PubMed

Development of a Data-Independent Targeted Metabolomics Method for Relative Quantification Using Liquid Chromatography Coupled with Tandem Mass Spectrometry. Anal Chem. 2017 Jun 02;: Authors: Chen Y, Zhou Z, Yang W, Bi N, Xu J, He J, Zhang R, Wang L, Abliz Z Abstract Quantitative metabolomics approaches can significantly improve the repeatability and reliability of metabolomics investi-gations but face critical technical challenges, owing to the vast number of unknown endogenous metabolites and the lack of authentic standards. The present study contributes to the development of a novel method known as "data-independent tar-geted quantitative metabolomics," (DITQM) which was used to investigate the label-free quantitative metabolomics of mul-tiple known and unknown metabolites in biofluid samples. This approach initially involved the acquisition of MS/MS data for all metabolites in biosamples using a sequentially stepped targeted MS/MS (sst-MS/MS) method, in which multiple prod-uct ion scans were performed by selecting all ions in the targeted mass ranges as the precursor ions. Subsequently, scheduled multiple reaction monitoring (MRM) by LC-MS/MS of the metabolome was established for 1,658 characteristic ion pairs of 1,324 metabolites. For sensitive and accurate quantification of these metabolites, mixed calibration curves were generated using sequentially diluted standard reference plasma samples using established MRM methods. Relative concentrations of all metabolites in each sample were calculated without using individual authentic standards. To evaluate the reliability and applicability of this new method, the performance of DITQM was validated by comparison to absolute quantification of twelve acylcarnitines using authentic standards and traditional metabolomics analysis for lung cancer. The results proved that the DITQM protocol is more reliable and can significantly improve clustering effects and repeatability in biomarker discovery. In this study, we established a novel methodology to standardize and quantify large-scale metabolome, providing a new choice for metabolomics research and its clinical applications. PMID: 28574715 [PubMed - as supplied by publisher]

A Novel Anti-Hepatitis C Virus and Antiproliferative Agent Alters Metabolic Networks in HepG2 and Hep3B Cells. Metabolites. 2017 Jun 02;7(2): Authors: Keogh A, Şenkardeş S, Idle JR, Küçükgüzel ŞG, Beyoğlu D Abstract A series of novel diflunisal hydrazide-hydrazones has been reported together with their anti-hepatitis C virus and antiproliferative activities in a number of human hepatoma cell lines. However, the mechanisms underlying the efficacy of these agents remain unclear. It was chosen to investigate the lead diflunisal hydrazide-hydrazone, 2',4'-difluoro-4-hydroxy-N'- [(pyridin-2-yl)methylidene]biphenyl-3-carbohydrazide (compound 3b), in two cultured human hepatoma cell lines-HepG2 and Hep3B-using a metabolomic protocol aimed at uncovering any effects of this agent on cellular metabolism. One sub-therapeutic concentration (2.5 μM) and one close to the IC50 for antimitotic effect (10 μM), after 72 h in cell culture, were chosen for both compound 3b and its inactive parent compound diflusinal as a control. A GCMS-based metabolomic investigation was performed on cell lysates after culture for 24 h. The intracellular levels of a total of 42 metabolites were found to be statistically significantly altered in either HepG2 or Hep3B cells, only eight of which were affected in both cell lines. It was concluded that compound 3b affected the following pathways-purine and pyrimidine catabolism, the glutathione cycle, and energy metabolism through glycolysis and the pentose phosphate pathway. Although the metabolomic findings occurred after 24 h in culture, significant cytotoxicity of compound 3b to both HepG2 and Hep3B cells at 10 μM were reported not to occur until 72 h in culture. These observations show that metabolomics can provide mechanistic insights into the efficacy of novel drug candidates prior to the appearance of their pharmacological effect. PMID: 28574427 [PubMed - in process]

