PubMed

Related Articles Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proc Natl Acad Sci U S A. 2016 Nov 18;: Authors: Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, Weckwerth W, Schleper C Abstract Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile "Ca. Nitrosotalea devanaterra" revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and "Ca Nitrosopelagicus brevis" proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs. PMID: 27864514 [PubMed - as supplied by publisher]

Related Articles Metabolites profiling reveals for antimicrobial compositional differences and action mechanism in the toothbrushing stick "miswak" Salvadora persica. J Pharm Biomed Anal. 2016 Nov 11;: Authors: Farag MA, Fahmy S, Choucry MA, Wahdan MO, Elsebai MF Abstract Among many plant species suitable for preparing toothbrushing sticks, miswak (Salvadora persica, family Salvadoraceae) is found the most effective tool for oral hygiene. S. persica possesses antibacterial, antiviral and antifungal effects against oral microbes, mostly due to its benzyl isothiocyanate content. To provide insight into S. persica chemical composition, volatile constituents from roots and stems of S. persica grown in Egypt and Saudi Arabia were profiled using solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). A total of 21 volatiles were identified with sulfur compounds amounting for the major volatile class. Orthogonal projection to latent structures-discriminant analysis (OPLS-DA) revealed for benzyl isothiocyanate (BITC) enrichment in roots versus stems. Primary metabolites contributing to S. persica taste viz. sugars and organic acids were profiled using GC-MS with silylation. Polyols (sugars) viz. arabitol, meso-erythritol, and mannitol were found to predominate sugars composition in S. persica stems being most enriched in meso-erythritol. The impact of saliva on S. persica aroma profile was further assessed and revealing for no enhancement in BITC production with salivation, and further not being detected in toothpaste preparation claimed to contain S. persica extract. This study provides the most complete profile of volatiles, sugars, and organic acids in S. persica organs and more rationalizing its use as a toothbrush. PMID: 27863835 [PubMed - as supplied by publisher]

Related Articles Chromatographic determination of some biomarkers of liver cirrhosis and hepatocellular carcinoma in Egyptian patients. Biomed Chromatogr. 2016 Nov 10;: Authors: Osman D, Ali O, Obada M, El-Mezayen H, El-Said H Abstract Metabolomics has been shown to be an effective tool for disease diagnosis, biomarker screening and characterization of biological pathways. A total of 140 subjects were included in this study; urine metabolomes of patients with liver cirrhosis (LC, n = 40), patients with HCC (n = 55) and healthy male subjects (n = 45); as control group, were studied. Gas chromatography/mass spectrometry based urine metabolomics profile was investigated for all participants. Diagnostic models were constructed with a combination of marker metabolites, using principal components analysis (PCA) and receiver operator characteristic curves. A total of 57 peaks could be auto-identified of which 13 marker metabolites (glycine, serine, threonine, proline, urea, phosphate, pyrimidine, arabinose, xylitol, hippuric acid, citric acid, xylonic acid, and glycerol) were responsible for the separation of HCC group from healthy subjects. Also, 8 markers metabolites (glycine, serine, threonine, proline, citric acid, urea, xylitol and arabinose) showed significant difference between LC group and healthy subjects. No significant difference was detected between HCC and LC groups regarding all these metabolites. Metabolomic profile using GC-MS established an optimized diagnostic model to discriminate between HCC patients and healthy subjects; also it could be useful for diagnosis of LC patients. However, it failed to differentiate between HCC and LC patients. PMID: 27862090 [PubMed - as supplied by publisher]

