs perfectly and pave the way to a personalized nutrition. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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12 pages, 961 KiB  
Article
Population-Level Analysis to Determine Parameters That Drive Variation in the Plasma Metabolite Profiles
by Mahmoud Al-Majdoub, Katharina Herzog, Bledar Daka, Martin Magnusson, Lennart Råstam, Ulf Lindblad and Peter Spégel
Metabolites 2018, 8(4), 78; https://doi.org/10.3390/metabo8040078 - 15 Nov 2018
Cited by 2 | Viewed by 3666
Abstract
The plasma metabolome is associated with multiple phenotypes and diseases. However, a systematic study investigating clinical determinants that control the metabolome has not yet been conducted. In the present study, therefore, we aimed to identify the major determinants of the plasma metabolite profile. [...] Read more.
The plasma metabolome is associated with multiple phenotypes and diseases. However, a systematic study investigating clinical determinants that control the metabolome has not yet been conducted. In the present study, therefore, we aimed to identify the major determinants of the plasma metabolite profile. We used ultra-high performance liquid chromatography (UHPLC) coupled to quadrupole time of flight mass spectrometry (QTOF-MS) to determine 106 metabolites in plasma samples from 2503 subjects in a cross-sectional study. We investigated the correlation structure of the metabolite profiles and generated uncorrelated metabolite factors using principal component analysis (PCA) and varimax rotation. Finally, we investigated associations between these factors and 34 clinical covariates. Our results suggest that liver function, followed by kidney function and insulin resistance show the strongest associations with the plasma metabolite profile. The association of specific phenotypes with several components may suggest multiple independent metabolic mechanisms, which is further supported by the composition of the associated factors. Full article
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15 pages, 1552 KiB  
Article
A Modified Kulka Micromethod for the Rapid and Safe Analysis of Fructose and 1-Deoxy-d-xylulose-5-phosphate
by Shreya Shaw and Robin Ghosh
Metabolites 2018, 8(4), 77; https://doi.org/10.3390/metabo8040077 - 08 Nov 2018
Cited by 1 | Viewed by 3794
Abstract
The Kulka resorcinol assay (Kulka, R.G., Biochemistry 1956, 63, 542–548) for ketoses has been widely used in the literature but suffers from two major disadvantages: (a) it employs large amounts of potentially harmful reagents for a general biology laboratory environment; and (b) [...] Read more.
The Kulka resorcinol assay (Kulka, R.G., Biochemistry 1956, 63, 542–548) for ketoses has been widely used in the literature but suffers from two major disadvantages: (a) it employs large amounts of potentially harmful reagents for a general biology laboratory environment; and (b) in its original formulation, it is unsuited for modern high-throughput applications. Here, we have developed a modified Kulka assay, which contains a safer formulation, employing approx. 5.4 M HCl in 250 µL aliquots, and is suitable for use in high-throughput systems biology or enzymatic applications. The modified assay has been tested extensively for the measurement of two ketoses—fructose (a common substrate in cell growth experiments) and 1-deoxy-d-xylulose-5-phosphate (DXP), the product of the DXP-synthase reaction—which until now has only been assayable using time-consuming chromatographic methods or radioactivity. The Kulka microassay has a sensitivity of 0–250 nmol fructose or 0–500 nmol DXP. The assay is suitable for monitoring the consumption of fructose in bacterial growth experiments but is too insensitive to be used directly for the measurement of DXP in in vitro enzyme assays. However, we show that after concentration of the DXP-enzyme mix by butanol extraction, the Kulka resorcinol method can be used for enzyme assays. Full article
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11 pages, 2682 KiB  
Article
Endogenous Anti-Inflammatory Very-Long-Chain Dicarboxylic Acids: Potential Chemopreventive Lipids
by Paul L. Wood
Metabolites 2018, 8(4), 76; https://doi.org/10.3390/metabo8040076 - 03 Nov 2018
Cited by 5 | Viewed by 2909
Abstract
In a paradigm shift, cancer research efforts are being dedicated to the discovery of chemopreventive agents. The goal of this approach is to delay or prevent the progression of augmented cell division to established cancer. Research has focused on dietary supplements, drugs, and [...] Read more.