Related Articles Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures. J Biomol NMR. 2017 Jun 01;: Authors: Li DW, Wang C, Brüschweiler R Abstract Characterization of the chemical components of complex mixtures in solution is important in many areas of biochemistry and chemical biology, including metabolomics. The use of 2D NMR total correlation spectroscopy (TOCSY) experiments has proven very useful for the identification of known metabolites as well as for the characterization of metabolites that are unknown by taking advantage of the good resolution and high sensitivity of this homonuclear experiment. Due to the complexity of the resulting spectra, automation is critical to facilitate and speed-up their analysis and enable high-throughput applications. To better meet these emerging needs, an automated spin-system identification algorithm of TOCSY spectra is introduced that represents the cross-peaks and their connectivities as a mathematical graph, for which all subgraphs are determined that are maximal cliques. Each maximal clique can be assigned to an individual spin system thereby providing a robust deconvolution of the original spectrum for the easy extraction of critical spin system information. The approach is demonstrated for a complex metabolite mixture consisting of 20 compounds and for E. coli cell lysate. PMID: 28573376 [PubMed - as supplied by publisher]

Related Articles Exposure Marker Discovery of Phthalates Using Mass Spectrometry. Mass Spectrom (Tokyo). 2017;6(Spec Iss):S0062 Authors: Hsu JY, Shih CL, Liao PC Abstract Phthalates are chemicals widely used in industry and the consequences on human health caused by exposure to these agents are of significant interest currently. The urinary metabolites of phthalates can be measured and used as exposure markers for the assessment of the actual internal contamination of phthalates coming from different sources and absorbed by various ways. The purpose of this paper is to review the markers for exposure and risk assessment of phthalates such as di-methyl phthalate (DMP), di-ethyl phthalate (DEP), di-butyl phthalate (DBP), benzylbutyl phthalate (BBP), di-(2-ethylhexyl)phthalate (DEHP), di-(2-propylheptyl)phthalate (DPHP), di-iso-nonyl phthalate (DINP), di-n-octyl phthalate (DnOP) and di-iso-decyl phthalate (DIDP), and introduction of the analytical approach of three metabolomics data processing approaches that can be used for chemical exposure marker discovery in urine with high-resolution mass spectrometry (HRMS) data. PMID: 28573083 [PubMed - in process]

Related Articles Erythrocyte Purinergic Signaling Components Underlie Hypoxia Adaptation. J Appl Physiol (1985). 2017 Jun 01;:jap.00155.2017 Authors: Sun K, Liu H, Song A, Manalo JM, D'Alessandro A, Hansen KC, Kellems RE, Eltzschig HK, Blackburn MR, Roach RC, Xia Y Abstract Erythrocytes are vital to human adaptation under hypoxic conditions because of their abundance in number and irreplaceable function of delivering oxygen (O2). However, although multiple large-scale altitude studies investigating the overall coordination of the human body for hypoxia adaptation have been conducted, detailed research with a focus on erythrocytes was missing due to lack of proper techniques. The recently maturing metabolomics profiling technology appears to be the answer to this limitation. Metabolomics profiling provides unbiased high-throughput screening data that reveal the overall metabolic status of erythrocytes. Recent studies have exploited this new technology and provided novel insight into erythrocyte physiology and pathology. In particular, a series of studies focusing on erythrocyte purinergic signaling have reported that adenosine signaling, coupled with 5' AMP-activated protein kinase (AMPK) and the production of erythrocyte-enriched bioactive signaling lipid sphingosine 1-phosphate, regulate erythrocyte glucose metabolism for more O2 delivery. Moreover, an adenosine-dependent "Erythrocyte Hypoxic Memory" was discovered which provides an explanation for fast acclimation upon re-ascent. These findings not only shed new light on our understanding of erythrocyte function and hypoxia adaptation but also offer a myriad of novel therapeutic possibilities to counteract various hypoxic conditions. PMID: 28572494 [PubMed - as supplied by publisher]