Related Articles Rule-Mining for the Early Prediction of Chronic Kidney Disease Based on Metabolomics and Multi-Source Data. PLoS One. 2016;11(11):e0166905 Authors: Luck M, Bertho G, Bateson M, Karras A, Yartseva A, Thervet E, Damon C, Pallet N Abstract 1H Nuclear Magnetic Resonance (NMR)-based metabolic profiling is very promising for the diagnostic of the stages of chronic kidney disease (CKD). Because of the high dimension of NMR spectra datasets and the complex mixture of metabolites in biological samples, the identification of discriminant biomarkers of a disease is challenging. None of the widely used chemometric methods in NMR metabolomics performs a local exhaustive exploration of the data. We developed a descriptive and easily understandable approach that searches for discriminant local phenomena using an original exhaustive rule-mining algorithm in order to predict two groups of patients: 1) patients having low to mild CKD stages with no renal failure and 2) patients having moderate to established CKD stages with renal failure. Our predictive algorithm explores the m-dimensional variable space to capture the local overdensities of the two groups of patients under the form of easily interpretable rules. Afterwards, a L2-penalized logistic regression on the discriminant rules was used to build predictive models of the CKD stages. We explored a complex multi-source dataset that included the clinical, demographic, clinical chemistry, renal pathology and urine metabolomic data of a cohort of 110 patients. Given this multi-source dataset and the complex nature of metabolomic data, we analyzed 1- and 2-dimensional rules in order to integrate the information carried by the interactions between the variables. The results indicated that our local algorithm is a valuable analytical method for the precise characterization of multivariate CKD stage profiles and as efficient as the classical global model using chi2 variable section with an approximately 70% of good classification level. The resulting predictive models predominantly identify urinary metabolites (such as 3-hydroxyisovalerate, carnitine, citrate, dimethylsulfone, creatinine and N-methylnicotinamide) as relevant variables indicating that CKD significantly affects the urinary metabolome. In addition, the simple knowledge of the concentration of urinary metabolites classifies the CKD stage of the patients correctly. PMID: 27861591 [PubMed - in process]

Related Articles Homozygous variants in pyrroline-5-carboxylate reductase 2 (PYCR2) in patients with progressive microcephaly and hypomyelinating leukodystrophy. Am J Med Genet A. 2016 Nov 11;: Authors: Meng L, Donti T, Xia F, Niu Z, Al Shamsi A, Hertecant J, Al-Jasmi F, Gibson JB, Nagakura H, Zhang J, He W, Eng C, Yang Y, Elsea SH Abstract Pyrroline-5-carboxylate reductase 2, encoded by PYCR2, is one of the three homologous enzymes that catalyze the last step of proline synthesis. Homozygous variants in PYCR2 have been reported in patients from multiple consanguineous families with hypomyelinating leukodystrophy 10 (HLD10) (MIM: 616420). Here, we report five additional patients from three families with homozygous nonsense or missense variants in PYCR2, identified through clinical exome sequencing. All patients presented with postnatally acquired microcephaly, moderate to profound global developmental delay, and failure to thrive. Brain MRI in these patients showed thin corpus callosum, delayed myelination, and generalized white-matter volume loss. Additional phenotypes that were less consistent among patients included seizures or seizure-like movements, spasticity and ataxic gait, recurrent vomiting, cortical blindness, dysmorphic features, joint contractures, and irritability. Exome sequencing identified homozygous variants in PYCR2 in the proband from each family: c.28C>T (p.(Glu10Ter)), c.796C>T (p.(Arg266Ter)), and c.577G>A (p.(Val193Met)). Subsequent targeted analyses demonstrated co-segregation of the disease with the variant in the family. Despite the metabolic role of PYCR2, routine serum metabolic test in these patients were normal. To further understand the disease etiology and functions of PYCR2, small molecule metabolomics profiling was performed in plasma from three severely affected patients. No significant changes were identified in proline biosynthesis pathway or related metabolites. Studying the clinical features and the metabolic profiles of the PYCR2-deficient patients provides a more comprehensive picture for this newly identified disorder and facilitates further research on the gene function and disease etiology. © 2016 Wiley Periodicals, Inc. PMID: 27860360 [PubMed - as supplied by publisher]