In a paradigm shift, cancer research efforts are being dedicated to the discovery of chemopreventive agents. The goal of this approach is to delay or prevent the progression of augmented cell division to established cancer. Research has focused on dietary supplements, drugs, and endogenous lipids that possess anti-inflammatory properties. We undertook a lipidomics analysis of potential endogenous anti-inflammatory/anti-proliferative lipids in human plasma. We performed high-resolution mass spectrometric lipidomics analyses of plasma samples from controls and patients with colorectal, kidney, pancreatic, glioblastoma, and breast cancers. We present evidence that endogenous very-long-chain dicarboxylic acids (VLCDCA) are anti-inflammatory lipids that possess chemopreventative properties. In a family of VLCDCAs, we characterized VLCDCA 28:4, which is decreased in the plasma of patients with colorectal, kidney, and pancreatic cancers. The structure of this biomarker was validated by derivatization strategies, synthesis of the analytical standard, and tandem mass spectrometry. Our data suggest that VLCDCA 28:4 may be a useful blood biomarker for a number of cancers and that resupplying this lipid, via a prodrug for example, may offer a new anti-inflammatory therapeutic strategy for delaying or preventing the progression of cancer and other inflammatory diseases. Full article
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18 pages, 726 KiB  
Article
Gas Chromatography Mass Spectrometry (GC-MS) Quantification of Metabolites in Stool Using 13C Labelled Compounds
by Oliver Gould, Ben De Lacy Costello, Amy Smart, Peter Jones, Angus Macmaster, Karen Ransley and Norman Ratcliffe
Metabolites 2018, 8(4), 75; https://doi.org/10.3390/metabo8040075 - 31 Oct 2018
Cited by 5 | Viewed by 3902
Abstract
It has become increasingly important to qualitatively and quantitatively assess the volatile metabolites in a range of bodily fluids for use in monitoring health. There has been relatively little work on the quantitative analysis of compounds, particularly with respect to the effects of [...] Read more.
It has become increasingly important to qualitatively and quantitatively assess the volatile metabolites in a range of bodily fluids for use in monitoring health. There has been relatively little work on the quantitative analysis of compounds, particularly with respect to the effects of ethnicity or geographic location. A novel method for the quantification of compounds in stool using 13C labelled compounds as internal standards is presented. Using thermal desorption gas chromatography mass spectrometry, stool samples from 38 healthy volunteers were analysed. The 13C labelled compounds, acetone, ethyl butanoate, ethanoic acid, butanoic acid, 3-methylbutanoic acid, and indole, were added as internal standards. This process mimics the solubility characteristics of the compounds and thus the method was able to quantify the compounds within the solid stool. In total, 15 compounds were quantified: Dimethyl sulphide (26–25,626 ng/g), acetone (442–3006 ng/g), ethyl butanoate (39–2468 ng/g), ethyl 2-methylbutanoate (0.3–180 ng/g), dimethyl disulphide (35–1303 ng/g), 1-octen-3-one (12 ng/g), dimethyl trisulphide (10–410 ng/g), 1-octen-3-ol (0.4–58 ng/g), ethanoic acid (672–12,963 ng/g), butanoic acid (2493–11,553 ng/g), 3-methylbutanoic acid (64–8262 ng/g), pentanoic acid (88–21,886 ng/g), indole (290–5477 ng/g), and 3-methyl indole (37–3483 ng/g). Moreover, by altering the pH of the stool to pH 13 in conjunction with the addition of 13C trimethylamine, the method was successful in detecting and quantifying trimethylamine for the first time in stool samples (range 40–5312 ng/g). Statistical analysis revealed that samples from U.K. origin had five significantly different compounds (ethyl butanoate, 1-octen-3-ol, ethanoic acid, butanoic acid, pentanoic acid, and indole) from those of South American origin. However, there were no significant differences between vegetarian and omnivore samples. These findings are supported by pre-existing literature evidence. Moreover, we have tentatively identified 12 compounds previously not reported as having been found in stool. Full article
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11 pages, 1896 KiB  
Article
Determination of Predominant Organic Acid Components in Malus Species: Correlation with Apple Domestication
by Baiquan Ma, Yangyang Yuan, Meng Gao, Cuiying Li, Collins Ogutu, Mingjun Li and Fengwang Ma
Metabolites 2018, 8(4), 74; https://doi.org/10.3390/metabo8040074 - 31 Oct 2018
Cited by 49 | Viewed by 4162
Abstract
Significant variation in organic acid components was detected in mature fruits of 101 apple accessions using high-performance liquid chromatography. The Malus species predominantly accumulated malic acid and citric acid, whereas wild fruits exhibited significantly higher levels of organic acid content than that in [...] Read more.