Related Articles Advantages and Limitations of Current Biomarker Research: From Experimental Research to Clinical Application. Curr Pharm Biotechnol. 2017 May 31;: Authors: Kim SH, Weiß C, Hoffmann U, Borggrefe M Abstract BACKGROUND: Biomarkers are indispensable tools for screening, diagnosis, and prognosis in cardiovascular diseases and their clinical application increases steadily. As cardiovascular diseases include various pathophysiological processes, no single biomarker, even natriuretic peptides, can be regarded as ideal fulfilling all necessary criteria for a comprehensive diagnostic or prognostic assessment revealing optimal clinical application. Hence, the multi-marker approaches using different biomarkers reflecting different pathophysiologies were highlighted recently. Advances in biomedical technologies expanded the spectrum of novel blood-derived biomarkers, such as micro-RNA (miRNA) or "omics"-data potentially providing a more advanced knowledge about pathogenesis of cardiovascular disease. CONCLUSION: This review describes the advantages and limitations of blood circulating biomarkers with regard to proteins, metabolomics and transcriptional level both within single as well as multi-marker strategies. Moreover, their usefulness is focused on clinical decision-making in cardiovascular diseases. PMID: 28571562 [PubMed - as supplied by publisher]

Related Articles Evolutionary Adaptation of the Essential tRNA Methyltransferase TrmD to the Signaling Molecule 3',5'-cAMP in Bacteria. J Biol Chem. 2017 Jan 06;292(1):313-327 Authors: Zhang Y, Agrebi R, Bellows LE, Collet JF, Kaever V, Gründling A Abstract The nucleotide signaling molecule 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) plays important physiological roles, ranging from carbon catabolite repression in bacteria to mediating the action of hormones in higher eukaryotes, including human. However, it remains unclear whether 3',5'-cAMP is universally present in the Firmicutes group of bacteria. We hypothesized that searching for proteins that bind 3',5'-cAMP might provide new insight into this question. Accordingly, we performed a genome-wide screen and identified the essential Staphylococcus aureus tRNA m(1)G37 methyltransferase enzyme TrmD, which is conserved in all three domains of life as a tight 3',5'-cAMP-binding protein. TrmD enzymes are known to use S-adenosyl-l-methionine (AdoMet) as substrate; we have shown that 3',5'-cAMP binds competitively with AdoMet to the S. aureus TrmD protein, indicating an overlapping binding site. However, the physiological relevance of this discovery remained unclear, as we were unable to identify a functional adenylate cyclase in S. aureus and only detected 2',3'-cAMP but not 3',5'-cAMP in cellular extracts. Interestingly, TrmD proteins from Escherichia coli and Mycobacterium tuberculosis, organisms known to synthesize 3',5'-cAMP, did not bind this signaling nucleotide. Comparative bioinformatics, mutagenesis, and biochemical analyses revealed that the highly conserved Tyr-86 residue in E. coli TrmD is essential to discriminate between 3',5'-cAMP and the native substrate AdoMet. Combined with a phylogenetic analysis, these results suggest that amino acids in the substrate binding pocket of TrmD underwent an adaptive evolution to accommodate the emergence of adenylate cyclases and thus the signaling molecule 3',5'-cAMP. Altogether this further indicates that S. aureus does not produce 3',5'-cAMP, which would otherwise competitively inhibit an essential enzyme. PMID: 27881678 [PubMed - indexed for MEDLINE]

Related Articles Characterisation of plasmalemmal shedding of vesicles induced by the cholesterol/sphingomyelin binding protein, ostreolysin A-mCherry. Biochim Biophys Acta. 2016 11;1858(11):2882-2893 Authors: Skočaj M, Yu Y, Grundner M, Resnik N, Bedina Zavec A, Leonardi A, Križaj I, Guella G, Maček P, Kreft ME, Frangež R, Veranič P, Sepčić K Abstract Ostreolysin A (OlyA) is a 15-kDa protein that binds selectively to cholesterol/sphingomyelin membrane nanodomains. This binding induces the production of extracellular vesicles (EVs) that comprise both microvesicles with diameters between 100nm and 1μm, and larger vesicles of around 10-μm diameter in Madin-Darby canine kidney cells. In this study, we show that vesiculation of these cells by the fluorescent fusion protein OlyA-mCherry is not affected by temperature, is not mediated via intracellular Ca(2+) signalling, and does not compromise cell viability and ultrastructure. Seventy-one proteins that are mostly of cytosolic and nuclear origin were detected in these shed EVs using mass spectroscopy. In the cells and EVs, 218 and 84 lipid species were identified, respectively, and the EVs were significantly enriched in lysophosphatidylcholines and cholesterol. Our collected data suggest that OlyA-mCherry binding to cholesterol/sphingomyelin membrane nanodomains induces specific lipid sorting into discrete patches, which promotes plasmalemmal blebbing and EV shedding from the cells. We hypothesize that these effects are accounted for by changes of local membrane curvature upon the OlyA-mCherry-plasmalemma interaction. We suggest that the shed EVs are a potentially interesting model for biophysical and biochemical studies of cell membranes, and larger vesicles could represent tools for non-invasive sampling of cytosolic proteins from cells and thus metabolic fingerprinting. PMID: 27591807 [PubMed - indexed for MEDLINE]