Related Articles Mediterranean diet-gene interactions: a targeted metabolomics study in Greek-Cypriot women. Mol Nutr Food Res. 2016 Nov 18;: Authors: Kakkoura MG, Sokratous K, Demetriou CA, Loizidou MA, Loucaides G, Kakouri E, Hadjisavvas A, Kyriacou K Abstract SCOPE: A high adherence to the Mediterranean diet (MD) was previously associated with a decreased risk of breast cancer (BC) among Greek-Cypriot women. Additionally, particular polymorphisms were shown to modulate this MD-BC association. Herein, we aimed to investigate the effect of polymorphisms-MD interactions on the levels of specific metabolites that could be related to dietary adherence or enzymatic activity, which is itself modulated by polymorphisms. METHODS AND RESULTS: Greek-Cypriot women who were BC controls and had the lowest or the highest MD adherence (vegetables, fruit, legumes, fish) as assessed by principal component analysis (n = 564) were included. Participants were previously genotyped for 9 polymorphisms of the one-carbon metabolism, oxidative stress and xenobiotic metabolism. The serum levels of 14 metabolites that are key players in the aforementioned pathways were measured by UPLC-MS/MS. ANCOVA was used to assess polymorphism-MD interactions on metabolites' levels within a multivariate linear regression model. Statistically significant interactions between GSTM1 deletion polymorphism and MD on flavin mononucleotide (FMN) and on 5-methyltetrahydrofolate (5-MTHF) concentrations were observed. The MTHFR rs1801133 interacted significantly with MD on 5-MTHF concentration. CONCLUSION: Serum levels of FMN and 5-MTHF were shown to be influenced by interactions between GSTM1 deletion or MTHFR (rs1801133) polymorphisms and a dietary pattern, characteristic of MD. This article is protected by copyright. All rights reserved. PMID: 27860207 [PubMed - as supplied by publisher]

Related Articles Peptidome characterization of the antipyretic fraction of Bubali Cornu aqueous extract by nano liquid chromatography with orbitrap mass spectrum detection. J Sep Sci. 2016 Nov 9;: Authors: Liu R, Huang Q, Duan JA, Zhu Z, Liu P, Bian Y, Tao J, Qian D Abstract In the present study, the antipyretic activity of Bubali Cornu (water buffalo horn) fraction and its metabolomics were investigated. The fraction decreased rat rectal temperature, and 13 endogenous metabolites were identified as potential biomarkers. Selected metabolites were involved in arachidonic acid metabolism and glycerophospholipid metabolism etc. Following treatment with the fraction, four metabolites, pyroglutamic acid, palmitelaidic acid, leukotriene A4, and prostaglandin A2 were reversed. In addition, the levels of interleukin-1β, tumor necrosis factor-α, prostaglandin E2 , and cyclic adenosine monophosphate in plasma were also reversed after treatment as determined by enzyme linked immunosorbent assay. Furthermore, nano-flow liquid chromatography with orbitrap mass spectrometry detection was used to analyze the peptides in the fraction. In total, 824 peptide sequences mainly from keratins were determined, with Keratin 14, Keratin 34, and Keratin 86 representing the three main types of keratin hydrolysis in water buffalo horn based on peptide heat maps. Of the identified peptides, 81.2% were hydrophilic and the molecular weight of 70.3% of identified peptides was lower than 2000 Da. According to the metabolomics- and peptidomics-based approach used in the present study, it is feasible to identify and analyze the active peptide matrix from animal-horn-derived traditional Chinese medicines. This article is protected by copyright. All rights reserved. PMID: 27860201 [PubMed - as supplied by publisher]