Significant variation in organic acid components was detected in mature fruits of 101 apple accessions using high-performance liquid chromatography. The Malus species predominantly accumulated malic acid and citric acid, whereas wild fruits exhibited significantly higher levels of organic acid content than that in cultivated fruits. Differential accumulation patterns during fruit developmental stages was detected between malic acid and citric acid, thus suggesting a complex genetic regulation mechanism of organic acid metabolism in apple fruit. A highly positive correlation was detected between fruit total organic acid content with malic acid and citric acid content, thus suggesting that malic acid and citric acid are the principal determinants of apple fruit acidity. In contrast to malic acid, citric acid was predominantly detected in partial wild apples, while extremely low to undetectable concentrations of citric acid were observed in cultivated apple fruits; this is likely due to the genetic effects of parental characters. Our results provide vital information that could be useful for future studies on genetic analysis and improvement of organic acid accumulation in apple fruits. Full article
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23 pages, 2364 KiB  
Article
Microbiota and Metabolite Profiling of Spoiled Spanish-Style Green Table Olives
by Antonio De Castro, Antonio Higinio Sánchez, Antonio López-López, Amparo Cortés-Delgado, Eduardo Medina and Alfredo Montaño
Metabolites 2018, 8(4), 73; https://doi.org/10.3390/metabo8040073 - 31 Oct 2018
Cited by 30 | Viewed by 3325
Abstract
The aim of the present study was to assess the malodorous spoilages of Spanish-style green table olives through microbial and metabolite composition using current measuring techniques (e.g., high-throughput DNA sequencing, headspace solid-phase microextraction combined with gas chromatography-mass spectrometry). Under different alkaline and washing [...] Read more.
The aim of the present study was to assess the malodorous spoilages of Spanish-style green table olives through microbial and metabolite composition using current measuring techniques (e.g., high-throughput DNA sequencing, headspace solid-phase microextraction combined with gas chromatography-mass spectrometry). Under different alkaline and washing conditions, the spoilage fermentations were reproduced with Gordal and Manzanilla olive cultivars using a low salt concentration (71 g L−1 NaCl) in the initial brine. The degradation of lactic acid and significant increases in volatile fatty acids and phenols were found in all the spoiled samples in comparison with the unspoiled control samples. According to high-throughput DNA sequencing, Cardiobacteriaceae and Ruminococcus were the dominant bacteria in the spoiled samples. PLS regression and Pearson’s correlation coefficient analyses revealed positive and negative correlations among microbial communities, metabolites, and sensory spoilage descriptors. Notably, the “zapatera” descriptor was significantly associated with Propionibacterium, which was positively correlated with acetic acid, propionic acid, succinic acid, and methyl propanoate; while the “butyric” descriptor exhibited a significant positive relationship with the genus Ruminococcus, which gave an almost significant correlation with propionic and butyric acids. Full article
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16 pages, 1296 KiB  
Article
Quenching for Microalgal Metabolomics: A Case Study on the Unicellular Eukaryotic Green Alga Chlamydomonas reinhardtii
by Rahul Vijay Kapoore and Seetharaman Vaidyanathan
Metabolites 2018, 8(4), 72; https://doi.org/10.3390/metabo8040072 - 31 Oct 2018
Cited by 4 | Viewed by 3881
Abstract
Capturing a valid snapshot of the metabolome requires rapid quenching of enzyme activities. This is a crucial step in order to halt the constant flux of metabolism and high turnover rate of metabolites. Quenching with cold aqueous methanol is treated as a gold [...] Read more.