19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2017/06/02PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2017/06/01PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles Epidermal bladder cells confer salinity stress tolerance in the halophyte quinoa and Atriplex species. Plant Cell Environ. 2017 May 30;: Authors: Kiani-Pouya A, Roessner U, Jayasinghe NS, Lutz A, Rupasinghe T, Bazihizina N, Bohm J, Alharbi S, Hedrich R, Shabala S Abstract Epidermal bladder cells (EBC) have been postulated to assist halophytes in coping with saline environments. However, little direct supporting evidence is available. Here, Chenopodium quinoa plants were grown under saline conditions for five weeks. One day prior to salinity treatment, EBC from all leaves and petioles were gently removed using a soft cosmetic brush and physiological, ionic and metabolic changes in brushed and non-brushed leaves were compared. Gentle removal of EBC neither initiated wound metabolism nor affected the physiology and biochemistry of control-grown plants but did have a pronounced effect on salt-grown plants, resulting in a salt-sensitive phenotype. Of 91 detected metabolites, more than half were significantly affected by salinity. Removal of EBC dramatically modified these metabolic changes, with the biggest differences reported for GABA, proline, sucrose and inositol, affecting ion transport across cellular membranes (as shown in electrophysiological experiments). This work provides the first direct evidence for a role of EBC in salt tolerance in halophytes and attributes this to (1) a key role of EBC as a salt dump for external sequestration of sodium; (2) improved K(+) retention in leaf mesophyll and (3) EBC as a storage space for several metabolites known to modulate plant ionic relations. PMID: 28558173 [PubMed - as supplied by publisher]

Related Articles Amino acid metabolites that regulate G protein signaling during osmotic stress. PLoS Genet. 2017 May 30;13(5):e1006829 Authors: Shellhammer JP, Morin-Kensicki E, Matson JP, Yin G, Isom DG, Campbell SL, Mohney RP, Dohlman HG Abstract All cells respond to osmotic stress by implementing molecular signaling events to protect the organism. Failure to properly adapt can lead to pathologies such as hypertension and ischemia-reperfusion injury. Mitogen-activated protein kinases (MAPKs) are activated in response to osmotic stress, as well as by signals acting through G protein-coupled receptors (GPCRs). For proper adaptation, the action of these kinases must be coordinated. To identify second messengers of stress adaptation, we conducted a mass spectrometry-based global metabolomics profiling analysis, quantifying nearly 300 metabolites in the yeast S. cerevisiae. We show that three branched-chain amino acid (BCAA) metabolites increase in response to osmotic stress and require the MAPK Hog1. Ectopic addition of these BCAA derivatives promotes phosphorylation of the G protein α subunit and dampens G protein-dependent transcription, similar to that seen in response to osmotic stress. Conversely, genetic ablation of Hog1 activity or the BCAA-regulatory enzymes leads to diminished phosphorylation of Gα and increased transcription. Taken together, our results define a new class of candidate second messengers that mediate cross talk between osmotic stress and GPCR signaling pathways. PMID: 28558063 [PubMed - as supplied by publisher]