Related Articles Metabolite profiling of whole murine embryos reveals metabolic perturbations associated with maternal valproate-induced neural tube closure defects. Birth Defects Res A Clin Mol Teratol. 2016 Nov 18;: Authors: Akimova D, Wlodarczyk BJ, Lin Y, Ross ME, Finnell RH, Chen Q, Gross SS Abstract BACKGROUND: Valproic acid (VPA) is prescribed therapeutically for multiple conditions, including epilepsy. When taken during pregnancy, VPA is teratogenic, increasing the risk of several birth and developmental defects including neural tube defects (NTDs). The mechanism by which VPA causes NTDs remains controversial and how VPA interacts with folic acid (FA), a vitamin commonly recommended for the prevention of NTDs, remains uncertain. We sought to address both questions by applying untargeted metabolite profiling analysis to neural tube closure (NTC) stage mouse embryos. METHODS: Pregnant SWV dams on either a 2 ppm or 10 ppm FA supplemented diet were injected with a single dose of VPA on gestational day E8.5. On day E9.5, the mouse embryos were collected and evaluated for NTC status. Liquid chromatography coupled to mass spectrometry metabolomics analysis was performed to compare metabolite profiles of NTD-affected VPA-exposed whole mouse embryos with profiles from embryos that underwent normal NTC from control dams. RESULTS: NTDs were observed in all embryos from VPA-treated dams and penetrance was not diminished by dietary FA supplementation. The most profound metabolic perturbations were found in the 10ppm FA VPA-exposed mouse embryos, compared with the other three treatment groups. Affected metabolites included amino acids, nucleobases and related phosphorylated nucleotides, lipids, and carnitines. CONCLUSION: Maternal VPA treatment markedly perturbed purine and pyrimidine metabolism in E9.5 embryos. In combination with a high FA diet, VPA treatment resulted in gross metabolic changes, likely caused by a multiplicity of mechanisms, including an apparent disruption of mitochondrial beta-oxidation. Birth Defects Research (Part A), 2016. © 2016 Wiley Periodicals, Inc. PMID: 27860192 [PubMed - as supplied by publisher]

Related Articles Quantitative Method to Investigate the Balance between Metabolism and Proteome Biomass: Starting from Glycine. Angew Chem Int Ed Engl. 2016 Nov 15;: Authors: Gu H, Carroll PA, Du J, Zhu J, Neto FC, Eisenman RN, Raftery D Abstract The balance between metabolism and biomass is very important in biological systems; however, to date there has been no quantitative method to characterize the balance. In this methodological study, we propose to use the distribution of amino acids in different domains to investigate this balance. It is well known that endogenous or exogenous amino acids in a biological system are either metabolized or incorporated into free amino acids (FAAs) or proteome amino acids (PAAs). Using glycine (Gly) as an example, we demonstrate a novel method to accurately determine the amounts of amino acids in various domains using serum, urine, and cell samples. As expected, serum and urine had very different distributions of FAA- and PAA-Gly. Using Tet21N human neuroblastoma cells, we also found that Myc(oncogene)-induced metabolic reprogramming included a higher rate of metabolizing Gly, which provides additional evidence that the metabolism of proliferating cells is adapted to facilitate producing new cells. It is therefore anticipated that our method will be very valuable for further studies of the metabolism and biomass balance that will lead to a better understanding of human cancers. PMID: 27860107 [PubMed - as supplied by publisher]

Related Articles Metabolic characterization of the early stage of hepatic fibrosis in rat using GC-TOF/MS and multivariate data analyses. Biomed Chromatogr. 2016 Nov 17;: Authors: Jiang H, Song JM, Gao PF, Qin XJ, Xu SZ, Zhang JF Abstract The aim of this study was to explore the changes in the urine metabolic spectrum in rats with the early stage of liver fibrosis using gas chromatography-time of flight/mass spectrometry (GC-TOF/MS), try to search for potential biomarkers and elucidate the probably metabonomic pathogenesis. The early stage of liver fibrosis was established with a single subcutaneously injection carbon tetrachloride (CCl4 ) twice each week for 4 weeks continuously. At the end of the experiment, GC-TOF/MS technology with multivariate statistical approaches such as principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) was used to analyze the changes in the metabolic spectrum trajectory and identify potential biomarkers. The results showed that twelve potential biomarkers in the model group such as succinic acid, threonine, lactose and so on were selected, which indicate that the metabonomic pathogenesis of the early stage of liver fibrosis may be related to disorders of energy metabolism, amino acid metabolism, fatty acid metabolism. PMID: 27859443 [PubMed - as supplied by publisher]