Capturing a valid snapshot of the metabolome requires rapid quenching of enzyme activities. This is a crucial step in order to halt the constant flux of metabolism and high turnover rate of metabolites. Quenching with cold aqueous methanol is treated as a gold standard so far, however, reliability of metabolomics data obtained is in question due to potential problems connected to leakage of intracellular metabolites. Therefore, we investigated the influence of various parameters such as quenching solvents, methanol concentration, inclusion of buffer additives, quenching time and solvent to sample ratio on intracellular metabolite leakage from Chlamydomonas reinhardtii. We measured the recovery of twelve metabolite classes using gas chromatography mass spectrometry (GC-MS) in all possible fractions and established mass balance to trace the fate of metabolites during quenching treatments. Our data demonstrate significant loss of intracellular metabolites with the use of the conventional 60% methanol, and that an increase in methanol concentration or quenching time also resulted in higher leakage. Inclusion of various buffer additives showed 70 mM HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) to be suitable. In summary, we recommend quenching with 60% aqueous methanol supplemented with 70 mM HEPES (−40 °C) at 1:1 sample to quenching solvent ratio, as it resulted in higher recoveries for intracellular metabolites with subsequent reduction in the metabolite leakage for all metabolite classes. Full article
(This article belongs to the Special Issue Metabolites from Phototrophic Prokaryotes and Algae Volume 2)
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10 pages, 1259 KiB  
Article
Metabolomic Profiling of Bile Acids in an Experimental Model of Prodromal Parkinson’s Disease
by Stewart F. Graham, Nolwen L. Rey, Zafer Ugur, Ali Yilmaz, Eric Sherman, Michael Maddens, Ray O. Bahado-Singh, Katelyn Becker, Emily Schulz, Lindsay K. Meyerdirk, Jennifer A. Steiner, Jiyan Ma and Patrik Brundin
Metabolites 2018, 8(4), 71; https://doi.org/10.3390/metabo8040071 - 31 Oct 2018
Cited by 34 | Viewed by 4871
Abstract
For people with Parkinson’s disease (PD), considered the most common neurodegenerative disease behind Alzheimer’s disease, accurate diagnosis is dependent on many factors; however, misdiagnosis is extremely common in the prodromal phases of the disease, when treatment is thought to be most effective. Currently, [...] Read more.
For people with Parkinson’s disease (PD), considered the most common neurodegenerative disease behind Alzheimer’s disease, accurate diagnosis is dependent on many factors; however, misdiagnosis is extremely common in the prodromal phases of the disease, when treatment is thought to be most effective. Currently, there are no robust biomarkers that aid in the early diagnosis of PD. Following previously reported work by our group, we accurately measured the concentrations of 18 bile acids in the serum of a prodromal mouse model of PD. We identified three bile acids at significantly different concentrations (p < 0.05) when mice representing a prodromal PD model were compared with controls. These include ω-murichoclic acid (MCAo), tauroursodeoxycholic acid (TUDCA) and ursodeoxycholic acid (UDCA). All were down-regulated in prodromal PD mice with TUDCA and UDCA at significantly lower levels (17-fold and 14-fold decrease, respectively). Using the concentration of three bile acids combined with logistic regression, we can discriminate between prodromal PD mice from control mice with high accuracy (AUC (95% CI) = 0.906 (0.777–1.000)) following cross validation. Our study highlights the need to investigate bile acids as potential biomarkers that predict PD and possibly reflect the progression of manifest PD. Full article
(This article belongs to the Special Issue Metabolomics in Neurodegenerative Disease)
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19 pages, 4052 KiB  
Review
No Country for Old Worms: A Systematic Review of the Application of C. elegans to Investigate a Bacterial Source of Environmental Neurotoxicity in Parkinson’s Disease
by Kim A. Caldwell, Jennifer L. Thies and Guy A. Caldwell
Metabolites 2018, 8(4), 70; https://doi.org/10.3390/metabo8040070 - 29 Oct 2018
Cited by 8 | Viewed by 4249
Abstract
While progress has been made in discerning genetic associations with Parkinson’s disease (PD), identifying elusive environmental contributors necessitates the application of unconventional hypotheses and experimental strategies. Here, we provide an overview of studies that we conducted on a neurotoxic metabolite produced by a [...] Read more.
