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Sheik Nadeem Elahee Doomun, Stella Loke, Sean O'Callaghan, Damien L Callahan
A simple method for tracing carbon fixation and lipid synthesis in microalgae was developed using a combination of solid-phase extraction (SPE) and negative ion chemical ionisation gas chromatography mass spectrometry (NCI-GC-MS). NCI-GC-MS is an extremely sensitive technique that can produce an unfragmented molecular ion making this technique particularly useful for stable isotope enrichment studies. Derivatisation of fatty acids using pentafluorobenzyl bromide (PFBBr) allows the coupling of the high separation efficiency of GC and the measurement of unfragmented molecular ions for each of the fatty acids by single quadrupole MS...
November 11, 2016: Metabolites
Philipp Gierok, Manuela Harms, Karen Methling, Falko Hochgräfe, Michael Lalk
The Gram positive opportunistic human pathogen Staphylococcus aureus induces a variety of diseases including pneumonia. S. aureus is the second most isolated pathogen in cystic fibrosis patients and accounts for a large proportion of nosocomial pneumonia. Inside the lung, the human airway epithelium is the first line in defence with regard to microbial recognition and clearance as well as regulation of the immune response. The metabolic host response is, however, yet unknown. To address the question of whether the infection alters the metabolome and metabolic activity of airway epithelial cells, we used a metabolomics approach...
November 9, 2016: Metabolites
Fidele Tugizimana, Paul A Steenkamp, Lizelle A Piater, Ian A Dubery
Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the "exhaustive" extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter...
November 3, 2016: Metabolites
Stefan Koch, Christoph Bueschl, Maria Doppler, Alexandra Simader, Jacqueline Meng-Reiterer, Marc Lemmens, Rainer Schuhmacher
Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented...
November 2, 2016: Metabolites
Yun Xu, Howbeer Muhamadali, Ali Sayqal, Neil Dixon, Royston Goodacre
Partial least squares (PLS) is one of the most commonly used supervised modelling approaches for analysing multivariate metabolomics data. PLS is typically employed as either a regression model (PLS-R) or a classification model (PLS-DA). However, in metabolomics studies it is common to investigate multiple, potentially interacting, factors simultaneously following a specific experimental design. Such data often cannot be considered as a "pure" regression or a classification problem. Nevertheless, these data have often still been treated as a regression or classification problem and this could lead to ambiguous results...
October 28, 2016: Metabolites
Hendrik Treutler, Steffen Neumann
Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92 % of the cases...
October 20, 2016: Metabolites
Eisuke Chikayama, Ryo Yamashina, Keiko Komatsu, Yuuri Tsuboi, Kenji Sakata, Jun Kikuchi, Yasuyo Sekiyama
Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness...
October 19, 2016: Metabolites
Sanad Alonezi, Jonans Tusiimire, Jennifer Wallace, Mark J Dufton, John A Parkinson, Louise C Young, Carol J Clements, Jin Kyu Park, Jong Woon Jeon, Valerie A Ferro, David G Watson
In the present study, liquid chromatography-mass spectrometry (LC-MS) was employed to characterise the metabolic profiles of two human ovarian cancer cell lines A2780 (cisplatin-sensitive) and A2780CR (cisplatin-resistant) in response to their exposure to melittin, a cytotoxic peptide from bee venom. In addition, the metabolomics data were supported by application of Biolog microarray technology to examine the utilisation of carbon sources by the two cell lines. Data extraction with MZmine 2.14 and database searching were applied to provide metabolite lists...
October 13, 2016: Metabolites
Victoria C Foletta, Michelle Palmieri, Joachim Kloehn, Shaun Mason, Stephen F Previs, Malcolm J McConville, Oliver M Sieber, Clinton R Bruce, Greg M Kowalski
Deuterated water (²H₂O), a stable isotopic tracer, provides a convenient and reliable way to label multiple cellular biomass components (macromolecules), thus permitting the calculation of their synthesis rates. Here, we have combined ²H₂O labelling, GC-MS analysis and a novel cell fractionation method to extract multiple biomass components (DNA, protein and lipids) from the one biological sample, thus permitting the simultaneous measurement of DNA (cell proliferation), protein and lipid synthesis rates...
October 13, 2016: Metabolites
Jorgelindo da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine Pérès, Loïc Paulevé, Marcel Levy Nogueira, Jean-Marc Steyaert, Laurent Schwartz
To better understand the energetic status of proliferating cells, we have measured the intracellular pH (pHi) and concentrations of key metabolites, such as adenosine triphosphate (ATP), nicotinamide adenine dinucleotide (NAD), and nicotinamide adenine dinucleotide phosphate (NADP) in normal and cancer cells, extracted from fresh human colon tissues. Cells were sorted by elutriation and segregated in different phases of the cell cycle (G0/G1/S/G2/M) in order to study their redox (NAD, NADP) and bioenergetic (ATP, pHi) status...
October 3, 2016: Metabolites
Anubhav Srivastava, Greg M Kowalski, Damien L Callahan, Peter J Meikle, Darren J Creek
This is a perspective from the peer session on stable isotope labelling and fluxomics at the Australian & New Zealand Metabolomics Conference (ANZMET) held from 30 March to 1 April 2016 at La Trobe University, Melbourne, Australia. This report summarizes the key points raised in the peer session which focused on the advantages of using stable isotopes in modern metabolomics and the challenges in conducting flux analyses. The session highlighted the utility of stable isotope labelling in generating reference standards for metabolite identification, absolute quantification, and in the measurement of the dynamic activity of metabolic pathways...