Related Articles Nuclear Magnetic Resonance metabolomics reveals an excretory metabolic signature of renal cell carcinoma. Sci Rep. 2016 Nov 18;6:37275 Authors: Monteiro MS, Barros AS, Pinto J, Carvalho M, Pires-Luís AS, Henrique R, Jerónimo C, Bastos ML, Gil AM, Guedes de Pinho P Abstract RCC usually develops and progresses asymptomatically and, when detected, it is frequently at advanced stages and metastatic, entailing a dismal prognosis. Therefore, there is an obvious demand for new strategies enabling an earlier diagnosis. The importance of metabolic rearrangements for carcinogenesis unlocked a new approach for cancer research, catalyzing the increased use of metabolomics. The present study aimed the NMR metabolic profiling of RCC in urine samples from a cohort of RCC patients (n = 42) and controls (n = 49). The methodology entailed variable selection of the spectra in tandem with multivariate analysis and validation procedures. The retrieval of a disease signature was preceded by a systematic evaluation of the impacts of subject age, gender, BMI, and smoking habits. The impact of confounders on the urine metabolomics profile of this population is residual compared to that of RCC. A 32-metabolite/resonance signature descriptive of RCC was unveiled, successfully distinguishing RCC patients from controls in principal component analysis. This work demonstrates the value of a systematic metabolomics workflow for the identification of robust urinary metabolic biomarkers of RCC. Future studies should entail the validation of the 32-metabolite/resonance signature found for RCC in independent cohorts, as well as biological validation of the putative hypotheses advanced. PMID: 27857216 [PubMed - in process]

Related Articles Topic modeling for untargeted substructure exploration in metabolomics. Proc Natl Acad Sci U S A. 2016 Nov 16;: Authors: van der Hooft JJ, Wandy J, Barrett MP, Burgess KE, Rogers S Abstract The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the system under study. Unfortunately, fragmentation spectra cannot identify molecules in isolation but require authentic standards or databases of known fragmented molecules. Fragmentation spectra are, however, replete with information pertaining to the biochemical processes present, much of which is currently neglected. Here, we present an analytical workflow that exploits all fragmentation data from a given experiment to extract biochemically relevant features in an unsupervised manner. We demonstrate that an algorithm originally used for text mining, latent Dirichlet allocation, can be adapted to handle metabolomics datasets. Our approach extracts biochemically relevant molecular substructures ("Mass2Motifs") from spectra as sets of co-occurring molecular fragments and neutral losses. The analysis allows us to isolate molecular substructures, whose presence allows molecules to be grouped based on shared substructures regardless of classical spectral similarity. These substructures, in turn, support putative de novo structural annotation of molecules. Combining this spectral connectivity to orthogonal correlations (e.g., common abundance changes under system perturbation) significantly enhances our ability to provide mechanistic explanations for biological behavior. PMID: 27856765 [PubMed - as supplied by publisher]

Related Articles Malonylation of glucosylated N-lauroylethanolamine: a new pathway that determines N-acylethanolamine metabolic fate in plants. J Biol Chem. 2016 Nov 17;: Authors: Khan BR, Wherritt DJ, Huhman D, Sumner LW, Chapman KD, Blancaflor EB Abstract N-acylethanolamines (NAEs) are bioactive fatty acid derivatives present in trace amounts in many eukaryotes. Although NAEs have signaling and physiological roles in animals, little is known about their metabolic fate in plants. Our previous microarray analyses showed that inhibition of Arabidopsis thaliana seedling growth by exogenous N-lauroylethanolamine (NAE 12:0) was accompanied by the differential expression of multiple genes encoding small molecule modifying enzymes. We focused on the gene, At5g39050, which encodes a phenolic glucoside malonyltransferase 1 (PMAT1) to better understand the biological significance of NAE 12:0-induced gene expression changes. PMAT1 expression was induced 3-5 fold by exogenous NAE 12:0. PMAT1 knockouts (pmat1) had reduced sensitivity to the growth inhibitory effects of NAE 12:0 compared to wild type leading to the hypothesis that PMAT1 might be a previously uncharacterized regulator of NAE metabolism in plants. To test this hypothesis, metabolic profiling of wild-type and pmat1 seedlings treated with NAE 12:0 was conducted. Wild-type seedlings treated with NAE 12:0 accumulated glucosylated and malonylated forms of this NAE species and structures were confirmed using Nuclear Magnetic Resonance (NMR) spectroscopy. By contrast, only the peak corresponding to NAE 12:0-glucoside was detected in pmat1. Recombinant PMAT1 catalyzed the reaction converting NAE 12:0-glucoside to NAE 12:0-mono or dimalonylglucosides providing direct evidence that this enzyme is involved in NAE 12:0-glucose malonylation. Taken together, our results indicate that glucosylation of NAE 12:0 by a yet to be determined glucosyltransferase and its subsequent malonylation by PMAT1 could represent a mechanism for modulating the biological activities of NAEs in plants. PMID: 27856641 [PubMed - as supplied by publisher]