While progress has been made in discerning genetic associations with Parkinson’s disease (PD), identifying elusive environmental contributors necessitates the application of unconventional hypotheses and experimental strategies. Here, we provide an overview of studies that we conducted on a neurotoxic metabolite produced by a species of common soil bacteria, Streptomyces venezuelae (S. ven), indicating that the toxicity displayed by this bacterium causes stress in diverse cellular mechanisms, such as the ubiquitin proteasome system and mitochondrial homeostasis. This dysfunction eventually leads to age and dose-dependent neurodegeneration in the nematode Caenorhabditis elegans. Notably, dopaminergic neurons have heightened susceptibility, but all of the neuronal classes eventually degenerate following exposure. Toxicity further extends to human SH-SY5Y cells, which also degenerate following exposure. Additionally, the neurons of nematodes expressing heterologous aggregation-prone proteins display enhanced metabolite vulnerability. These mechanistic analyses collectively reveal a unique metabolomic fingerprint for this bacterially-derived neurotoxin. In considering that epidemiological distinctions in locales influence the incidence of PD, we surveyed soils from diverse regions of Alabama, and found that exposure to ~30% of isolated Streptomyces species caused worm dopaminergic neurons to die. In addition to aging, one of the few established contributors to PD appears to be a rural lifestyle, where exposure to soil on a regular basis might increase the risk of interaction with bacteria producing such toxins. Taken together, these data suggest that a novel toxicant within the Streptomyces genus might represent an environmental contributor to the progressive neurodegeneration that is associated with PD. Full article
(This article belongs to the Special Issue Metabolomics in Neurodegenerative Disease)
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16 pages, 787 KiB  
Article
Evidence That Parietal Lobe Fatty Acids May Be More Profoundly Affected in Moderate Alzheimer’s Disease (AD) Pathology Than in Severe AD Pathology
by Muhammad L. Nasaruddin, Xiaobei Pan, Bernadette McGuinness, Peter Passmore, Patrick G. Kehoe, Christian Hölscher, Stewart F. Graham and Brian D. Green
Metabolites 2018, 8(4), 69; https://doi.org/10.3390/metabo8040069 - 26 Oct 2018
Cited by 16 | Viewed by 3922
Abstract
Brain is a lipid-rich tissue, and fatty acids (FAs) play a crucial role in brain function, including neuronal cell growth and development. This study used GC-MS to survey all detectable FAs in the human parietal cortex (Brodmann area 7). These FAs were accurately [...] Read more.
Brain is a lipid-rich tissue, and fatty acids (FAs) play a crucial role in brain function, including neuronal cell growth and development. This study used GC-MS to survey all detectable FAs in the human parietal cortex (Brodmann area 7). These FAs were accurately quantified in 27 cognitively normal age-matched controls, 16 cases of moderate Alzheimer’s disease (AD), 30 severe AD, and 14 dementia with Lewy bodies (DLB). A total of 24 FA species were identified. Multiple comparison procedures, using stepdown permutation tests, noted higher levels of 13 FAs but the majority of changes were in moderate AD and DLB, rather than severe AD. Subjects with moderate AD and DLB pathology exhibited significantly higher levels of a number of FAs (13 FAs and 12 FAs, respectively). These included nervonic, lignoceric, cis-13,16-docosadienoic, arachidonic, cis-11,14,17-eicosatrienoic, erucic, behenic, α-linolenic, stearic, oleic, cis-10-heptanoic, and palmitic acids. The similarities between moderate AD and DLB were quite striking—arachidic acid was the only FA which was higher in moderate AD than control, and was not similarly affected in DLB. Furthermore, there were no significant differences between moderate AD and DLB. The associations between each FA and a number of variables, including diagnosis, age, gender, Aβ plaque load, tau load, and frontal tissue pH, were also investigated. To conclude, the development of AD or DLB pathology affects brain FA composition but, intriguingly, moderate AD neuropathology impacts this to a much greater extent. Post-mortem delay is a potential confounding factor, but the findings here suggest that there could be a more dynamic metabolic response in the earlier stages of the disease pathology. Full article
(This article belongs to the Special Issue Metabolomics in Neurodegenerative Disease)
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18 pages, 2105 KiB  
Article
Partial Least Squares Discriminant Analysis and Bayesian Networks for Metabolomic Prediction of Childhood Asthma
by Rachel S. Kelly, Michael J. McGeachie, Kathleen A. Lee-Sarwar, Priyadarshini Kachroo, Su H. Chu, Yamini V. Virkud, Mengna Huang, Augusto A. Litonjua, Scott T. Weiss and Jessica Lasky-Su
Metabolites 2018, 8(4), 68; https://doi.org/10.3390/metabo8040068 - 23 Oct 2018
Cited by 17 | Viewed by 4254
Abstract
To explore novel methods for the analysis of metabolomics data, we compared the ability of Partial Least Squares Discriminant Analysis (PLS-DA) and Bayesian networks (BN) to build predictive plasma metabolite models of age three asthma status in 411 three year olds (n [...] Read more.