Related Articles Overexpression of the human DEK oncogene reprograms cellular metabolism and promotes glycolysis. PLoS One. 2017;12(5):e0177952 Authors: Matrka MC, Watanabe M, Muraleedharan R, Lambert PF, Lane AN, Romick-Rosendale LE, Wells SI Abstract The DEK oncogene is overexpressed in many human malignancies including at early tumor stages. Our reported in vitro and in vivo models of squamous cell carcinoma have demonstrated that DEK contributes functionally to cellular and tumor survival and to proliferation. However, the underlying molecular mechanisms remain poorly understood. Based on recent RNA sequencing experiments, DEK expression was necessary for the transcription of several metabolic enzymes involved in anabolic pathways. This identified a possible mechanism whereby DEK may drive cellular metabolism to enable cell proliferation. Functional metabolic Seahorse analysis demonstrated increased baseline and maximum extracellular acidification rates, a readout of glycolysis, in DEK-overexpressing keratinocytes and squamous cell carcinoma cells. DEK overexpression also increased the maximum rate of oxygen consumption and therefore increased the potential for oxidative phosphorylation (OxPhos). To detect small metabolites that participate in glycolysis and the tricarboxylic acid cycle (TCA) that supplies substrate for OxPhos, we carried out NMR-based metabolomics studies. We found that high levels of DEK significantly reprogrammed cellular metabolism and altered the abundances of amino acids, TCA cycle intermediates and the glycolytic end products lactate, alanine and NAD+. Taken together, these data support a scenario whereby overexpression of the human DEK oncogene reprograms keratinocyte metabolism to fulfill energy and macromolecule demands required to enable and sustain cancer cell growth. PMID: 28558019 [PubMed - in process]

Related Articles Metabolomics approach to evaluate a Baltic Sea-sourced diet for cultured Arctic char (Salvelinus alpinus L.). J Agric Food Chem. 2017 May 30;: Authors: Cheng K, Müllner E, Moazzami AA, Carlberg H, Brännäs E, Pickova J Abstract Aqua-feeds traditionally rely on fishmeal as a protein source, which is costly and unsustainable. A new feed was formulated in the study with Baltic Sea-sourced decontaminated fishmeal, Mytilus edulis and Saccharomyces cerevisiae, and given to Arctic char (Salvelinus alpinus) for ten months. The diet-induced changes on metabolic profile in fish plasma, liver and muscle were studied relative to a fishmeal-based standard diet by using a 1H NMR-based metabolomics approach. Fish fed the test diet had higher content of betaine, and lower levels of trimethylamine-N-oxide and aromatic amino acids in plasma and/or tissues, which were mainly caused by the diet. The metabolomics results are useful to understand the mechanism of lower body mass, smaller Fulton's condition factor and a tendency of less lipid content observed in fish fed the test diet. Thus, modifications on the dietary levels of these compounds in the feed are needed to achieve better growth performance. PMID: 28557427 [PubMed - as supplied by publisher]

Related Articles Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds. Microb Biotechnol. 2017 May 29;: Authors: Tyc O, de Jager VCL, van den Berg M, Gerards S, Janssens TKS, Zaagman N, Kai M, Svatos A, Zweers H, Hordijk C, Besselink H, de Boer W, Garbeva P Abstract Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date about interspecific interactions between Gram-positive and Gram-negative bacteria. In this study, we aimed to understand how the interspecific interaction between the Gram-positive Paenibacillus sp. AD87 and the Gram-negative Burkholderia sp. AD24 affects the fitness, gene expression and the production of soluble and volatile secondary metabolites of both bacteria. To obtain better insight into this interaction, transcriptome and metabolome analyses were performed. Our results revealed that the interaction between the two bacteria affected their fitness, gene expression and the production of secondary metabolites. During interaction, the growth of Paenibacillus was not affected, whereas the growth of Burkholderia was inhibited at 48 and 72 h. Transcriptome analysis revealed that the interaction between Burkholderia and Paenibacillus caused significant transcriptional changes in both bacteria as compared to the monocultures. The metabolomic analysis revealed that the interaction increased the production of specific volatile and soluble antimicrobial compounds such as 2,5-bis(1-methylethyl)-pyrazine and an unknown Pederin-like compound. The pyrazine volatile compound produced by Paenibacillus was subjected to bioassays and showed strong inhibitory activity against Burkholderia and a range of plant and human pathogens. Moreover, strong additive antimicrobial effects were observed when soluble extracts from the interacting bacteria were combined with the pure 2,5-bis(1-methylethyl)-pyrazine. The results obtained in this study highlight the importance to explore bacterial interspecific interactions to discover novel secondary metabolites and to perform simultaneously metabolomics of both, soluble and volatile compounds. PMID: 28557379 [PubMed - as supplied by publisher]