Related Articles Sulfur fumigation reducing systemic exposure of ginsenosides and weakening immunomodulatory activity of ginseng. J Ethnopharmacol. 2016 Nov 14;: Authors: Ma B, Ting Kan WL, Zhu H, Li SL, Lin G Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Ginseng (Ginseng Radix et Rhizoma) is used worldwide for its miracle tonic effects, especially for its immunomodulatory activities. Sulfur fumigation, a fast and convenient method to prevent pesticidal and bacterial contamination in the food industry, has been recently employed during post-harvest processing of ginseng. Our previous studies demonstrated that sulfur fumigation significantly altered the chemical profile of the bioactive ingredients in ginseng. However, the effects of sulfur fumigation on the pharmacokinetics and bioactivities of ginseng remain unknown. AIM OF THE STUDY: To examine the effects of sulfur fumigation on the pharmacokinetics and immunomodulatory activities of ginseng. MATERIALS AND METHODS: For pharmacokinetic studies, male Sprague-Dawley rats exposed to single/multiple dosages of non-fumigated ginseng (NFG) and sulfur fumigated ginseng (SFG) were investigated using HPLC-MS/MS analysis. For bioactivity studies, male ICR mice were used to compare the immunomodulatory effects of NFG or SFG under both normal and cyclophosphamide (CY)-induced immunocompromised conditions using white blood cell counts, serum cytokine levels, and spleen and thymus weight indices. RESULTS: Sulfur fumigation significantly reduced the contents of the bioactive ginsenosides in ginseng, which resulted in drastically low systemic exposure of ginsenosides in SFG-treatment group compared to NFG-treatment group. This observation was consistent with the bioactivities obtained in NFG- and SFG-treatment groups. The bioactivity studies also demonstrated the immunomodulatory effects of NFG but not SFG in the CY-induced immunosuppressed mice. CONCLUSION: Sulfur fumigation significantly reduced contents of bioactive ginsenosides in ginseng, leading to dramatic decrease in the systemic exposure of these ginsenosides in the body and detrimental reduction of immunomodulatory effects of ginseng. Our results provided scientific evidences and laid a solid foundation for the needs of thorough evaluation of the significant impact of sulfur fumigation on ginseng and other medicinal herbs. PMID: 27856301 [PubMed - as supplied by publisher]

Related Articles Characterization of the Clostridium difficile volatile metabolome using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Nov 9;1039:8-16 Authors: Rees CA, Shen A, Hill JE Abstract Clostridium difficile is a bacterial pathogen capable of causing life-threatening infections of the gastrointestinal tract characterized by severe diarrhea. Exposure to certain classes of antibiotics, advanced age, and prolonged hospitalizations are known risk factors for infection by this organism. Anecdotally, healthcare providers have reported that they can smell C. difficile infections in their patients, and several studies have suggested that there may indeed be an olfactory signal associated with C. difficile-associated diarrhea. In this study, we sought to characterize the volatile molecules produced by an epidemic strain of C. difficile (R20291) using headspace solid-phase microextraction (HS-SPME) followed by two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS). We report on a set of 77 volatile compounds, of which 59 have not previously been associated with C. difficile growth in vitro. Amongst these reported compounds, we detect both straight-chain and branched-chain carboxylic acids, as well as p-cresol, which have been the primary foci of C. difficile volatile metabolomic studies to-date. We additionally report on novel sulfur-containing and carbonyl-containing molecules that have not previously been reported for C. difficile. With the identification of these novel C. difficile-associated volatile compounds, we demonstrate the superior resolution and sensitivity of GC×GC-TOFMS relative to traditional GC-MS. PMID: 27855313 [PubMed - as supplied by publisher]