To explore novel methods for the analysis of metabolomics data, we compared the ability of Partial Least Squares Discriminant Analysis (PLS-DA) and Bayesian networks (BN) to build predictive plasma metabolite models of age three asthma status in 411 three year olds (n = 59 cases and 352 controls) from the Vitamin D Antenatal Asthma Reduction Trial (VDAART) study. The standard PLS-DA approach had impressive accuracy for the prediction of age three asthma with an Area Under the Curve Convex Hull (AUCCH) of 81%. However, a permutation test indicated the possibility of overfitting. In contrast, a predictive Bayesian network including 42 metabolites had a significantly higher AUCCH of 92.1% (p for difference < 0.001), with no evidence that this accuracy was due to overfitting. Both models provided biologically informative insights into asthma; in particular, a role for dysregulated arginine metabolism and several exogenous metabolites that deserve further investigation as potential causative agents. As the BN model outperformed the PLS-DA model in both accuracy and decreased risk of overfitting, it may therefore represent a viable alternative to typical analytical approaches for the investigation of metabolomics data. Full article
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12 pages, 591 KiB  
Review
Current Applications of Metabolomics in Cirrhosis
by Vinshi Khan, Nagireddy Putluri, Arun Sreekumar and Ayse L. Mindikoglu
Metabolites 2018, 8(4), 67; https://doi.org/10.3390/metabo8040067 - 22 Oct 2018
Cited by 14 | Viewed by 2940
Abstract
Metabolomics is the identification and quantification of all or specified metabolites in a living system under a specific condition or disease. Metabolomics in cirrhosis can be used in diagnosing complications, determining prognosis and assessment of response to therapy. In this review, we summarized [...] Read more.
Metabolomics is the identification and quantification of all or specified metabolites in a living system under a specific condition or disease. Metabolomics in cirrhosis can be used in diagnosing complications, determining prognosis and assessment of response to therapy. In this review, we summarized representative applications of metabolomics in cirrhosis and significant metabolites associated with cirrhosis and its complications. Full article
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13 pages, 2021 KiB  
Article
Intracellular Fate of Universally Labelled 13C Isotopic Tracers of Glucose and Xylose in Central Metabolic Pathways of Xanthomonas oryzae
by Manu Shree and Shyam K. Masakapalli
Metabolites 2018, 8(4), 66; https://doi.org/10.3390/metabo8040066 - 15 Oct 2018
Cited by 6 | Viewed by 5007
Abstract
The goal of this study is to map the metabolic pathways of poorly understood bacterial phytopathogen, Xanthomonas oryzae (Xoo) BXO43 fed with plant mimicking media XOM2 containing glutamate, methionine and either 40% [13C5] xylose or 40% [13C [...] Read more.
The goal of this study is to map the metabolic pathways of poorly understood bacterial phytopathogen, Xanthomonas oryzae (Xoo) BXO43 fed with plant mimicking media XOM2 containing glutamate, methionine and either 40% [13C5] xylose or 40% [13C6] glucose. The metabolic networks mapped using the KEGG mapper and the mass isotopomer fragments of proteinogenic amino acids derived from GC-MS provided insights into the activities of Xoo central metabolic pathways. The average 13C in histidine, aspartate and other amino acids confirmed the activities of PPP, the TCA cycle and amino acid biosynthetic routes, respectively. The similar labelling patterns of amino acids (His, Ala, Ser, Val and Gly) from glucose and xylose feeding experiments suggests that PPP would be the main metabolic route in Xoo. Owing to the lack of annotated gene phosphoglucoisomerase in BXO43, the 13C incorporation in alanine could not be attributed to the competing pathways and hence warrants additional positional labelling experiments. The negligible presence of 13C incorporation in methionine brings into question its potential role in metabolism and pathogenicity. The extent of the average 13C labelling in several amino acids highlighted the contribution of pre-existing pools that need to be accounted for in 13C-flux analysis studies. This study provided the first qualitative insights into central carbon metabolic pathway activities in Xoo. Full article
(This article belongs to the Special Issue Pathway Mapping)
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