Related Articles Characterization of Metabolite Profile in Phyllanthus niruri and Correlation with Bioactivity Elucidated by Nuclear Magnetic Resonance Based Metabolomics. Molecules. 2017 May 30;22(6): Authors: Mediani A, Abas F, Maulidiani M, Khatib A, Tan CP, Ismail IS, Shaari K, Ismail A Abstract Phyllanthus niruri is an important medicinal plant. To standardize the extract and guarantee its maximum benefit, processing methods optimization ought to be amenable and beneficial. Herein, three dried P. niruri samples, air (AD), freeze (FD) and oven (OD), extracted with various ethanol to water ratios (0%, 50%, 70%, 80% and 100%) were evaluated for their metabolite changes using proton nuclear magnetic resonance (¹H-NMR)-based metabolomics approach. The amino acids analysis showed that FD P. niruri exhibited higher content of most amino acids compared to the other dried samples. Based on principal component analysis (PCA), the FD P. niruri extracted with 80% ethanol contained higher amounts of hypophyllanthin and phenolic compounds based on the loading plot. The partial least-square (PLS) results showed that the phytochemicals, including hypophyllanthin, catechin, epicatechin, rutin, quercetin and chlorogenic, caffeic, malic and gallic acids were correlated with antioxidant and α-glucosidase inhibitory activities, which were higher in the FD material extracted with 80% ethanol. This report optimized the effect of drying and ethanol ratios and these findings demonstrate that NMR-based metabolomics was an applicable approach. The FD P. niruri extracted with 80% ethanol can be used as afunctional food ingredient for nutraceutical or in medicinal preparation. PMID: 28556789 [PubMed - in process]

Related Articles Fasting serum hippuric acid is elevated after bilberry (Vaccinium myrtillus) consumption and associates with improvement of fasting glucose levels and insulin secretion in persons at high risk of developing type 2 diabetes. Mol Nutr Food Res. 2017 May 29;: Authors: Df de Mello V, A Lankinen M, Lindström J, Puupponen-Pimiä R, E Laaksonen D, Pihlajamäki J, Lehtonen M, Uusitupa M, Tuomilehto J, Kolehmainen M, Törrönen R, Hanhineva K Abstract SCOPE: Urinary hippuric acid has been proposed as a biomarker for fruit, vegetable and polyphenol consumption. We assessed how serum hippuric acid changes after a bilberry-enriched diet (BB; high anthocyanin intake) and another berry diet including strawberries, raspberries and cloudberries (SRC; lower anthocyanin intake) and how these changes associate with insulin and glucose metabolism. METHODS AND RESULTS: Hippuric acid was measured with LC-QTOF-MS metabolite profiling analysis from fasting serum samples at baseline and after an 8-week intervention in 47 individuals with features of the metabolic syndrome who were randomized to either a BB diet (n = 15), a SRC diet (n = 20) or a control diet (n = 12). Fasting serum hippuric acid increased significantly (3.5-fold, p = 0.001) only in the BB group and correlated with changes in fasting plasma glucose concentration (r = -0.54, p < 0.05) and insulin secretion (r = 0.59, p < 0.05). These associations were confirmed in the Finnish Diabetes Prevention Study (n = 198). CONCLUSION: Fasting serum hippuric acid is increased after consumption of anthocyanin-rich bilberries, and may contribute to the beneficial effect of bilberry consumption through its associations with better glycemic control and β-cell function. This article is protected by copyright. All rights reserved. PMID: 28556578 [PubMed - as supplied by publisher]