Related Articles Comparison of Chemical Compositions in Pseudostellariae Radix from Different Cultivated Fields and Germplasms by NMR-Based Metabolomics. Molecules. 2016 Nov 15;21(11): Authors: Hua Y, Hou Y, Wang S, Ma Y, Liu Z, Zou L, Liu X, Luo Y, Liu J Abstract Pseudostellariae Radix (PR) is an important traditional Chinese medicine (TCM), which is consumed commonly for its positive health effects. However, the chemical differences of PR from different cultivated fields and germplasms are still unknown. In order to comprehensively compare the chemical compositions of PR from different cultivated fields, in this study, ¹H-NMR-based metabolomics coupled with high performance liquid chromatography (HPLC) were used to investigate the different metabolites in PR from five germplasms (jr, zs1, zs2, sb, and xc) cultivated in traditional fields (Jurong, Jiangsu, JSJR) and cultivated fields (Zherong, Fujian, FJZR). A total of 34 metabolites were identified based on ¹H-NMR data, and fourteen of them were found to be different in PR from JSJR and FJZR. The relative contents of alanine, lactate, lysine, taurine, sucrose, tyrosine, linolenic acid, γ-aminobutyrate, and hyperoside in PR from JSJR were higher than that in PR from FJZR, while PR from FJZR contained higher levels of glutamine, raffinose, xylose, unsaturated fatty acid, and formic acid. The contents of Heterophyllin A and Heterophyllin B were higher in PR from FJZR. This study will provide the basic information for exploring the influence law of ecological environment and germplasm genetic variation on metabolite biosynthesis of PR and its quality formation mechanism. PMID: 27854294 [PubMed - in process]

Related Articles Role of the lipid-regulated NF-κB/IL-6/STAT3 axis in alpha-naphthyl isothiocyanate-induced liver injury. Arch Toxicol. 2016 Nov 16; Authors: Fang ZZ, Tanaka N, Lu D, Jiang CT, Zhang WH, Zhang C, Du Z, Fu ZW, Gao P, Cao YF, Sun HZ, Zhu ZT, Cai Y, Krausz KW, Yao Z, Gonzalez FJ Abstract Alpha-naphthyl isothiocyanate (ANIT)-induced liver damage is regarded as a useful model to study drug-induced cholestatic hepatitis. Ultra-performance liquid chromatography coupled with electrospray ionization quadrupole mass spectrometry (UPLC-ESI-QTOF MS)-based metabolomics revealed clues to the mechanism of ANIT-induced liver injury, which facilitates the elucidation of drug-induced liver toxicity. 1-Stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC 18:0) and 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC 18:1) were significantly increased in serum from ANIT-treated mice, and this increase resulted from altered expression of genes encoding the lipid metabolism enzymes Chka and Scd1. ANIT also increased NF-κB/IL-6/STAT3 signaling, and in vitro luciferase reporter gene assays revealed that LPC 18:0 and LPC 18:1 can activate NF-κB in a concentration-dependent manner. Activation of PPARα through feeding mice a Wy-14,643-containing diet (0.1%) reduced ANIT-induced liver injury, as indicated by lowered ALT and AST levels, and liver histology. In conclusion, the present study demonstrated a role for the lipid-regulated NF-κB/IL-6/STAT3 axis in ANIT-induced hepatotoxicity, and that PPARα may be a potential therapeutic target for the prevention of drug-induced cholestatic liver injury. PMID: 27853831 [PubMed - as supplied by publisher]