October 1, 2016: Metabolites
Miroslava Cuperlovic-Culf, NandhaKishore Rajagopalan, Dan Tulpan, Michele C Loewen
Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a devastating disease of wheat. Partial resistance to FHB of several wheat cultivars includes specific metabolic responses to inoculation. Previously published studies have determined major metabolic changes induced by pathogens in resistant and susceptible plants. Functionality of the majority of these metabolites in resistance remains unknown. In this work we have made a compilation of all metabolites determined as selectively accumulated following FHB inoculation in resistant plants...
September 30, 2016: Metabolites
Philipp Eisenmann, Mona Ehlers, Christoph H Weinert, Pavleta Tzvetkova, Mara Silber, Manuela J Rist, Burkhard Luy, Claudia Muhle-Goll
Metabolome analyses by NMR spectroscopy can be used in quality control by generating unique fingerprints of different species. Hundreds of components and their variation between different samples can be analyzed in a few minutes/hours with high accuracy and low cost of sample preparation. Here, apple peel and pulp extracts of a variety of apple cultivars were studied to assess their suitability to discriminate between the different varieties. The cultivars comprised mainly newly bred varieties or ones that were brought onto the market in recent years...
September 19, 2016: Metabolites
Nahoko Tanaka, Shotaro Masuoka, Natsuko Kusunoki, Toshihiro Nanki, Shinichi Kawai
Adipokines are important regulators of several processes, including inflammation and atherosclerosis. In patients with systemic autoimmune diseases, atherosclerosis is accelerated with higher cardiovascular morbidity and mortality. We prospectively investigated the association of adipokines and glucocorticoid therapy with progression of premature atherosclerosis in 38 patients starting glucocorticoid therapy for systemic autoimmune diseases. To detect premature atherosclerosis, carotid ultrasonography was performed at initiation of glucocorticoid therapy and after a mean three-year follow-up period...
September 16, 2016: Metabolites
Benjamin Görling, Stefan Bräse, Burkhard Luy
Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine...
September 2, 2016: Metabolites
Brice Fermier, Hélène Blasco, Emmanuel Godat, Cinzia Bocca, Joseph Moënne-Loccoz, Patrick Emond, Christian R Andres, Marc Laffon, Martine Ferrandière
BACKGROUND: Shock includes different pathophysiological mechanisms not fully understood and remains a challenge to manage. Exhaled breath condensate (EBC) may contain relevant biomarkers that could help us make an early diagnosis or better understand the metabolic perturbations resulting from this pathological situation. OBJECTIVE: we aimed to establish the metabolomics signature of EBC from patients in shock with acute respiratory failure in a pilot study. MATERIAL AND METHODS: We explored the metabolic signature of EBC in 12 patients with shock compared to 14 controls using LC-HRMS...
September 1, 2016: Metabolites
Fei Gao, Justice McDaniel, Emily Y Chen, Hannah Rockwell, Matthew D Lynes, Yu-Hua Tseng, Rangaprasad Sarangarajan, Niven R Narain, Michael A Kiebish
Monoacylglycerols (MAGs) are structural and bioactive metabolites critical for biological function. Development of facile tools for measuring MAG are essential to understand its role in different diseases and various pathways. A data-independent acquisition method, MS/MS(ALL), using electrospray ionization (ESI) coupled quadrupole time of flight mass spectrometry (MS), was utilized for the structural identification and quantitative analysis of individual MAG molecular species. Compared with other acylglycerols, diacylglycerols (DAG) and triacylglycerols (TAG), MAG characteristically presented as a dominant protonated ion, [M + H]⁺, and under low collision energy as fatty acid-like fragments due to the neutral loss of the glycerol head group...
August 17, 2016: Metabolites
Aoibhe M Pasieka, Alex Rafacho
Glucocorticoids (GCs) are steroid hormones that exert important physiological actions on metabolism. Given that GCs also exert potent immunosuppressive and anti-inflammatory actions, synthetic GCs such as prednisolone and dexamethasone were developed for the treatment of autoimmune- and inflammatory-related diseases. The synthetic GCs are undoubtedly efficient in terms of their therapeutic effects, but are accompanied by significant adverse effects on metabolism, specifically glucose metabolism. Glucose intolerance and reductions in insulin sensitivity are among the major concerns related to GC metabolic side effects, which may ultimately progress to type 2 diabetes mellitus...
August 3, 2016: Metabolites
Arjun Sengupta, Saikumari Y Krishnaiah, Seth Rhoades, Jacqueline Growe, Barry Slaff, Anand Venkataraman, Anthony O Olarerin-George, Chi Van Dang, John B Hogenesch, Aalim M Weljie
Oscillations in circadian metabolism are crucial to the well being of organism. Our understanding of metabolic rhythms has been greatly enhanced by recent advances in high-throughput systems biology experimental techniques and data analysis. In an in vitro setting, metabolite rhythms can be measured by time-dependent sampling over an experimental period spanning one or more days at sufficent resolution to elucidate rhythms. We hypothesized that cellular metabolic effects over such a time course would be influenced by both oscillatory and circadian-independent cell metabolic effects...
July 27, 2016: Metabolites
Farhana R Pinu, Samuel de Carvalho-Silva, Ana Paula Trovatti Uetanabaro, Silas G Villas-Boas
Balsamic vinegar is a popular food condiment produced from cooked grape must by two successive fermentation (anaerobic and aerobic) processes. Although many studies have been performed to determine the composition of major metabolites, including sugars and aroma compounds, no study has been undertaken yet to characterize the comprehensive metabolite composition of balsamic vinegars. Here, we present the first metabolomics study of commercial balsamic vinegars by gas chromatography coupled to mass spectrometry (GC-MS)...
July 23, 2016: Metabolites
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