Related Articles Demonstration of the utility of biomarkers for dietary intake assessment; proline betaine as an example. Mol Nutr Food Res. 2017 May 28;: Authors: Gibbons H, Michielsen CJR, Rundle M, Frost G, McNulty BA, Nugent AP, Walton J, Flynn A, Gibney MJ, Brennan L Abstract SCOPE: There is a dearth of studies demonstrating the use of dietary biomarkers for determination of food intake. The objective of this study was to develop calibration curves for use in quantifying citrus intakes in an independent cohort. METHODS AND RESULTS: Participants (n = 50) from the NutriTech food-intake study consumed standardized breakfasts for three consecutive days over three consecutive weeks. Orange juice intake decreased over the weeks. Urine samples were analyzed by NMR-spectroscopy and proline betaine was quantified and normalized to osmolality. Calibration curves were developed and used to predict citrus intake in an independent cohort; the Irish National Adult Nutrition Survey (NANS) (n = 565). Proline betaine displayed a dose-response relationship to orange juice intake in 24h and fasting samples (p<0.001). In a test set, predicted orange juice intakes displayed excellent agreement with true intake. There were significant associations between predicted intake measured in 24h and fasting samples and true intake(r = 0.710-0.919). Citrus intakes predicted for the NANS cohort demonstrated good agreement with self-reported intake and this agreement improved following normalization to osmolality. CONCLUSION: The developed calibration curves successfully predicted citrus intakes in an independent cohort. Expansion of this approach to other foods will be important for the development of objective intake measurements. This article is protected by copyright. All rights reserved. PMID: 28556565 [PubMed - as supplied by publisher]

Related Articles Serum extracellular vesicles contain protein biomarkers for primary sclerosing cholangitis and cholangiocarcinoma. Hepatology. 2017 May 26;: Authors: Arbelaiz A, Azkargorta M, Krawczyk M, Santos-Laso A, Lapitz A, Perugorria MJ, Erice O, Gonzalez E, Jimenez-Agüero R, Lacasta A, Ibarra C, Sanchez-Campos A, Jimeno JP, Lammert F, Milkiewicz P, Marzioni M, Macias RIR, Marin JJG, Patel T, Gores GJ, Martinez I, Elortza F, Falcon-Perez JM, Bujanda L, Banales JM Abstract Cholangiocarcinoma (CCA) includes a heterogeneous group of biliary cancers with poor prognosis. Several conditions such as primary sclerosing cholangitis (PSC) are risk factors. Non-invasive differential diagnosis between intrahepatic CCA (iCCA) and hepatocellular carcinoma (HCC) is sometimes difficult. Accurate non-invasive biomarkers for PSC, CCA or HCC are not available. In the search of novel biomarkers, serum extracellular vesicles (EV) were isolated from CCA (n=43), PSC (n=30) or HCC (n=29) patients, and healthy individuals (control, n=32), and their protein content was characterized. By using nanoparticle tracking analysis (NTA), serum EV concentration was found higher in HCC than all the other groups. Round morphology (by transmission electron microscopy), size (∼180 nm diameter by NTA) and markers (CD9, CD63 and CD81 by immunoblot) indicated that most serum EV were exosomes. Proteome profiles (by mass spectrometry) revealed multiple differentially expressed proteins among groups. Several of these proteins showed high diagnostic values with maximum area under the ROC curve (AUC) of 0.878 for CCA vs control, 0.905 for CCA stage I-I vs control, 0.789 for PSC vs control, 0.806 for PSC non-cirrhotic vs control, 0.796 for CCA vs PSC, 0.956 for CCA stage I-I vs PSC, 0.904 for HCC vs control, and 0.894 for iCCA vs HCC. The proteomic analysis of EV derived from CCA human cells in vitro revealed higher abundance of oncogenic proteins compared to EV released by normal human cholangiocytes. Orthotopic implant of CCA human cells in the liver of immunodeficient mice resulted in the release to serum of EV containing some similar human oncogenic proteins. CONCLUSION: novel proteomic signatures found in serum EV of CCA, PSC and HCC patients show potential usefulness as diagnostic tools. This article is protected by copyright. All rights reserved. PMID: 28555885 [PubMed - as supplied by publisher]

Related Articles Bioinformatics can boost metabolomics research. J Biotechnol. 2017 May 26;: Authors: Meier R, Ruttkies C, Treutler H, Neumann S Abstract Metabolomics is the modern term for the field of small molecule research in biology and biochemistry. Currently, metabolomics is undergoing a transition where the classic analytical chemistry is combined with modern cheminformatics and bioinformatics methods, paving the way for large-scale data analysis. We give some background on past developments, highlight current state-of-the-art approaches, and give a perspective on future requirements. PMID: 28554829 [PubMed - as supplied by publisher]