Related Articles Homeostasis of metabolites in Escherichia coli on transition from anaerobic to aerobic conditions and the transient secretion of pyruvate. R Soc Open Sci. 2016 Aug;3(8):160187 Authors: Yasid NA, Rolfe MD, Green J, Williamson MP Abstract We have developed a method for rapid quenching of samples taken from chemostat cultures of Escherichia coli that gives reproducible and reliable measurements of extracellular and intracellular metabolites by (1)H NMR and have applied it to study the major central metabolites during the transition from anaerobic to aerobic growth. Almost all metabolites showed a gradual change after perturbation with air, consistent with immediate inhibition of pyruvate formate-lyase, dilution of overflow metabolites and induction of aerobic enzymes. Surprisingly, although pyruvate showed almost no change in intracellular concentration, the extracellular concentration transiently increased. The absence of intracellular accumulation of pyruvate suggested that one or more glycolytic enzymes might relocate to the cell membrane. To test this hypothesis, chromosomal pyruvate kinase (pykF) was modified to express either PykF-green fluorescent protein or PykF-FLAG fusion proteins. Measurements showed that PykF-FLAG relocates to the cell membrane within 5 min of aeration and then slowly returns to the cytoplasm, suggesting that on aeration, PykF associates with the membrane to facilitate secretion of pyruvate to maintain constant intracellular levels. PMID: 27853594 [PubMed - in process]

Related Articles Structured plant metabolomics for the simultaneous exploration of multiple factors. Sci Rep. 2016 Nov 17;6:37390 Authors: Vasilev N, Boccard J, Lang G, Grömping U, Fischer R, Goepfert S, Rudaz S, Schillberg S Abstract Multiple factors act simultaneously on plants to establish complex interaction networks involving nutrients, elicitors and metabolites. Metabolomics offers a better understanding of complex biological systems, but evaluating the simultaneous impact of different parameters on metabolic pathways that have many components is a challenging task. We therefore developed a novel approach that combines experimental design, untargeted metabolic profiling based on multiple chromatography systems and ionization modes, and multiblock data analysis, facilitating the systematic analysis of metabolic changes in plants caused by different factors acting at the same time. Using this method, target geraniol compounds produced in transgenic tobacco cell cultures were grouped into clusters based on their response to different factors. We hypothesized that our novel approach may provide more robust data for process optimization in plant cell cultures producing any target secondary metabolite, based on the simultaneous exploration of multiple factors rather than varying one factor each time. The suitability of our approach was verified by confirming several previously reported examples of elicitor-metabolite crosstalk. However, unravelling all factor-metabolite networks remains challenging because it requires the identification of all biochemically significant metabolites in the metabolomics dataset. PMID: 27853298 [PubMed - in process]

Related Articles Intestinal PPARγ signalling is required for sympathetic nervous system activation in response to caloric restriction. Sci Rep. 2016 Nov 17;6:36937 Authors: Duszka K, Picard A, Ellero-Simatos S, Chen J, Defernez M, Paramalingam E, Pigram A, Vanoaica L, Canlet C, Parini P, Narbad A, Guillou H, Thorens B, Wahli W Abstract Nuclear receptor PPARγ has been proven to affect metabolism in multiple tissues, and has received considerable attention for its involvement in colon cancer and inflammatory disease. However, its role in intestinal metabolism has been largely ignored. To investigate this potential aspect of PPARγ function, we submitted intestinal epithelium-specific PPARγ knockout mice (iePPARγKO) to a two-week period of 25% caloric restriction (CR), following which iePPARγKO mice retained more fat than their wild type littermates. In attempting to explain this discrepancy, we analysed the liver, skeletal muscle, intestinal lipid trafficking, and the microbiome, none of which appeared to contribute to the adiposity phenotype. Interestingly, under conditions of CR, iePPARγKO mice failed to activate their sympathetic nervous system (SNS) and increase CR-specific locomotor activity. These KO mice also manifested a defective control of their body temperature, which was overly reduced. Furthermore, the white adipose tissue of iePPARγKO CR mice showed lower levels of both hormone-sensitive lipase, and its phosphorylated form. This would result from impaired SNS signalling and possibly cause reduced lipolysis. We conclude that intestinal epithelium PPARγ plays an essential role in increasing SNS activity under CR conditions, thereby contributing to energy mobilization during metabolically stressful episodes. PMID: 27853235 [PubMed - in process]